Setubal JC

References (14)

Title : The complete genome sequence of 'Candidatus Liberibacter americanus', associated with Citrus huanglongbing - Wulff_2014_Mol.Plant.Microbe.Interact_27_163
Author(s) : Wulff NA , Zhang S , Setubal JC , Almeida NF , Martins EC , Harakava R , Kumar D , Rangel LT , Foissac X , Bove JM , Gabriel DW
Ref : Mol Plant Microbe Interact , 27 :163 , 2014
Abstract : Liberibacter spp. form a Rhizobiaceae clade of phloem-limited pathogens of limited host range. Two obligately parasitic species have been sequenced: 'Candidatus Liberibacter asiaticus', which causes citrus huanglongbing (HLB) worldwide, and 'Ca. L. solanacearum', which causes potato "zebra chip" disease. A third (proposed) species, Liberibacter crescens, was isolated from mountain papaya, grown in axenic culture, and sequenced. In an effort to identify common host determinants, the complete genomic DNA sequence of a second HLB species, 'Ca. L. americanus' strain 'Sao Paulo' was determined. The circular genome of 1,195,201 bp had an average 31.12% GC content and 983 predicted protein encoding genes, 800 (81.4%) of which had a predicted function. There were 658 genes common to all sequenced Liberibacter spp. and only 8 genes common to 'Ca. L. americanus' and 'Ca. L. asiaticus' but not found in 'Ca. L. solanacearum'. Surprisingly, most of the lipopolysaccharide biosynthetic genes were missing from the 'Ca. L. americanus' genome, as well as OmpA and a key regulator of flagellin, all indicating a 'Ca. L. americanus' strategy of avoiding production of major pathogen-associated molecular patterns present in 'Ca. L. asiaticus' and 'Ca. L. solanacearum'. As with 'Ca. L. asiaticus', one of two 'Ca. L. americanus' prophages replicated as an excision plasmid and carried potential lysogenic conversion genes that appeared fragmentary or degenerated in 'Ca. L. solanacearum'.
ESTHER : Wulff_2014_Mol.Plant.Microbe.Interact_27_163
PubMedSearch : Wulff_2014_Mol.Plant.Microbe.Interact_27_163
PubMedID: 24200077
Gene_locus related to this paper: 9rhiz-u6b5g7

Title : Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity - Jalan_2011_J.Bacteriol_193_6342
Author(s) : Jalan N , Aritua V , Kumar D , Yu F , Jones JB , Graham JH , Setubal JC , Wang N
Ref : Journal of Bacteriology , 193 :6342 , 2011
Abstract : Xanthomonas axonopodis pv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence of X. axonopodis pv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrus Xanthomonas pathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogen X. campestris pv. vesicatoria 85-10, with a completely different host range. We also compared X. axonopodis pv. citrumelo to the genome of citrus canker pathogen X. axonopodis pv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition to pthA, effectors such as xopE3, xopAI, and hrpW were absent from X. axonopodis pv. citrumelo while present in X. axonopodis pv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that of X. axonopodis pv. citri. We also identified unique effectors in X. axonopodis pv. citrumelo that may be related to the different host range as compared to that of X. axonopodis pv. citri. X. axonopodis pv. citrumelo also lacks various genes, such as syrE1, syrE2, and RTX toxin family genes, which were present in X. axonopodis pv. citri. These may be associated with the distinct virulences of X. axonopodis pv. citrumelo and X. axonopodis pv. citri. Comparison of the complete genome sequence of X. axonopodis pv. citrumelo to those of X. axonopodis pv. citri and X. campestris pv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.
ESTHER : Jalan_2011_J.Bacteriol_193_6342
PubMedSearch : Jalan_2011_J.Bacteriol_193_6342
PubMedID: 21908674
Gene_locus related to this paper: xanax-XAC2987 , xanax-XAC4055 , xanor-q5h5n1 , 9xant-a0a0g8v5k2

