Zhao GP

References (17)

Title : Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens - Liu_2013_PLoS.One_8_e55185
Author(s) : Liu G , Zhang L , Wei X , Zou G , Qin Y , Ma L , Li J , Zheng H , Wang S , Wang C , Xun L , Zhao GP , Zhou Z , Qu Y
Ref : PLoS ONE , 8 :e55185 , 2013
Abstract : Many Penicillium species could produce extracellular enzyme systems with good lignocellulose hydrolysis performance. However, these species and their enzyme systems are still poorly understood and explored due to the lacking of genetic information. Here, we present the genomic and secretomic analyses of Penicillium decumbens that has been used in industrial production of lignocellulolytic enzymes in China for more than fifteen years. Comparative genomics analysis with the phylogenetically most similar species Penicillium chrysogenum revealed that P. decumbens has evolved with more genes involved in plant cell wall degradation, but fewer genes in cellular metabolism and regulation. Compared with the widely used cellulase producer Trichoderma reesei, P. decumbens has a lignocellulolytic enzyme system with more diverse components, particularly for cellulose binding domain-containing proteins and hemicellulases. Further, proteomic analysis of secretomes revealed that P. decumbens produced significantly more lignocellulolytic enzymes in the medium with cellulose-wheat bran as the carbon source than with glucose. The results expand our knowledge on the genetic information of lignocellulolytic enzyme systems in Penicillium species, and will facilitate rational strain improvement for the production of highly efficient enzyme systems used in lignocellulose utilization from Penicillium species.
ESTHER : Liu_2013_PLoS.One_8_e55185
PubMedSearch : Liu_2013_PLoS.One_8_e55185
PubMedID: 23383313
Gene_locus related to this paper: peno1-s7zjd1 , peno1-s8aym9 , peno1-s7zcd7 , peno1-s8aui7 , peno1-s7zba9 , peno1-s7z7w2 , peno1-s7zkn6 , peno1-s8ak78 , peno1-s7z721 , peno1-s8ajn6 , peno1-s7zqw4 , peno1-s8bba0 , peno1-s8b4w2 , peno1-s7zta4 , peno1-s8a1h3 , peno1-s8aiq5 , peno1-s8ba66 , peno1-s7zxp5 , penox-poxo

Title : Complete genome sequence of Amycolatopsis mediterranei S699 based on de novo assembly via a combinatorial sequencing strategy - Tang_2012_J.Bacteriol_194_5699
Author(s) : Tang B , Zhao W , Zheng H , Zhuo Y , Zhang L , Zhao GP
Ref : Journal of Bacteriology , 194 :5699 , 2012
Abstract : The genome of Amycolatopsis mediterranei S699 was resequenced and assembled de novo. By comparing the sequences of S699 previously released and that of A. mediterranei U32, about 10 kb of major indels was found to differ between the two S699 genomes, and the differences are likely attributable to their different assembly strategies.
ESTHER : Tang_2012_J.Bacteriol_194_5699
PubMedSearch : Tang_2012_J.Bacteriol_194_5699
PubMedID: 23012281
Gene_locus related to this paper: amymu-d8hpp2 , amyms-g0fkj6

Title : Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana - Xiao_2012_Sci.Rep_2_483
Author(s) : Xiao G , Ying SH , Zheng P , Wang ZL , Zhang S , Xie XQ , Shang Y , St Leger RJ , Zhao GP , Wang C , Feng MG
Ref : Sci Rep , 2 :483 , 2012
Abstract : The ascomycete fungus Beauveria bassiana is a pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. We sequenced the genome of B. bassiana and a phylogenomic analysis confirmed that ascomycete entomopathogenicity is polyphyletic, but also revealed convergent evolution to insect pathogenicity. We also found many species-specific virulence genes and gene family expansions and contractions that correlate with host ranges and pathogenic strategies. These include B. bassiana having many more bacterial-like toxins (suggesting an unsuspected potential for oral toxicity) and effector-type proteins. The genome also revealed that B. bassiana resembles the closely related Cordyceps militaris in being heterothallic, although its sexual stage is rarely observed. A high throughput RNA-seq transcriptomic analysis revealed that B. bassiana could sense and adapt to different environmental niches by activating well-defined gene sets. The information from this study will facilitate further development of B. bassiana as a cost-effective mycoinsecticide.
ESTHER : Xiao_2012_Sci.Rep_2_483
PubMedSearch : Xiao_2012_Sci.Rep_2_483
PubMedID: 22761991
Gene_locus related to this paper: beab2-j4kp85 , beab2-j4kq23 , beab2-j4ugv0 , beab2-j4ujz3 , beab2-j4urc2 , beab2-j4ut21 , beab2-j4uti2 , beab2-j4vvv1 , beab2-j4wbg2 , beab2-j5jde3 , beab2-j5jzt0 , beab2-j4wjh2 , beaba-a0a2s7xwt2 , 9hypo-a0a167hq40 , beab2-ops1

