Genome Sequence of
            <i>Aeromonas hydrophila</i>
            ATCC 7966
            <sup>T</sup>
            : Jack of All Trades

Seshadri, Rekha; Joseph, Sam W.; Chopra, Ashok K.; Sha, Jian; Shaw, Jonathan G.; Graf, Joerg; Haft, Daniel H.; Wu, Martin; Ren, Qinghu; Rosovitz, M. J.; Madupu, Ramana; Tallon, Luke J.; Kim, Mary; Jin, Shao-Hua; Vuong, Hue; Stine, O. Colin; Ali, Afsar; Horneman, Amy J.; Heidelberg, John F.

doi:10.1128/jb.00621-06

Cited by 337 publications

(339 citation statements)

References 110 publications

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“…For example, relationships among the gammaproteobacteria Aeromonas hydrophila, Vibrio cholerae and Escherichia coli in the 16S rRNA gene-based tree are consistent with the phylogeny shown in a previous study using 31 concatenated protein sequences and comprising a large group of gammaproteobacteria (Seshadri et al, 2006), but the DnaJ tree shows a different relationship.…”

Section: The Proteobacteriasupporting

confidence: 72%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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In the past, bacterial phylogeny relied almost exclusively on 16S rRNA gene sequence analysis. More recently, multilocus sequence analysis has been used to infer organismal phylogenies. In this study, the dnaJ chaperone gene was investigated as a marker for phylogeny studies in alphaproteobacteria. Preliminary analysis of G+C contents and G+C3s contents (the G+C content of the synonymous third codon position) showed no clear evidence of horizontal transfer of this gene in proteobacteria. dnaJ-based phylogenies were then analysed at three taxonomic levels: the Proteobacteria, the Alphaproteobacteria and the genus Mesorhizobium. Dendrograms based on DnaJ and 16S rRNA gene sequences revealed the same topology described previously for the Proteobacteria. These results indicate that the DnaJ phylogenetic signal is able to reproduce the accepted relationships among the five classes of the Proteobacteria. At a lower taxonomic level, using 20 alphaproteobacteria, the 16S rRNA gene-based phylogeny is distinct from the one based on DnaJ sequence analysis. Although the same clusters are generated, only the topology of the DnaJ tree is consistent with broader phylogenies from recent studies based on concatenated alignments of multiple core genes. For example, the DnaJ tree shows the two clusters within the Rhizobiales as closely related, as expected, while the 16S rRNA gene-based phylogeny shows them as distantly related. In order to evaluate the phylogenetic performance of dnaJ at the genus level, a multilocus analysis based on five housekeeping genes (atpD, gapA, gyrB, recA and rplB) was performed for ten Mesorhizobium species. In contrast to the 16S rRNA gene, the DnaJ sequence analysis generated a tree similar to the multilocus dendrogram. For identification of chickpea mesorhizobium isolates, a dnaJ nucleotide sequence-based tree was used. Despite different topologies, 16S rRNA gene-and dnaJ-based trees led to the same species identification. This study suggests that the dnaJ gene is a good phylogenetic marker, particularly for the class Alphaproteobacteria, since its phylogeny is consistent with phylogenies based on multilocus approaches. INTRODUCTIONThe phylum Proteobacteria is composed of five classes, the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria (Garrity et al., 2005;Stackebrandt et al., 1988). By the end of 2008, more than 380 complete genomes of proteobacteria were available in public databases (http://www. ncbi.nlm.nih.gov/genomes/lproks.cgi). Alphaproteobacteria exhibit an enormous diversity in their morphological and metabolic characteristics and the class is presently recognized solely as a clade in the 16S rRNA gene-based phylogeny (Stackebrandt et al., 1988). Based on 16S rRNA gene trees, the Alphaproteobacteria has been divided into seven orders: Caulobacterales, Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Parvularculales (Kersters et al., 2006). The Alphaproteobacteria includes important bacteria tha...