Title : Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper - Potnis_2011_BMC.Genomics_12_146
Author(s) : Potnis N , Krasileva K , Chow V , Almeida NF , Patil PB , Ryan RP , Sharlach M , Behlau F , Dow JM , Momol M , White FF , Preston JF , Vinatzer BA , Koebnik R , Setubal JC , Norman DJ , Staskawicz BJ , Jones JB
Ref : BMC Genomics , 12 :146 , 2011
Abstract : BACKGROUND: Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10.
RESULTS: We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity.
CONCLUSIONS: Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.
ESTHER : Potnis_2011_BMC.Genomics_12_146
PubMedSearch : Potnis_2011_BMC.Genomics_12_146
PubMedID: 21396108
Gene_locus related to this paper: 9xant-f0bam8 , 9xant-f0bb73 , 9xant-f0bea2 , 9xant-f0bfp7 , 9xant-f0c1j5 , 9xant-f0c9f8 , 9xant-f0c729 , xanax-CATD , xanax-CPO , xanax-ENTF2 , xanax-estA1 , xanax-GAA , xanax-PTRB , xanax-XAC0198 , xanax-XAC0262 , xanax-XAC0515 , xanax-XAC0591 , xanax-XAC0619 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC0805 , xanax-XAC1213 , xanax-XAC1713 , xanax-XAC2532 , xanax-XAC2541 , xanax-XAC2987 , xanax-XAC2990 , xanax-XAC3315 , xanax-XAC4046 , xanax-XAC4055 , xanax-XAC4106 , xanax-XAC4316 , xanc5-q3bqi2 , xanca-impep , xanca-XCC0266 , xanca-XCC1105 , xanca-XCC2566 , xanca-XCC2722 , xanca-XCC3296 , xanca-XCC3961 , xanor-acvB , xanor-metx , 9xant-f0bgj0 , 9xant-f0cdj1 , 9xant-a0a0g8v5k2 , 9xant-f0cdg7

Title : Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid - Wibberg_2011_J.Biotechnol_155_50
Author(s) : Wibberg D , Blom J , Jaenicke S , Kollin F , Rupp O , Scharf B , Schneiker-Bekel S , Sczcepanowski R , Goesmann A , Setubal JC , Schmitt R , Puhler A , Schluter A
Ref : J Biotechnol , 155 :50 , 2011
Abstract : Agrobacterium sp. H13-3, formerly known as Rhizobium lupini H13-3, is a soil bacterium that was isolated from the rhizosphere of Lupinus luteus. The isolate has been established as a model system for studying novel features of flagellum structure, motility and chemotaxis within the family Rhizobiaceae. The complete genome sequence of Agrobacterium sp. H13-3 has been established and the genome structure and phylogenetic assignment of the organism was analysed. For de novo sequencing of the Agrobacterium sp. H13-3 genome, a combined strategy comprising 454-pyrosequencing on the Genome Sequencer FLX platform and PCR-based amplicon sequencing for gap closure was applied. The finished genome consists of three replicons and comprises 5,573,770 bases. Based on phylogenetic analyses, the isolate could be assigned to the genus Agrobacterium biovar I and represents a genomic species G1 strain within this biovariety. The highly conserved circular chromosome (2.82 Mb) of Agrobacterium sp. H13-3 mainly encodes housekeeping functions characteristic for an aerobic, heterotrophic bacterium. Agrobacterium sp. H13-3 is a motile bacterium driven by the rotation of several complex flagella. Its behaviour towards external stimuli is regulated by a large chemotaxis regulon and a total of 17 chemoreceptors. Comparable to the genome of Agrobacterium tumefaciens C58, Agrobacterium sp. H13-3 possesses a linear chromosome (2.15 Mb) that is related to its reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid pAspH13-3a (0.6 Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3 indicating that it is a non-virulent isolate.
ESTHER : Wibberg_2011_J.Biotechnol_155_50
PubMedSearch : Wibberg_2011_J.Biotechnol_155_50
PubMedID: 21329740
Gene_locus related to this paper: agrsh-f0l326 , agrsh-f0lb16 , agrsh-f0lfg1 , agrsh-f0lgt6 , agrt5-a9cfs8 , agrt5-q7d1j0 , agrt5-q7d1j3 , agrtu-ATU2126 , agrtu-ATU2481 , agrsh-f0lfk1

