Ren Q

References (44)

Title : Clinical and genetic characteristics of CEL-MODY (MODY8): a literature review and screening in Chinese individuals diagnosed with early-onset type 2 diabetes - Sun_2023_Endocrine__
Author(s) : Sun S , Gong S , Li M , Wang X , Wang F , Cai X , Liu W , Luo Y , Zhang S , Zhang R , Zhou L , Zhu Y , Ma Y , Ren Q , Zhang X , Chen J , Chen L , Wu J , Gao L , Zhou X , Li Y , Zhong L , Han X , Ji L
Ref : Endocrine , : , 2023
Abstract : OBJECTIVE: CEL-related maturity-onset diabetes of the young (CEL-MODY, MODY8) is a special type of monogenetic diabetes caused by mutations in the carboxyl-ester lipase (CEL) gene. This study aimed to summarize the genetic and clinical characteristics of CEL-MODY patients and to determine the prevalence of the disease among Chinese patients with early-onset type 2 diabetes (EOD). METHODS: We systematically reviewed the literature associated with CEL-MODY in PubMed, Embase, Web of Science, China National Knowledge Infrastructure and Wanfang Data to analyze the features of patients with CEL-MODY. We screened and evaluated rare variants of the CEL gene in a cohort of 679 Chinese patients with EOD to estimate the prevalence of CEL-MODY in China. RESULTS: In total, 21 individuals reported in previous studies were diagnosed with CEL-MODY based on the combination of diabetes and pancreatic exocrine dysfunction as well as frameshift mutations in exon 11 of the CEL gene. CEL-MODY patients were nonobese and presented with exocrine pancreatic affection (e.g., chronic pancreatitis, low fecal elastase levels, pancreas atrophy and lipomatosis) followed by insulin-dependent diabetes. No carriers of CEL missense mutations were reported with exocrine pancreatic dysfunction. Sequencing of CEL in Chinese EOD patients led to the identification of the variant p.Val736Cysfs*22 in two patients. However, these patients could not be diagnosed with CEL-MODY because there were no signs that the exocrine pancreas was afflicted. CONCLUSION: CEL-MODY is a very rare disease caused by frameshift mutations affecting the proximal VNTR segments of the CEL gene. Signs of exocrine pancreatic dysfunction provide diagnostic clues for CEL-MODY, and genetic testing is vital for proper diagnosis. Further research in larger cohorts is needed to investigate the characteristics and prevalence of CEL-MODY in the Chinese population.
ESTHER : Sun_2023_Endocrine__
PubMedSearch : Sun_2023_Endocrine__
PubMedID: 37726640

Title : Eucommia ulmoides Olive Male Flower Extracts Ameliorate Alzheimer's Disease-Like Pathology in Zebrafish via Regulating Autophagy, Acetylcholinesterase, and the Dopamine Transporter - Sun_2022_Front.Mol.Neurosci_15_901953
Author(s) : Sun C , Zhang S , Ba S , Dang J , Ren Q , Zhu Y , Liu K , Jin M
Ref : Front Mol Neurosci , 15 :901953 , 2022
Abstract : Alzheimer's disease (AD) is the most prevalent neural disorder. However, the therapeutic agents for AD are limited. Eucommia ulmoides Olive (EUO) is widely used as a traditional Chinese herb to treat various neurodegenerative disorders. Therefore, we investigated whether the extracts of EUO male flower (EUMF) have therapeutic effects against AD. We focused on the flavonoids of EUMF and identified the composition using a targeted HPLC-MS analysis. As a result, 125 flavonoids and flavanols, 32 flavanones, 22 isoflavonoids, 11 chalcones and dihydrochalcones, and 17 anthocyanins were identified. Then, the anti-AD effects of the EUMF were tested by using zebrafish AD model. The behavioral changes were detected by automated video-tracking system. Abeta deposition was assayed by thioflavin S staining. Ache activity and cell apoptosis in zebrafish were tested by, Acetylcholine Assay Kit and TUNEL assay, respectively. The results showed that EUMF significantly rescued the dyskinesia of zebrafish and inhibited Abeta deposition, Ache activity, and occurrence of cell apoptosis in the head of zebrafish induced by AlCl(3). We also investigated the mechanism underlying anti-AD effects of EUMF by RT-qPCR and found that EUMF ameliorated AD-like symptoms possibly through inhibiting excessive autophagy and the abnormal expressions of ache and slc6a3 genes. In summary, our findings suggested EUMF can be a therapeutic candidate for AD treatment.
ESTHER : Sun_2022_Front.Mol.Neurosci_15_901953
PubMedSearch : Sun_2022_Front.Mol.Neurosci_15_901953
PubMedID: 35754707

Title : Biology and applications of Clonostachys rosea - Sun_2020_J.Appl.Microbiol__
Author(s) : Sun ZB , Li SD , Ren Q , Xu JL , Lu X , Sun MH
Ref : J Appl Microbiol , : , 2020
Abstract : Clonostachys rosea is a promising saprophytic filamentous fungus that belongs to phylum Ascomycota. Clonostachys rosea is widespread around the world and exists in many kinds of habitats, with the highest frequency in soil. As an excellent mycoparasite, C. rosea exhibits strong biological control ability against numerous fungal plant pathogens, nematodes and insects. These behaviours are based on the activation of multiple mechanisms such as secreted cell-wall-degrading enzymes, production of antifungal secondary metabolites and induction of plant defence systems. Besides having significant biocontrol activity, C. rosea also functions in the biodegradation of plastic waste, biotransformation of bioactive compounds, as a bioenergy sources and in fermentation. This mini review summarizes information about the biology and various applications of C. rosea and expands on its possible uses.
ESTHER : Sun_2020_J.Appl.Microbiol__
PubMedSearch : Sun_2020_J.Appl.Microbiol__
PubMedID: 32115828

Title : The seasonal development dynamics of the yak hair cycle transcriptome - Bao_2020_BMC.Genomics_21_355
Author(s) : Bao P , Luo J , Liu Y , Chu M , Ren Q , Guo X , Tang B , Ding X , Qiu Q , Pan H , Wang K , Yan P
Ref : BMC Genomics , 21 :355 , 2020
Abstract : BACKGROUND: Mammalian hair play an important role in mammals' ability to adapt to changing climatic environments. The seasonal circulation of yak hair helps them adapt to high altitude but the regulation mechanisms of the proliferation and differentiation of hair follicles (HFs) cells during development are still unknown. Here, using time series data for transcriptome and hormone contents, we systematically analyzed the mechanism regulating the periodic expression of hair development in the yak and reviewed how different combinations of genetic pathways regulate HFs development and cycling. RESULTS: This study used high-throughput RNA sequencing to provide a detailed description of global gene expression in 15 samples from five developmental time points during the yak hair cycle. According to clustering analysis, we found that these 15 samples could be significantly grouped into three phases, which represent different developmental periods in the hair cycle. A total of 2316 genes were identified in these three consecutive developmental periods and their expression patterns could be divided into 9 clusters. In the anagen, genes involved in activating hair follicle growth are highly expressed, such as the WNT pathway, FGF pathway, and some genes related to hair follicle differentiation. In the catagen, genes that inhibit differentiation and promote hair follicle cell apoptosis are highly expressed, such as BMP4, and Wise. In the telogen, genes that inhibit hair follicle activity are highly expressed, such as DKK1 and BMP1. Through co-expression analysis, we revealed a number of modular hub genes highly associated with hormones, such as SLF2, BOP1 and DPP8. They may play unique roles in hormonal regulation of events associated with the hair cycle. CONCLUSIONS: Our results revealed the expression pattern and molecular mechanisms of the seasonal hair cycle in the yak. The findings will be valuable in further understanding the alpine adaptation mechanism in the yak, which is important in order to make full use of yak hair resources and promote the economic development of pastoral plateau areas.
ESTHER : Bao_2020_BMC.Genomics_21_355
PubMedSearch : Bao_2020_BMC.Genomics_21_355
PubMedID: 32393236

Title : Key role of soluble epoxide hydrolase in the neurodevelopmental disorders of offspring after maternal immune activation - Ma_2019_Proc.Natl.Acad.Sci.U.S.A_116_7083
Author(s) : Ma M , Ren Q , Yang J , Zhang K , Xiong Z , Ishima T , Pu Y , Hwang SH , Toyoshima M , Iwayama Y , Hisano Y , Yoshikawa T , Hammock BD , Hashimoto K
Ref : Proc Natl Acad Sci U S A , 116 :7083 , 2019
Abstract : Maternal infection during pregnancy increases risk of neurodevelopmental disorders such as schizophrenia and autism spectrum disorder (ASD) in offspring. In rodents, maternal immune activation (MIA) yields offspring with schizophrenia- and ASD-like behavioral abnormalities. Soluble epoxide hydrolase (sEH) plays a key role in inflammation associated with neurodevelopmental disorders. Here we found higher levels of sEH in the prefrontal cortex (PFC) of juvenile offspring after MIA. Oxylipin analysis showed decreased levels of epoxy fatty acids in the PFC of juvenile offspring after MIA, supporting increased activity of sEH in the PFC of juvenile offspring. Furthermore, expression of sEH (or EPHX2) mRNA in induced pluripotent stem cell-derived neurospheres from schizophrenia patients with the 22q11.2 deletion was higher than that of healthy controls. Moreover, the expression of EPHX2 mRNA in postmortem brain samples (Brodmann area 9 and 40) from ASD patients was higher than that of controls. Treatment with 1-trifluoromethoxyphenyl-3-(1-propionylpiperidin-4-yl)urea (TPPU), a potent sEH inhibitor, in juvenile offspring from prenatal day (P) 28 to P56 could prevent cognitive deficits and loss of parvalbumin (PV) immunoreactivity in the medial PFC of adult offspring after MIA. In addition, dosing of TPPU to pregnant mothers from E5 to P21 could prevent cognitive deficits, and social interaction deficits and PV immunoreactivity in the medial prefrontal cortex of juvenile offspring after MIA. These findings suggest that increased activity of sEH in the PFC plays a key role in the etiology of neurodevelopmental disorders in offspring after MIA. Therefore, sEH represents a promising prophylactic or therapeutic target for neurodevelopmental disorders in offspring after MIA.
ESTHER : Ma_2019_Proc.Natl.Acad.Sci.U.S.A_116_7083
PubMedSearch : Ma_2019_Proc.Natl.Acad.Sci.U.S.A_116_7083
PubMedID: 30890645

