Type III secretion chaperones ShcS1 and ShcO1 from Pseudomonas syringae pv. tomato DC3000 bind more than one effector

MolPhase, an advanced prediction algorithm for protein phase separation

We introduce MolPhase, an advanced algorithm for predicting protein phase separation (PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical features and extensive experimental datasets. MolPhase applies a user-friendly interface to compare distinct biophysical features side-by-side along protein sequences. By additional comparison with structural predictions, MolPhase enables efficient predictions of new phase-separating proteins and guides hypothesis generation and experimental design. Key contributing factors underlying MolPhase include electrostatic pi-interactions, disorder, and prion-like domains. As an example, MolPhase finds that phytobacterial type III effectors (T3Es) are highly prone to homotypic PS, which was experimentally validated in vitro biochemically and in vivo in plants, mimicking their injection and accumulation in the host during microbial infection. The physicochemical characteristics of T3Es dictate their patterns of association for multivalent interactions, influencing the material properties of phase-separating droplets based on the surrounding microenvironment in vivo or in vitro. Robust integration of MolPhase's effective prediction and experimental validation exhibit the potential to evaluate and explore how biomolecule PS functions in biological systems.

Regulation of Effector Delivery by Type III Secretion Chaperone Proteins in Erwinia amylovora

Type III secretion (TTS) chaperones are critical for the delivery of many effector proteins from Gram-negative bacterial pathogens into host cells, functioning in the stabilization and hierarchical delivery of the effectors to the type III secretion system (TTSS). The plant pathogen Erwinia amylovora secretes at least four TTS effector proteins: DspE, Eop1, Eop3, and Eop4. DspE specifically interacts with the TTS chaperone protein DspF, which stabilizes the effector protein in the cytoplasm and promotes its efficient translocation through the TTSS. However, the role of E. amylovora chaperones in regulating the delivery of other secreted effectors is unknown. In this study, we identified functional interactions between the effector proteins DspE, Eop1, and Eop3 with the TTS chaperones DspF, Esc1 and Esc3 in yeast. Using site-directed mutagenesis, secretion, and translocation assays, we demonstrated that the three TTS chaperones have additive roles for the secretion and translocation of DspE into plant cells whereas DspF negatively affects the translocation of Eop1 and Eop3. Collectively, these results indicate that TTS chaperone proteins exhibit a cooperative behavior to orchestrate the effector secretion and translocation dynamics in E. amylovora.

Visualizing the relevance of bacterial blue- and red-light receptors during plant-pathogen interaction

The foliar pathogen Pseudomonas syringae pv. tomato DC3000 (Pst) leads to consistent losses in tomato crops, urging to multiply investigations on the physiological bases for its infectiveness. As other P. syringae pathovars, Pst is equipped with photoreceptors for blue and red light, mimicking the photosensing ability of host plants. In this work we have investigated Pst strains lacking the genes for a blue-light sensing protein (PstLOV), for a bacteriophytochrome (PstBph1) or for heme-oxygenase-1. When grown in culturing medium, all deletion mutants presented a larger growth than wild-type (WT) Pst under all other light conditions, with the exception of blue light which, under our experimental conditions (photon fluence rate = 40 μmol m(-2) s(-1)), completely suppressed the growth of the deletion mutants. Each of the knockout mutants shows stronger virulence towards Arabidopsis thaliana than PstWT, as evidenced by macroscopic damages in the host tissues of infected leaves. Mutated bacteria were also identified in districts distant from the infection site using scanning electron microscopy. These results underscore the importance of Pst photoreceptors in responding to environmental light inputs and the partial protective role that they exert towards host plants during infection, diminishing virulence and invasiveness.