Title : Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii - Moreira_2010_BMC.Genomics_11_238
Author(s) : Moreira LM , Almeida NF, Jr. , Potnis N , Digiampietri LA , Adi SS , Bortolossi JC , da Silva AC , da Silva AM , de Moraes FE , de Oliveira JC , de Souza RF , Facincani AP , Ferraz AL , Ferro MI , Furlan LR , Gimenez DF , Jones JB , Kitajima EW , Laia ML , Leite RP, Jr. , Nishiyama MY , Rodrigues Neto J , Nociti LA , Norman DJ , Ostroski EH , Pereira HA, Jr. , Staskawicz BJ , Tezza RI , Ferro JA , Vinatzer BA , Setubal JC
Ref : BMC Genomics , 11 :238 , 2010
Abstract : BACKGROUND: Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C.
RESULTS: We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. CONCLUSION: We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.
ESTHER : Moreira_2010_BMC.Genomics_11_238
PubMedSearch : Moreira_2010_BMC.Genomics_11_238
PubMedID: 20388224
Gene_locus related to this paper: xanax-CATD , xanax-ENTF2 , xanax-estA1 , xanax-GAA , xanax-PTRB , xanax-XAC0198 , xanax-XAC0515 , xanax-XAC0591 , xanax-XAC0619 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC0805 , xanax-XAC1213 , xanax-XAC1713 , xanax-XAC1752 , xanax-XAC2393 , xanax-XAC2532 , xanax-XAC2541 , xanax-XAC2987 , xanax-XAC3315 , xanax-XAC3371 , xanax-XAC4046 , xanax-XAC4055 , xanax-XAC4106 , xanax-XYNB , xanc5-q3bqi2 , xanca-impep , xanca-XCC1105 , xanca-XCC2566 , xanca-XCC2722 , xanor-acvB , xanor-metx , 9xant-a0a0g8v5k2

Title : A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000 - Almeida_2009_Mol.Plant.Microbe.Interact_22_52
Author(s) : Almeida NF , Yan S , Lindeberg M , Studholme DJ , Schneider DJ , Condon B , Liu H , Viana CJ , Warren A , Evans C , Kemen E , Maclean D , Angot A , Martin GB , Jones JD , Collmer A , Setubal JC , Vinatzer BA
Ref : Mol Plant Microbe Interact , 22 :52 , 2009
Abstract : Diverse gene products including phytotoxins, pathogen-associated molecular patterns, and type III secreted effectors influence interactions between Pseudomonas syringae strains and plants, with additional yet uncharacterized factors likely contributing as well. Of particular interest are those interactions governing pathogen-host specificity. Comparative genomics of closely related pathogens with different host specificity represents an excellent approach for identification of genes contributing to host-range determination. A draft genome sequence of Pseudomonas syringae pv. tomato T1, which is pathogenic on tomato but nonpathogenic on Arabidopsis thaliana, was obtained for this purpose and compared with the genome of the closely related A. thaliana and tomato model pathogen P. syringae pv. tomato DC3000. Although the overall genetic content of each of the two genomes appears to be highly similar, the repertoire of effectors was found to diverge significantly. Several P. syringae pv. tomato T1 effectors absent from strain DC3000 were confirmed to be translocated into plants, with the well-studied effector AvrRpt2 representing a likely candidate for host-range determination. However, the presence of avrRpt2 was not found sufficient to explain A. thaliana resistance to P. syringae pv. tomato T1, suggesting that other effectors and possibly type III secretion system-independent factors also play a role in this interaction.
ESTHER : Almeida_2009_Mol.Plant.Microbe.Interact_22_52
PubMedSearch : Almeida_2009_Mol.Plant.Microbe.Interact_22_52
PubMedID: 19061402
Gene_locus related to this paper: pse14-q48ia0 , psesm-e2mn04 , psesm-IRP1 , psesm-METX , psesm-q88a39 , psesm-q881b4 , psesy-ESTA , psesy-IRP4 , psesy-PIP , psesy-PSPTO0421 , psesy-PSPTO0508 , psesy-PSPTO1504 , psesy-PSPTO1559 , psesy-PSPTO1766 , psesy-PSPTO2005 , psesy-PSPTO2134 , psesy-PSPTO2150 , psesy-PSPTO3135 , psesy-PSPTO3138 , psesy-PSPTO3306 , psesy-PSPTO4277 , psesy-PSPTO4519 , psesy-PSPTO4540 , psesy-PSPTO4964 , psesy-PSPTO5299 , psesy-PSPTO5537 , pseub-e2mf08