Title : Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601 - Zhong_2011_Cell.Res_21_1210
Author(s) : Zhong Y , Chang X , Cao XJ , Zhang Y , Zheng H , Zhu Y , Cai C , Cui Z , Li YY , Jiang XG , Zhao GP , Wang S , Li Y , Zeng R , Li X , Guo XK
Ref : Cell Res , 21 :1210 , 2011
Abstract : The virulence-attenuated Leptospira interrogans serovar Lai strain IPAV was derived by prolonged laboratory passage from a highly virulent ancestral strain isolated in China. We studied the genetic variations of IPAV that render it avirulent via comparative analysis against the pathogenic L. interrogans serovar Lai strain 56601. The complete genome sequence of the IPAV strain was determined and used to compare with, and then rectify and reannotate the genome sequence of strain 56601. Aside from their highly similar genomic structure and gene order, a total of 33 insertions, 53 deletions and 301 single-nucleotide variations (SNVs) were detected throughout the genome of IPAV directly affecting 101 genes, either in their 5' upstream region or within their coding region. Among them, the majority of the 44 functional genes are involved in signal transduction, stress response, transmembrane transport and nitrogen metabolism. Comparative proteomic analysis based on quantitative liquid chromatography (LC)-MS/MS data revealed that among 1 627 selected pairs of orthologs, 174 genes in the IPAV strain were upregulated, with enrichment mainly in classes of energy production and lipid metabolism. In contrast, 228 genes in strain 56601 were upregulated, with the majority enriched in the categories of protein translation and DNA replication/repair. The combination of genomic and proteomic approaches illustrated that altered expression or mutations in critical genes, such as those encoding a Ser/Thr kinase, carbon-starvation protein CstA, glutamine synthetase, GTP-binding protein BipA, ribonucleotide-diphosphate reductase and phosphate transporter, and alterations in the translational profile of lipoproteins or outer membrane proteins are likely to account for the virulence attenuation in strain IPAV.
ESTHER : Zhong_2011_Cell.Res_21_1210
PubMedSearch : Zhong_2011_Cell.Res_21_1210
PubMedID: 21423275
Gene_locus related to this paper: lepin-q72tt9

Title : Genome sequence of a porcine extraintestinal pathogenic Escherichia coli strain - Tan_2011_J.Bacteriol_193_5038
Author(s) : Tan C , Xu Z , Zheng H , Liu W , Tang X , Shou J , Wu B , Wang S , Zhao GP , Chen H
Ref : Journal of Bacteriology , 193 :5038 , 2011
Abstract : Extraintestinal pathogenic Escherichia coli (ExPEC) is an important pathogen which can infect humans and animals and cause many diseases outside the intestine. Here, we report the first draft genome sequence of a porcine ExPEC strain, PCN033, isolated from a pig with meningitis.
ESTHER : Tan_2011_J.Bacteriol_193_5038
PubMedSearch : Tan_2011_J.Bacteriol_193_5038
PubMedID: 21742868
Gene_locus related to this paper: ecoli-IROD , ecoli-IROE , ecoli-ycfp , ecoli-YFBB , ecoli-ypt1 , ecoli-yqia