Title : Regulation of hippocampal long term depression by Neuroligin 1 - Dang_2018_Neuropharmacol_143_205
Author(s) : Dang R , Qi J , Liu A , Ren Q , Lv D , Han L , Zhou Z , Cao F , Xie W , Jia Z
Ref : Neuropharmacology , 143 :205 , 2018
Abstract : Neuroligins (NLGs) are postsynaptic adhesion molecules known to play essential roles in synapse development and maturation, but their effects on synaptic plasticity at mature synapses remain unclear. In this study, we investigate the involvement of NLG1 in hippocampal long-term depression (LTD), a key form of long lasting synaptic plasticity, critical for memory formation and brain disorders, by using mice deficient in the expression of NLG1. We find that although NLG1 homozygous (NLG1-/-) mice show no impairments in either NMDA receptor- (NMDAR-LTD) or metabotropic glutamate receptor-dependent LTD (mGluR-LTD), the heterozygous (NLG1+/-) mice are significantly altered in both forms of LTD characterized by the absence of NMDAR-LTD but enhanced mGluR-LTD. Accordingly, the NLG1+/-, but not the NLG1-/- mice are altered in synaptic proteins, including PSD95, GluA2 and phosphorylated GluA1 at serine 845, all of which are involved in the expression of LTD. The NLG1+/- mice also exhibit autistic-like behaviors including increased grooming and impaired recognition memory. We further show that the expression of NLG3, a close family member of NLG1, is elevated in the NLG1-/-, but not in NLG1+/- mice, suggesting that the lack of LTD deficits in the NLG1-/- mice might be due to the increased NLG3. Our results reveal a gene dosage dependent role for NLG1 in the regulation of LTD and suggest that moderate changes in NLG1 protein level may be sufficient to cause synaptic and behavior deficits in brain disorders where copy number variants and hemizygosity of gene mutations are common.
ESTHER : Dang_2018_Neuropharmacol_143_205
PubMedSearch : Dang_2018_Neuropharmacol_143_205
PubMedID: 30266599

Title : Lycodine-type alkaloids from Lycopodiastrum casuarinoides and their cholinesterase inhibitory activities - Liu_2018_Fitoterapia_130_203
Author(s) : Liu Y , Xu PS , Ren Q , Chen X , Zhou G , Li D , Li XM , Xu KP , Yu X , Tan GS
Ref : Fitoterapia , 130 :203 , 2018
Abstract : Four new trace alkaloids with lycodine-related structures, Lycocasuarinines A-D (1-4), together with seven known analogues (5-11), were isolated from the chloroform extract of Lycopodiastrum casuarinoides. The structures and stereochemistry of 1-4 were elucidated by spectroscopic analysis (IR, UV, MS, NMR, HRESIMS and CD) and comparison with known ones. The acetylcholinesterase (AChE) and butyrocholinesterase (BuChE) inhibitory activities of nine isolates were evaluated. Lycocasuarinine D (4) showed the most potent AChE inhibitory effect. In addition, a plausible biogenetic pathway of compound 4 was proposed.
ESTHER : Liu_2018_Fitoterapia_130_203
PubMedSearch : Liu_2018_Fitoterapia_130_203
PubMedID: 30213757

Title : The Role of AChE in Swimming Behavior of Daphnia magna: Correlation Analysis of Both Parameters Affected by Deltamethrin and Methomyl Exposure - Ren_2017_J.Toxicol_2017_3265727
Author(s) : Ren Q , Zhao R , Wang C , Li S , Zhang T , Ren Z , Yang M , Pan H , Xu S , Zhu J , Wang X
Ref : J Toxicol , 2017 :3265727 , 2017
Abstract : The unpredictable toxicity of insecticides may cause behavior disorder of biological organisms. In order to assess the role of acetylcholinesterase (AChE) in swimming behavior of Daphnia magna, a correlation analysis of both parameters in 24 h exposure of deltamethrin (DM) and methomyl (MT) was investigated. The behavior responses of D. magna in DM (13.36 mug/L and 33.40 mug/L) and MT (19.66 mug/L and 49.15 mug/L) suggested that recovery behavior in the adjustment phase was crucial, and behavior homeostasis provided them with an optimal way to achieve a wider tolerance against environmental stress. During the experiment, positive effects on AChE activity occurred in the beginning of the exposure. Even though the de novo synthesis of AChE in D. magna might help it recover, the AChE inhibition in different treatments could be observed. Some induction effects on AChE activity at the beginning of exposure occurred, and a 50% decrease may cause toxic effects on behavior. In most treatments, the results showed that both behavior strength and AChE activity stayed in the same field within a correlation circle. These results illustrated that the environmental stress caused by both DM and MT could inhibit AChE activity and subsequently induce a stepwise behavior response, though both pesticides affect it as direct and indirect inhibitors, respectively.
ESTHER : Ren_2017_J.Toxicol_2017_3265727
PubMedSearch : Ren_2017_J.Toxicol_2017_3265727
PubMedID: 29201050
Gene_locus related to this paper: dapul-ACHE1

Title : Does time difference of the acetylcholinesterase (AChE) inhibition in different tissues exist? A case study of zebra fish (Danio rerio) exposed to cadmium chloride and deltamethrin - Zhang_2017_Chemosphere_168_908
Author(s) : Zhang T , Yang M , Pan H , Li S , Ren B , Ren Z , Xing N , Qi L , Ren Q , Xu S , Song J , Ma J
Ref : Chemosphere , 168 :908 , 2017
Abstract : In order to illustrate time difference in toxic effects of cadmium chloride (CdCl2) and deltamethrin (DM), AChE activities were measured in different tissues, liver, muscle, brain, and gill, of Zebra fish (Danio rerio) across different concentrations in this research. The average AChE activity decreased comparing to 0.0 TU with DM (82.81% in 0.1 TU, 56.14% in 1.0 TU and 44.68% in 2.0 TU) and with CdCl2 (74.68% in 0.1 TU, 52.05% in 1.0 TU and 50.14% in 2.0 TU) showed an overall decrease with the increase of exposure concentrations. According to Self-Organizing Map (SOM), the AChE activities were characterized in relation with experimental conditions, showing an inverse relationship with exposure time. As the exposure time was longer, the AChE activities were correspondingly lower. The AChE inhibition showed time delay in sublethal treatments (0.1 TU) in different tissues: the AChE was first inhibited in brain by chemicals followed by gill, muscle and liver (brain > gill > muscle > liver). The AChE activity was almost inhibited synchronously in higher environmental stress (1.0 TU and 2.0 TU). As the AChE inhibition can induce abnormal of behavior movement, these results will be helpful to the mechanism of stepwise behavior responses according to the time difference in different tissues rather than the whole body AChE activity.
ESTHER : Zhang_2017_Chemosphere_168_908
PubMedSearch : Zhang_2017_Chemosphere_168_908
PubMedID: 27825714

Title : Gene deficiency and pharmacological inhibition of soluble epoxide hydrolase confers resilience to repeated social defeat stress - Ren_2016_Proc.Natl.Acad.Sci.U.S.A_113_E1944
Author(s) : Ren Q , Ma M , Ishima T , Morisseau C , Yang J , Wagner KM , Zhang JC , Yang C , Yao W , Dong C , Han M , Hammock BD , Hashimoto K
Ref : Proc Natl Acad Sci U S A , 113 :E1944 , 2016
Abstract : Depression is a severe and chronic psychiatric disease, affecting 350 million subjects worldwide. Although multiple antidepressants have been used in the treatment of depressive symptoms, their beneficial effects are limited. The soluble epoxide hydrolase (sEH) plays a key role in the inflammation that is involved in depression. Thus, we examined here the role of sEH in depression. In both inflammation and social defeat stress models of depression, a potent sEH inhibitor, TPPU, displayed rapid antidepressant effects. Expression of sEH protein in the brain from chronically stressed (susceptible) mice was higher than of control mice. Furthermore, expression of sEH protein in postmortem brain samples of patients with psychiatric diseases, including depression, bipolar disorder, and schizophrenia, was higher than controls. This finding suggests that increased sEH levels might be involved in the pathogenesis of certain psychiatric diseases. In support of this hypothesis, pretreatment with TPPU prevented the onset of depression-like behaviors after inflammation or repeated social defeat stress. Moreover, sEH KO mice did not show depression-like behavior after repeated social defeat stress, suggesting stress resilience. The sEH KO mice showed increased brain-derived neurotrophic factor (BDNF) and phosphorylation of its receptor TrkB in the prefrontal cortex, hippocampus, but not nucleus accumbens, suggesting that increased BDNF-TrkB signaling in the prefrontal cortex and hippocampus confer stress resilience. All of these findings suggest that sEH plays a key role in the pathophysiology of depression, and that epoxy fatty acids, their mimics, as well as sEH inhibitors could be potential therapeutic or prophylactic drugs for depression.
ESTHER : Ren_2016_Proc.Natl.Acad.Sci.U.S.A_113_E1944
PubMedSearch : Ren_2016_Proc.Natl.Acad.Sci.U.S.A_113_E1944
PubMedID: 26976569
Gene_locus related to this paper: mouse-hyes

Title : Self-assembly of MPG1, a hydrophobin protein from the rice blast fungus that forms functional amyloid coatings, occurs by a surface-driven mechanism - Pham_2016_Sci.Rep_6_25288
Author(s) : Pham CL , Rey A , Lo V , Soules M , Ren Q , Meisl G , Knowles TP , Kwan AH , Sunde M
Ref : Sci Rep , 6 :25288 , 2016
Abstract : Rice blast is a devastating disease of rice caused by the fungus Magnaporthe oryzae and can result in loss of a third of the annual global rice harvest. Two hydrophobin proteins, MPG1 and MHP1, are highly expressed during rice blast infections. These hydrophobins have been suggested to facilitate fungal spore adhesion and to direct the action of the enzyme cutinase 2, resulting in penetration of the plant host. Therefore a mechanistic understanding of the self-assembly properties of these hydrophobins and their interaction with cutinase 2 is crucial for the development of novel antifungals. Here we report details of a study of the structure, assembly and interactions of these proteins. We demonstrate that, in vitro, MPG1 assembles spontaneously into amyloid structures while MHP1 forms a non-fibrillar film. The assembly of MPG1 only occurs at a hydrophobic:hydrophilic interface and can be modulated by MHP1 and other factors. We further show that MPG1 assemblies can much more effectively retain cutinase 2 activity on a surface after co-incubation and extensive washing compared with other protein coatings. The assembly and interactions of MPG1 and MHP1 at hydrophobic surfaces thereby provide the basis for a possible mechanism by which the fungus can develop appropriately at the infection interface.
ESTHER : Pham_2016_Sci.Rep_6_25288
PubMedSearch : Pham_2016_Sci.Rep_6_25288
PubMedID: 27142249

