Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains
BMC Microbiology volume 12, Article number: 188 (2012)
The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. Some Pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterized Hrc1 T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. The aim of this study is to perform an in silico analysis of T3SS-2, and to compare it with other known T3SSs.
Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of the P. syringae pv. phaseolicola strain is grouped with a second T3SS found in the pNGR234b plasmid of Rhizobium sp. These additional T3SS gene clusters define a subgroup within the Rhizobium T3SS family. Although, T3SS-2 is not distributed as widely as the Hrc1 T3SS in P. syringae strains, it was found to be constitutively expressed in P. syringae pv phaseolicola through RT-PCR experiments.
The relatedness of the P. syringae T3SS-2 to a second T3SS from the pNGR234b plasmid of Rhizobium sp., member of subgroup II of the rhizobial T3SS family, indicates common ancestry and/or possible horizontal transfer events between these species. Functional analysis and genome sequencing of more rhizobia and P. syringae pathovars may shed light into why these bacteria maintain a second T3SS gene cluster in their genome.
Gram-negative proteobacteria deploy various types of protein secretion systems for exporting selected sets of proteins to the cell surface, the extracellular space or into host cells [1, 2]. Type III Secretion Systems (T3SS) are directly related to pathogenicity or to symbiosis with higher organisms and constitute essential mediators of the interactions between gram-negative bacterial cells and eukaryotic ones [3–8] as the T3SS efficiently translocates bacterial proteins (effectors) directly into the host cell cytoplasm when fully developed.
The T3SS apparatus comprises three distinct parts: a) the basal body, which forms a cylindrical base that penetrates the two bacterial membranes and the periplasmic space; b) the extracellular part with the needle or the pilus as its main feature which is formed through the polymerization of specialized protein subunits that are T3SS substrates themselves; and c) the cytoplasmic part, which forms the export gate for secretion control. This apparatus is built by specific core proteins encoded by a conserved subset of genes tightly organized in gene clusters with counterparts in the bacterial flagellum [6, 7].
Phylogenetic analyses of the core T3SS proteins revealed that the T3S systems evolved into seven distinct families that spread between bacteria by horizontal gene transfer. (1) The Ysc-T3SS family, named after the archetypal Yersinia system, is present in α-, β-, γ-, and δ- proteobacteria. At least in α-proteobacteria the system confers resistance to phagocytosis and triggers macrophage apoptosis. (2) The Ssa-Esc-T3SS family is named after the archetypal T3SS of enteropathogenic and enterohemorrhagic E.coli. (3) The Inv-Mxi-Spa-T3SS family named after the Inv-Spa system of Salmonella enterica and the Inv-Mxi T3S system of Shigella spp. The family members trigger bacterial uptake by nonphagocytic cells.(4) The Hrc-Hrp1- and (5) the Hrc-Hrp2-T3SS families are present in plant pathogenic bacteria of the genus Pseudomonas, Erwinia, Ralstonia and Xanthomonas. The two families are differentiated on the basis of their genetic loci organization and regulatory systems. (6) The Rhizobiales-T3SS family (hereafter referred to as Rhc-T3SS) is dedicated to the intimate endosymbiosis serving nitrogen fixation in the roots of leguminous plants. (7) Finally the Chlamydiales-T3SS is present only in these strictly intracellular nonproteobacteria pathogens [8, 9]. The phylogenetic trees obtained by the above analysis were totally incongruent with the evolutionary tree of bacteria based on 16S rRNA sequences. These results imply that T3S systems did not originate within their present host bacteria, but spread through horizontal gene transfer events . 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.
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 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 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 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 . Coiled coil predictions and assignment of the heptad repeat positions in proteins were produced in COILS  and MATCHER  respectively. Sequence threading techniques and fold-recognition algorithms were used to identify distant homologs. 3-D structural profiles for T3SS proteins were predicted from sequence data was performed using the PHYRE pipeline . The program Memstat3  was used for the prediction of membrane α-helices in proteins.
Nucleotide sequence analysis
The gene synteny of the T3SS-2 clusters of P. syringae pv phaseolicola 1448a, P. syringae pv oryzae str. 1_6, P. syringae pv tabaci ATCC11528, Rhizobium spp. NGR234 and the gene synteny of the unique T3SS gene clusters of B. japonicum USDA 110, R. etli CIAT 652, R. etli CNF 42, were compared to other known T3SS gene clusters of various bacteria using the BLASTN and BLASTP tools of the Genbank. Codon Usage Bias analysis was performed using DnaSP v5 .
T3SS core protein sequences were retrieved using Psi-BLAST searches with the P. syringae pv phaseolicola 1448a T3SS-2 gene cluster coding frames and were aligned with the multiple alignment method ClustalW, version 1.8 .
Phylogenetic relations were inferred using the neighbour-joining method  implemented in the MEGA4 software . The bootstrap consensus tree inferred from 1000 replicates  is taken to represent the evolutionary history of the amino acid sequences analyzed . Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches . The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method  and are in the units of the number of amino acid substitutions per site. All positions containing alignment gaps and missing data were eliminated only in pair wise sequence comparisons.
