These results imply that T3S systems did not originate within their present host bacteria, but spread through horizontal gene transfer events . selleck compound Furthermore, apart from a high degree of gene homologies within the T3SS families, the overall genetic organization
(synteny) is also conserved . In this study, we present a detailed phylogenetic and gene synteny analysis of core T3SS proteins. This analysis reveals the presence of three distinct Rhc-T3SS family subgroups. From these subgroups, the one designated as subgroup II was found to comprise T3S systems from various Pseudomonas syringae strains as well as from Rhizobium sp. NGR234. The T3SS of subgroup II will be hereafter referred to as T3SS-2, because these systems exist in their bacterial hosts next to the well-studied T3SS from the pNGR234a plasmid of Rhizobium sp. and the Hrc1-Hrp1 T3S system of P. syringae. Interestingly, at least two of the genes from the additional T3SS-2
gene cluster in P. syringae pv phaseolicola strain 1448a were found to be transcriptionally active. Methods Sequence analysis Genomic regions The regions comprising and surrounding the T3SS-2 gene clusters of P. syringae pv phaseolicola 1448a, P. syringae pv oryzae str. 1_6, P. syringae pv tabaci ATCC11528, Rhizobium spp. NGR234 and the regions comprising and surrounding the unique T3SS gene clusters of Bradyrhizobium japonicum USDA 110, Rhizobium etli CIAT 652 and R. etli CNF 42 were retrieved from the NCBI Genome database. In the cases of
P. syringae Selleckchem A1155463 pv tabaci ATCC11528 and P. syringae pv aesculi the nucleotide sequence in the region close to the T3SS gene cluster was retrieved (GenBank: N° ACHU01000133 and N° ACXS01000083.1 respectively) after being identified through MegaBLAST searches and found to be present in P. syringae pv phaseolicola 1448a, but find more absent from P. syringae pv tomato DC3000 and Pseudomonas syringae pv syringae B728A; coding sequences were identified with NCBI’s ORF Finder tool. Amino acid sequence analysis Each coding sequence annotated in the T3SS gene clusters of P. syringae pv phaseolicola 1448a, R. etli CIAT 652 and Rhizobium spp. NGR234 was analyzed Farnesyltransferase by Psi-BLAST searches  against the NCBI non-redundant database reduced for bacteria using the following parameters: BLOSUM 65 substitution matrix; expected threshold 10; word size 3; gap costs: existence: 11, extension 1; the filter for low complexity regions was set to on. The number of descriptions and alignments to be reported was set to 500 and conditional compositional adjustments were on. The program FoldIndex© was used with default parameters for the prediction of structural disorder propensity from the amino acid sequences . Secondary structure predictions were performed with PSIPRED . Physical and chemical parameters of sequences under study were estimated by ProtParam .