Title : The acetylcholinesterase (AChE) inhibition analysis of medaka (Oryzias latipes) in the exposure of three insecticides - Zhu_2015_Pak.J.Pharm.Sci_28_671
Author(s) : Zhu J , Huan C , Si G , Yang H , Yin L , Ren Q , Ren B , Fu R , Miao M , Ren Z
Ref : Pak J Pharm Sci , 28 :671 , 2015
Abstract : The continuous effects on Acetylcholinesterase (AChE) activity of medaka (Oryzias latipes) caused by dichlorvos, methomyl and deltamethrin in vivo were investigated, and the trends of AChE activity inhibition due to the influence of these insecticides were discussed. The LC50-24h of dichlorvos, methomyl and deltamethrin on medaka were 2.3 mg/L, 0.2 mg/L, and 2.9x10(-3) mg/L respectively. The result suggested that at the beginning of the exposure, the AChE activity might increase, and the AChE activity in dead individuals was obviously lower than the live individuals. Though the de novo synthesis of AChE in medaka might help the AChE activity recover, the trends during the exposure in different treatments were downward, and it showed both exposure time and concentration dependent. Meanwhile, higher temperature might cause the AChE inhibition earlier due to the higher metabolic rate. Therefore, as a specific biomarker for organophosphate, carbamate pesticides and pyrethroids, the degree of the AChE inhibition with in vivo conditions is a good tool in continuous monitoring of insecticides, which may induce the nerve conduction disorders.
ESTHER : Zhu_2015_Pak.J.Pharm.Sci_28_671
PubMedSearch : Zhu_2015_Pak.J.Pharm.Sci_28_671
PubMedID: 25796143

Title : Influence of growth stage on activities of polyhydroxyalkanoate (PHA) polymerase and PHA depolymerase in Pseudomonas putida U - Ren_2010_BMC.Microbiol_10_254
Author(s) : Ren Q , de Roo G , Witholt B , Zinn M , Thony-Meyer L
Ref : BMC Microbiol , 10 :254 , 2010
Abstract : BACKGROUND: Medium chain length (mcl-) polyhydroxyalkanoates (PHA) are synthesized by many bacteria in the cytoplasm as storage compounds for energy and carbon. The key enzymes for PHA metabolism are PHA polymerase (PhaC) and depolymerase (PhaZ). Little is known of how mcl-PHA accumulation and degradation are controlled. It has been suggested that overall PHA metabolism is regulated by the beta-oxidation pathway of which the flux is governed by intracellular ratios of [NADH]/[NAD] and [acetyl-CoA]/[CoA]. Another level of control could relate to modulation of the activities of PhaC and PhaZ. In order to investigate the latter, assays for in vitro activity measurements of PhaC and PhaZ in crude cell extracts are necessary. RESULTS: Two in vitro assays were developed which allow the measurement of PhaC and PhaZ activities in crude cell extracts of Pseudomonas putida U. Using the assays, it was demonstrated that the activity of PhaC decreased 5-fold upon exponential growth on nitrogen limited medium and octanoate. In contrast, the activity of PhaZ increased only 1.5-fold during growth. One reason for the changes in the enzymatic activity of PhaC and PhaZ could relate to a change in interaction with the phasin surface proteins on the PHA granule. SDS-PAGE analysis of isolated PHA granules demonstrated that during growth, the ratio of [phasins]/[PHA] decreased. In addition, it was found that after eliminating phasins (PhaF and PhaI) from the granules PhaC activity decreased further. CONCLUSION: Using the assays developed in this study, we followed the enzymatic activities of PhaC and PhaZ during growth and correlated them to the amount of phasins on the PHA granules. It was found that in P. putida PhaC and PhaZ are concomitantly active, resulting in parallel synthesis and degradation of PHA. Moreover PhaC activity was found to be decreased, whereas PhaZ activity increased during growth. Availability of phasins on PHA granules affected the activity of PhaC.
ESTHER : Ren_2010_BMC.Microbiol_10_254
PubMedSearch : Ren_2010_BMC.Microbiol_10_254
PubMedID: 20937103

Title : The complete genome sequence of Haloferax volcanii DS2, a model archaeon - Hartman_2010_PLoS.One_5_e9605
Author(s) : Hartman AL , Norais C , Badger JH , Delmas S , Haldenby S , Madupu R , Robinson J , Khouri H , Ren Q , Lowe TM , Maupin-Furlow J , Pohlschroder M , Daniels C , Pfeiffer F , Allers T , Eisen JA
Ref : PLoS ONE , 5 :e9605 , 2010
Abstract : BACKGROUND: Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS: We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE: The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
ESTHER : Hartman_2010_PLoS.One_5_e9605
PubMedSearch : Hartman_2010_PLoS.One_5_e9605
PubMedID: 20333302
Gene_locus related to this paper: halvd-d4gpd7 , halvd-d4gtr7 , halvd-d4gug3 , halvd-d4gug9 , halvd-d4gz20 , halvd-metxa

Title : Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7 - Roy_2010_PLoS.One_5_e8842
Author(s) : Roy PH , Tetu SG , Larouche A , Elbourne L , Tremblay S , Ren Q , Dodson R , Harkins D , Shay R , Watkins K , Mahamoud Y , Paulsen IT
Ref : PLoS ONE , 5 :e8842 , 2010
Abstract : Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is multiresistant to antibiotics. We first sequenced gyrA, gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found that PA7 is a taxonomic outlier. We report here the complete sequence of the 6,588,339 bp genome, which has only about 95% overall identity to other strains. PA7 has multiple novel genomic islands and a total of 51 occupied regions of genomic plasticity. These islands include antibiotic resistance genes, parts of transposons, prophages, and a pKLC102-related island. Several PA7 genes not present in PAO1 or PA14 are putative orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7 appears to be closely related to the known taxonomic outlier DSM1128 (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin type II. Preliminary proteomic studies indicate numerous differences with PAO1, some of which are probably a consequence of a frameshift mutation in the mvfR quorum sensing regulatory gene.
ESTHER : Roy_2010_PLoS.One_5_e8842
PubMedSearch : Roy_2010_PLoS.One_5_e8842
PubMedID: 20107499
Gene_locus related to this paper: pseae-PA5384 , psea7-a6vca5 , psea7-a6v8b2 , psea7-a6v754

Title : Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils - Ward_2009_Appl.Environ.Microbiol_75_2046
Author(s) : Ward NL , Challacombe JF , Janssen PH , Henrissat B , Coutinho PM , Wu M , Xie G , Haft DH , Sait M , Badger J , Barabote RD , Bradley B , Brettin TS , Brinkac LM , Bruce D , Creasy T , Daugherty SC , Davidsen TM , DeBoy RT , Detter JC , Dodson RJ , Durkin AS , Ganapathy A , Gwinn-Giglio M , Han CS , Khouri H , Kiss H , Kothari SP , Madupu R , Nelson KE , Nelson WC , Paulsen I , Penn K , Ren Q , Rosovitz MJ , Selengut JD , Shrivastava S , Sullivan SA , Tapia R , Thompson LS , Watkins KL , Yang Q , Yu C , Zafar N , Zhou L , Kuske CR
Ref : Applied Environmental Microbiology , 75 :2046 , 2009
Abstract : The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
ESTHER : Ward_2009_Appl.Environ.Microbiol_75_2046
PubMedSearch : Ward_2009_Appl.Environ.Microbiol_75_2046
PubMedID: 19201974
Gene_locus related to this paper: korve-q1ihr9 , korve-q1ii02 , korve-q1iit0 , korve-q1ilk4 , korve-q1imj9 , korve-q1ims4 , korve-q1iqj0 , korve-q1isy7 , korve-q1itj5 , korve-q1itz6 , korve-q1ivc8 , acic5-c1f1u6 , acic5-c1f2i7 , acic5-c1f4m6 , acic5-c1f4y4 , acic5-c1f5a7 , acic5-c1f5u2 , acic5-c1f7a9 , acic5-c1f7x6 , acic5-c1f8y9 , acic5-c1f9m2 , acic5-c1f594 , acic5-c1f609 , acic5-c1f692 , acic5-c1f970 , acic5-c1fa52 , korve-q1iiw2 , korve-q1ivn9 , solue-q01nb0 , solue-q01qj6 , solue-q01r37 , solue-q01rq8 , solue-q01rz0 , solue-q01t44 , solue-q01t57 , solue-q01ts5 , solue-q01tv4 , solue-q01vd8 , solue-q01vr3 , solue-q01vw5 , solue-q01w12 , solue-q01wt9 , solue-q01y40 , solue-q01ym8 , solue-q01z24 , solue-q01z97 , solue-q01zl4 , solue-q01zm0 , solue-q01zm5 , solue-q01zm7 , solue-q02aa4 , solue-q02ab9 , solue-q02b72 , solue-q02bs8 , solue-q02bt7 , solue-q02cp0 , solue-q02d61 , solue-q020h3 , solue-q020i8 , solue-q021i6 , solue-q022b1 , solue-q022p8 , solue-q022q2 , solue-q022q3 , solue-q022x2 , solue-q022x5 , solue-q022x6 , solue-q022x8 , solue-q023e7 , solue-q024d9 , solue-q025c1 , solue-q026j1 , solue-q026k6 , solue-q026r6 , solue-q027p2 , solue-q027r8 , solue-q01zt5 , korve-q1itw6 , solue-q01yh7 , solue-q02ad6 , korve-q1imj6 , korve-q1iuf6 , acic5-c1f891 , solue-q026h7