P. syringae strains were routinely grown at 28°C in LB medium. Bacteria of overnight culture were collected at an OD (optical density) of 0.8. The bacterial pellet was washed with 10 mM MgCl2 and the cells were resuspended (OD: 0.6-0.7) in Hrp-induction media  for overnight cultivation at 28°C. The next day the bacterial cells were collected (OD: 0.7-0.8) for RNA extraction.
For the RT-PCR reactions, total RNA was extracted from overnight bacterial cultures of P. syringae pv phaseolicola 1448a and P. syringae pv tomato DC3000, using both LB and Hrp-induction media . Total RNA was treated with RNase-free DNase I for 45 min at 37°C . From both culture conditions equal amounts of the extracted total RNA were subjected to RT-PCR with gene specific primers for the PSPPH_2530, PSPPH_2524 and 16S rDNA genes, using the OneStep RT-PCR kit according to the manufacturer’s instructions (QIAGEN). For negative control, PCR was performed on the total RNA without Reverse Transcriptase assay, using the 16S rDNA primers, in order to accredit no DNA contamination in the total RNA isolation samples. The RT-PCR products were then analyzed by agarose gel electrophoresis. Primers sequences for 16S RNA were 5′-CGGGTACTTGTACCTGGTGGC-3′ and 5′-CTTGCCAGTTTTGGATGCAGTTC-3′, for PSPPH_2530 were 5′-AGGCCCTGACGACGCTGCTG-3′ and 5′-CCAGGTGCCTGTGTTCGGCAGT-3′ and for PSPPH_2524 5′-TCCTGCTGTGCCTGTTATCCGGCG-3′ and 5′-GACGGTCGGTAGCGACTTGAGTGAC-3′.
Results and discussion
Analysis of core components of P. syringae T3SS-2 and the Rhc-T3SS family
Phylogenetic analysis of core proteins
In the subsequent sections the unified nomenclature for T3SS proteins (Table 1) will be followed . The phylogenetic analysis of various T3SS core proteins (including T3SS-2 proteins), e.g. SctU (RhcU/HrcU/YscU/FlhB and their homologues), SctV (RhcV/HrcV/LcrD/FlhA homolog proteins), SctQ (RhcQ/HrcQ/YscQ/FliN/ and their homologues) and the T3SS ATPases SctN (RhcN/HrcN/YscN/FliI and homologues), confirmed the broad classification of the non-flagellar T3SS into seven families. However, the T3SS-2 proteins were grouped in the same clade with the Rhc T3SS proteins with high bootstrap values, suggesting that these lineages share a more recent common origin than with other T3SS families.
Interestingly, the Rhc T3SS family can be further subdivided into three subgroups: Subgroup I is represented by the well-known T3SSs of Rhizobium sp. NGR234, and B. japonicum USDA 110 while subgroup III is represented by the T3SS present in R. etli. Proteins from the T3SS-2 system of various P. syringae strains are grouped closer to the T3SS-2 of Rhizobium sp. NGR234 (Figure 1, 2, Additional files 1, Additional file 2 & Additional file 3: Figures S1, S2 & S3), forming the subgroup II of the Rhc T3SS family.
All required core T3SS components are present in the T3SS- of P. syringae strains
BLASTP and Psi-BLAST searches revealed the main T3SS components of the novel T3SS-2 gene cluster of P. syringae pv phaseolicola 1448a which are also conserved in P. syringae pv oryzae str. 1_6, P. syringae pv tabaci ATCC11528 (Additional file 4: Table S1) and P. syringae pv aesculi. Similar searches and comparisons were also carried out with the T3SSs of R. etli CNF 42, R. etli CIAT 652 and Rhizobium sp. strain NGR234. In the following, the prefix Hrc II will be used to specify the conserved T3SS-2 proteins of P. syringae pv phaseolicola 1448a, P. syringae pv oryzae str. 1_6 and P. syringae pv tabaci, while the prefix Rhc II will be used to distinguish the Rhc proteins of the T3SS-2 gene cluster found in plasmid pNGR234b of Rhizobium sp. NGR234 (see below). The T3SS protein nomenclature when used is indicated by the prefix Sct according to Table 1.
All major T3SS core proteins were found in the T3SS gene clusters mentioned above, including the T3SS ATPase protein SctN (RhcN/HrcN/YscN/FliI homolog), its negative regulator SctL (NolV/HrpE/YscL/FliH homolog), the two T3SS gate proteins SctU and SctV (RhcU/HrcU/YscU/FlhB and RhcV/HrcV/LcrD/FlhA homologs respectively), the protein building the inner ring of the T3SS basal body SctJ (RhcJ/HrcJ/YscJ homolog), the protein building the cytoplasmic ring SctQ (RhcQ/HrcQ/YscQ/FliY homolog) and the three core membrane proteins SctR, SctS, SctT (RhcRST/HrcRST/YscRST/FliPQR homologs) (Additional file 4: Table S1).
It is noteworthy that the promoter regions of the T3SS-2 ORFs/operons of P. syringae pv phaseolicola 1448a, do not appear to harbor "hrp box" elements like those which have been described for the T3SS-1 genes of various P. syringae strains . This, coupled with the low expression level seen in minimal media (Figure 3), leave open the question whether T3SS-2 in this or other P. syringae strains is expressed under in planta conditions and whether it is plays a role in their phytopathogenic potential or in any other aspect of their life cycle.
