Regulation of type III secretion system in Pseudomonas syringae

Pseudomonas syringae is a model phytopathogenic bacterium that uses the type III secretion system (T3SS) to cause lethal diseases in staple crops and thus presents a threat to food security worldwide. Great progress has been made in delineating the biochemical mechanisms and cellular targets of T3SS effectors, but less is known about the signalling pathways and molecular mechanisms of T3SS regulators. In recent years, thanks to the popularity and power of genome-wide mutant screening and high-throughput sequencing, new regulatory proteins (such as RhpR, AefR, AlgU and CvsR) and proteases (such as Lon and RhpP) have been identified as T3SS regulators in P. syringae pathovars. The detailed mechanisms of previously illustrated regulators (such as HrpRS, HrpL and HrpGV) have also been further studied. Notably, the two-component system RhpRS has been determined to play key roles in the modulation of T3SS via direct regulation of hrpRS and other virulence-related pathways by sensing changes in environmental signals. In addition, secondary messengers (such as c-di-GMP and ppGpp) have been shown to fine-tune the activity of T3SS. Overall, these studies have suggested the existence of a highly intricate regulatory network for T3SS, which controls the pathogenicity of P. syringae. This short review summarizes studies of P. syringae T3SS regulation and the known mechanisms of key regulators.     

Two-component sensor RhpS promotes induction of Pseudomonas syringae type III secretion system by repressing negative regulator RhpR

The Pseudomonas syringae type III secretion system (T3SS) is induced during interaction with the plant or culture in minimal medium (MM). How the bacterium senses these environments to activate the T3SS is poorly understood. Here, we report the identification of a novel two-component system (TCS), RhpRS, that regulates the induction of P. syringae T3SS genes. The rhpR and rhpS genes are organized in an operon with rhpR encoding a putative TCS response regulator and rhpS encoding a putative biphasic sensor kinase. Transposon insertion in rhpS severely reduced the induction of P. syringae T3SS genes in the plant as well as in MM and significantly compromised the pathogenicity on host plants and hypersensitive response-inducing activity on nonhost plants. However, deletion of the rhpRS locus allowed the induction of T3SS genes to the same level as in the wild-type strain and the recovery of pathogenicity upon infiltration into plants. Overexpression of RhpR in the deltarhpRS deletion strain abolished the induction of T3SS genes. However, overexpression of RhpR in the wild-type strain or overexpression of RhpR(D70A), a mutant of the predicted phosphorylation site of RhpR, in the deltarhpRS deletion strain only slightly reduced the induction of T3SS genes. Based on these results, we propose that the phosphorylated RhpR represses the induction of T3SS genes and that RhpS reverses phosphorylation of RhpR under the T3SS-inducing conditions. Epistasis analysis indicated that rhpS and rhpR act upstream of hrpR to regulate T3SS genes.     

丁香假单胞菌中的III型分泌系统及其调控机制研究进展

丁香假单胞菌(Pseudomonas syringae)是引起许多作物病害的一种革兰氏阴性病原细菌。该细菌入侵寄主植物细胞主要通过其III型分泌系统(type III secretion system,T3SS)将效应蛋白转入到寄主真核细胞内,抑制寄主免疫功能,以达到成功侵染和定殖的目的。III型分泌系统的主调控因子RhpR/S通过感受环境信号的变化直接调控hrpR/S及其他毒力相关通路。同时III型分泌系统基因的表达也受到其他调控因子的影响,包括σ因子HrpL、双组分系统GacA/S、Lon蛋白酶、第二信使分子和环境信号等。本文在简要介绍丁香假单胞菌III型分泌系统组成和功能的基础上,综述丁香假单胞菌III型分泌系统调控机制的最新研究进展,以期为深入探究病原菌的致病机制提供参考和思路。     

Pseudomonas syringae lytic transglycosylases coregulated with the type III secretion system contribute to the translocation of effector proteins into plant cells

