Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation.
ABSTRACT Repetitive extragenic palindromic (REPs) sequences were first described in enterobacteriacea and later in Pseudomonas putida. We have detected a new variant (51 base pairs) of REP sequences that appears to be disseminated in more than 300 copies in the Pseudomonas syringae DC3000 genome. The finding of REP sequences in P. syringae confirms the broad presence of this type of repetitive sequence in bacteria. We analyzed the distribution of REP sequences and the structure of the clusters, and we show that palindromy is conserved. REP sequences appear to be allocated to the extragenic space, with a special preference for the intergenic spaces limited by convergent genes, while their presence is scarce between divergent genes. Using REP sequences as markers of extragenicity we re-annotated a set of genes of the P. syringae DC3000 genome demonstrating that REP sequences can be used for refinement of annotation of a genome. The similarity detected between virulence genes from evolutionarily distant pathogenic bacteria suggests the acquisition of clusters of virulence genes by horizontal gene transfer. We did not detect the presence of P. syringae REP elements in the principal pathogenicity gene clusters. This absence suggests that genome fragments lacking REP sequences could point to regions recently acquired from other organisms, and REP sequences might be new tracers for gaining insight into key aspects of bacterial genome evolution, especially when studying pathogenicity acquisition. In addition, as the P. syringae REP sequence is species-specific with respect to the sequenced genomes, it is an exceptional candidate for use as a fingerprint in precise genotyping and epidemiological studies.
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ABSTRACT: The genome of Stenotrophomonas maltophilia is peppered with palindromic elements called SMAG (Stenotrophomonas maltophilia GTAG) because they carry at one terminus the tetranucleotide GTAG. The repeats are species-specific variants of the superfamily of repetitive extragenic palindromes (REPs), DNA sequences spread in the intergenic space in many prokaryotic genomes. The genomic organization and the functional features of SMAG elements are described herein. A total of 1650 SMAG elements were identified in the genome of the S. maltophilia K279a strain. The elements are 22-25 bp in size, and can be sorted into five distinct major subfamilies because they have different stem and loop sequences. One fifth of the SMAG family is comprised of single units, 2/5 of elements located at a close distance from each other and 2/5 of elements grouped in tandem arrays of variable lengths. Altogether, SMAGs and intermingled DNA occupy 13% of the intergenic space, and make up 1.4% of the chromosome. Hundreds of genes are immediately flanked by SMAGs, and the level of expression of many may be influenced by the folding of the repeats in the mRNA. Expression analyses suggested that SMAGs function as RNA control sequences, either stabilizing upstream transcripts or favoring their degradation.FEMS Microbiology Letters 07/2010; 308(2):185-92. DOI:10.1111/j.1574-6968.2010.02010.x · 2.72 Impact Factor
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ABSTRACT: The ability of Pseudomonas syringae pv. phaseolicola to cause halo blight of bean is dependent on its ability to translocate effector proteins into host cells via the hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS). To identify genes encoding type III effectors and other potential virulence factors that are regulated by the HrpL alternative sigma factor, we used a hidden Markov model, weight matrix model, and type III targeting-associated patterns to search the genome of P. syringae pv. phaseolicola 1448A, which recently was sequenced to completion. We identified 44 high-probability putative Hrp promoters upstream of genes encoding the core T3SS machinery, 27 candidate effectors and related T3SS substrates, and 10 factors unrelated to the Hrp system. The expression of 13 of these candidate HrpL regulon genes was analyzed by real-time polymerase chain reaction, and all were found to be upregulated by HrpL. Six of the candidate type III effectors were assayed for T3SS-dependent translocation into plant cells using the Bordetella pertussis calmodulin-dependent adenylate cyclase (Cya) translocation reporter, and all were translocated. PSPPH1855 (ApbE-family protein) and PSPPH3759 (alcohol dehydrogenase) have no apparent T3SS-related function; however, they do have homologs in the model strain P. syringae pv. tomato DC3000 (PSPTO2105 and PSPTO0834, respectively) that are similarly upregulated by HrpL. Mutations were constructed in the DC3000 homologs and found to reduce bacterial growth in host Arabidopsis leaves. These results establish the utility of the bioinformatic or candidate gene approach to identifying effectors and other genes relevant to pathogenesis in P. syringae genomes.Molecular Plant-Microbe Interactions 12/2006; 19(11):1193-206. DOI:10.1094/MPMI-19-1193 · 4.46 Impact Factor
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ABSTRACT: Tesis Univ. Granada. Departamento de Genética. Leída el 13 de julio de 2006