The split secretin gene
A distinguishing feature of gene organization in Rhc T3SS clusters is a split gene coding for the outer membrane secretin protein SctC, i.e. a HrcC/YscC homologue . This is also true for the subgroup II Rhc T3SS gene clusters. In the T3SS-2 clusters of the three P. syringae pathovars the secretin gene is split in two ORFs (Figure 4, Additional file 4: Table S1). In P. syringae pv phaseolicola 1448a, loci PSPPH_2524 (hrc II C1) and PSPPH_2521 (hrc II C2) code for the N-terminal and the C-terminal part of secretin, respectively, of a HrcC/YscC homolog. Comparisons of Hrc II C1 and Hrc II C2 with the RhcC1 and Rhc2 proteins of Rhizobium sp. NGR234 are given in Additional file 5: Figure S4, respectively. A similar situation occurs in P. syringae pv oryzae str. 1_6 while in P. syringae pv tabaci ATCC11528 hrc II C2 gene is further split into two parts. However in P. syringae pv phaseolicola 1448a and P. syringae pv tabaci ATCC11528 the two hrc II C1, hrc II C2 genes are only separated by an opposite facing ORF coding for a TPR-protein, while in the subgroup I Rhc T3SS these two genes are separated even further (Figure 4). Although the functional significance of the split secretin gene is not known, there are reports of constitutive expression of the rhcC1 gene in contrast to the rest of the T3SS operons in rhizobia [29, 30]. In subgroup III only the rhcC1 could be identified (RHECIAT_PB0000097 in the R. etli CIAT 652 and RHE_PD00065 in R. etli CNF 42) in Psi-BLAST searches using the Hrc ΙΙ C1 protein sequence as query (25% identity to RhcC1 of Rhizobium sp. NGR234) (Figure 4).
The HrcIIQ protein
The PSPPH_2534 locus (designated hrc II Q) in the T3SS-2 cluster of P. syringae pv phaseolicola 1448A codes for a polypeptide chain of 301 residues, which has sequence similarities with members of the HrcQ/YscQ/FliY family. Members of this family usually consist of two autonomous regions  which either are organized as two domains of a single protein or can be split up into two polypeptide chains. The Hrc II Q is comparable in length with the long proteins of the family. The same is true in the Rhc-T3SS case, where an HrcQ ortholog is found. In agreement with the other HrcQ/YscQ/FliY members the sequence conservation is especially high at the C-terminus [31, 32]. In the originally described T3SS-1 (Hrc-Hrp1) of P. syringae strains this gene is split into two adjacent ORFs coding for separate polypeptides (HrcQA and HrcQB). No splitting occurs however in the T3SS-2 clusters of the P. syringae strains.
The HrpO-like protein
A conserved feature in gene organization of T3SS gene clusters and the flagellum is the presence of a small ORF downstream of the gene coding for the ATPase (hrcN/yscN/fliI homologue). These ORFs code for proteins of the HrpO/YscO/FliJ family, a diverse group characterized by low sequence similarity, and heptad repeat motifs suggesting a high tendency for coiled-coil formation and a propensity for structural disorder . Such a gene is also present in the Rhizobium NGR234 T3SS-2 but is absent from the subgroup III Rhc- T3SS where the rhcQ gene is immediately downstream of the rhcN gene (Figure 4). In the P. syringae pathovars included in Figure 4 there is a small ORF (PSPPH_2532 in strain P. syringae pv phaseolicola 1448A, Figure 4) coding for a polypeptide wrongly annotated as Myosin heavy chain B (MHC B) in the NCBI protein database. Sequence analysis of this protein and its homologs in the other two P. syringae strains using BLASTP searches did not reveal any significant similarities to other proteins. However, these small proteins are predicted as unfolded in their entire length, while heptad repeat patterns are recognizable in the largest part of their sequence, thus strongly resembling the properties of members of the HrpO/YscO/FliJ family , (Additional file 6: Figure S5). A potentially important feature in the P. syringae pv phaseolicola 1448a T3SS-2 cluster is a predicted transposase gene between the ORF coding for the above described HrpO/YscO/FliJ family member and the ORF for the HrcIIN ATPase (Figure 4); this gene is absent from the P. syringae pv tabaci and P. syringae pv oryzae str.1_6 T3SS-2 clusters. The insertion of the transposase gene does not disrupt genes hrc II N or hrp II O as concluded by amino acid sequence comparison with other members of the SctN and SctO protein families respectively (including ORFs from other T3SS-2 P. syringae strains). These genes are capable of producing the respective full-length proteins and no premature termination, due to transposase insertion, is observed.