Pseudomonas syringae translocates virulence effector proteins into plant cells via a type III secretion system (T3SS) encoded by hrp (for hypersensitive response and pathogenicity) genes. Three genes coregulated with the Hrp T3SS system in P. syringae pv. tomato DC3000 have predicted lytic transglycosylase domains: PSPTO1378 (here designated hrpH), PSPTO2678 (hopP1), and PSPTO852 (hopAJ1). hrpH is located between hrpR and avrE1 in the Hrp pathogenicity island and is carried in the functional cluster of P. syringae pv. syringae 61 hrp genes cloned in cosmid pHIR11. Strong expression of DC3000 hrpH in Escherichia coli inhibits bacterial growth unless the predicted catalytic glutamate at position 148 is mutated. Translocation tests involving C-terminal fusions with a Cya (Bordetella pertussis adenylate cyclase) reporter indicate that HrpH and HopP1, but not HopAJ1, are T3SS substrates. Pseudomonas fluorescens carrying a pHIR11 derivative lacking hrpH is poorly able to translocate effector HopA1, and this deficiency can be restored by HopP1 and HopAJ1, but not by HrpH(E148A) or HrpH_1-241. DC3000 mutants lacking hrpH or hrpH, hopP1, and hopAJ1 combined are variously reduced in effector translocation, elicitation of the hypersensitive response, and virulence. However, the mutants are not reduced in secretion of T3SS substrates in culture. When produced in wild-type DC3000, the HrpH(E148A) and HrpH_1-241 variants have a dominant-negative effect on the ability of DC3000 to elicit the hypersensitive response in nonhost tobacco and to grow and cause disease in host tomato. The three Hrp-associated lytic transglycosylases in DC3000 appear to have overlapping functions in contributing to T3SS functions during infection.     

Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats,are phylogenetically diverse and can be pathogenic

The type III secretion system (T3SS) is an important virulence factor of pathogenic bacteria, but the natural occurrence of variants of bacterial plant pathogens with deficiencies in their T3SS raises questions about the significance of the T3SS for fitness. Previous work on T3SS-deficient plant pathogenic bacteria has focused on strains from plants or plant debris. Here we have characterized T3SS-deficient strains of Pseudomonas syringae from plant and nonplant substrates in pristine nonagricultural contexts, many of which represent recently described clades not yet found associated with crop plants. Strains incapable of inducing a hypersensitive reaction (HR⁻) in tobacco were detected in 65% of 126 samples from headwaters of rivers (mountain creeks and lakes), snowpack, epilithic biofilms, wild plants and leaf litter and constituted 2 to 100% of the P. syringae population associated with each sample. All HR⁻ strains lacked at least one gene in the canonical hrp/hrc locus or the associated conserved effector locus, but most lacked all six of the genes tested (hrcC, hrpL, hrpK1, avrE1 and hrpW1) and represented several disparate phylogenetic clades. Although most HR⁻ strains were incapable of causing symptoms on cantaloupe seedlings as expected, strains in the recently described TA-002 clade caused severe symptoms in spite of the absence of any of the six conserved genes of the canonical T3SS according to PCR and Southern blot assays. The phylogenetic context of the T3SS variants we observed provides insight into the evolutionary history of P. syringae as a pathogen and as an environmental saprophyte.     

Type III secretion system genes of Dickeya dadantii 3937 are induced by plant phenolic acids

Background

Dickeya dadantii is a broad-host range phytopathogen. D. dadantii 3937 (Ech3937) possesses a type III secretion system (T3SS), a major virulence factor secretion system in many Gram-negative pathogens of plants and animals. In Ech3937, the T3SS is regulated by two major regulatory pathways, HrpX/HrpY-HrpS-HrpL and GacS/GacA-rsmB-RsmA pathways. Although the plant apoplast environment, low pH, low temperature, and absence of complex nitrogen sources in media have been associated with the induction of T3SS genes of phytobacteria, no specific inducer has yet been identified.

Methodology/Principal Findings

In this work, we identified two novel plant phenolic compounds, o-coumaric acid (OCA) and t-cinnamic acid (TCA), that induced the expression of T3SS genes dspE (a T3SS effector), hrpA (a structural protein of the T3SS pilus), and hrpN (a T3SS harpin) in vitro. Assays by qRT-PCR showed higher amounts of mRNA of hrpL (a T3SS alternative sigma factor) and rsmB (an untranslated regulatory RNA), but not hrpS (a σ⁵⁴-enhancer binding protein) of Ech3937 when these two plant compounds were supplemented into minimal medium (MM). However, promoter activity assays using flow cytometry showed similar promoter activities of hrpN in rsmB mutant Ech148 grown in MM and MM supplemented with these phenolic compounds. Compared with MM alone, only slightly higher promoter activities of hrpL were observed in bacterial cells grown in MM supplemented with OCA/TCA.

Conclusion/Significance

The induction of T3SS expression by OCA and TCA is moderated through the rsmB-RsmA pathway. This is the first report of plant phenolic compounds that induce the expression T3SS genes of plant pathogenic bacteria.     