Type III chaperones & Co in bacterial plant pathogens: a set of specialized bodyguards mediating effector delivery

Gram-negative plant pathogenic bacteria possess a type III secretion system (T3SS) to inject bacterial proteins, called type III effectors (T3Es), into host cells through a specialized syringe structure. T3Es are virulence factors that can suppress plant immunity but they can also conversely be recognized by the plant and trigger specific resistance mechanisms. The T3SS and injected T3Es play a central role in determining the outcome of a host-pathogen interaction. Still little is known in plant pathogens on the assembly of the T3SS and the regulatory mechanisms involved in the temporal control of its biosynthesis and T3E translocation. However, recent insights point out the role of several proteins as prime candidates in the role of regulators of the type III secretion (T3S) process. In this review we report on the most recent advances on the regulation of the T3S by focusing on protein players involved in secretion/translocation regulations, including type III chaperones (T3Cs), type III secretion substrate specificity switch (T3S4) proteins and other T3S orchestrators.

Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria

Flagellar and translocation-associated type III secretion (T3S) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. The architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated T3S systems. The needle/pilus is connected to a bacterial translocon that is inserted into the host plasma membrane and mediates the transkingdom transport of bacterial effector proteins into eukaryotic cells. During the last 3 to 5 years, significant progress has been made in the characterization of membrane-associated core components and extracellular structures of T3S systems. Furthermore, transcriptional and posttranscriptional regulators that control T3S gene expression and substrate specificity have been described. Given the architecture of the T3S system, it is assumed that extracellular components of the secretion apparatus are secreted prior to effector proteins, suggesting that there is a hierarchy in T3S. The aim of this review is to summarize our current knowledge of T3S system components and associated control proteins from both plant- and animal-pathogenic bacteria.

Gene Ontology for type III effectors: capturing processes at the host-pathogen interface

Disease development is determined by the interplay of host defense processes and pathogen factors that subvert defenses and remodel the host for parasitic benefit. The goal of the Plant-Associated Microbe Gene Ontology (PAMGO) interest group is the development of Gene Ontology (GO) terms that capture the range of biological processes occurring between hosts and symbionts (from mutualists to pathogens). Here, the application of the new GO terms to type III effector proteins (T3Es) from the plant pathogen Pseudomonas syringae serves as an example to systematically document the available extensive data and to reveal shared aspects of interactions with various host plants. Extending the comparison to T3Es deployed by animal pathogens further highlights how GO can uncover the common strategies employed by diverse symbionts as they exploit the host niche. Future application of GO terms to gene products mediating pathogenic or mutualistic interactions involving other microbes will enhance researchers' abilities to identify fundamental patterns among diverse systems and generate new hypotheses based on associations among annotations.

Arabidopsis HARMLESS TO OZONE LAYER protein methylates a glucosinolate breakdown product and functions in resistance to Pseudomonas syringae pv. maculicola

Almost all of the chlorine-containing gas emitted from natural sources is methyl chloride (CH(3)Cl), which contributes to the destruction of the stratospheric ozone layer. Tropical and subtropical plants emit substantial amounts of CH(3)Cl. A gene involved in CH(3)Cl emission from Arabidopsis was previously identified and designated HARMLESS TO OZONE LAYER (hereafter AtHOL1) based on the mutant phenotype. Our previous studies demonstrated that AtHOL1 and its homologs, AtHOL2 and AtHOL3, have S-adenosyl-l-methionine-dependent methyltransferase activities. However, the physiological functions of AtHOLs have yet to be elucidated. In the present study, our comparative kinetic analyses with possible physiological substrates indicated that all of the AtHOLs have low activities toward chloride. AtHOL1 was highly reactive to thiocyanate (NCS(-)), a pseudohalide, synthesizing methylthiocyanate (CH(3)SCN) with a very high k(cat)/K(m) value. We demonstrated in vivo that substantial amounts of NCS(-) were synthesized upon tissue damage in Arabidopsis and that NCS(-) was largely derived from myrosinase-mediated hydrolysis of glucosinolates. Analyses with the T-DNA insertion Arabidopsis mutants (hol1, hol2, and hol3) revealed that only hol1 showed increased sensitivity to NCS(-) in medium and a concomitant lack of CH(3)SCN synthesis upon tissue damage. Bacterial growth assays indicated that the conversion of NCS(-) into CH(3)SCN dramatically increased antibacterial activities against Arabidopsis pathogens that normally invade the wound site. Furthermore, hol1 seedlings showed an increased susceptibility toward an Arabidopsis pathogen, Pseudomonas syringae pv. maculicola. Here we propose that AtHOL1 is involved in glucosinolate metabolism and defense against phytopathogens. Moreover, CH(3)Cl synthesized by AtHOL1 could be considered a byproduct of NCS(-) metabolism.