The HrpQ-like protein
Another common feature of P. syringae T3SS-2 and the Rhizobium T3SSs excluding subgroup III, is a gene usually positioned upstream of the sctV gene (rhcV/hrcV/lcrD/flhA homolog) and in close proximity to it. Psi-BLAST searches for the PSPPH_2517 encoded protein revealed moderate similarities to the HrpQ/YscD family of T3SS proteins; these were confirmed by sequence threading techniques. For example, a segment of of PSPPH_2517 corresponding to 45% of its amino acid sequence scores an E-value of 2e-05 and a 26% identity with YscD protein from Yersinia enterocolitica (ref|YP_006007912.1); the same segment scores an E-value of 1e-13 with 25% identity to the 90% of its sequence with the equivalent protein from B. japonicum USDA110 (ref| NP_768443.1). The chosen folding templates belong to various forkhead - associated (FHA) protein domains from different origins. FHA cytoplasmic domains characterize the YscD/EscD protein family and may suggest phosphopeptide recognition interactions . A protein with the above characteristics is present in the B. japonicum USDA110 T3SS cluster (encoded by the y4yQ gene) while an ortholog could not be identified in the R. etli T3SS.
Gene clusters organization in the Rhc- T3SS family and the P. syringae T3SS-2
Subgroup I of the Rhc-T3SS family comprises the first described and well characterized T3SS-1 of Rhizobium NGR234 present in the plasmid pNGR234a , along with that of B. japonicum USDA110 and others . The T3SS core genes in this case are organized in three segments. The biggest segment harbors the genes rhcU, rhcT, rhcS, rhcR, rhcQ, y4yJ, rhcN, nolV, nolU, rhcJ, nolB, in the same DNA strand with the rhcC1 gene flanking the nolB gene in the opposite strand (Figure 4, Subgroup I). The second one harbors the rhcV gene usually between the y4yS and y4yQ genes, all in the same orientation. In the case of the B. japonicum USDA110 however there are two additional open reading frames (ORFs) between the rhcV and the y4yQ gene in the same orientation (Figure 4, Subgroup I). The third segment harbors the rhcC2 gene usually between the y4xI and the y4xK genes.
Subgroup III of the Rhc-T3SS family includes the T3SS of R. etli strains CIAT652 (plasmid b) and CNF42 (plasmid d) . The gene organization is very different from that of subgroup I in that there is no rhcC2 gene, while the rhcV gene is in close proximity to the biggest segment. In the biggest segment the genes y4yJ (hrpO/yscO/fliJ homolog) and nolB are missing. Additional genes present in the subgroup III are coding for a HrpK-like protein (hypothetical translocator of the Hrc-Hrp1 T3SS) and a HrpW-like protein.
Gene clusters of subgroup II of the Rhc T3SS family, represented by the the T3SS-2 of Rhizobium NGR234 (pNGR234b plasmid)  and the recently identified T3SS-2 gene clusters of the P. syringae, possesses various characteristics that classify them as intermediates between the T3SS subgroups I and III. On one hand, subgroup II clusters share the sctO, sctD and sctC2 genes with subgroup I clusters and but not with subgroup III; on the other hand, some subgroup II clusters posses putative translocator genes present in subgroup III, but absent from subgroup I.
The T3SS-2 clusters of the P. syringae strains are essentially syntenic, with the exceptions of an IS element (insertion sequence element) being present between the Hrc II N and Hrp II O coding frames in the P. syringae pv phaseolicola 1448a cluster and the absence of a TPR (tetratricopeptide repeats) protein coding frame in the P. syringae pv oryzae str.1_6 cluster. The Rhizobium sp. NGR234 pNGR234b-plasmid borne cluster has two extended regions of synteny with those of the P. syringae strains. One is the region from hrc II C 1 to hrc II T, [not including the IS element in the P. syringae pv phaseolicola 1448a cluster (see above)]. The other is the region from hrp II Q to PSPPH_2522 which, however, is inverted in the Rhizobium sp. NGR234 pNGR234b T3SS cluster relative to those in the pseudomonads. The coding frame for the RhcU/HrcU/YscU/FhlB homolog in the NGR234 cluster is transposed in relation to the Pseudomonas cluster (position which is maintained in the R.etli and B. japonicum clusters). In subgroup II of Rhc- T3SS gene clusters an hrc II C2 gene can be identified in synteny to the subgroup I cluster. A common property of subgroups II and III of Rhc-T3SS gene clusters is the presence of hrpK-like genes.
Common to all Rhc-T3SS subgroups is the absence of a hrpP/yscP –like gene which usually resides between the hrpO/yscO-like gene and the hrcQ/yscQ homolog gene. A hrpO/yscO- like gene is absent from the subgroup III cluster. Subgroup I and III clusters maintain synteny with the P. syringae T3SS-2 clusters for most of the core T3SS ORFs. Finally, a gene coding for a HrpW homolog is found only in the R. etli clusters.