A revised model for the role of GacS/GacA in regulating type III secretion by Pseudomonas syringae pv. tomato DC3000

GacS/GacA is a conserved two-component system that functions as a master regulator of virulence-associated traits in many bacterial pathogens, including Pseudomonas spp., that collectively infect both plant and animal hosts. Among many GacS/GacA-regulated traits, type III secretion of effector proteins into host cells plays a critical role in bacterial virulence. In the opportunistic plant and animal pathogen Pseudomonas aeruginosa, GacS/GacA negatively regulates the expression of type III secretion system (T3SS)-encoding genes. However, in the plant pathogenic bacterium Pseudomonas syringae, strain-to-strain variation exists in the requirement of GacS/GacA for T3SS deployment, and this variability has limited the development of predictive models of how GacS/GacA functions in this species. In this work we re-evaluated the function of GacA in P. syringae pv. tomato DC3000. Contrary to previous reports, we discovered that GacA negatively regulates the expression of T3SS genes in DC3000, and that GacA is not required for DC3000 virulence inside Arabidopsis leaf tissue. However, our results show that GacA is required for full virulence of leaf surface-inoculated bacteria. These data significantly revise current understanding of GacS/GacA in regulating P. syringae virulence.     

Global Analysis of the HrpL Regulon in the Plant Pathogen Pseudomonas syringae pv. tomato DC3000 Reveals New Regulon Members with Diverse Functions

The type III secretion system (T3SS) is required for virulence in the gram-negative plant pathogen Pseudomonas syringae pv. tomato DC3000. The alternative sigma factor HrpL directly regulates expression of T3SS genes via a promoter sequence, often designated as the “hrp promoter.” Although the HrpL regulon has been extensively investigated in DC3000, it is not known whether additional regulon members remain to be found. To systematically search for HrpL-regulated genes, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) and bulk mRNA sequencing (RNA-Seq) to identify HrpL-binding sites and likely hrp promoters. The analysis recovered 73 sites of interest, including 20 sites that represent new hrp promoters. The new promoters lie upstream of a diverse set of genes encoding potential regulators, enzymes and hypothetical proteins. PSPTO_5633 is the only new HrpL regulon member that is potentially an effector and is now designated HopBM1. Deletions in several other new regulon members, including PSPTO_5633, PSPTO_0371, PSPTO_2130, PSPTO_2691, PSPTO_2696, PSPTO_3331, and PSPTO_5240, in either DC3000 or ΔhopQ1-1 backgrounds, do not affect the hypersensitive response or in planta growth of the resulting strains. Many new HrpL regulon members appear to be unrelated to the T3SS, and orthologs for some of these can be identified in numerous non-pathogenic bacteria. With the identification of 20 new hrp promoters, the list of HrpL regulon members is approaching saturation and most likely includes all DC3000 effectors.     

Pseudomonas syringae HrpP Is a Type III Secretion Substrate Specificity Switch Domain Protein That Is Translocated into Plant Cells but Functions Atypically for a Substrate-Switching Protein