Title : Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria - Slater_2009_J.Bacteriol_191_2501
Author(s) : Slater SC , Goldman BS , Goodner B , Setubal JC , Farrand SK , Nester EW , Burr TJ , Banta L , Dickerman AW , Paulsen I , Otten L , Suen G , Welch R , Almeida NF , Arnold F , Burton OT , Du Z , Ewing A , Godsy E , Heisel S , Houmiel KL , Jhaveri J , Lu J , Miller NM , Norton S , Chen Q , Phoolcharoen W , Ohlin V , Ondrusek D , Pride N , Stricklin SL , Sun J , Wheeler C , Wilson L , Zhu H , Wood DW
Ref : J. Bacteriol , 191 :2501 , 2009
Abstract : The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.
ESTHER : Slater_2009_J.Bacteriol_191_2501
PubMedSearch : Slater_2009_J.Bacteriol_191_2501
PubMedID: 19251847
Gene_locus related to this paper: agrrk-b9j7k2 , agrrk-b9j8e4 , agrrk-b9j8g5 , agrrk-b9j9n4 , agrrk-b9j9p4 , agrrk-b9ja88 , agrrk-b9jbs5 , agrrk-b9jd67 , agrrk-b9jd85 , agrrk-b9jfh5 , agrrk-b9jfj6 , agrrk-b9jfu6 , agrrk-b9jfy6 , agrrk-b9jh78 , agrrk-b9ji04 , agrrk-b9jih5 , agrrk-b9jih7 , agrrk-b9jj14 , agrrk-b9jjt5 , agrrk-b9jjt6 , agrrk-b9jk42 , agrrk-b9jki6 , agrrk-b9jkt4 , agrrk-b9jla0 , agrrk-b9jlc3 , agrrk-b9jlj1 , agrrk-b9jlj2 , agrrk-b9jlr1 , agrrk-b9jmj9 , agrrk-b9jml0 , agrrk-b9jmn1 , agrrk-b9jnw6 , agrrk-b9jq01 , agrrk-b9jq11 , agrrk-b9jq35 , agrtu-DHAA , agrvs-b9jqv2 , agrvs-b9jr09 , agrvs-b9js24 , agrvs-b9js61 , agrvs-b9ju03 , agrvs-b9jw40 , agrvs-b9jx20 , agrvs-b9jy84 , agrvs-b9k1h8 , agrvs-b9k2m9 , agrvs-b9k3r6 , agrvs-b9k5p9 , agrvs-b9k093 , agrvs-b9k188 , agrvs-b9k312 , agrrk-b9jls9 , agrrk-b9jca1 , agrvs-b9jur1 , agrrk-rutd

Title : Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes - Setubal_2009_J.Bacteriol_191_4534
Author(s) : Setubal JC , dos Santos P , Goldman BS , Ertesvag H , Espin G , Rubio LM , Valla S , Almeida NF , Balasubramanian D , Cromes L , Curatti L , Du Z , Godsy E , Goodner B , Hellner-Burris K , Hernandez JA , Houmiel K , Imperial J , Kennedy C , Larson TJ , Latreille P , Ligon LS , Lu J , Maerk M , Miller NM , Norton S , O'Carroll IP , Paulsen I , Raulfs EC , Roemer R , Rosser J , Segura D , Slater S , Stricklin SL , Studholme DJ , Sun J , Viana CJ , Wallin E , Wang B , Wheeler C , Zhu H , Dean DR , Dixon R , Wood D
Ref : Journal of Bacteriology , 191 :4534 , 2009
Abstract : Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins.
ESTHER : Setubal_2009_J.Bacteriol_191_4534
PubMedSearch : Setubal_2009_J.Bacteriol_191_4534
PubMedID: 19429624
Gene_locus related to this paper: azovd-c1dex6 , azovd-c1df21 , azovd-c1dfb5 , azovd-c1dg75 , azovd-c1dgm6 , azovd-c1dh91 , azovd-c1di03 , azovd-c1dib3 , azovd-c1dif2 , azovd-c1dIq5 , azovd-c1dir1 , azovd-c1dis2 , azovd-c1djq5 , azovd-c1djw3 , azovd-c1dk37 , azovd-c1dkb2 , azovd-c1dkj0 , azovd-c1dli6 , azovd-c1dng8 , azovd-c1dni5 , azovd-c1dpr0 , azovd-c1dqu3 , azovd-c1dri5 , azovd-c1drx0 , azovd-c1dsl7 , azovd-c1dsq7 , azovd-c1dss1 , azovd-metx , azovi-PHBC , azovd-c1dem4