Non-conserved T3SS proteins
The translocator of the P. syringae T3SS-2
A common feature of the R. etli Rhc T3SS (subgroup III) and the T3SS-2 of P. syringae pathovars (but not of the Rhizobium sp. NGR234 T3SS-2) is the presence of an ORF coding for a hypothetical translocator protein: The PSPPH_2540 locus of the P. syringae pv phaseolicola 1448a T3SS-2 codes for a large protein of 1106 residues. The C-terminal part of this protein (residues 421 – 1106) is homologous to the HrpK proteins of the Hrc-Hrp1 T3SS family based on Psi-BLAST searches (25% identity with HrpK of Erwinia amylovora). HrpK shares low similarity with the putative translocator, HrpF, from Xantomonas campestris pv vesicatoria. Furthermore, the C-terminal part of the protein coded by PSPPH_2540 also possesses two predicted transmembrane α-helices comprising residues 879–898 and 1029–1047 (MEMSAT3 analysis). The subgroup I Rhc T3SS lacks a hrpK ortholog. The HrpK protein was initially identified as a component of the Hrc-Hrp1 family of T3S systems . Interestingly, the R. etli T3SS gene cluster possesses two copies of hrpK-like genes, plus an additional hrpW-like gene, coding for an Hrp-secreted protein homologous to class III pectate lyases which is absent from the P. syringae pv phaseolicola 1448a T3SS-2 gene cluster but present in the extremity of the Hrc-Hrp1 gene cluster of P. syringae pv phaseolicola 1448a. These differences possibly suggest variations in the mode of interaction of these bacteria with their hosts.
The two unknown ORFs upstream of the rhcV gene in subgroup II Rhc-T3SS gene clusters
The choice of the B. japonicum USDA 110 T3SS as archetypal for subgroup I in the Rhc family (Figure 4) and for synteny comparisons with the subgroup II gene clusters, was based on the DNA segment encompassing rhcV (y4yQ-y4yS). The presence of two small open reading frames upstream of the rhcV gene and downstream of the y4yQ gene of the known Rhizobium T3SS resembled the case of the P. syringae pv phaseolicola 1448a T3SS-2 where loci PSPPH_2518 and PSPPH_2519 are found between the ORF coding for the SctV protein (RhcV/HrcV/LcrD/FlhA homolog) and the ORF coding for the SctD protein (HrpQ/YscD homolog).
The PSPPH_2519 locus, upstream of the hrc II V gene of P. syringae pv phaseolicola 1448a genome, encodes for a 112 long polypeptide with sequence similarities to the VscY protein of Vibrio parahaemolyticus, according to Psi-BLAST searches (E-value = 0.005). The vscY gene is located upstream of the vcrD gene and this synteny is also conserved in the Ysc T3SS gene cluster family. Proteins YscY, VscY and PSPPH_2519 all possess TPR repeats (Tetratricopeptide Repeats) as predicted by Psi-BLAST searches and fold recognition methods. YscY has been found to directly bind the YscX protein, a secreted component of the Ysc T3SS . The bll1801 locus of B. japonicum USDA110 encodes for a 142 long polypeptide with TPR repeats and sequence similarities to the AscY (Aeromonas salmonicida) and YscY proteins according to Psi-BLAST searches. The position of bll1801 is likewise upstream of the rhcV gene in B. japonicum USDA110 T3SS gene cluster. A protein with the above characteristics could not be identified for the R. etli T3SS (subgroup III), however it is present in the T3SS-2 of Rhizobium NGR234.
Transcription regulators in P. syringae T3SS-2
The Hrc-Hrp2 and the Rhc T3S (subgroup I) systems possess transcription regulators that belong to the AraC/XylS in contrast to the Hrc-Hrp1 T3SS that depends on the alternative sigma factor HrpL. The known transcription factors are related to the T3SS regulation of AraC and LuxR/UhaP families of transcription regulators and characterized by two α-helix-turn-α-helix (HTH) motifs in a tetrahelical bundle.
However, the PSPPH_2539 locus of P. syringae T3SS-2 codes for a hypothetical transcription regulator with different characteristics. The N-terminal part of the hypothetical protein (Figure 5, blue-purple area) is predicted to adopt a structure similar to the DNA-binding domains of the PhoB transcription factor. The characteristic HTH motif is a common feature of transcription factors. Although the PSPPH_2539 ORF is annotated in the NCBI as a LuxR-type of transcription regulator, the choice of the DNA-binding domain of PhoB as a structural template indicates that PSPPH_2539 probably has an α-/β- doubly wound fold (distinguished by the presence of a C-terminal β-strand hairpin unit that packs against the shallow cleft of the partially open tri-helical HTH core) motif. Transcription factors are usually multidomain proteins, thus the assignment of PSPPH_2539 as a LuxR-type transcription regulator in the NCBI is probably due to full-length inadequate Psi-BLAST searches biased by the presence of Tetratricopeptide Repeats (TPR) in the large carboxyterminal domain.
The middle part of the protein (Figure 5, yellow area) was found homologous to the AAA+ ATPases (COG3903) based on fold-recognition algorithms and Psi-BLAST searches. These ATPases are associated with diverse cellular activities and are able to induce conformational changes in their targets . In the context of the transcription process, AAA+ ATPase domains are involved in the remodeling of σ54 RNA polymerases. Especially the residues 195 to 300 probably possess the receiver or ligand binding domain of the hypothetical transcription factor (green area, Figure 5).
TPR-repeats proteins present in P. syringae T3SS-2
Apart from the PSPPH_2539 C-terminal domain, there are two more ORFs, PSPPH_2519 and PSPPH_2523, from the P. syringae pv phaseolicola 1448a T3SS-2 that are predicted to code for proteins that possess TPR domains. TPR domains are typically found in class II chaperones of T3S systems - chaperones of the translocators - as well as in transcriptional regulators of the T3S systems, e.g. the HrpB protein of Ralstonia solanacearum, HilA of Salmonella enterica and SicA, of Salmonella typhimurium involved in the activations of T3SS virulence genes . Proteins with TPR repeats also exist in the Hrc-Hrp2 T3S system of X. campestris (HrpB2 protein) and in the T3S system of Rhizobia (e.g. the 182 residue long Y4yS protein). On the other hand, the Hrc-Hrp1 system of P. syringae does not possess proteins with TPR repeats.
