Comparison of the genomes of two Xanthomonas pathogens with differing host specificities

Silva, A. C. R. da; Ferro, J. A.; Reinach, Fernando C.; Farah, Chuck S.; Furlan, L. R.; Quaggio, Ronaldo Bento; Monteiro-Vitorello, Cláudia Barros; Sluys, Marie Anne Van; Almeida, Nalvo F.; Alves, L. M. C.; Amaral, Alexandre Morais do; Bertolini, Maria Célia; Camargo, L. E. A.; Camarotte, Giovana; Cannavan, Fabiana S.; Cardozo, JP; Chambergo, Felipe S.; Ciapina, Luciane Prioli; Cicarelli, Regina Maria Barreto; Coutinho, Luiz Lehmann; Cursino‐Santos, Jeny R.; El-Dorry, Hamza A.; Faria, Juarez Braz de; Ferreira, Ari J. S.; Ferreira, Rita de Cássia Café; Ferro, Maria Inês Tiraboschi; Formighieri, Eduardo Fernandes; Franco, Maribel; Greggio, Christian C.; Gruber, Arthur; Katsuyama, Angela M.; Kishi, Luciano Takeshi; Leite, Rui Pereira; Lemos, Eliana Gertrudes Macedo; Lemos, Manoel Victor Franco; Locali, E. C.; Machado, Marcos Antônio; Madeira, Alda Maria Backx Noronha; Martinez-Rossi, Nilce M.; Martins, E. C.; Meidânis, João; Menck, Carlos Frederico Martins; Miyaki, Cristina Yumi; Moon, David Henry; Moreira, Leandro Márcio; Novo, Maria Teresa Marques; Okura, Vagner Katsumi; Oliveira, Mariana C.; Oliveira, V R; Pereira, H. A.; Rossi, Antônio; Sena, Janete Apparecida Desidério; Silva, C.; Souza, Robson Francisco de; Spinola, L. A. F.; Takita, Marco Aurélio; Tamura, Rodrigo Esaki; Teixeira, Elaine Cristina; Tezza, R. I. D.; Santos, M. Tadeu dos; Truffi, Daniela; Tsai, Siu Mui; White, Frank F.; Setúbal, João Carlos; Kitajima, João Paulo

doi:10.1038/417459a

Cited by 1,030 publications

(1,077 citation statements)

References 26 publications

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“…Several of the strain-specific genes have no homologs in any database ('orphan genes') and are interesting targets for further research, because they may account for P. gallaeciensis strain-specific metabolic traits and may also influence the host specificity (Mira, 2002;Silva et al, 2002). Our survey also suggests strain differentiation in the regulatory networks of extracytoplasmic function s factors and small RNAs (Supplementary Materials S12 and 13).…”

Section: Resultsmentioning

confidence: 83%

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

et al. 2012

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Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.

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Section: Resultsmentioning

confidence: 83%

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

et al. 2012

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“…To identify those ORFs of E. coli MG1655 that are restricted to clades of different phylogenetic depths, we narrowed our analysis to the gene contents of sequenced enteric bacteria, currently the best represented bacterial group, including five strains of E. coli (Blattner et al 1997;Hayashi et al 2001;Perna et al 2001;Welch et al 2002;Wei et al 2003), two subspecies/serovars of S. enterica (McClelland et al 2001;Parkhill et al 2001a), two species of Buchnera (Shigenobu et al 2000;Tamas et al 2002), and two strains of Yersinia pestis (Parkhill et al 2001b;Deng et al 2002) as well as those of several other ␥-Proteobacteria, including Vibrio cholerae (Schoolnik and Yildiz 2000), Vibrio parahaemolyticus (Makino et al 2003), Haemophilus influenzae (Fleischmann et al 1995), Pasteurella multocida (May et al 2001), Pseudomonas aeruginosa (Stover et al 2000), Xylella fastidiosa (Simpson et al 2000), Xanthomonas campestris, and Xanthomonas citri (da Silva et al 2002). (Species are listed in order of increasing genetic distance to E.…”

Section: Methods Delimiting Orfans In Clades Of Different Phylogenetimentioning

confidence: 99%

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Daubin¹,

Ochman²

2004

Genome Res.

241

253

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Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uniqueness of ORFans within a genome has precluded the use of a comparative approach to examine their function and evolution. However, by identifying sequences unique to monophyletic groups at increasing phylogenetic depths, we can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Relative to the genes ancestral to γ-Proteobacteria and to those genes distributed sporadically in other prokaryotic species, ORFans in the E. coli lineage are short, A+T rich, and evolve quickly. Moreover, most encode functional proteins. Based on these features, ORFans are not attributable to errors in gene annotation, limitations of current databases, or to failure of methods for detecting homology. Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions

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“…citristr 306. 19) suggested that the proteinase from Rvi. gelatinosus KDDS1 was a serine-type of proteinase.…”

Section: Characteristics Of the Enzymementioning

confidence: 99%

Purification and Characterization of Alkaline Serine Proteinase from Photosynthetic Bacterium,Rubrivivax gelatinosusKDDS1

Oda

Tanskul

Oyama

et al. 2004

Bioscience, Biotechnology, and Biochemistry

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In order to reduce the protein content of wastewater, photosynthetic bacteria producing proteinases were screened from wastewater of various sources and stocked in culture. An isolated strain, KDDS1, was identified as Rubrivivax gelatinosus, a purple nonsulfur bacterium that secretes proteinase under micro-aerobic conditions under light at 35 C. Molecular weight of the purified enzyme was estimated to be 32.5 kDa. The enzyme showed the highest activity at 45 C and pH 9.6, and the activity was completely inhibited by phenylmethyl sulfonyl fluoride (PMSF), but not by EDTA. The amino-terminal 24 amino acid sequence of the enzyme showed about 50% identity to those of serine proteinases from Pseudoalteromonas piscicida strain O-7 and Burkholderia pseudomallei. Thus, the enzyme from Rvi. gelatinosus KDDS1 was thought to be a serine-type proteinase. This was the first serine proteinase characterized from photosynthetic bacteria.

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Comparison of the genomes of two Xanthomonas pathogens with differing host specificities

Cited by 1,030 publications

References 26 publications

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Purification and Characterization of Alkaline Serine Proteinase from Photosynthetic Bacterium,Rubrivivax gelatinosusKDDS1

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