Pseudomonas syringae delivers virulence effector proteins into plant cells via an Hrp1 type III secretion system (T3SS). P. syringae pv. tomato DC3000 HrpP has a C-terminal, putative T3SS substrate specificity switch domain, like Yersinia YscP. A ΔhrpP DC3000 mutant could not cause disease in tomato or elicit a hypersensitive response (HR) in tobacco, but the HR could be restored by expression of HrpP in trans. Though HrpP is a relatively divergent protein in the T3SS of different P. syringae pathovars, hrpP from P. syringae pv. syringae 61 and P. syringae pv. phaseolicola 1448A restored HR elicitation and pathogenicity to DC3000 ΔhrpP. HrpP was translocated into Nicotiana benthamiana cells via the DC3000 T3SS when expressed from its native promoter, but it was not secreted in culture. N- and C-terminal truncations of HrpP were tested for their ability to be translocated and to restore HR elicitation activity to the ΔhrpP mutant. No N-terminal truncation completely abolished translocation, implying that HrpP has an atypical T3SS translocation signal. Deleting more than 20 amino acids from the C terminus abolished the ability to restore HR elicitation. HrpP fused to green fluorescent protein was no longer translocated but could restore HR elicitation activity to the ΔhrpP mutant, suggesting that translocation is not essential for the function of HrpP. No T3SS substrates were detectably secreted by DC3000 ΔhrpP except the pilin subunit HrpA, which unexpectedly was secreted poorly. HrpP may function somewhat differently than YscP because the P. syringae T3SS pilus likely varies in length due to differing plant cell walls.Many proteobacterial pathogens use a type III secretion system (T3SS) as their primary mechanism to overcome and infect eukaryotic hosts. T3SSs are complex macromolecular machines that span both the bacterial cell envelope and host cell barriers to deliver proteins, commonly termed effectors, from the bacterial cytoplasm into the host cytoplasm (13, 19). After delivery into the host, effector proteins manipulate host cell function and suppress host defenses, allowing bacterial proliferation and disease development (6, 20). Bacteria that rely on T3SS to cause disease include plant pathogens such as Pseudomonas syringae, Ralstonia solanacearum, Erwinia and Xanthomonas species and animal pathogens in the genera Yersinia, Salmonella, Shigella, Escherichia, and Pseudomonas. While the repertoire of effectors delivered by a given T3SS is unique, the T3SS machinery is more universal (13). T3SS includes a core set of eight conserved proteins. These proteins, which are also conserved in bacterial flagellar biogenesis machines, make up the multiringed base structure, or basal body, that spans the bacterial membranes and cell wall. T3SS machines are also comprised of less-conserved and unique proteins that vary between systems. These include regulatory proteins that orchestrate construction of the machine and the extracellular components that function to translocate effectors across host barriers.The extracellular portion of the T3SS is comprised of the pilus or needle appendage (in plant or animal pathogens, respectively), which acts as a conduit for effector delivery, and the translocon complex, which creates the pore in the host cell membrane. These substructures vary between different T3SSs; presumably these external structures have adapted to allow different bacteria to infect different types of host cells. For Yersinia enterocolitica to infect macrophage cells, the T3SS needle must be a particular length (∼58 nm) to bridge the lipopolysaccharides extending from the bacterial outer membrane and reach the host cell membrane (35). Several other animal pathogens have T3SS needles of a defined length (48). Enteropathogenic Escherichia coli also has an additional extension beyond the needle called the EspA filament that functions to span the mucous layer found outside enterocyte cells (13). In plant pathogens, however, the extracellular gap between a bacterium and a plant cell includes a thick plant cell wall that is variable in width between plant species. Consequently, plant pathogenic Pseudomonas syringae has a pilus that can measure over 1 μm in vitro (25).Another major difference between the T3SS machineries of animal and plant pathogens is their translocon complexes. In animal pathogens, these are typically comprised of three essential proteins, but there is growing evidence that plant pathogen translocons employ diverse, functionally redundant components (28). There is growing interest in understanding the regulatory players that orchestrate the construction of diverse machinery. It is hypothesized that the assembly of the T3SS must involve several tightly regulated steps that allow secretion of the required components, followed by that of effectors upon completion. Of particular interest here is the control of pilus/needle subunit secretion, which is necessary when the pilus/needle is being constructed but would presumably compete with translocon and effector secretion after the T3SS is complete.We study the model plant pathogen P. syringae pv. tomato (Pto) DC3000, the causal agent of bacterial speck of tomato and Arabidopsis thaliana (8). DC3000 has a T3SS that delivers ca. 28 effectors and is essential for pathogenesis (11, 12, 30, 43). The P. syringae T3SS is encoded by hrp and hrc genes (hypersensitive response and pathogenicity/conserved), which are located in a pathogenicity island on the chromosome (4). hrc genes encode the conserved core components present in every T3SS. hrp genes encode T3SS components that are divergent or unique to P. syringae and enterobacterial plant pathogens, which also possess Hrp1 class T3SS (13). In contrast, plant pathogenic Ralstonia and Xanthomonas spp. have Hrp2 class T3SS, as indicated by several different Hrp proteins and distinct regulatory systems.To better understand the T3SS machinery, we previously conducted a survey of the hrp genes of P. syringae pv. syringae (Psy) 