DNA characteristics of the P. syringae T3SS-2 gene cluster
The T3SS-2 cluster of P. syringae pv phaseolicola 1448a is separated by 1.42 Mb from the well-characterized Hrc-Hrp1 T3SS cluster in the main chromosome. Both clusters are located on DNA segments with GC content similar to their neighbouring areas. No sequences associated with HrpL-responsive promoters (characteristic for the regulation of the Hrc-Hrp1 operons in P. syringae pathovars) were found in the T3SS-2 gene cluster  indicating a different way of regulation from the Hrc-Hrp1 system. The ORF PSPPH_2539 that resides between the core genes and the hrpK homolog PSPPH_2540, codes for a hypothetical transcription regulator (Figure 4, 5). No t RNA genes, however, have been found in the vicinity of this cluster, while two insertion sequence (IS) elements occur in the border and in the middle region of the T3SS-2 gene cluster (Figure 4).
The GC content of the T3SS-2 cluster in the P. syringae strains is close to the chromosome average (58–61%), which might suggest that it has been resident in the P. syringae’s genome for a long time . The codon usage indexes (Additional file 7: Table S2) of the T3SS-2 cluster show the same degree of codon usage bias as the hrc-hrp1 T3SS cluster of P. syringae pv phaseolicola 1448a. Furthermore, the GC content in the third coding position (GC3) of various genes across the T3SS-2 is close to the respective mean of the genome GC3, as in the case of Hrc-Hrp1 (Additional file 7: Table S2). These equal GC levels could indicate an ancient acquisition of the T3SS-2 gene cluster by P. syringae that was lost in some of its strains. However the scenario of a more recent acquisition from a hypothetical donor with equal GC levels can not be excluded.
Evidence for expression of the P. syringae T3SS-2
There are no reports so far for the expression or function of T3SS-2 in members of P. syringae. To obtain preliminary expression evidence of functional putative RNA transcripts, the hrc II N (sctN) and hrc II C1 (sctC) from P. syringae pv phaseolicola 1448a were detected by RT-PCR in total RNA extracts from cultures grown in rich (LB) and minimal (M9) media, after exhaustive treatment with RNase-free DNase I (Supplier Roche Applied Science). Putative transcripts were detected under both growth conditions that were tested, using equal amounts of the extracted total RNA as an RT-PCR template. Interestingly, the detected transcript levels were remarkably higher in LB medium (Figure 3), compared to minimal (M9) medium, probably indicating that the genes are expressed in both cultivation conditions.
Rhizobia are α-proteobacteria that are able to induce the formation of nodules on leguminous plant roots, where nitrogen fixation takes place with T3SS being one important determinant of this symbiosis [36, 46, 47]. Sequences of the symbiotic plasmids of Rhizobium strains NGR234 and R. etli CFN42 together with the chromosomal symbiotic regions of B. japonicum USDA110 and Mesorhizobium loti R7A have been recently reported [36–38]. An unusual feature of the Rhizobium strains NGR234 , is the presence of an additional T3SS gene cluster.
Members of the P. syringae species are gram negative plant-associated γ-proteobacteria that can exist both as harmless epiphytes and as pathogens of major agricultural crops [48–52]. Pathogenic varieties of this species utilize a Hrc-Hrp1 T3SS to inject effector proteins and thus subvert signalling pathways of their plant hosts. This secretion system (Hrc-Hrp1 T3SS) and its effector proteins are responsible for the development of the characteristic disease symptoms on susceptible plants and the triggering of the Hypersensitive Response (HR) in resistant plants [26, 49, 50, 52].
Comparative genomics of closely related isolates or species of pathogenic bacteria provides a powerful tool for rapid identification of genes involved in host specificity and virulence . In this work, we reported sequence similarity searches, phylogeny analysis and prediction of the physicochemical characteristics of the hypothetical T3SS-2 proteins, as well as gene synteny analysis of the T3SS-2 gene cluster in P. syringae pv phaseolicola 1448a, P. syringae pv oryzae str. 1_6 and P. syringae pv tabaci ATCC11528 in order to characterize this recently identified gene cluster. This analysis revealed that the T3SS-2 most closely resembles the T3SS of the Rhc-T3SS family. It further typifies a second discrete subfamily (subgroup II) within the Rhc-T3SS family in addition to the ones represented by the R. etli T3SS (subgroup III) and the known Rhizobium-T3SS (subgroup I). Usually, the presence of two T3SS gene clusters in the same genome is not the result of gene duplication inside the species but rather the result of independent horizontal gene transfers. This may reflect progressive coevolution of the plant patho/symbio-system to either colonize various hosts or interact with the plant in different disease/symbiotic stages.