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Section: The Proteobacteriasupporting

confidence: 72%

dnaJ is a useful phylogenetic marker for alphaproteobacteria

Alexandre

Laranjo

Young

et al. 2008

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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“…In this study, we identified additional hcp and vgrG genes (designated hcp-1 and vgrG-1) located at distal genomic sites (outside of the T6SS cluster) of A. hydrophila SSU. Interestingly, hcp-1 and vgrG-1 genes were genetically linked through a 263 bp non-coding intergenic region, as was also seen in V. cholerae and A. hydrophila ATCC 7966 genomes (Pukatzki et al, 2006;Seshadri et al, 2006). The hcp-1 and hcp-2 genes of A. hydrophila SSU encoded almost identical proteins with 172 amino acid residues; the only differences observed were at positions 84 and 146, in which alanine and methionine in Hcp-1 were replaced with serine and leucine in Hcp-2, respectively (Fig.…”

Section: T6ss Gene Cluster and Functionmentioning

confidence: 94%

“…Based on the genome sequences of V. cholerae (Pukatzki et al, 2006;Seshadri et al, 2006), additional copies of hcp and vgrG genes, designated hcp-1 and vgrG-1, were identified that mapped to chromosomal regions outside of the T6SS gene cluster. During our T6SS characterization, we noticed that two PCR amplicons/products of lengths 450 and 650 bp were amplified using the primer pair Pv1 and Pv2, which corresponded to the 39 end of hcp-2 and the 59 end of vgrG-2, respectively (Table S1, available in Microbiology Online).…”

Section: Methodsmentioning

confidence: 99%

“…Indeed, multiple copies of hcps and vgrGs have commonly been seen across all the bacteria that possess the T6SS, and, interestingly, some bacteria even possess multiple copies of the T6SS cluster (Mougous et al, 2006;Podladchikova et al, 2011). In A. hydrophila, the two effector proteins (Hcps and VgrGs) that disarm host defences by targeting genes important for innate immune cells (among other genes) cluster to only one region of the chromosome (Seshadri et al, 2006;Suarez et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of the roles played by Hcp and VgrG type 6 secretion system effectors in Aeromonas hydrophila SSU pathogenesis

et al. 2013

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Aeromonas hydrophila, a Gram-negative bacterium, is an emerging human pathogen equipped with both a type 3 and a type 6 secretion system (T6SS). In this study, we evaluated the roles played by paralogous T6SS effector proteins, hemolysin co-regulated proteins (Hcp-1 and -2) and valine glycine repeat G (VgrG-1, -2 and -3) protein family members in A. hydrophila SSU pathogenesis by generating various combinations of deletion mutants of the their genes. In addition to their predicted roles as structural components and effector proteins of the T6SS, our data clearly demonstrated that paralogues of Hcp and VgrG also influenced bacterial motility, protease production and biofilm formation. Surprisingly, there was limited to no observed functional redundancy among and/or between the aforementioned T6SS effector paralogues in multiple assays. Our data indicated that Hcp and VgrG paralogues located within the T6SS cluster were more involved in forming T6SS structures, while the primary roles of Hcp-1 and VgrG-1, located outside of the T6SS cluster, were as T6SS effectors. In terms of influence on bacterial physiology, Hcp-1, but not Hcp-2, influenced bacterial motility and protease production, and in its absence, increases in both of the aforementioned activities were observed. Likewise, VgrG-1 played a major role in regulating bacterial protease production, while VgrG-2 and VgrG-3 were critical in regulating bacterial motility and biofilm formation. In an intraperitoneal murine model of infection, all Hcp and VgrG paralogues were required for optimal bacterial virulence and dissemination to mouse peripheral organs. Importantly, the observed phenotypic alterations of the T6SS mutants could be fully complemented. Taking these results together, we have further established the roles played by the two known T6SS effectors of A. hydrophila by defining their contributions to T6SS function and virulence in both in vitro and in vivo models of infection.

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“…The oligonucleotide primers used in this study (Table 2) were designed based on the A. hydrophila ATCC 7966 T genome sequence. 18) Homology searches were performed using the National Center for Biotechnology Information Basic Local Alignment Search Tool (BLAST; http://blast.ncbi.nlm.nih.gov/). A putative AraC-binding site (AraC box) sequence was identified using the Virtual Footprint promoter analysis software based on the PRODORIC Release 8.9 (http://www.prodoric.de/) online database.…”

Section: Methodsmentioning

confidence: 99%