Title : Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine - Zheng_2011_Genome.Biol_12_R116
Author(s) : Zheng P , Xia Y , Xiao G , Xiong C , Hu X , Zhang S , Zheng H , Huang Y , Zhou Y , Wang S , Zhao GP , Liu X , St Leger RJ , Wang C
Ref : Genome Biol , 12 :R116 , 2011
Abstract : BACKGROUND: Species in the ascomycete fungal genus Cordyceps have been proposed to be the teleomorphs of Metarhizium species. The latter have been widely used as insect biocontrol agents. Cordyceps species are highly prized for use in traditional Chinese medicines, but the genes responsible for biosynthesis of bioactive components, insect pathogenicity and the control of sexuality and fruiting have not been determined.
RESULTS: Here, we report the genome sequence of the type species Cordyceps militaris. Phylogenomic analysis suggests that different species in the Cordyceps/Metarhizium genera have evolved into insect pathogens independently of each other, and that their similar large secretomes and gene family expansions are due to convergent evolution. However, relative to other fungi, including Metarhizium spp., many protein families are reduced in C. militaris, which suggests a more restricted ecology. Consistent with its long track record of safe usage as a medicine, the Cordyceps genome does not contain genes for known human mycotoxins. We establish that C. militaris is sexually heterothallic but, very unusually, fruiting can occur without an opposite mating-type partner. Transcriptional profiling indicates that fruiting involves induction of the Zn2Cys6-type transcription factors and MAPK pathway; unlike other fungi, however, the PKA pathway is not activated.
CONCLUSIONS: The data offer a better understanding of Cordyceps biology and will facilitate the exploitation of medicinal compounds produced by the fungus.
ESTHER : Zheng_2011_Genome.Biol_12_R116
PubMedSearch : Zheng_2011_Genome.Biol_12_R116
PubMedID: 22112802
Gene_locus related to this paper: cormm-g3jhe4 , cormm-g3j5w5 , cormm-g3jjs8 , cormm-g3jj84 , cormm-g3j580 , cormm-g3jkl0 , cormi-a0a2h4sj63 , cormm-g3jpf2

Title : Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum - Gao_2011_PLoS.Genet_7_e1001264
Author(s) : Gao Q , Jin K , Ying SH , Zhang Y , Xiao G , Shang Y , Duan Z , Hu X , Xie XQ , Zhou G , Peng G , Luo Z , Huang W , Wang B , Fang W , Wang S , Zhong Y , Ma LJ , St Leger RJ , Zhao GP , Pei Y , Feng MG , Xia Y , Wang C
Ref : PLoS Genet , 7 :e1001264 , 2011
Abstract : Metarhizium spp. are being used as environmentally friendly alternatives to chemical insecticides, as model systems for studying insect-fungus interactions, and as a resource of genes for biotechnology. We present a comparative analysis of the genome sequences of the broad-spectrum insect pathogen Metarhizium anisopliae and the acridid-specific M. acridum. Whole-genome analyses indicate that the genome structures of these two species are highly syntenic and suggest that the genus Metarhizium evolved from plant endophytes or pathogens. Both M. anisopliae and M. acridum have a strikingly larger proportion of genes encoding secreted proteins than other fungi, while ~30% of these have no functionally characterized homologs, suggesting hitherto unsuspected interactions between fungal pathogens and insects. The analysis of transposase genes provided evidence of repeat-induced point mutations occurring in M. acridum but not in M. anisopliae. With the help of pathogen-host interaction gene database, ~16% of Metarhizium genes were identified that are similar to experimentally verified genes involved in pathogenicity in other fungi, particularly plant pathogens. However, relative to M. acridum, M. anisopliae has evolved with many expanded gene families of proteases, chitinases, cytochrome P450s, polyketide synthases, and nonribosomal peptide synthetases for cuticle-degradation, detoxification, and toxin biosynthesis that may facilitate its ability to adapt to heterogeneous environments. Transcriptional analysis of both fungi during early infection processes provided further insights into the genes and pathways involved in infectivity and specificity. Of particular note, M. acridum transcribed distinct G-protein coupled receptors on cuticles from locusts (the natural hosts) and cockroaches, whereas M. anisopliae transcribed the same receptor on both hosts. This study will facilitate the identification of virulence genes and the development of improved biocontrol strains with customized properties.
ESTHER : Gao_2011_PLoS.Genet_7_e1001264
PubMedSearch : Gao_2011_PLoS.Genet_7_e1001264
PubMedID: 21253567
Gene_locus related to this paper: metaq-dapb , metaq-e9dr02 , metaq-e9dr46 , metaq-e9dx32 , metaq-e9dy00 , metaq-e9e6i5 , metaq-e9e332 , metaq-e9e873 , metaq-e9eaq4 , metaq-e9ebs3 , metaq-e9ebt3 , metaq-e9edi2 , metaq-e9edr0 , metaq-e9ee29 , metaq-e9eej3 , metaq-e9ef60 , metaq-e9ef98 , metaq-e9efc1 , metaq-e9eg97 , metaq-e9egz7 , metaq-kex1 , metar-dapb , metar-e9ej81 , metar-e9ejw6 , metar-e9ek06 , metar-e9eka7 , metar-e9eku9 , metar-e9em68 , metar-e9emd0 , metar-e9enf9 , metar-e9eny8 , metar-e9ep20 , metar-e9ep60 , metar-e9eqh0 , metar-e9etb2 , metar-e9etp6 , metar-e9euh9 , metar-e9ey62 , metar-e9eyx6 , metar-e9ezk2 , metar-e9f3f2 , metar-e9f3j3 , metar-e9f3l3 , metar-e9f3z5 , metar-e9f6q5 , metar-e9f6t6 , metar-e9f7y7 , metar-e9f9h2 , metar-e9f029 , metar-e9f205 , metar-e9f721 , metar-e9fa63 , metar-e9fab1 , metar-e9fas3 , metar-e9fbn5 , metar-e9fbt1 , metar-e9fd34 , metaq-e9eej8 , metaq-e9dx35 , metar-e9f3e9 , metar-e9f0w8 , metan-a0a086npb7 , 9hypo-a0a014p983 , metan-a0a086nhe0 , 9hypo-a0a0a1v7e9 , metaq-e9e0y0 , metan-a0a0d9pev7 , metaq-e9edt7 , metra-e9ewg3 , metra-pks2 , metaf-pks1 , metaq-pks2 , metaq-e9e9z0