Title : The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli - Monteiro-Vitorello_2004_Mol.Plant.Microbe.Interact_17_827
Author(s) : Monteiro-Vitorello CB , Camargo LE , Van Sluys MA , Kitajima JP , Truffi D , do Amaral AM , Harakava R , de Oliveira JC , Wood D , de Oliveira MC , Miyaki C , Takita MA , da Silva AC , Furlan LR , Carraro DM , Camarotte G , Almeida NF, Jr. , Carrer H , Coutinho LL , El-Dorry HA , Ferro MI , Gagliardi PR , Giglioti E , Goldman MH , Goldman GH , Kimura ET , Ferro ES , Kuramae EE , Lemos EG , Lemos MV , Mauro SM , Machado MA , Marino CL , Menck CF , Nunes LR , Oliveira RC , Pereira GG , Siqueira W , de Souza AA , Tsai SM , Zanca AS , Simpson AJ , Brumbley SM , Setubal JC
Ref : Mol Plant Microbe Interact , 17 :827 , 2004
Abstract : The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.
ESTHER : Monteiro-Vitorello_2004_Mol.Plant.Microbe.Interact_17_827
PubMedSearch : Monteiro-Vitorello_2004_Mol.Plant.Microbe.Interact_17_827
PubMedID: 15305603
Gene_locus related to this paper: leixx-q6ack2 , leixx-q6acm6 , leixx-q6acw2 , leixx-q6ad78 , leixx-q6adb9 , leixx-q6aed1 , leixx-q6aee6 , leixx-q6af15 , leixx-q6agt3 , leixx-q6ah78

Title : Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis - Nascimento_2004_J.Bacteriol_186_2164
Author(s) : Nascimento AL , Ko AI , Martins EA , Monteiro-Vitorello CB , Ho PL , Haake DA , Verjovski-Almeida S , Hartskeerl RA , Marques MV , Oliveira MC , Menck CF , Leite LC , Carrer H , Coutinho LL , Degrave WM , Dellagostin OA , El-Dorry H , Ferro ES , Ferro MI , Furlan LR , Gamberini M , Giglioti EA , Goes-Neto A , Goldman GH , Goldman MH , Harakava R , Jeronimo SM , Junqueira-de-Azevedo IL , Kimura ET , Kuramae EE , Lemos EG , Lemos MV , Marino CL , Nunes LR , de Oliveira RC , Pereira GG , Reis MS , Schriefer A , Siqueira WJ , Sommer P , Tsai SM , Simpson AJ , Ferro JA , Camargo LE , Kitajima JP , Setubal JC , Van Sluys MA
Ref : Journal of Bacteriology , 186 :2164 , 2004
Abstract : Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.
ESTHER : Nascimento_2004_J.Bacteriol_186_2164
PubMedSearch : Nascimento_2004_J.Bacteriol_186_2164
PubMedID: 15028702
Gene_locus related to this paper: lepin-AXEA , lepin-ESTA , lepin-LA0357 , lepin-LA0587 , lepin-LA0932 , lepin-LA1069 , lepin-LA1345 , lepin-LA1541 , 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-LA3672 , lepin-LA3788 , lepin-LA3851 , lepin-LA3897 , lepin-LA3998 , lepin-METX , lepin-q8f7a8 , lepin-q72tt9