In our phylogenetic analysis proteins encoded in the T3SS-2 cluster of P. syringae strains are grouped together with the Rhizobium NGR234 T3SS-2. This finding suggests the possibility of an ancient acquisition from a common ancestor for Rhizobium NGR234 T3SS-2 and the P. syringae T3SS-2. T3SSs of the Rhizobium family possesses a GC-content in same range (59-62%), a value lower than the chromosome average. Since the GC content of T3SS-2 is almost the same as that of the genome of the P. syringae strains, it is difficult to characterize the second T3SS gene cluster as a genomic island based solely on this criterion. However, the genome sequencing of two other members of P. syringae [pathovars tomato DC3000, syringae B728A] revealed the total absence of a T3SS-2 like cluster.
The T3SS-2 gene cluster found in P. syringae pv phaseolicola 1448a, P. syringae pv oryzae str.1_6, P. syringae pv tabaci and of Rhizobium sp. NGR234, is also present in P. syringae pv aesculi (strains NCPPB 3681 and 2250), P. syringae pv savastanoi (str. NCPPB 3335) , P. syringae pv glycinea (strains: B076 and race 4) , P. syringae pv lachrymans str. M301315 (GenBank: AEAF01000091.1), P. syringae pv actinidiae str. M302091 (GenBank: AEAL01000073.1), P. syringae pv. morsprunorum str. M302280PT (GenBank: AEAE01000259.1) and P. syringae Cit 7 (GenBank: AEAJ01000620.1). This T3SS-2 defines a distinct lineage in the Rhc T3SS family of at least the same evolutionary age as the split between the NGR234 T3SS-2 from the other rhizobial T3SSs.
In light of these findings, there are two plausible scenarios. One is that P. syringae acquired the T3SS-2 cluster from an ancient donor which is common both to P. syringae and the Rhizobium sp. NGR234 T3SS-2, before the diversification of the P. syringae pathovars from each other, followed by subsequent loss from certain members of the group. Another scenario is that multiple horizontal transfers from hypothetical donors into selected pathovars/strains occurred after their diversification. The present data set does not allow us to consider whether the hypothesis of an earlier acquisition followed by subsequent loss from members such as P. syringae pv tomato DC3000 might be considered more likely than several independent acquisitions.
The genes hrc II N and hrc II V in P. syringae pv tabaci and P. syringae pv oryzae T3SS-2 clusters were split into at least two open reading frames in various positions suggesting possibly that they might be degenerate pseudogenes, while the hrc II C2 gene in P. syringae pv tabaci is further split in two ORFs as well (Figure 4). However, this is not the case for the P. syringae pv phaseolicola 1448a, P. syringae pv savastanoi and P. syringae pv aesculi T3SS-2 where all these genes remain intact while hrc II C1 and hrc II N transcripts were observed in P. syringae pv phaseolicola 1448a T3SS-2 case (Figure 4). Remarkably, the T3SS-2 genes expression was even higher in rich compared to minimal medium (Figure 3). Minimal media of slightly acidic pH are thought to simulate in planta conditions and promote expression of the P. syringae T3SS-1 and effectors [24, 57, 58]. Such genes typically possess conserved motifs (hrp boxes) in their promoter regions and are transcriptionally controlled by the alternative sigma factor HrpL. However, the T3SS-2 operons in the P. syringae pv phaseolicola 1448a genome do not appear to have hrp boxes like those found in T3SS-1 genes of P. syringae strains . This suggests that Psph 1448a does restrict T3SS-2 expression to in planta conditions and the potential contribution of the T3SS-2 in P. syringae life cycle may not be connected with the phytopathogenic potential of this species. Further functional studies are thus needed to reveal the exact biological roles of this secretion system in bacterium-plant interactions or other aspects of the bacterial life cycle. Suppression of other secretion systems under the T3SS-1 inducing conditions has also been reported for the T6SS of P. syringae pv syringae B728a  as well as for the P. aeruginosa T3SS , which do not appear to play a role in plant pathogenesis [59, 61, 62].
Gene transfer between phylogenetically remote bacteria would be favored by colonization of the same environmental niche . In nature, Rhizobium is normally viewed as a microbe that survives saprophytically in soil, in nitrogen fixing nodules of legumes or as endophytes in gramineous plants, for example field grown  and wild rice . P. syringae pv phaseolicola 1448A and P. syringae pv oryzae str.1_6 are pathogens of the common bean and rice, respectively, while Rhizobium sp. NGR234 forms nitrogen fixing nodules with more legumes than any other microsymbiont . Thus, there is ample opportunity for niche overlap between at least one of the P. syringae pathovars possessing T3SS-2 and Rhizobium sp. NGR234. At this point, a role for T3SS-2 in host-bacterium interactions for the rhizobia or the P. syringae strains possessing the system remains to be established and it is not obvious why these bacteria maintain a second T3SS gene cluster in their genome. Functional analysis and genome sequencing of more rhizobia that share common niches with P. syringae as well as the sequencing of more P. syringae pathovar genomes may shed light into these questions.