Title : The 2008 update of the Aspergillus nidulans genome annotation: a community effort - Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2
Author(s) : Wortman JR , Gilsenan JM , Joardar V , Deegan J , Clutterbuck J , Andersen MR , Archer D , Bencina M , Braus G , Coutinho P , von Dohren H , Doonan J , Driessen AJ , Durek P , Espeso E , Fekete E , Flipphi M , Estrada CG , Geysens S , Goldman G , de Groot PW , Hansen K , Harris SD , Heinekamp T , Helmstaedt K , Henrissat B , Hofmann G , Homan T , Horio T , Horiuchi H , James S , Jones M , Karaffa L , Karanyi Z , Kato M , Keller N , Kelly DE , Kiel JA , Kim JM , van der Klei IJ , Klis FM , Kovalchuk A , Krasevec N , Kubicek CP , Liu B , Maccabe A , Meyer V , Mirabito P , Miskei M , Mos M , Mullins J , Nelson DR , Nielsen J , Oakley BR , Osmani SA , Pakula T , Paszewski A , Paulsen I , Pilsyk S , Pocsi I , Punt PJ , Ram AF , Ren Q , Robellet X , Robson G , Seiboth B , van Solingen P , Specht T , Sun J , Taheri-Talesh N , Takeshita N , Ussery D , vanKuyk PA , Visser H , van de Vondervoort PJ , de Vries RP , Walton J , Xiang X , Xiong Y , Zeng AP , Brandt BW , Cornell MJ , van den Hondel CA , Visser J , Oliver SG , Turner G
Ref : Fungal Genet Biol , 46 Suppl 1 :S2 , 2009
Abstract : The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.
ESTHER : Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2
PubMedSearch : Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2
PubMedID: 19146970
Gene_locus related to this paper: emeni-axe1 , emeni-c8v4m7 , emeni-faec , emeni-ppme1 , emeni-q5ara9 , emeni-q5arf0 , emeni-q5as30 , emeni-q5ase8 , emeni-q5av79 , emeni-q5aw09 , emeni-q5awc3 , emeni-q5awc7 , emeni-q5awu9 , emeni-q5aww4 , emeni-q5ax50 , emeni-q5ay37 , emeni-q5ay57 , emeni-q5ay59 , emeni-q5ayk9 , emeni-q5ays5 , emeni-q5az32 , emeni-q5az91 , emeni-q5az97 , emeni-q5azp1 , emeni-q5b0i6 , emeni-q5b1h2 , emeni-q5b2a9 , emeni-q5b2p7 , emeni-q5b3d2 , emeni-q5b4q7 , emeni-q5b5u7 , emeni-q5b5y4 , emeni-q5b9e7 , emeni-q5b9i0 , emeni-q5b364 , emeni-q5b446 , emeni-q5b938 , emeni-q5ba78 , emeni-q5bcd1 , emeni-q5bcd2 , emeni-q5bde7 , emeni-q5bdr0 , emeni-q5bf92 , emeni-q7si80 , emeni-q5bdv9 , emeni-c8vu15 , 9euro-a0a3d8t644 , emeni-q5b719 , emeni-q5ax97 , emeni-tdia , emeni-afoc , emeni-dbae

Title : Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans - Haas_2009_Nature_461_393
Author(s) : Haas BJ , Kamoun S , Zody MC , Jiang RH , Handsaker RE , Cano LM , Grabherr M , Kodira CD , Raffaele S , Torto-Alalibo T , Bozkurt TO , Ah-Fong AM , Alvarado L , Anderson VL , Armstrong MR , Avrova A , Baxter L , Beynon J , Boevink PC , Bollmann SR , Bos JI , Bulone V , Cai G , Cakir C , Carrington JC , Chawner M , Conti L , Costanzo S , Ewan R , Fahlgren N , Fischbach MA , Fugelstad J , Gilroy EM , Gnerre S , Green PJ , Grenville-Briggs LJ , Griffith J , Grunwald NJ , Horn K , Horner NR , Hu CH , Huitema E , Jeong DH , Jones AM , Jones JD , Jones RW , Karlsson EK , Kunjeti SG , Lamour K , Liu Z , Ma L , Maclean D , Chibucos MC , McDonald H , McWalters J , Meijer HJ , Morgan W , Morris PF , Munro CA , O'Neill K , Ospina-Giraldo M , Pinzon A , Pritchard L , Ramsahoye B , Ren Q , Restrepo S , Roy S , Sadanandom A , Savidor A , Schornack S , Schwartz DC , Schumann UD , Schwessinger B , Seyer L , Sharpe T , Silvar C , Song J , Studholme DJ , Sykes S , Thines M , van de Vondervoort PJ , Phuntumart V , Wawra S , Weide R , Win J , Young C , Zhou S , Fry W , Meyers BC , van West P , Ristaino J , Govers F , Birch PR , Whisson SC , Judelson HS , Nusbaum C
Ref : Nature , 461 :393 , 2009
Abstract : Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $$6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
ESTHER : Haas_2009_Nature_461_393
PubMedSearch : Haas_2009_Nature_461_393
PubMedID: 19741609
Gene_locus related to this paper: phyin-ENDO2 , phyin-q2m440 , phyin-q58g92 , phyit-d0mqp1 , phyit-d0mqp2 , phyit-d0mt75 , phyit-d0muv1 , phyit-d0mv34 , phyit-d0mv35 , phyit-d0mwf9 , phyit-d0mxu5 , phyit-d0n935 , phyit-d0nax9 , phyit-d0nfs3 , phyit-d0nhj2 , phyit-d0nhj4 , phyit-d0nhj8 , phyit-d0ni28 , phyit-d0nj14 , phyit-d0nj53 , phyit-d0nj54 , phyit-d0njf2 , phyit-d0nkm4 , phyit-d0nr53 , phyit-d0nrb1 , phyit-d0nrk9 , phyit-d0nrl4 , phyit-d0ns26 , phyit-d0ns42 , phyit-d0ns43 , phyit-d0nsr8 , phyit-d0nu41 , phyit-d0nvt3 , phyit-d0nwb6 , phyit-d0nwm8 , phyit-d0nzc0 , phyit-d0nzc1 , phyit-d0p0z1 , phyit-d0p3z2 , phyit-kex1 , phyit-d0n6q6 , phyit-d0n4i8 , phyit-d0mqf7 , phyit-d0n5g6

Title : Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum - Wu_2009_PLoS.One_4_e4207
Author(s) : Wu D , Raymond J , Wu M , Chatterji S , Ren Q , Graham JE , Bryant DA , Robb F , Colman A , Tallon LJ , Badger JH , Madupu R , Ward NL , Eisen JA
Ref : PLoS ONE , 4 :e4207 , 2009
Abstract : In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.
ESTHER : Wu_2009_PLoS.One_4_e4207
PubMedSearch : Wu_2009_PLoS.One_4_e4207
PubMedID: 19148287
Gene_locus related to this paper: therp-b9kxz7 , therp-b9l2i8 , therp-b9l396

Title : Comparative genomics of the neglected human malaria parasite Plasmodium vivax - Carlton_2008_Nature_455_757
Author(s) : Carlton JM , Adams JH , Silva JC , Bidwell SL , Lorenzi H , Caler E , Crabtree J , Angiuoli SV , Merino EF , Amedeo P , Cheng Q , Coulson RM , Crabb BS , Del Portillo HA , Essien K , Feldblyum TV , Fernandez-Becerra C , Gilson PR , Gueye AH , Guo X , Kang'a S , Kooij TW , Korsinczky M , Meyer EV , Nene V , Paulsen I , White O , Ralph SA , Ren Q , Sargeant TJ , Salzberg SL , Stoeckert CJ , Sullivan SA , Yamamoto MM , Hoffman SL , Wortman JR , Gardner MJ , Galinski MR , Barnwell JW , Fraser-Liggett CM
Ref : Nature , 455 :757 , 2008
Abstract : The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non-human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species.
ESTHER : Carlton_2008_Nature_455_757
PubMedSearch : Carlton_2008_Nature_455_757
PubMedID: 18843361
Gene_locus related to this paper: plakh-b3lb44 , plavi-a5kcq0 , plavs-a5k2k6 , plavs-a5k3z4 , plavs-a5k4s6 , plavs-a5k5e4 , plavs-a5k7t5 , plavs-a5k686 , plavs-a5kaa1 , plavs-a5kaa3 , plavs-a5kas6 , plavs-a5kcm2

Title : Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans - Sievert_2008_Appl.Environ.Microbiol_74_1145
Author(s) : Sievert SM , Scott KM , Klotz MG , Chain PS , Hauser LJ , Hemp J , Hugler M , Land M , Lapidus A , Larimer FW , Lucas S , Malfatti SA , Meyer F , Paulsen IT , Ren Q , Simon J
Ref : Applied Environmental Microbiology , 74 :1145 , 2008
Abstract : Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
ESTHER : Sievert_2008_Appl.Environ.Microbiol_74_1145
PubMedSearch : Sievert_2008_Appl.Environ.Microbiol_74_1145
PubMedID: 18065616
Gene_locus related to this paper: suldn-q30ua6 , suldn-q30rs9

Title : Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice - Fouts_2008_PLoS.Genet_4_e1000141
Author(s) : Fouts DE , Tyler HL , DeBoy RT , Daugherty S , Ren Q , Badger JH , Durkin AS , Huot H , Shrivastava S , Kothari S , Dodson RJ , Mohamoud Y , Khouri H , Roesch LF , Krogfelt KA , Struve C , Triplett EW , Methe BA
Ref : PLoS Genet , 4 :e1000141 , 2008
Abstract : We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.
ESTHER : Fouts_2008_PLoS.Genet_4_e1000141
PubMedSearch : Fouts_2008_PLoS.Genet_4_e1000141
PubMedID: 18654632
Gene_locus related to this paper: klep3-b5xp56 , klep3-b5xqp6 , klep3-b5xzn5 , klep3-b5xzy8 , klep3-bioh , klep3-menh , klep7-a6t8q2 , klep7-a6t9v6 , klep7-a6tb98 , klep7-mhpc , klep7-y243 , klep7-y1077 , klepn-c4x8q1 , klepn-w8uta0 , klep3-rutd