Title : Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa - Van Sluys_2003_J.Bacteriol_185_1018
Author(s) : Van Sluys MA , de Oliveira MC , Monteiro-Vitorello CB , Miyaki CY , Furlan LR , Camargo LE , da Silva AC , Moon DH , Takita MA , Lemos EG , Machado MA , Ferro MI , da Silva FR , Goldman MH , Goldman GH , Lemos MV , El-Dorry H , Tsai SM , Carrer H , Carraro DM , de Oliveira RC , Nunes LR , Siqueira WJ , Coutinho LL , Kimura ET , Ferro ES , Harakava R , Kuramae EE , Marino CL , Giglioti E , Abreu IL , Alves LM , do Amaral AM , Baia GS , Blanco SR , Brito MS , Cannavan FS , Celestino AV , da Cunha AF , Fenille RC , Ferro JA , Formighieri EF , Kishi LT , Leoni SG , Oliveira AR , Rosa VE, Jr. , Sassaki FT , Sena JA , de Souza AA , Truffi D , Tsukumo F , Yanai GM , Zaros LG , Civerolo EL , Simpson AJ , Almeida NF, Jr. , Setubal JC , Kitajima JP
Ref : Journal of Bacteriology , 185 :1018 , 2003
Abstract : Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.
ESTHER : Van Sluys_2003_J.Bacteriol_185_1018
PubMedSearch : Van Sluys_2003_J.Bacteriol_185_1018
PubMedID: 12533478
Gene_locus related to this paper: xylfa-ACVB , xylfa-cxest , xylfa-metx , xylfa-PD1038 , xylfa-PD1211 , xylfa-PD1300 , xylfa-PD1702 , xylfa-PD2024 , xylfa-pip , xylfa-XF0015 , xylfa-XF0357 , xylfa-XF0754 , xylfa-XF0863 , xylfa-XF1029 , xylfa-XF1181 , xylfa-XF1253 , xylfa-XF1282 , xylfa-XF1356 , xylfa-XF1479 , xylfa-XF1965 , xylfa-XF2330 , xylfa-XF2551

Title : Comparison of the genomes of two Xanthomonas pathogens with differing host specificities - da Silva_2002_Nature_417_459
Author(s) : da Silva ACR , Ferro JA , Reinach FC , Farah CS , Furlan LR , Quaggio RB , Monteiro-Vitorello CB , Van Sluys MA , Almeida Jr NF , Alves LMC , do Amaral AM , Bertolini MC , Camargo LEA , Camarotte G , Cannavan F , Cardozo J , Chambergo F , Ciapina LP , Cicarelli RMB , Coutinho LL , Cursino-Santos JR , El-Dorry H , Faria JB , Ferreira AJS , Ferreira RCC , Ferro MIT , Formighieri EF , Franco MC , Greggio CC , Gruber A , Katsuyama AM , Kishi LT , Leite JrRP , Lemos EGM , Lemos MVF , Locali EC , Machado MA , Madeira AMBN , Martinez-Rossi NM , Martins EC , Meidanis J , Menck CFM , Miyaki CY , Moon DH , Moreira LM , Novo MTM , Okura VK , Oliveira MC , Oliveira VR , Pereira Jr HA , Rossi A , Sena JAD , Silva C , de Souza RF , Spinola LAF , Takita MA , Tamura RE , Teixeira EC , Tezza RID , Trindade dos Santos M , Truffi D , Tsai SM , White FF , Setubal JC , Kitajima JP
Ref : Nature , 417 :459 , 2002
Abstract : The genus Xanthomonas is a diverse and economically important group of bacterial phytopathogens, belonging to the gamma-subdivision of the Proteobacteria. Xanthomonas axonopodis pv. citri (Xac) causes citrus canker, which affects most commercial citrus cultivars, resulting in significant losses worldwide. Symptoms include canker lesions, leading to abscission of fruit and leaves and general tree decline. Xanthomonas campestris pv. campestris (Xcc) causes black rot, which affects crucifers such as Brassica and Arabidopsis. Symptoms include marginal leaf chlorosis and darkening of vascular tissue, accompanied by extensive wilting and necrosis. Xanthomonas campestris pv. campestris is grown commercially to produce the exopolysaccharide xanthan gum, which is used as a viscosifying and stabilizing agent in many industries. Here we report and compare the complete genome sequences of Xac and Xcc. Their distinct disease phenotypes and host ranges belie a high degree of similarity at the genomic level. More than 80% of genes are shared, and gene order is conserved along most of their respective chromosomes. We identified several groups of strain-specific genes, and on the basis of these groups we propose mechanisms that may explain the differing host specificities and pathogenic processes.
ESTHER : da Silva_2002_Nature_417_459
PubMedSearch : da Silva_2002_Nature_417_459
PubMedID: 12024217
Gene_locus related to this paper: xanac-q8phx9 , xanac-q8pmm6 , xanax-ACVB , xanax-BIOH , xanax-CATD , xanax-CPO , xanax-DHAA , xancp-OleB , xanax-ENTF2 , xanax-estA1 , xanax-GAA , xanax-META , xanax-METX , xanax-PCAD , xanax-PHBC , xanax-PTRB , xanax-Q8PMQ8 , xanax-Q8PQP0 , xanax-XAC0198 , xanax-XAC0262 , xanax-XAC0279 , xanax-XAC0319 , xanax-XAC0372 , xanax-XAC0375 , xanax-XAC0501 , xanax-XAC0515 , xanax-XAC0574 , xanax-XAC0591 , xanax-XAC0619 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC0805 , xanax-XAC0874 , xanax-XAC0916 , xanax-XAC1200 , xanax-XAC1213 , xanax-XAC1591 , xanax-XAC1713 , xanax-XAC1752 , xanax-XAC2126 , xanax-XAC2393 , xanax-XAC2532 , xanax-XAC2541 , xanax-XAC2907 , xanax-XAC2981 , xanax-XAC2987 , xanax-XAC2990 , xanax-XAC3037 , xanax-XAC3053 , xanax-XAC3152 , xanax-XAC3173 , xanax-XAC3315 , xanax-XAC3371 , xanax-XAC3619 , xanax-XAC3674 , xanax-XAC3770 , xanax-XAC3967 , xanax-XAC3999 , xanax-XAC4046 , xanax-XAC4055 , xanax-XAC4106 , xanax-XAC4221 , xanax-XAC4316 , xanax-XYNB , 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-XCC0260 , xanca-XCC0266 , xanca-XCC0372 , xanca-XCC0375 , xanca-XCC0753 , xanca-XCC0757 , xanca-XCC0800 , xanca-XCC0843 , xanca-XCC1105 , xanca-XCC1541 , 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-XCC2957 , xanca-XCC3028 , xanca-XCC3164 , xanca-XCC3219 , xanca-XCC3296 , xanca-XCC3300 , xanca-XCC3308 , xanca-XCC3320 , xanca-XCC3514 , xanca-XCC3548 , xanca-XCC3555 , xanca-XCC3623 , xanca-XCC3885 , xanca-XCC3915 , xanca-XCC3961 , xanca-XCC3970 , xanca-XCC4016 , xanca-XCC4096 , xanca-XCC4180 , xanca-XYNB , xanca-XYNB2 , xancb-b0rq23 , xancp-q8pax3 , xancp-y2094