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We thank Ioanna Eleftheriadou for assistance in the initial search for T3SS related ORFs in the P. syringae pv phaseolicola 1448a genome. This work was supported by PENED, PYTHAGORAS and PEP (KP-15) grants from the Greek Ministry of Education, GSRT and the EPEAEK-Plant Molecular Biology and Biotechnology and the Protein Biotechnology graduate programs. S.N.C. was recipient of an Onassis Foundation fellowship and a GSRT post-doctoral grant. V.E.F is supported by a Marie Curie Reintegration Grant.
ADG performed research, helped draft the manuscript, analysed results and prepared figures. PFS, VEF, SNC and NM performed research, analysed results and critically appraised the manuscript. NJP and MK designed research, supervised work, organized financial support and critically appraised the manuscript. All authors read and approved the final manuscript.
Nicholas J Panopoulos and Michael Kokkinidis contributed equally to this work.
Electronic supplementary material
Additional file 1: Figure S1: Unrooted neighbor-joining phylogenetic tree of SctQ proteins of flagellar and non-flagellar T3S proteins. The tree was calculated by CLUSTALW (1.82) using bootstrapping (500 replicates) as a method for deriving confidence values for the groupings and was drawn by MEGA 4.0. Bootstrap values are indicated in each branching point. Scale bar represents numbers of substitution per site. The arrow indicates a possible position of root so that the tree will be compatible with the monophyly of the flagellar T3SS. Consistently with phylograms based on other conserved proteins of the Pph T3SS-2, the Hrc II Q polypeptide does not fall into any of the two Hrc1/Hrc2 T3SS families but it is grouped with the Rhc family. (PDF 388 KB)
Additional file 2: Figure S2.: Unrooted neighboring joining tree including all known SctV T3SS families and the flagelar proteins. Bootstrap values are percentages of 500 repetitions taking place. Multiple alignment performed with ClustalW. (PDF 163 KB)
Additional file 3: Figure S3: Evolutionary relationships of 250 HrcN/YscN/FliI proteins. A. The phylogram of 253 SctN sequences subdivided in seven main families, depicted with different colors and named according to , while the flagellum proteins are depicted in black. The evolutionary history was inferred as in case of Figure 2. B. The Rhc T3SS clade as derived from the phylogram in A, groups clearly the P. syringae Hrc II V sequences close to the Rhc II V protein of the Rhizobium sp. NGR234 T3SS-2. The values at the nodes are the bootstrap percentages out of 1000 replicates. The locus numbers or the protein accession number of each sequence is indicated. (PDF 182 KB)
Additional file 4: Table S1: Sequence comparisons of T3SS-2 proteins with proteins from from subgroups I-III of Rhc T3SS gene clusters. Percentage identities of various T3SS proteins in comparison to the Pph T3SS-2 proteins. Pph T3SS-2 cluster shares a higher degree of common genes with T3SS-2 of Rhizobium sp. NGR234 than with Rhc T3SS gene clusters of subgroup I or III. Shading in grayscale is according to percentage identity. (PDF 105 KB)
Additional file 5: Figure S4: Multiple alignements with ClustalW version 1.8  for A) RhcC1 proteins (ref|YP 274720.1| HrcIIC1 Pseudomonas syringae pv. phaseolicola 1448a], ref|ZP 04589253.1| HrcIIC1 Pseudomonas syringae pv. oryzae str. 1_6], ref|YP 002824487.1| RhcIIC Rhizobium sp. NGR234], ref|NP 444156.1| NolW Rhizobium sp. NGR234], ref|NP 106861.1| NOLW Mesorhizobium loti MAFF303099], ref|NP 768451.1| RhcC1 Bradyrhizobium japonicum USDA 110] and B) RhcC2 proteins (ref|ZP 04589255.1|HrpIIC2 Pseudomonas syringae pv. oryzae str. 1_6], ref|YP 002824481.1| RhcIIC2 Rhizobium sp. NGR234], ref|NP 106858.1| RhcC2 Mesorhizobium loti MAFF303099], ref|NP 768482.1| RhcC2 Bradyrhizobium japonicum USDA 110] and ref|NP 444146.1| Y4xJ Rhizobium sp. NGR234]. Visualization of the alignment was performed in http://www.bioinformatics.org/sms2/color_align_cons.html. (PDF 107 KB)
Additional file 6: Figure S5: Sequence analysis for HrpO-like proteins. The analysis of PSPPH_2532 (HrpIIO) indicates that this hypothetical protein belongs to the HrpO/YscO/FliJ family of T3SS proteins [5, 33]. The same is evident for the sequence annotated as RhcZ in the T3SS-2 of Rhizobium sp. NGR342. Residues predicted in α-helical conformation are indicated in yellow and unfolded regions in red. Green areas indicate ordered regions. Residues for which a high propensity for coiled-coil formation is predicted are indicated in blue rectangular. Here α-helix prediction was performed with PsiPRED, disordered prediction with FOLDINDEX and coiled coils prediction with COILS. Accession numbers or loci numbers are: AAC25065 (HrpO), P25613 (FliJ), AAB72198 (YscO), PSPPH_2532 (HrpIIO), NGR_b22960 (RhcZ), NGR234_462 (Y4yJ). (PDF 82 KB)
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Gazi, A.D., Sarris, P.F., Fadouloglou, V.E. et al. Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains. BMC Microbiol 12, 188 (2012). https://doi.org/10.1186/1471-2180-12-188