Title : Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis - Carlton_2007_Science_315_207
Author(s) : Carlton JM , Hirt RP , Silva JC , Delcher AL , Schatz M , Zhao Q , Wortman JR , Bidwell SL , Alsmark UC , Besteiro S , Sicheritz-Ponten T , Noel CJ , Dacks JB , Foster PG , Simillion C , Van de Peer Y , Miranda-Saavedra D , Barton GJ , Westrop GD , Muller S , Dessi D , Fiori PL , Ren Q , Paulsen I , Zhang H , Bastida-Corcuera FD , Simoes-Barbosa A , Brown MT , Hayes RD , Mukherjee M , Okumura CY , Schneider R , Smith AJ , Vanacova S , Villalvazo M , Haas BJ , Pertea M , Feldblyum TV , Utterback TR , Shu CL , Osoegawa K , de Jong PJ , Hrdy I , Horvathova L , Zubacova Z , Dolezal P , Malik SB , Logsdon JM, Jr. , Henze K , Gupta A , Wang CC , Dunne RL , Upcroft JA , Upcroft P , White O , Salzberg SL , Tang P , Chiu CH , Lee YS , Embley TM , Coombs GH , Mottram JC , Tachezy J , Fraser-Liggett CM , Johnson PJ
Ref : Science , 315 :207 , 2007
Abstract : We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
ESTHER : Carlton_2007_Science_315_207
PubMedSearch : Carlton_2007_Science_315_207
PubMedID: 17218520
Gene_locus related to this paper: triva-a2d7i4 , triva-a2d9w5 , triva-a2d766 , triva-a2dah5 , triva-a2dlx9 , triva-a2dul1 , triva-a2dy49 , triva-a2e6h5 , triva-a2e7p9 , triva-a2e9l3 , triva-a2e414 , triva-a2e613 , triva-a2e983 , triva-a2eau8 , triva-a2ekb9 , triva-a2en58 , triva-a2erp5 , triva-a2et59 , triva-a2f7u4 , triva-a2f801 , triva-a2fa76 , triva-a2fbq3 , triva-a2fe47 , triva-a2fgl0 , triva-a2fhp7 , triva-a2fie6 , triva-a2fk22 , triva-a2fla2 , triva-a2fqm0 , triva-a2fqq2 , triva-a2frq0 , triva-a2frr3 , triva-a2fsq9 , triva-a2fsz5 , triva-a2fux4 , triva-a2fz57 , triva-a2g2h0 , triva-a2g9x0 , triva-a2fqi4

Title : The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation - Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
Author(s) : Palenik B , Grimwood J , Aerts A , Rouze P , Salamov A , Putnam N , Dupont C , Jorgensen R , Derelle E , Rombauts S , Zhou K , Otillar R , Merchant SS , Podell S , Gaasterland T , Napoli C , Gendler K , Manuell A , Tai V , Vallon O , Piganeau G , Jancek S , Heijde M , Jabbari K , Bowler C , Lohr M , Robbens S , Werner G , Dubchak I , Pazour GJ , Ren Q , Paulsen I , Delwiche C , Schmutz J , Rokhsar D , Van de Peer Y , Moreau H , Grigoriev IV
Ref : Proc Natl Acad Sci U S A , 104 :7705 , 2007
Abstract : The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
ESTHER : Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedSearch : Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedID: 17460045
Gene_locus related to this paper: ostlu-a4rrl5 , ostlu-a4ruh2 , ostlu-a4rut7 , ostlu-a4ruy3 , ostlu-a4rxn1 , ostlu-a4ry37 , ostlu-a4s2e6 , ostlu-a4s2y4 , ostlu-a4s3d7 , ostlu-a4s4v4 , ostlu-a4s5e4 , ostlu-a4s5y6 , ostlu-a4s7a8 , ostlu-a4s7z5 , ostlu-a4s8g3 , ostlu-a4s8n8 , ostlu-a4s8s1 , ostlu-a4s958 , ostlu-a4sac2 , ostlu-a4saz3 , ostlu-a4sbb7 , ostlu-a4s6q5 , ostlu-a4s1q9 , ostlu-a4s8b2 , ostlu-a4s262

Title : The Chlamydomonas genome reveals the evolution of key animal and plant functions - Merchant_2007_Science_318_245
Author(s) : Merchant SS , Prochnik SE , Vallon O , Harris EH , Karpowicz SJ , Witman GB , Terry A , Salamov A , Fritz-Laylin LK , Marechal-Drouard L , Marshall WF , Qu LH , Nelson DR , Sanderfoot AA , Spalding MH , Kapitonov VV , Ren Q , Ferris P , Lindquist E , Shapiro H , Lucas SM , Grimwood J , Schmutz J , Cardol P , Cerutti H , Chanfreau G , Chen CL , Cognat V , Croft MT , Dent R , Dutcher S , Fernandez E , Fukuzawa H , Gonzalez-Ballester D , Gonzalez-Halphen D , Hallmann A , Hanikenne M , Hippler M , Inwood W , Jabbari K , Kalanon M , Kuras R , Lefebvre PA , Lemaire SD , Lobanov AV , Lohr M , Manuell A , Meier I , Mets L , Mittag M , Mittelmeier T , Moroney JV , Moseley J , Napoli C , Nedelcu AM , Niyogi K , Novoselov SV , Paulsen IT , Pazour G , Purton S , Ral JP , Riano-Pachon DM , Riekhof W , Rymarquis L , Schroda M , Stern D , Umen J , Willows R , Wilson N , Zimmer SL , Allmer J , Balk J , Bisova K , Chen CJ , Elias M , Gendler K , Hauser C , Lamb MR , Ledford H , Long JC , Minagawa J , Page MD , Pan J , Pootakham W , Roje S , Rose A , Stahlberg E , Terauchi AM , Yang P , Ball S , Bowler C , Dieckmann CL , Gladyshev VN , Green P , Jorgensen R , Mayfield S , Mueller-Roeber B , Rajamani S , Sayre RT , Brokstein P , Dubchak I , Goodstein D , Hornick L , Huang YW , Jhaveri J , Luo Y , Martinez D , Ngau WC , Otillar B , Poliakov A , Porter A , Szajkowski L , Werner G , Zhou K , Grigoriev IV , Rokhsar DS , Grossman AR
Ref : Science , 318 :245 , 2007
Abstract : Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.
ESTHER : Merchant_2007_Science_318_245
PubMedSearch : Merchant_2007_Science_318_245
PubMedID: 17932292
Gene_locus related to this paper: chlre-a0a2k3e2k6 , chlre-a8hmd4 , chlre-a8hqa9 , chlre-a8htq0 , chlre-a8hus6.1 , chlre-a8hus6.2 , chlre-a8icg4 , chlre-a8iwm0 , chlre-a8ize5 , chlre-a8j2s9 , chlre-a8j5w6 , chlre-a8j7f8 , chlre-a8j8u9 , chlre-a8j8v0 , chlre-a8j9u6 , chlre-a8j143 , chlre-a8j248 , chlre-a8jd32 , chlre-a8jd42 , chlre-a8jgj2 , chlre-a8jhc8 , chlre-a8jhe5 , chlre-a8iwj1 , chlre-a8j7d5 , chlre-a0a2k3dii0

Title : Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus - Myers_2007_Nat.Biotechnol_25_569
Author(s) : Myers GS , Parker D , Al-Hasani K , Kennan RM , Seemann T , Ren Q , Badger JH , Selengut JD , DeBoy RT , Tettelin H , Boyce JD , McCarl VP , Han X , Nelson WC , Madupu R , Mohamoud Y , Holley T , Fedorova N , Khouri H , Bottomley SP , Whittington RJ , Adler B , Songer JG , Rood JI , Paulsen IT
Ref : Nat Biotechnol , 25 :569 , 2007
Abstract : Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.
ESTHER : Myers_2007_Nat.Biotechnol_25_569
PubMedSearch : Myers_2007_Nat.Biotechnol_25_569
PubMedID: 17468768
Gene_locus related to this paper: dicnv-a5evg0 , dicnv-a5ewn0 , dicnv-a5ewp3

Title : Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa - Brayton_2007_PLoS.Pathog_3_1401
Author(s) : Brayton KA , Lau AO , Herndon DR , Hannick L , Kappmeyer LS , Berens SJ , Bidwell SL , Brown WC , Crabtree J , Fadrosh D , Feldblum T , Forberger HA , Haas BJ , Howell JM , Khouri H , Koo H , Mann DJ , Norimine J , Paulsen IT , Radune D , Ren Q , Smith RK, Jr. , Suarez CE , White O , Wortman JR , Knowles DP, Jr. , McElwain TF , Nene VM
Ref : PLoS Pathog , 3 :1401 , 2007
Abstract : Babesia bovis is an apicomplexan tick-transmitted pathogen of cattle imposing a global risk and severe constraints to livestock health and economic development. The complete genome sequence was undertaken to facilitate vaccine antigen discovery, and to allow for comparative analysis with the related apicomplexan hemoprotozoa Theileria parva and Plasmodium falciparum. At 8.2 Mbp, the B. bovis genome is similar in size to that of Theileria spp. Structural features of the B. bovis and T. parva genomes are remarkably similar, and extensive synteny is present despite several chromosomal rearrangements. In contrast, B. bovis and P. falciparum, which have similar clinical and pathological features, have major differences in genome size, chromosome number, and gene complement. Chromosomal synteny with P. falciparum is limited to microregions. The B. bovis genome sequence has allowed wide scale analyses of the polymorphic variant erythrocyte surface antigen protein (ves1 gene) family that, similar to the P. falciparum var genes, is postulated to play a role in cytoadhesion, sequestration, and immune evasion. The approximately 150 ves1 genes are found in clusters that are distributed throughout each chromosome, with an increased concentration adjacent to a physical gap on chromosome 1 that contains multiple ves1-like sequences. ves1 clusters are frequently linked to a novel family of variant genes termed smorfs that may themselves contribute to immune evasion, may play a role in variant erythrocyte surface antigen protein biology, or both. Initial expression analysis of ves1 and smorf genes indicates coincident transcription of multiple variants. B. bovis displays a limited metabolic potential, with numerous missing pathways, including two pathways previously described for the P. falciparum apicoplast. This reduced metabolic potential is reflected in the B. bovis apicoplast, which appears to have fewer nuclear genes targeted to it than other apicoplast containing organisms. Finally, comparative analyses have identified several novel vaccine candidates including a positional homolog of p67 and SPAG-1, Theileria sporozoite antigens targeted for vaccine development. The genome sequence provides a greater understanding of B. bovis metabolism and potential avenues for drug therapies and vaccine development.
ESTHER : Brayton_2007_PLoS.Pathog_3_1401
PubMedSearch : Brayton_2007_PLoS.Pathog_3_1401
PubMedID: 17953480
Gene_locus related to this paper: babbo-a7amu4 , babbo-a7as90 , babbo-a7au28 , babbo-a7avh4