Title : Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism - Zhao_2010_Cell.Res_20_1096
Author(s) : Zhao W , Zhong Y , Yuan H , Wang J , Zheng H , Wang Y , Cen X , Xu F , Bai J , Han X , Lu G , Zhu Y , Shao Z , Yan H , Li C , Peng N , Zhang Z , Zhang Y , Lin W , Fan Y , Qin Z , Hu Y , Zhu B , Wang S , Ding X , Zhao GP
Ref : Cell Res , 20 :1096 , 2010
Abstract : Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimycobacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10,236,715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9,228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel 'quasi-core' with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.
ESTHER : Zhao_2010_Cell.Res_20_1096
PubMedSearch : Zhao_2010_Cell.Res_20_1096
PubMedID: 20567260
Gene_locus related to this paper: amyme-ester , amymu-d8hj63 , amymu-d8hka5 , amymu-d8hl19 , amymu-d8hp99 , amymu-d8hpp2 , amymu-d8htc9 , amymu-d8hu68 , amymu-d8hu87 , amymu-d8hy40 , amymu-d8hy73 , amymu-d8i2j5 , amymu-d8i4g6 , amymu-d8i8i8 , amymu-d8hri1 , amymu-d8hsx7 , amymu-d8hzu8 , amymu-d8i5g7 , amyms-g0g7f0 , amymu-a0a0h3cwx4 , amymu-a0a0h3d2a5 , amymu-a0a0h3d6r8

Title : Complete genome sequence of Bifidobacterium longum JDM301 - Wei_2010_J.Bacteriol_192_4076
Author(s) : Wei YX , Zhang ZY , Liu C , Zhu YZ , Zhu YQ , Zheng H , Zhao GP , Wang S , Guo XK
Ref : Journal of Bacteriology , 192 :4076 , 2010
Abstract : Bifidobacteria, known as probiotic bacteria, are high-G+C Gram-positive bacteria which naturally inhabit the human gastrointestinal tract and vagina. Recently, we completely sequenced Bifidobacterium longum JDM301, which is a widely used Chinese commercial strain with several probiotic properties.
ESTHER : Wei_2010_J.Bacteriol_192_4076
PubMedSearch : Wei_2010_J.Bacteriol_192_4076
PubMedID: 20525832
Gene_locus related to this paper: biflj-d6zvy3 , biflo-BL0073 , biflo-BL0336 , biflo-BL0581 , biflo-BL0582 , biflo-BL1109 , biflo-BL1514 , biflo-PTRB , bifln-c2gtr2

