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Author Report for: Deboy R

Title: Genome sequence of the deltaproteobacterial strain NaphS2 and analysis of differential gene expression during anaerobic growth on naphthalene
DiDonato RJ, Jr., Young ND, Butler JE, Chin KJ, Hixson KK, Mouser P, Lipton MS, Deboy R, Methe BA
Ref: PLoS ONE, 5:e14072, 2010 : PubMed
Abstract


ESTHER: Didonato_2010_PLoS.ONE_5_E14072
PubMedSearch: Didonato 2010 PLoS.ONE 5 E14072
PubMedID: 21124915
Gene_locus related to this paper: 9delt-d8f3r8, 9delt-d8ffq6

Abstract

BACKGROUND: Anaerobic polycyclic hydrocarbon (PAH) degradation coupled to sulfate reduction may be an important mechanism for in situ remediation of contaminated sediments. Steps involved in the anaerobic degradation of 2-methylnaphthalene have been described in the sulfate reducing strains NaphS3, NaphS6 and N47. Evidence from N47 suggests that naphthalene degradation involves 2-methylnaphthalene as an intermediate, whereas evidence in NaphS2, NaphS3 and NaphS6 suggests a mechanism for naphthalene degradation that does not involve 2-methylnaphthalene. To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined.
RESULTS: Draft genome sequencing, gene expression analysis, and proteomic analysis revealed that NaphS2 degrades naphthoyl-CoA in a manner analogous to benzoyl-CoA degradation. Genes including the previously characterized NmsA, thought to encode an enzyme necessary for 2-methylnaphthalene metabolism, were not upregulated during growth of NaphS2 on naphthalene, nor were the corresponding protein products. NaphS2 may possess a non-classical dearomatizing enzyme for benzoate degradation, similar to one previously characterized in Geobacter metallireducens. Identification of genes involved in toluene degradation in NaphS2 led us to determine that NaphS2 degrades toluene, a previously unreported capacity. The genome sequence also suggests that NaphS2 may degrade other monoaromatic compounds. CONCLUSION: This study demonstrates that steps leading to the degradation of 2-naphthoyl-CoA are conserved between NaphS2 and N47, however while NaphS2 possesses the capacity to degrade 2-methylnaphthalene, naphthalene degradation likely does not proceed via 2-methylnaphthalene. Instead, carboxylation or another form of activation may serve as the first step in naphthalene degradation. Degradation of toluene and 2-methylnaphthalene, and the presence of at least one bss-like and bbs-like gene cluster in this organism, suggests that NaphS2 degrades both compounds via parallel mechanisms. Elucidation of the key genes necessary for anaerobic naphthalene degradation may provide the ability to track naphthalene degradation through in situ transcript monitoring.



        

Title: Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition
Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS and Buell CR <22 more author(s)> Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR (- 22)
Ref: Journal of Bacteriology, 187:6488, 2005 : PubMed
Abstract


ESTHER: Joardar_2005_J.Bacteriol_187_6488
PubMedSearch: Joardar 2005 J.Bacteriol 187 6488
PubMedID: 16159782
Gene_locus related to this paper: pse14-q48cb3, pse14-q48ck7, pse14-q48cs3, pse14-q48ct2, pse14-q48d82, pse14-q48da3, pse14-q48dj9, pse14-q48dq5, pse14-q48e33, pse14-q48es1, pse14-q48f84, pse14-q48fg2, pse14-q48g47, pse14-q48g51, pse14-q48gq9, pse14-q48h40, pse14-q48ha4, pse14-q48hb4, pse14-q48he1, pse14-q48hq0, pse14-q48hq2, pse14-q48ia0, pse14-q48im0, pse14-q48j48, pse14-q48ji2, pse14-q48k54, pse14-q48k55, pse14-q48k63, pse14-q48kc1, pse14-q48kt9, pse14-q48ku0, pse14-q48lb6, pse14-q48lj1, pse14-q48ln2, pse14-q48m56, pse14-q48mh5, pse14-q48mq7, pse14-q48nt0, pse14-q48p24, pse14-q48pi7, pse14-q48pi8, pse14-q48pi9, pse14-q48pq2, pse14-q48pq5, psesm-METX, psesm-q87y20, psesm-q889k3, psesy-PIP, psesy-PSPTO0162, psesy-PSPTO1766, psesy-PSPTO2134, psesy-PSPTO3135, pseu2-q4zwv7, psesg-e7p3i0

Abstract

Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.



        

Title: Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C and Eisen JA <20 more author(s)> Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C, Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS, Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB, Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE, Tettelin H, O'Neill SL, Eisen JA (- 20)
Ref: PLoS Biol, 2:E69, 2004 : PubMed
Abstract


ESTHER: Wu_2004_PLoS.Biol_2_E69
PubMedSearch: Wu 2004 PLoS.Biol 2 E69
PubMedID: 15024419
Gene_locus related to this paper: wolpm-q73gf0, wolpm-q73gx7

Abstract

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.