Title : Genome sequence of Aedes aegypti, a major arbovirus vector - Nene_2007_Science_316_1718
Author(s) : Nene V , Wortman JR , Lawson D , Haas B , Kodira C , Tu ZJ , Loftus B , Xi Z , Megy K , Grabherr M , Ren Q , Zdobnov EM , Lobo NF , Campbell KS , Brown SE , Bonaldo MF , Zhu J , Sinkins SP , Hogenkamp DG , Amedeo P , Arensburger P , Atkinson PW , Bidwell S , Biedler J , Birney E , Bruggner RV , Costas J , Coy MR , Crabtree J , Crawford M , Debruyn B , Decaprio D , Eiglmeier K , Eisenstadt E , El-Dorry H , Gelbart WM , Gomes SL , Hammond M , Hannick LI , Hogan JR , Holmes MH , Jaffe D , Johnston JS , Kennedy RC , Koo H , Kravitz S , Kriventseva EV , Kulp D , LaButti K , Lee E , Li S , Lovin DD , Mao C , Mauceli E , Menck CF , Miller JR , Montgomery P , Mori A , Nascimento AL , Naveira HF , Nusbaum C , O'Leary S , Orvis J , Pertea M , Quesneville H , Reidenbach KR , Rogers YH , Roth CW , Schneider JR , Schatz M , Shumway M , Stanke M , Stinson EO , Tubio JM , Vanzee JP , Verjovski-Almeida S , Werner D , White O , Wyder S , Zeng Q , Zhao Q , Zhao Y , Hill CA , Raikhel AS , Soares MB , Knudson DL , Lee NH , Galagan J , Salzberg SL , Paulsen IT , Dimopoulos G , Collins FH , Birren B , Fraser-Liggett CM , Severson DW
Ref : Science , 316 :1718 , 2007
Abstract : We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
ESTHER : Nene_2007_Science_316_1718
PubMedSearch : Nene_2007_Science_316_1718
PubMedID: 17510324
Gene_locus related to this paper: aedae-ACHE , aedae-ACHE1 , aedae-glita , aedae-q0iea6 , aedae-q0iev6 , aedae-q0ifn6 , aedae-q0ifn8 , aedae-q0ifn9 , aedae-q0ifp0 , aedae-q0ig41 , aedae-q1dgl0 , aedae-q1dh03 , aedae-q1dh19 , aedae-q1hqe6 , aedae-Q8ITU8 , aedae-Q8MMJ6 , aedae-Q8T9V6 , aedae-q16e91 , aedae-q16f04 , aedae-q16f25 , aedae-q16f26 , aedae-q16f28 , aedae-q16f29 , aedae-q16f30 , aedae-q16gq5 , aedae-q16iq5 , aedae-q16je0 , aedae-q16je1 , aedae-q16je2 , aedae-q16ks8 , aedae-q16lf2 , aedae-q16lv6 , aedae-q16m61 , aedae-q16mc1 , aedae-q16mc6 , aedae-q16mc7 , aedae-q16md1 , aedae-q16ms7 , aedae-q16nk5 , aedae-q16rl5 , aedae-q16rz9 , aedae-q16si8 , aedae-q16t49 , aedae-q16wf1 , aedae-q16x18 , aedae-q16xp8 , aedae-q16xu6 , aedae-q16xw5 , aedae-q16xw6 , aedae-q16y04 , aedae-q16y05 , aedae-q16y06 , aedae-q16y07 , aedae-q16y39 , aedae-q16y40 , aedae-q16yg4 , aedae-q16z03 , aedae-q17aa7 , aedae-q17av1 , aedae-q17av2 , aedae-q17av3 , aedae-q17av4 , aedae-q17b28 , aedae-q17b29 , aedae-q17b30 , aedae-q17b31 , aedae-q17b32 , aedae-q17bm3 , aedae-q17bm4 , aedae-q17bv7 , aedae-q17c44 , aedae-q17cz1 , aedae-q17d32 , aedae-q17g39 , aedae-q17g40 , aedae-q17g41 , aedae-q17g42 , aedae-q17g43 , aedae-q17g44 , aedae-q17gb8 , aedae-q17gr3 , aedae-q17if7 , aedae-q17if9 , aedae-q17ig1 , aedae-q17ig2 , aedae-q17is4 , aedae-q17l09 , aedae-q17m26 , aedae-q17mg9 , aedae-q17mv4 , aedae-q17mv5 , aedae-q17mv6 , aedae-q17mv7 , aedae-q17mw8 , aedae-q17mw9 , aedae-q17nw5 , aedae-q17nx5 , aedae-q17pa4 , aedae-q17q69 , aedae-q170k7 , aedae-q171y4 , aedae-q172e0 , aedae-q176i8 , aedae-q176j0 , aedae-q177k1 , aedae-q177k2 , aedae-q177l9 , aedae-j9hic3 , aedae-q179r9 , aedae-u483 , aedae-j9hj23 , aedae-q17d68 , aedae-q177c7 , aedae-q0ifp1 , aedae-a0a1s4fx83 , aedae-a0a1s4g2m0 , aedae-q1hr49

Title : Draft genome of the filarial nematode parasite Brugia malayi - Ghedin_2007_Science_317_1756
Author(s) : Ghedin E , Wang S , Spiro D , Caler E , Zhao Q , Crabtree J , Allen JE , Delcher AL , Guiliano DB , Miranda-Saavedra D , Angiuoli SV , Creasy T , Amedeo P , Haas B , El-Sayed NM , Wortman JR , Feldblyum T , Tallon L , Schatz M , Shumway M , Koo H , Salzberg SL , Schobel S , Pertea M , Pop M , White O , Barton GJ , Carlow CK , Crawford MJ , Daub J , Dimmic MW , Estes CF , Foster JM , Ganatra M , Gregory WF , Johnson NM , Jin J , Komuniecki R , Korf I , Kumar S , Laney S , Li BW , Li W , Lindblom TH , Lustigman S , Ma D , Maina CV , Martin DM , McCarter JP , McReynolds L , Mitreva M , Nutman TB , Parkinson J , Peregrin-Alvarez JM , Poole C , Ren Q , Saunders L , Sluder AE , Smith K , Stanke M , Unnasch TR , Ware J , Wei AD , Weil G , Williams DJ , Zhang Y , Williams SA , Fraser-Liggett C , Slatko B , Blaxter ML , Scott AL
Ref : Science , 317 :1756 , 2007
Abstract : Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the approximately 90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict approximately 11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during approximately 350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design.
ESTHER : Ghedin_2007_Science_317_1756
PubMedSearch : Ghedin_2007_Science_317_1756
PubMedID: 17885136
Gene_locus related to this paper: bruma-a8ndk6 , bruma-a8njt8 , bruma-a8nl88 , bruma-a8npi4 , bruma-a8npi6 , bruma-a8p6g9 , bruma-a8pah3 , bruma-a8pc38 , bruma-a8pek5 , bruma-a8piq4 , bruma-a8pnw8 , bruma-a8psu4 , bruma-a8pte1 , bruma-a8q606 , bruma-a8q632 , bruma-a8q937 , bruma-a8qav5 , bruma-a8qbd9 , bruma-a8qgj6 , bruma-a8qh78 , bruma-a8q143 , bruma-a0a024mej5 , bruma-a0a0k0jju9 , bruma-a0a0i9n517

Title : Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades - Seshadri_2006_J.Bacteriol_188_8272
Author(s) : Seshadri R , Joseph SW , Chopra AK , Sha J , Shaw J , Graf J , Haft D , Wu M , Ren Q , Rosovitz MJ , Madupu R , Tallon L , Kim M , Jin S , Vuong H , Stine OC , Ali A , Horneman AJ , Heidelberg JF
Ref : Journal of Bacteriology , 188 :8272 , 2006
Abstract : The complete genome of Aeromonas hydrophila ATCC 7966(T) was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate List because of its potential to cause human disease. The 4.7-Mb genome of this emerging pathogen shows a physiologically adroit organism with broad metabolic capabilities and considerable virulence potential. A large array of virulence genes, including some identified in clinical isolates of Aeromonas spp. or Vibrio spp., may confer upon this organism the ability to infect a wide range of hosts. However, two recognized virulence markers, a type III secretion system and a lateral flagellum, that are reported in other A. hydrophila strains are not identified in the sequenced isolate, ATCC 7966(T). Given the ubiquity and free-living lifestyle of this organism, there is relatively little evidence of fluidity in terms of mobile elements in the genome of this particular strain. Notable aspects of the metabolic repertoire of A. hydrophila include dissimilatory sulfate reduction and resistance mechanisms (such as thiopurine reductase, arsenate reductase, and phosphonate degradation enzymes) against toxic compounds encountered in polluted waters. These enzymes may have bioremediative as well as industrial potential. Thus, the A. hydrophila genome sequence provides valuable insights into its ability to flourish in both aquatic and host environments.
ESTHER : Seshadri_2006_J.Bacteriol_188_8272
PubMedSearch : Seshadri_2006_J.Bacteriol_188_8272
PubMedID: 16980456
Gene_locus related to this paper: aerhh-a0kes5 , aerhh-a0keu7 , aerhh-a0kf11 , aerhh-a0kfl9 , aerhh-a0kfn7 , aerhh-a0kgz2 , aerhh-a0khk1 , aerhh-a0kin3 , aerhh-a0kiv7 , aerhh-a0kkc6 , aerhh-a0kkj8 , aerhh-a0klc3 , aerhh-a0kme3 , aerhh-a0knr1 , aerhh-a0knu8 , aerhh-a0kp50 , aerhh-a0kpk1 , aerhh-a0kr22 , aerhy-PHAC , aerpu-PEP , aerhh-a0khd8 , aerhh-a0kle4 , aerhy-a0a028v5g9

Title : Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus - Badger_2006_J.Bacteriol_188_6841
Author(s) : Badger JH , Hoover TR , Brun YV , Weiner RM , Laub MT , Alexandre G , Mrazek J , Ren Q , Paulsen IT , Nelson KE , Khouri HM , Radune D , Sosa J , Dodson RJ , Sullivan SA , Rosovitz MJ , Madupu R , Brinkac LM , Durkin AS , Daugherty SC , Kothari SP , Giglio MG , Zhou L , Haft DH , Selengut JD , Davidsen TM , Yang Q , Zafar N , Ward NL
Ref : Journal of Bacteriology , 188 :6841 , 2006
Abstract : The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.
ESTHER : Badger_2006_J.Bacteriol_188_6841
PubMedSearch : Badger_2006_J.Bacteriol_188_6841
PubMedID: 16980487
Gene_locus related to this paper: hypna-q0bwt8 , hypna-q0bwv5 , hypna-q0bww7 , hypna-q0bxb2 , hypna-q0bxr5 , hypna-q0by84 , hypna-q0byl3 , hypna-q0bz23 , hypna-q0bzi5 , hypna-q0c0f7 , hypna-q0c0f8 , hypna-q0c2v8 , hypna-q0c2w1 , hypna-q0c2w4 , hypna-q0c3g0 , hypna-q0c4j0 , hypna-q0c4n1 , hypna-q0c4q9 , hypna-q0c4v5 , hypna-q0c386 , hypna-q0c539 , hypna-q0c611