Title : Complete genome sequence of Lactobacillus plantarum JDM1 - Zhang_2009_J.Bacteriol_191_5020
Author(s) : Zhang ZY , Liu C , Zhu YZ , Zhong Y , Zhu YQ , Zheng HJ , Zhao GP , Wang SY , Guo XK
Ref : Journal of Bacteriology , 191 :5020 , 2009
Abstract : Lactobacillus plantarum is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.
ESTHER : Zhang_2009_J.Bacteriol_191_5020
PubMedSearch : Zhang_2009_J.Bacteriol_191_5020
PubMedID: 19465650
Gene_locus related to this paper: lacpl-EST1 , lacpl-EST2 , lacpl-HPO , lacpl-LP.0796 , lacpl-LP.0973 , lacpl-LP.1002 , lacpl-LP.1156 , lacpl-LP.1165 , lacpl-LP.1935 , lacpl-LP.2586 , lacpl-LP.2737 , lacpl-LP.2923 , lacpl-LP.3205 , lacpl-LP.3561 , lacpl-PEPI , lacpl-PEPR1 , lacpl-PEPR2 , lacpl-pepx , lacpl-tanL

Title : The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments - Ma_2009_Appl.Environ.Microbiol_75_6812
Author(s) : Ma YF , Zhang Y , Zhang JY , Chen DW , Zhu Y , Zheng H , Wang SY , Jiang CY , Zhao GP , Liu SJ
Ref : Applied Environmental Microbiology , 75 :6812 , 2009
Abstract : Members of the gram-negative, strictly aerobic genus Comamonas occur in various environments. Here we report the complete genome of Comamonas testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open reading frames (ORFs) were identified; 3,514 of these ORFs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 ORFs encode hypothetical proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2 genome has many genes for transportation (22%) and signal transduction (6%), which allows the cells to respond and adapt to changing environments. Strain CNB-2 does not assimilate carbohydrates due to the lack of genes encoding proteins involved in glycolysis and pentose phosphate pathways, and it contains many genes encoding proteins involved in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to take up and metabolize a range of carboxylic acids. This nutritional bias for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy unique niches in environments. Four different sets of terminal oxidases for the respiratory system were identified, and they putatively functioned at different oxygen concentrations. This study conclusively revealed at the genomic level that the genetic versatility of C. testosteroni is vital for competition with other bacteria in its special niches.
ESTHER : Ma_2009_Appl.Environ.Microbiol_75_6812
PubMedSearch : Ma_2009_Appl.Environ.Microbiol_75_6812
PubMedID: 19734336
Gene_locus related to this paper: comt2-d0iwv3 , comt2-d0iyk2 , comt2-d0izv6 , comt2-d0j1z3 , comt2-d0j233 , comte-b7wt77 , comte-b7wvy1 , comte-b7wwl1 , comte-b7wz02 , comte-b7x0f1 , comte-b7x2b9 , comte-b7x5l7 , comte-d8d555 , comte-TESD , comte-b7wth6 , comt2-d0j2k4

Title : Genome biology of Actinobacillus pleuropneumoniae JL03, an isolate of serotype 3 prevalent in China - Xu_2008_PLoS.One_3_e1450
Author(s) : Xu Z , Zhou Y , Li L , Zhou R , Xiao S , Wan Y , Zhang S , Wang K , Li W , Jin H , Kang M , Dalai B , Li T , Liu L , Cheng Y , Zhang L , Xu T , Zheng H , Pu S , Wang B , Gu W , Zhang XL , Zhu GF , Wang S , Zhao GP , Chen H
Ref : PLoS ONE , 3 :e1450 , 2008
Abstract : Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a cause of considerable world wide economic losses in the swine industry. We sequenced the complete genome of A. pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its genome is a single chromosome of 2,242,062 base pairs containing 2,097 predicted protein-coding sequences, six ribosomal rRNA operons, and 63 tRNA genes. Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen. We identified a full spectrum of genes related to its characteristic chemoheterotrophic catabolism of fermentation and respiration with an incomplete TCA system for anabolism. In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 5'-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03. Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)-specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.
ESTHER : Xu_2008_PLoS.One_3_e1450
PubMedSearch : Xu_2008_PLoS.One_3_e1450
PubMedID: 18197260
Gene_locus related to this paper: actp2-a3n347 , actp7-b3h2v1 , actp7-b3h2x2 , actpj-b0bpm3 , actpj-b0bqd8 , actpj-b0brq2