Title : The genome of the natural genetic engineer Agrobacterium tumefaciens C58 - Wood_2001_Science_294_2317
Author(s) : Wood DW , Setubal JC , Kaul R , Monks DE , Kitajima JP , Okura VK , Zhou Y , Chen L , Wood GE , Almeida NF, Jr. , Woo L , Chen Y , Paulsen IT , Eisen JA , Karp PD , Bovee D, Sr. , Chapman P , Clendenning J , Deatherage G , Gillet W , Grant C , Kutyavin T , Levy R , Li MJ , McClelland E , Palmieri A , Raymond C , Rouse G , Saenphimmachak C , Wu Z , Romero P , Gordon D , Zhang S , Yoo H , Tao Y , Biddle P , Jung M , Krespan W , Perry M , Gordon-Kamm B , Liao L , Kim S , Hendrick C , Zhao ZY , Dolan M , Chumley F , Tingey SV , Tomb JF , Gordon MP , Olson MV , Nester EW
Ref : Science , 294 :2317 , 2001
Abstract : The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.
ESTHER : Wood_2001_Science_294_2317
PubMedSearch : Wood_2001_Science_294_2317
PubMedID: 11743193
Gene_locus related to this paper: agrt5-a9cf94 , agrt5-a9cfa9 , agrt5-a9cfs8 , agrt5-a9cfu7 , agrt5-a9cie7 , agrt5-a9cj11 , agrt5-a9cjp2 , agrt5-a9cki2 , agrt5-a9ckr2 , agrt5-a9ckt2 , agrt5-a9cle4 , agrt5-a9clq8 , agrt5-a9clq9 , agrt5-q7cx24 , agrt5-q7d1j0 , agrt5-q7d1j3 , agrt5-q7d3m5 , agrt5-y5261 , agrtu-ACVB , agrtu-ATTS , agrtu-ATU0253 , agrtu-ATU0403 , agrtu-ATU0841 , agrtu-ATU1045 , agrtu-ATU1102 , agrtu-ATU1572 , agrtu-ATU1617 , agrtu-ATU1826 , agrtu-ATU1842 , agrtu-ATU2061 , agrtu-ATU2126 , agrtu-ATU2171 , agrtu-ATU2409 , agrtu-ATU2452 , agrtu-ATU2481 , agrtu-ATU2497 , agrtu-ATU2576 , agrtu-ATU3428 , agrtu-ATU3651 , agrtu-ATU3652 , agrtu-ATU4238 , agrtu-ATU5190 , agrtu-ATU5193 , agrtu-ATU5275 , agrtu-ATU5296 , agrtu-ATU5348 , agrtu-ATU5389 , agrtu-ATU5446 , agrtu-ATU5495 , agrtu-CPO , agrtu-DHAA , agrtu-DLHH , agrtu-EPHA , agrtu-GRST , agrtu-PCA , agrtu-PCAD , agrtu-PHBC , agrtu-PTRB , agrt5-a9cji8