Title : Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens - Myers_2006_Genome.Res_16_1031
Author(s) : Myers GS , Rasko DA , Cheung JK , Ravel J , Seshadri R , DeBoy RT , Ren Q , Varga J , Awad MM , Brinkac LM , Daugherty SC , Haft DH , Dodson RJ , Madupu R , Nelson WC , Rosovitz MJ , Sullivan SA , Khouri H , Dimitrov GI , Watkins KL , Mulligan S , Benton J , Radune D , Fisher DJ , Atkins HS , Hiscox T , Jost BH , Billington SJ , Songer JG , McClane BA , Titball RW , Rood JI , Melville SB , Paulsen IT
Ref : Genome Res , 16 :1031 , 2006
Abstract : Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique "genomic islands" identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
ESTHER : Myers_2006_Genome.Res_16_1031
PubMedSearch : Myers_2006_Genome.Res_16_1031
PubMedID: 16825665
Gene_locus related to this paper: clope-CPE0307 , clope-CPE0432 , clope-CPE1581 , clope-CPE1596 , clope-CPE1989 , clope-CPE2231 , clope-lipa , clope-LIPB , clope-PLDB

Title : Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment - Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
Author(s) : Palenik B , Ren Q , Dupont CL , Myers GS , Heidelberg JF , Badger JH , Madupu R , Nelson WC , Brinkac LM , Dodson RJ , Durkin AS , Daugherty SC , Sullivan SA , Khouri H , Mohamoud Y , Halpin R , Paulsen IT
Ref : Proc Natl Acad Sci U S A , 103 :13555 , 2006
Abstract : Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
ESTHER : Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
PubMedSearch : Palenik_2006_Proc.Natl.Acad.Sci.U.S.A_103_13555
PubMedID: 16938853
Gene_locus related to this paper: syns3-q0i8r7 , syns3-q0i9w2 , syns3-q0i996 , syns3-q0ia13 , syns3-q0ia55 , syns3-q0ib73 , syns3-q0ibm2 , syns3-q0ibp1 , syns3-q0iby1 , syns9-q3ax89 , syns3-q0ibv4

Title : Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote - Eisen_2006_PLoS.Biol_4_e286
Author(s) : Eisen JA , Coyne RS , Wu M , Wu D , Thiagarajan M , Wortman JR , Badger JH , Ren Q , Amedeo P , Jones KM , Tallon LJ , Delcher AL , Salzberg SL , Silva JC , Haas BJ , Majoros WH , Farzad M , Carlton JM , Smith RK, Jr. , Garg J , Pearlman RE , Karrer KM , Sun L , Manning G , Elde NC , Turkewitz AP , Asai DJ , Wilkes DE , Wang Y , Cai H , Collins K , Stewart BA , Lee SR , Wilamowska K , Weinberg Z , Ruzzo WL , Wloga D , Gaertig J , Frankel J , Tsao CC , Gorovsky MA , Keeling PJ , Waller RF , Patron NJ , Cherry JM , Stover NA , Krieger CJ , del Toro C , Ryder HF , Williamson SC , Barbeau RA , Hamilton EP , Orias E
Ref : PLoS Biol , 4 :e286 , 2006
Abstract : The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
ESTHER : Eisen_2006_PLoS.Biol_4_e286
PubMedSearch : Eisen_2006_PLoS.Biol_4_e286
PubMedID: 16933976
Gene_locus related to this paper: tetts-i7mam3 , tetts-i7ml33

Title : Comparative genomics of emerging human ehrlichiosis agents - Dunning Hotopp_2006_PLoS.Genet_2_e21
Author(s) : Dunning Hotopp JC , Lin M , Madupu R , Crabtree J , Angiuoli SV , Eisen JA , Seshadri R , Ren Q , Wu M , Utterback TR , Smith S , Lewis M , Khouri H , Zhang C , Niu H , Lin Q , Ohashi N , Zhi N , Nelson W , Brinkac LM , Dodson RJ , Rosovitz MJ , Sundaram J , Daugherty SC , Davidsen T , Durkin AS , Gwinn M , Haft DH , Selengut JD , Sullivan SA , Zafar N , Zhou L , Benahmed F , Forberger H , Halpin R , Mulligan S , Robinson J , White O , Rikihisa Y , Tettelin H
Ref : PLoS Genet , 2 :e21 , 2006
Abstract : Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens.
ESTHER : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedSearch : Dunning Hotopp_2006_PLoS.Genet_2_e21
PubMedID: 16482227
Gene_locus related to this paper: anapz-q2gj80 , anapz-q2gle9 , anapz-q2glf0 , anapz-q2gln7 , ehrch-q40iu0 , ehrch-q40jj7 , ehrcr-q2gfq9 , neosm-q2gcq8 , neosm-q2gdf2 , neosm-q2gcn8 , anapz-q2gk48 , ehrcr-q2ggj6

Title : The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2 - Scott_2006_PLoS.Biol_4_e383
Author(s) : Scott KM , Sievert SM , Abril FN , Ball LA , Barrett CJ , Blake RA , Boller AJ , Chain PS , Clark JA , Davis CR , Detter C , Do KF , Dobrinski KP , Faza BI , Fitzpatrick KA , Freyermuth SK , Harmer TL , Hauser LJ , Hugler M , Kerfeld CA , Klotz MG , Kong WW , Land M , Lapidus A , Larimer FW , Longo DL , Lucas S , Malfatti SA , Massey SE , Martin DD , McCuddin Z , Meyer F , Moore JL , Ocampo LH, Jr. , Paul JH , Paulsen IT , Reep DK , Ren Q , Ross RL , Sato PY , Thomas P , Tinkham LE , Zeruth GT
Ref : PLoS Biol , 4 :e383 , 2006
Abstract : Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
ESTHER : Scott_2006_PLoS.Biol_4_e383
PubMedSearch : Scott_2006_PLoS.Biol_4_e383
PubMedID: 17105352
Gene_locus related to this paper: thicr-q31fm2 , thicr-q31ih5

Title : Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes - Gardner_2005_Science_309_134
Author(s) : Gardner MJ , Bishop R , Shah T , de Villiers EP , Carlton JM , Hall N , Ren Q , Paulsen IT , Pain A , Berriman M , Wilson RJ , Sato S , Ralph SA , Mann DJ , Xiong Z , Shallom SJ , Weidman J , Jiang L , Lynn J , Weaver B , Shoaibi A , Domingo AR , Wasawo D , Crabtree J , Wortman JR , Haas B , Angiuoli SV , Creasy TH , Lu C , Suh B , Silva JC , Utterback TR , Feldblyum TV , Pertea M , Allen J , Nierman WC , Taracha EL , Salzberg SL , White OR , Fitzhugh HA , Morzaria S , Venter JC , Fraser CM , Nene V
Ref : Science , 309 :134 , 2005
Abstract : We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated.
ESTHER : Gardner_2005_Science_309_134
PubMedSearch : Gardner_2005_Science_309_134
PubMedID: 15994558
Gene_locus related to this paper: thepa-q4mzr2 , thepa-q4n0b4 , thepa-q4n2i4 , thepa-q4n4i8 , thepa-q4n5d6 , thepa-q4n5m4 , thepa-q4n006 , thepa-q4n9g7 , thepa-q4n315 , thepa-q4n349 , thepa-q4n803

Title : Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 - Paulsen_2005_Nat.Biotechnol_23_873
Author(s) : Paulsen IT , Press CM , Ravel J , Kobayashi DY , Myers GS , Mavrodi DV , DeBoy RT , Seshadri R , Ren Q , Madupu R , Dodson RJ , Durkin AS , Brinkac LM , Daugherty SC , Sullivan SA , Rosovitz MJ , Gwinn ML , Zhou L , Schneider DJ , Cartinhour SW , Nelson WC , Weidman J , Watkins K , Tran K , Khouri H , Pierson EA , Pierson LS, 3rd , Thomashow LS , Loper JE
Ref : Nat Biotechnol , 23 :873 , 2005
Abstract : Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.
ESTHER : Paulsen_2005_Nat.Biotechnol_23_873
PubMedSearch : Paulsen_2005_Nat.Biotechnol_23_873
PubMedID: 15980861
Gene_locus related to this paper: psef5-metx , psef5-q4k3c9 , psef5-q4k4b4 , psef5-q4k4t4 , psef5-q4k4u7 , psef5-q4k4y2 , psef5-q4k5b5 , psef5-q4k5k6 , psef5-q4k5w4 , psef5-q4k6z9 , psef5-q4k7i6 , psef5-q4k7u9 , psef5-q4k8j2 , psef5-q4k9i3 , psef5-q4k458 , psef5-q4k713 , psef5-q4k717 , psef5-q4k873 , psef5-q4k906 , psef5-q4k982 , psef5-q4k989 , psef5-q4k993 , psef5-q4kax4 , psef5-q4kay8 , psef5-q4kaz0 , psef5-q4kaz4 , psef5-q4kb21 , psef5-q4kbd7 , psef5-q4kbs3 , psef5-q4kbs6 , psef5-q4kc18 , psef5-q4kc21 , psef5-q4kcd3 , psef5-q4kch8 , psef5-q4kcj3 , psef5-q4kck4 , psef5-q4kcn8 , psef5-q4kcq2 , psef5-q4kcx3 , psef5-q4kd54 , psef5-q4kda1 , psef5-q4kdb4 , psef5-q4ke18 , psef5-q4keh1 , psef5-q4kej0 , psef5-q4keq4 , psef5-q4kes9 , psef5-q4kf14 , psef5-q4kfj4 , psef5-q4kfw0 , psef5-q4kfw1 , psef5-q4kfx7 , psef5-q4kgg3 , psef5-q4kgj9 , psef5-q4kgs6 , psef5-q4kh30 , psef5-q4kha2 , psef5-q4khf1 , psef5-q4khl0 , psef5-q4khv5 , psef5-q4ki42 , psef5-q4kj24 , psef5-q4kj95 , psef5-q4kjk5 , psef5-q4kjk7 , psef5-q4kjm8 , psef5-q4kjt7 , psef5-q4kk20 , psef5-q4kk22 , psef5-q4kk59 , psef5-q4kkf7 , psefl-PLTG , psepf-PHAZ , psef5-q4kfd8