Title : cvhA gene of Streptomyces hygroscopicus 10-22 encodes a negative regulator for mycelia development - Wang_2006_Acta.Biochim.Biophys.Sin_38_271
Author(s) : Wang HA , Qin L , Lu P , Pang ZX , Deng ZX , Zhao GP
Ref : Acta Biochim Biophys Sin (Shanghai) , 38 :271 , 2006
Abstract : A five-gene cluster cvhABCDE was identified from Streptomyces hygroscopicus 10-22. As the first gene of this cluster, cvhA encoded a putative sensor histidine kinase with a predicted sensor domain consisting of two trans-membrane segments at the N-terminus and a conserved HATPase_c domain at the C-terminus. The C-terminus polypeptide of CvhA expressed in Escherichia coli was purified and shown to be autophosphorylated with [gamma-32P]ATP in vitro. The phosphoryl group was acid-labile and basic-stable, which supported histidine as the phosphorylation residue. No obvious difference of mycelia development was observed between the null mutant of cvhA generated by targeted gene replacement and the wild-type parental strain 10-22 grown on solid soya flour medium with 2%-8% glucose or sucrose, but the cvhA mutant could form much more abundant aerial mycelia and spores than the wild-type strain on solid soya flour medium supplemented with 6%-8% mannitol, 6%-8% sorbitol, 4%-6% mannose, or 4%-6% fructose. This phenotype was complemented by the cloned wild-type cvhA gene, and no difference was observed for growth curves of the cvhA mutant and the wild strain in liquid minimal medium with the tested sugars at a concentration of 4%, 6% and 8%. We thus propose that CvhA is likely a sensor histidine kinase and negatively regulates the morphological differentiation in a sugar-dependent manner in S. hygroscopicus 10-22.
ESTHER : Wang_2006_Acta.Biochim.Biophys.Sin_38_271
PubMedSearch : Wang_2006_Acta.Biochim.Biophys.Sin_38_271
PubMedID: 16604267
Gene_locus related to this paper: strhy-SHY9