61 to complete the inventory of all those encoding proteins capable of traveling the T3SS into plant cells when expressed from a constitutive promoter (39). We hypothesized that these proteins might aid in pilus or translocon construction or regulate the construction process. HrpP was one protein found to be a T3SS substrate and important for secretion and translocation of the model effector AvrPto. Importantly, HrpP is related to a well-studied protein from Yersinia enterocolitica, YscP, which is a T3SS-secreted protein and a regulator responsible for switching the T3SS from secreting needle subunits to secreting effector proteins (15, 38, 47). It has also been shown that secretion of YscP into the culture medium is not essential for the switch function and that there may be two type III secretion signals embedded in YscP (2).The phenotype of a yscP mutant is unregulated secretion of the needle subunit, no secretion of effectors, and production of needles of indeterminate length. The switching phenotype requires a domain at the C terminus of YscP called the type III secretion substrate specificity switch (T3S4) domain, which is a conserved feature unifying its homologs (1). YscP has been proposed to act as a molecular ruler because the length of the YscP protein is directly correlated with the length of the Ysc needle (26). According to this model, when the needle has reached its proper length, YscP signals to the T3SS machinery to stop secreting needle subunits and begin secreting effector proteins. However, other functional models have been hypothesized for homologs of YscP. A recent study of the Salmonella enterica serovar Typhimurium YscP homolog InvJ showed that an invJ mutant lacked an inner rod. When the inner rod protein PrgJ was overexpressed, the length of the needle decreased relative to that of the wild type, leading the researchers to conclude that InvJ controls the inner rod, which in turn controls needle length (33). Recent evidence in Yersinia has lent more support to this model. YscP was found to negatively control secretion of YscI, the inner rod protein (51). Also, certain YscI mutations affected needle assembly but not effector secretion, implying that YscI may be a key player in substrate switching. Little is known about HrpB, the inner rod homolog in P. syringae (22), other than that the protein can be translocated into plant cells and is essential for T3SS function (39).Other models for length control/substrate switching have been proposed, such as the “C-ring cup model” in flagella, which was based on the observation that certain mutations in proteins that make up the inner membrane C ring of the basal body lead to shorter hooks (the flagellar equivalent of the needle), thus suggesting that C-ring capacity controls hook length (32). A more recent, flagellar “molecular-clock” model suggests that because overexpression of hook subunits leads to longer hooks and hook polymerization-defective mutants make shorter hooks, hook polymerization initiates a countdown, and the timing, in cooperation with the YscP homolog FliK, determines final hook length (34).HrpP is considered a member of the YscP/FliK family due mostly to the presence of a T3S4 domain at its C terminus. HrpP is also proline rich (10.6%), which is considered a characteristic of the family. The most striking feature of HrpP is its small size; the protein is 189 amino acids, compared with YscP from Y. enterocolitica, which is 453 amino acids and 8.4% proline. We were intrigued by how HrpP functions in P. syringae to regulate a pilus that can measure several hundred nanometers in length. Also, unlike animal pathogen needles and flagellar hooks, the pilus of P. syringae is predicted to be indeterminate in length, based on the fact that plant cell walls vary in width between species (40).We hypothesized that HrpP would be a main player in regulating pilus construction in P. syringae by allowing the system to make the transition between secretion of pilus subunits and secretion of translocon or effector proteins, though perhaps by a novel mechanism. In this study, we more precisely define the role of HrpP in the P. syringae T3SS. We show that HrpP is a T3SS substrate in DC3000, is translocated into plant cells at levels equivalent to those of effectors, and is essential for the function of the T3SS. Though it is highly translocated and variable, we found that HrpP from different P. syringae pathovars could complement the DC3000 hrpP mutant. Analysis of truncations of HrpP and an impassible HrpP-green fluorescent protein (GFP) fusion suggests that it has structural similarities to YscP, but surprisingly, HrpP was found to be required for full secretion of the pilus subunit HrpA as well as for translocation of HrpB.     

The type II secretion system (Xcp) of Pseudomonas putida is active and involved in the secretion of phosphatases

The genome of the Gram‐negative bacterium Pseudomonas putida harbours a complete set of xcp genes for a type II protein secretion system (T2SS). This study shows that expression of these genes is induced under inorganic phosphate (P_i) limitation and that the system enables the utilization of various organic phosphate sources. A phosphatase of the PhoX family, previously designated UxpB, was identified, which was produced under low P_i conditions and transported across the cell envelope in an Xcp‐dependent manner demonstrating that the xcp genes encode an active T2SS. The signal sequence of UxpB contains a twin‐arginine translocation (Tat) motif as well as a lipobox, and both processing by leader peptidase II and Tat dependency were experimentally confirmed. Two different tat gene clusters were detected in the P. putida genome, of which one, named tat‐1, is located adjacent to the uxpB and xcp genes. Both Tat systems appeared to be capable of transporting the UxpB protein. However, expression of the tat‐1 genes was strongly induced by low P_i levels, indicating a function of this system in survival during P_i starvation.