Title : Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 - Wu_2005_PLoS.Genet_1_e65
Author(s) : Wu M , Ren Q , Durkin AS , Daugherty SC , Brinkac LM , Dodson RJ , Madupu R , Sullivan SA , Kolonay JF , Haft DH , Nelson WC , Tallon LJ , Jones KM , Ulrich LE , Gonzalez JM , Zhulin IB , Robb FT , Eisen JA
Ref : PLoS Genet , 1 :e65 , 2005
Abstract : We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a "minimal" model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously.
ESTHER : Wu_2005_PLoS.Genet_1_e65
PubMedSearch : Wu_2005_PLoS.Genet_1_e65
PubMedID: 16311624
Gene_locus related to this paper: carhz-metx , carhz-q3abd5 , carhz-q3adp4

Title : Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment - Moran_2004_Nature_432_910
Author(s) : Moran MA , Buchan A , Gonzalez JM , Heidelberg JF , Whitman WB , Kiene RP , Henriksen JR , King GM , Belas R , Fuqua C , Brinkac L , Lewis M , Johri S , Weaver B , Pai G , Eisen JA , Rahe E , Sheldon WM , Ye W , Miller TR , Carlton J , Rasko DA , Paulsen IT , Ren Q , Daugherty SC , DeBoy RT , Dodson RJ , Durkin AS , Madupu R , Nelson WC , Sullivan SA , Rosovitz MJ , Haft DH , Selengut J , Ward N
Ref : Nature , 432 :910 , 2004
Abstract : Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
ESTHER : Moran_2004_Nature_432_910
PubMedSearch : Moran_2004_Nature_432_910
PubMedID: 15602564
Gene_locus related to this paper: silpo-q5lke5 , silpo-q5lke7 , silpo-q5lke8 , silpo-q5lkk5 , silpo-q5lkv2 , silpo-q5lln9 , silpo-q5llu0 , silpo-q5llu2 , silpo-q5llx5 , silpo-q5lm66 , silpo-q5lmb9 , silpo-q5lml9 , silpo-q5lnp6 , silpo-q5lp28 , silpo-q5lp48 , silpo-q5lp56 , silpo-q5lpa5 , silpo-q5lpf7 , silpo-q5lpy6 , silpo-q5lrk1 , silpo-q5lsn7 , silpo-q5ltb5 , silpo-q5ltk0 , silpo-q5ltm5 , silpo-q5ltw8 , silpo-q5ltw9 , silpo-q5ltx1 , silpo-q5ltx5 , silpo-q5lu02 , silpo-q5lv12 , silpo-q5lv17 , silpo-q5lv53 , silpo-q5lvg9 , silpo-q5lw35 , silpo-q5lwk9 , silpo-q5lws0

Title : Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes - Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
Author(s) : Seshadri R , Myers GS , Tettelin H , Eisen JA , Heidelberg JF , Dodson RJ , Davidsen TM , DeBoy RT , Fouts DE , Haft DH , Selengut J , Ren Q , Brinkac LM , Madupu R , Kolonay J , Durkin SA , Daugherty SC , Shetty J , Shvartsbeyn A , Gebregeorgis E , Geer K , Tsegaye G , Malek J , Ayodeji B , Shatsman S , McLeod MP , Smajs D , Howell JK , Pal S , Amin A , Vashisth P , McNeill TZ , Xiang Q , Sodergren E , Baca E , Weinstock GM , Norris SJ , Fraser CM , Paulsen IT
Ref : Proc Natl Acad Sci U S A , 101 :5646 , 2004
Abstract : We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
ESTHER : Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
PubMedSearch : Seshadri_2004_Proc.Natl.Acad.Sci.U.S.A_101_5646
PubMedID: 15064399
Gene_locus related to this paper: trede-q73j01 , trede-q73kf5 , trede-q73kp3 , trede-q73ks1 , trede-q73nf8 , trede-q73qt5 , trede-q73qv0 , trede-q73ra4 , trede-q73ri8 , trede-Q93EK3 , trede-TDE0521

Title : Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) - Ward_2004_PLoS.Biol_2_e303
Author(s) : Ward N , Larsen O , Sakwa J , Bruseth L , Khouri H , Durkin AS , Dimitrov G , Jiang L , Scanlan D , Kang KH , Lewis M , Nelson KE , Methe B , Wu M , Heidelberg JF , Paulsen IT , Fouts D , Ravel J , Tettelin H , Ren Q , Read T , DeBoy RT , Seshadri R , Salzberg SL , Jensen HB , Birkeland NK , Nelson WC , Dodson RJ , Grindhaug SH , Holt I , Eidhammer I , Jonasen I , Vanaken S , Utterback T , Feldblyum TV , Fraser CM , Lillehaug JR , Eisen JA
Ref : PLoS Biol , 2 :e303 , 2004
Abstract : Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.
ESTHER : Ward_2004_PLoS.Biol_2_e303
PubMedSearch : Ward_2004_PLoS.Biol_2_e303
PubMedID: 15383840
Gene_locus related to this paper: metca-q60a38 , metca-q60bu6 , metca-q60cn0 , metca-q605j8 , metca-q606x9 , metca-q607f7 , metca-q607m2 , metca-q609v0

Title : Complete genome sequence of an M1 strain of Streptococcus pyogenes - Ferretti_2001_Proc.Natl.Acad.Sci.U.S.A_98_4658
Author(s) : Ferretti JJ , McShan WM , Ajdic D , Savic DJ , Savic G , Lyon K , Primeaux C , Sezate S , Suvorov AN , Kenton S , Lai HS , Lin SP , Qian Y , Jia HG , Najar FZ , Ren Q , Zhu H , Song L , White J , Yuan X , Clifton SW , Roe BA , McLaughlin R
Ref : Proc Natl Acad Sci U S A , 98 :4658 , 2001
Abstract : The 1,852,442-bp sequence of an M1 strain of Streptococcus pyogenes, a Gram-positive pathogen, has been determined and contains 1,752 predicted protein-encoding genes. Approximately one-third of these genes have no identifiable function, with the remainder falling into previously characterized categories of known microbial function. Consistent with the observation that S. pyogenes is responsible for a wider variety of human disease than any other bacterial species, more than 40 putative virulence-associated genes have been identified. Additional genes have been identified that encode proteins likely associated with microbial "molecular mimicry" of host characteristics and involved in rheumatic fever or acute glomerulonephritis. The complete or partial sequence of four different bacteriophage genomes is also present, with each containing genes for one or more previously undiscovered superantigen-like proteins. These prophage-associated genes encode at least six potential virulence factors, emphasizing the importance of bacteriophages in horizontal gene transfer and a possible mechanism for generating new strains with increased pathogenic potential.
ESTHER : Ferretti_2001_Proc.Natl.Acad.Sci.U.S.A_98_4658
PubMedSearch : Ferretti_2001_Proc.Natl.Acad.Sci.U.S.A_98_4658
PubMedID: 11296296
Gene_locus related to this paper: strpy-ESTA , strpy-PEPXP , strpy-Q8K5W4 , strpy-SPY1308 , strpy-SPYM18.1727

Title : The DNA sequence of human chromosome 22 - Dunham_1999_Nature_402_489
Author(s) : Dunham I , Hunt AR , Collins JE , Bruskiewich R , Beare DM , Clamp M , Smink LJ , Ainscough R , Almeida JP , Babbage AK , Bagguley C , Bailey J , Barlow KF , Bates KN , Beasley OP , Bird CP , Blakey SE , Bridgeman AM , Buck D , Burgess J , Burrill WD , Burton J , Carder C , Carter NP , Chen Y , Clark G , Clegg SM , Cobley VE , Cole CG , Collier RE , Connor R , Conroy D , Corby NR , Coville GJ , Cox AV , Davis J , Dawson E , Dhami PD , Dockree C , Dodsworth SJ , Durbin RM , Ellington AG , Evans KL , Fey JM , Fleming K , French L , Garner AA , Gilbert JGR , Goward ME , Grafham DV , Griffiths MND , Hall C , Hall RE , Hall-Tamlyn G , Heathcott RW , Ho S , Holmes S , Hunt SE , Jones MC , Kershaw J , Kimberley AM , King A , Laird GK , Langford CF , Leversha MA , Lloyd C , Lloyd DM , Martyn ID , Mashreghi-Mohammadi M , Matthews LH , Mccann OT , Mcclay J , Mclaren S , McMurray AA , Milne SA , Mortimore BJ , Odell CN , Pavitt R , Pearce AV , Pearson D , Phillimore BJCT , Phillips SH , Plumb RW , Ramsay H , Ramsey Y , Rogers L , Ross MT , Scott CE , Sehra HK , Skuce CD , Smalley S , Smith ML , Soderlund C , Spragon L , Steward CA , Sulston JE , Swann RM , Vaudin M , Wall M , Wallis JM , Whiteley MN , Willey DL , Williams L , Williams SA , Williamson H , Wilmer TE , Wilming L , Wright CL , Hubbard T , Bentley DR , Beck S , Rogers J , Shimizu N , Minoshima S , Kawasaki K , Sasaki T , Asakawa S , Kudoh J , Shintani A , Shibuya K , Yoshizaki Y , Aoki N , Mitsuyama S , Roe BA , Chen F , Chu L , Crabtree J , Deschamps S , Do A , Do T , Dorman A , Fang F , Fu Y , Hu P , Hua A , Kenton S , Lai H , Lao HI , Lewis J , Lewis S , Lin S-P , Loh P , Malaj E , Nguyen T , Pan H , Phan S , Qi S , Qian Y , Ray L , Ren Q , Shaull S , Sloan D , Song L , Wang Q , Wang Y , Wang Z , White J , Willingham D , Wu H , Yao Z , Zhan M , Zhang G , Chissoe S , Murray J , Miller N , Minx P , Fulton R , Johnson D , Bemis G , Bentley D , Bradshaw H , Bourne S , Cordes M , Du Z , Fulton L , Goela D , Graves T , Hawkins J , Hinds K , Kemp K , Latreille P , Layman D , Ozersky P , Rohlfing T , Scheet P , Walker C , Wamsley A , Wohldmann P , Pepin K , Nelson J , Korf I , Bedell JA , Hillier L , Mardis E , Waterston R , Wilson R , Emanuel BS , Shaikh T , Kurahashi H , Saitta S , Budarf ML , McDermid HE , Johnson A , Wong ACC , Morrow BE , Edelmann L , Kim UJ , Shizuya H , Simon MI , Dumanski JP , Peyrard M , Kedra D , Seroussi E , Fransson I , Tapia I , Bruder CE , O'Brien KP
Ref : Nature , 402 :489 , 1999
Abstract : Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.
ESTHER : Dunham_1999_Nature_402_489
PubMedSearch : Dunham_1999_Nature_402_489
PubMedID: 10591208
Gene_locus related to this paper: human-CES5A , human-SERHL2