Title : Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris - Qian_2005_Genome.Res_15_757
Author(s) : Qian W , Jia Y , Ren SX , He YQ , Feng JX , Lu LF , Sun Q , Ying G , Tang DJ , Tang H , Wu W , Hao P , Wang L , Jiang BL , Zeng S , Gu WY , Lu G , Rong L , Tian Y , Yao Z , Fu G , Chen B , Fang R , Qiang B , Chen Z , Zhao GP , Tang JL , He C
Ref : Genome Res , 15 :757 , 2005
Abstract : Xanthomonas campestris pathovar campestris (Xcc) is the causative agent of crucifer black rot disease, which causes severe losses in agricultural yield world-wide. This bacterium is a model organism for studying plant-bacteria interactions. We sequenced the complete genome of Xcc 8004 (5,148,708 bp), which is highly conserved relative to that of Xcc ATCC 33913. Comparative genomics analysis indicated that, in addition to a significant genomic-scale rearrangement cross the replication axis between two IS1478 elements, loss and acquisition of blocks of genes, rather than point mutations, constitute the main genetic variation between the two Xcc strains. Screening of a high-density transposon insertional mutant library (16,512 clones) of Xcc 8004 against a host plant (Brassica oleraceae) identified 75 nonredundant, single-copy insertions in protein-coding sequences (CDSs) and intergenic regions. In addition to known virulence factors, full virulence was found to require several additional metabolic pathways and regulatory systems, such as fatty acid degradation, type IV secretion system, cell signaling, and amino acids and nucleotide metabolism. Among the identified pathogenicity-related genes, three of unknown function were found in Xcc 8004-specific chromosomal segments, revealing a direct correlation between genomic dynamics and Xcc virulence. The present combination of comparative and functional genomic analyses provides valuable information about the genetic basis of Xcc pathogenicity, which may offer novel insight toward the development of efficient methods for prevention of this important plant disease.
ESTHER : Qian_2005_Genome.Res_15_757
PubMedSearch : Qian_2005_Genome.Res_15_757
PubMedID: 15899963
Gene_locus related to this paper: xanax-DHAA , xanax-ENTF2 , xanax-GAA , xanax-PTRB , xanax-XAC0515 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC1713 , xanca-acvB , xanca-BIOH , xanca-CATD , xanca-CPO , xanca-estA1 , xanca-impep , xanca-META , xanca-METX , xanca-PCAD , xanca-PHBC , xanca-Q8PB04 , xanca-W78 , xanca-XCC0080 , xanca-XCC0180 , xanca-XCC0243 , xanca-XCC0266 , xanca-XCC0372 , xanca-XCC0375 , xanca-XCC0753 , xanca-XCC0800 , xanca-XCC0843 , xanca-XCC1105 , xanca-XCC1734 , xanca-XCC2285 , xanca-XCC2374 , xanca-XCC2397 , xanca-XCC2405 , xanca-XCC2566 , xanca-XCC2722 , xanca-XCC2737 , xanca-XCC2811 , xanca-XCC2817 , xanca-XCC2854 , xanca-XCC2869 , xanca-XCC3028 , xanca-XCC3164 , xanca-XCC3219 , xanca-XCC3296 , xanca-XCC3320 , xanca-XCC3514 , xanca-XCC3548 , xanca-XCC3555 , xanca-XCC3623 , xanca-XCC3915 , xanca-XCC3961 , xanca-XCC3970 , xanca-XCC4016 , xanca-XCC4096 , xanca-XCC4180 , xanca-XYNB , xanca-XYNB2 , xancb-b0rq23 , xancp-q8pax3 , xancp-y2094

Title : DNA sequence and comparative analysis of chimpanzee chromosome 22 - Watanabe_2004_Nature_429_382
Author(s) : Watanabe H , Fujiyama A , Hattori M , Taylor TD , Toyoda A , Kuroki Y , Noguchi H , BenKahla A , Lehrach H , Sudbrak R , Kube M , Taenzer S , Galgoczy P , Platzer M , Scharfe M , Nordsiek G , Blocker H , Hellmann I , Khaitovich P , Paabo S , Reinhardt R , Zheng HJ , Zhang XL , Zhu GF , Wang BF , Fu G , Ren SX , Zhao GP , Chen Z , Lee YS , Cheong JE , Choi SH , Wu KM , Liu TT , Hsiao KJ , Tsai SF , Kim CG , S OO , Kitano T , Kohara Y , Saitou N , Park HS , Wang SY , Yaspo ML , Sakaki Y
Ref : Nature , 429 :382 , 2004
Abstract : Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.
ESTHER : Watanabe_2004_Nature_429_382
PubMedSearch : Watanabe_2004_Nature_429_382
PubMedID: 15164055
Gene_locus related to this paper: pantr-a0a2j8lmv7