Title : The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis - Simpson_2000_Nature_406_151
Author(s) : Simpson AJ , Reinach FC , Arruda P , Abreu FA , Acencio M , Alvarenga R , Alves LM , Araya JE , Baia GS , Baptista CS , Barros MH , Bonaccorsi ED , Bordin S , Bove JM , Briones MR , Bueno MR , Camargo AA , Camargo LE , Carraro DM , Carrer H , Colauto NB , Colombo C , Costa FF , Costa MC , Costa-Neto CM , Coutinho LL , Cristofani M , Dias-Neto E , Docena C , El-Dorry H , Facincani AP , Ferreira AJ , Ferreira VC , Ferro JA , Fraga JS , Franca SC , Franco MC , Frohme M , Furlan LR , Garnier M , Goldman GH , Goldman MH , Gomes SL , Gruber A , Ho PL , Hoheisel JD , Junqueira ML , Kemper EL , Kitajima JP , Krieger JE , Kuramae EE , Laigret F , Lambais MR , Leite LC , Lemos EG , Lemos MV , Lopes SA , Lopes CR , Machado JA , Machado MA , Madeira AM , Madeira HM , Marino CL , Marques MV , Martins EA , Martins EM , Matsukuma AY , Menck CF , Miracca EC , Miyaki CY , Monteriro-Vitorello CB , Moon DH , Nagai MA , Nascimento AL , Netto LE , Nhani A, Jr. , Nobrega FG , Nunes LR , Oliveira MA , de Oliveira MC , de Oliveira RC , Palmieri DA , Paris A , Peixoto BR , Pereira GA , Pereira HA, Jr. , Pesquero JB , Quaggio RB , Roberto PG , Rodrigues V , de MRAJ , de Rosa VE, Jr. , de Sa RG , Santelli RV , Sawasaki HE , da Silva AC , da Silva AM , da Silva FR , da Silva WA, Jr. , da Silveira JF , Silvestri ML , Siqueira WJ , de Souza AA , de Souza AP , Terenzi MF , Truffi D , Tsai SM , Tsuhako MH , Vallada H , Van Sluys MA , Verjovski-Almeida S , Vettore AL , Zago MA , Zatz M , Meidanis J , Setubal JC
Ref : Nature , 406 :151 , 2000
Abstract : Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.
ESTHER : Simpson_2000_Nature_406_151
PubMedSearch : Simpson_2000_Nature_406_151
PubMedID: 10910347
Gene_locus related to this paper: xylfa-ACVB , xylfa-cxest , xylfa-metx , xylfa-PD2024 , xylfa-pip , xylfa-q9pdj5 , xylfa-XF0015 , xylfa-XF0357 , xylfa-XF0358 , xylfa-XF0754 , xylfa-XF0863 , xylfa-XF0992 , xylfa-XF1029 , xylfa-XF1181 , xylfa-XF1253 , xylfa-XF1282 , xylfa-XF1356 , xylfa-XF1479 , xylfa-XF1743 , xylfa-XF1745 , xylfa-XF1750 , xylfa-XF1829 , xylfa-XF1965 , xylfa-XF2151 , xylfa-XF2260 , xylfa-XF2330 , xylfa-XF2551 , xylfa-XFA0032