        

Title: The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium
Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC and Fraser CM <25 more author(s)> Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM (- 25)
Ref: Proceedings of the National Academy of Sciences of the United States of America, 99:9509, 2002 : PubMed
Abstract


ESTHER: Eisen_2002_Proc.Natl.Acad.Sci.U.S.A_99_9509
PubMedSearch: Eisen 2002 Proc.Natl.Acad.Sci.U.S.A 99 9509
PubMedID: 12093901
Gene_locus related to this paper: chlte-CT0177, chlte-CT0524, chlte-CT0717, chlte-CT0947, chlte-CT1208, chlte-CT1253, chlte-CT1301, chlte-CT1312, chlte-CT1856, chlte-CT1908, chlte-CT2087, chlte-CT2271, chlte-MENH, chlte-MET2, chlte-q4w546, chlte-q8kgb8

Abstract

The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species.



        

Title: Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains
Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, Deboy R, Dodson R, Gwinn M and Fraser CM <16 more author(s)> Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, Deboy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs Jr WR, Jr., Venter JC, Fraser CM (- 16)
Ref: Journal of Bacteriology, 184:5479, 2002 : PubMed
Abstract


ESTHER: Fleischmann_2002_J.Bacteriol_184_5479
PubMedSearch: Fleischmann 2002 J.Bacteriol 184 5479
PubMedID: 12218036
Gene_locus related to this paper: myctu-a85a, myctu-a85b, myctu-a85c, myctu-bpoC, myctu-d5yk66, myctu-ephA, myctu-ephB, myctu-ephc, myctu-ephd, myctu-ephE, myctu-ephF, myctu-hpx, myctu-linb, myctu-lipG, myctu-LPQP, myctu-MBTB, myctu-metx, myctu-mpt51, myctu-MT3441, myctu-p71654, myctu-p95011, myctu-PKS6, myctu-PKS13, myctu-ppe42, myctu-ppe63, myctu-Rv1430, myctu-RV0045C, myctu-Rv0077c, myctu-Rv0151c, myctu-Rv0152c, myctu-Rv0159c, myctu-Rv0160c, myctu-rv0183, myctu-Rv0217c, myctu-Rv0220, myctu-Rv0272c, myctu-RV0293C, myctu-RV0421C, myctu-RV0457C, myctu-RV0519C, myctu-RV0774C, myctu-RV0782, myctu-RV0840C, myctu-Rv1069c, myctu-Rv1076, myctu-RV1123C, myctu-Rv1184c, myctu-Rv1190, myctu-Rv1191, myctu-RV1192, myctu-RV1215C, myctu-Rv1399c, myctu-Rv1400c, myctu-RV1639C, myctu-RV1683, myctu-RV1758, myctu-Rv1800, myctu-Rv1833c, myctu-Rv2045c, myctu-RV2054, myctu-Rv2284, myctu-RV2296, myctu-Rv2385, myctu-Rv2485c, myctu-RV2627C, myctu-RV2672, myctu-RV2695, myctu-RV2765, myctu-RV2800, myctu-RV2854, myctu-Rv2970c, myctu-Rv3084, myctu-Rv3097c, myctu-rv3177, myctu-Rv3312c, myctu-RV3452, myctu-Rv3487c, myctu-Rv3569c, myctu-Rv3591c, myctu-RV3724, myctu-Rv3802c, myctu-Rv3822, myctu-y0571, myctu-y963, myctu-Y1834, myctu-y1835, myctu-y2079, myctu-Y2307, myctu-yc88, myctu-ym23, myctu-ym24, myctu-YR15, myctu-yt28

Abstract

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.



        

Title: Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T and Fraser CM <15 more author(s)> Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, Deboy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM (- 15)
Ref: Nucleic Acids Research, 28:1397, 2000 : PubMed
Abstract


ESTHER: Read_2000_Nucleic.Acids.Res_28_1397
PubMedSearch: Read 2000 Nucleic.Acids.Res 28 1397
PubMedID: 10684935
Gene_locus related to this paper: chlmu-TC0345, chlmu-TC0413, chlmu-TC0426, chlmu-TC0478, chlpn-CPJ0152, chlpn-CPJ0342, chlpn-CPN0161, chlpn-CPN0271, chlpn-q9jrv1, chlpn-q9js10, chlpn-q9k1u7, chlpn-q9z6x9

Abstract

The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an approximately 50 kb 'plasticity zone' near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli O157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C. pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens.



        

Title: Complete genome sequence of Neisseria meningitidis serogroup B strain MC58
Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF and Venter JC <32 more author(s)> Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, Deboy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC (- 32)
Ref: Science, 287:1809, 2000 : PubMed
Abstract


ESTHER: Tettelin_2000_Science_287_1809
PubMedSearch: Tettelin 2000 Science 287 1809
PubMedID: 10710307
Gene_locus related to this paper: neigo-pip, neima-metx, neimb-q9k0t9, neime-ESD, neime-NMA2216, neime-NMB0276, neime-NMB0868, neime-NMB1828, neime-NMB1877

Abstract

The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.