Title : Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing - Ren_2003_Nature_422_888
Author(s) : Ren SX , Fu G , Jiang XG , Zeng R , Miao YG , Xu H , Zhang YX , Xiong H , Lu G , Lu LF , Jiang HQ , Jia J , Tu YF , Jiang JX , Gu WY , Zhang YQ , Cai Z , Sheng HH , Yin HF , Zhang Y , Zhu GF , Wan M , Huang HL , Qian Z , Wang SY , Ma W , Yao ZJ , Shen Y , Qiang BQ , Xia QC , Guo XK , Danchin A , Saint Girons I , Somerville RL , Wen YM , Shi MH , Chen Z , Xu JG , Zhao GP
Ref : Nature , 422 :888 , 2003
Abstract : Leptospirosis is a widely spread disease of global concern. Infection causes flu-like episodes with frequent severe renal and hepatic damage, such as haemorrhage and jaundice. In more severe cases, massive pulmonary haemorrhages, including fatal sudden haemoptysis, can occur. Here we report the complete genomic sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae consisting of a 4.33-megabase large chromosome and a 359-kilobase small chromosome, with a total of 4,768 predicted genes. In terms of the genetic determinants of physiological characteristics, the facultatively parasitic L. interrogans differs extensively from two other strictly parasitic pathogenic spirochaetes, Treponema pallidum and Borrelia burgdorferi, although similarities exist in the genes that govern their unique morphological features. A comprehensive analysis of the L. interrogans genes for chemotaxis/motility and lipopolysaccharide synthesis provides a basis for in-depth studies of virulence and pathogenesis. The discovery of a series of genes possibly related to adhesion, invasion and the haematological changes that characterize leptospirosis has provided clues about how an environmental organism might evolve into an important human pathogen.
ESTHER : Ren_2003_Nature_422_888
PubMedSearch : Ren_2003_Nature_422_888
PubMedID: 12712204
Gene_locus related to this paper: lepin-AXEA , lepin-ESTA , lepin-LA0357 , lepin-LA0587 , lepin-LA0823 , lepin-LA0932 , lepin-LA1069 , lepin-LA1345 , lepin-LA1541 , lepin-LA1702 , lepin-LA1861 , lepin-LA1902 , lepin-LA1936 , lepin-LA1955 , lepin-LA2034 , lepin-LA2132 , lepin-LA2501 , lepin-LA2505 , lepin-LA2526 , lepin-LA2544 , lepin-LA2857 , lepin-LA2958 , lepin-LA3100 , lepin-LA3107 , lepin-LA3147 , lepin-LA3604 , lepin-LA3661 , lepin-LA3669 , lepin-LA3672 , lepin-LA3770 , lepin-LA3788 , lepin-LA3851 , lepin-LA3897 , lepin-LA3998 , lepin-LA4247 , lepin-LB147 , lepin-LB264 , lepin-LB265 , lepin-METX , lepin-q8f7a8 , lepin-q72tt9

Title : Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228) - Zhang_2003_Mol.Microbiol_49_1577
Author(s) : Zhang YQ , Ren SX , Li HL , Wang YX , Fu G , Yang J , Qin ZQ , Miao YG , Wang WY , Chen RS , Shen Y , Chen Z , Yuan ZH , Zhao GP , Qu D , Danchin A , Wen YM
Ref : Molecular Microbiology , 49 :1577 , 2003
Abstract : Staphylococcus epidermidis strains are diverse in their pathogenicity; some are invasive and cause serious nosocomial infections, whereas others are non-pathogenic commensal organisms. To analyse the implications of different virulence factors in Staphylococcus epidermidis infections, the complete genome of Staphylococcus epidermidis strain ATCC 12228, a non-biofilm forming, non-infection associated strain used for detection of residual antibiotics in food products, was sequenced. This strain showed low virulence by mouse and rat experimental infections. The genome consists of a single 2499 279 bp chromosome and six plasmids. The chromosomal G + C content is 32.1% and 2419 protein coding sequences (CDS) are predicted, among which 230 are putative novel genes. Compared to the virulence factors in Staphylococcus aureus, aside from delta-haemolysin and beta-haemolysin, other toxin genes were not found. In contrast, the majority of adhesin genes are intact in ATCC 12228. Most strikingly, the ica operon coding for the enzymes synthesizing interbacterial cellular polysaccharide is missing in ATCC 12228 and rearrangements of adjacent genes are shown. No mec genes, IS256, IS257, were found in ATCC 12228. It is suggested that the absence of the ica operon is a genetic marker in commensal Staphylococcus epidermidis strains which are less likely to become invasive.
ESTHER : Zhang_2003_Mol.Microbiol_49_1577
PubMedSearch : Zhang_2003_Mol.Microbiol_49_1577
PubMedID: 12950922
Gene_locus related to this paper: staep-GEHD , staep-lipas , staep-SE0011 , staep-SE0226 , staep-SE0386 , staep-SE0389 , staep-SE0424 , staep-SE0564 , staep-SE0714 , staep-SE0745 , staep-SE0980 , staep-SE1436 , staep-SE1460 , staep-SE1510 , staep-SE1780 , staep-SE1929 , staep-SERP2035 , staep-SE2050 , staep-SE2095 , staep-SE2213 , staep-SE2328 , staep-SE2403