Multiple approaches to a complete inventory of Pseudomonas syringae pv. tomato DC3000 type III secretion system effector proteins

Pseudomonas syringae pv. tomato DC3000 is a pathogen of tomato and Arabidopsis that translocates virulence effector proteins into host cells via a type III secretion system (T3SS). Many effector-encoding hypersensitive response and pathogenicity (Hrp) outer protein (hop) genes have been identified previously in DC3000 using bioinformatic methods based on Hrp promoter sequences and characteristic N-terminal amino acid patterns that are associated with T3SS substrates. To approach completion of the Hop/effector inventory in DC3000, 44 additional candidates were tested by the Bordetella pertussis calmodulin-dependent adenylate cyclase (Cya) translocation reporter assay; 10 of the high-probability candidates were confirmed as T3SS substrates. Several previously predicted hop genes were tested for their ability to be expressed in an HrpL-dependent manner in culture or to be expressed in planta. The data indicate that DC3000 harbors 53 hop/avr genes and pseudogenes (encoding both injected effectors and T3SS substrates that probably are released to the apoplast); 33 of these genes are likely functional in DC3000, 12 are nonfunctional members of valid Hop families, and 8 are less certain regarding their production at functional levels. Growth of DC3000 in tomato and Arabidopsis Col-0 was not impaired by constitutive expression of repaired versions of two hops that were disrupted naturally by transposable elements or of hop genes that are naturally cryptic. In summary, DC3000 carries a complex mixture of active and inactive hop genes, and the hop genes in P. syringae can be identified efficiently by bioinformatic methods; however, a precise inventory of the subset of Hops that are important in pathogenesis awaits more knowledge based on mutant phenotypes and functions within plants.

Different versions of Pseudomonas syringae pv. tomato DC3000 exist due to the activity of an effector transposon

SUMMARY The plant pathogenic bacterium Pseudomonas syringae pv. tomato strain DC3000 is a key model organism to study plant-pathogen interactions. We realized that two versions of this strain, which carry plasmids of different sizes, exist in our strain collections. The difference was located to a 9.4-kb deletion within the larger of the two endogenous plasmids encompassing the partitioning genes parA and parB and a putative mobile element encoding the type III effector hopAM1-2 (formerly avrPpiB2). Both plasmid variants are lost in similar frequency, indicating that the partitioning genes are not essential for stability of the plasmid. In addition, the deletion derivative strain DC3001 exhibited the same virulence towards Arabidopsis as strain DC3000. The deletion site in DC3001 is located immediately adjacent to a putative transposon that carries the effector hopX1 (formerly avrPphE), suggesting that the deletion originated from an aberrant transposition event of this element. By tagging the hopX1 transposon with an antibiotic resistance cassette on a suicide plasmid it was shown that the element is functional and produces a target site duplication of 5 bp. The plasmid also integrated into the chromosome in several cases, possibly mediated by one-ended transposition of the hopX1 transposon. This is the first report that describes an active effector-transposon. Comparison of DC3000 strains from several sources revealed that strains exist with differences in the endogenous plasmid composition.

Who comes first? How plant pathogenic bacteria orchestrate type III secretion

The type III secretion system (T3SS) is a key pathogenicity factor of many Gram-negative plant and animal pathogens and is also present in some symbiotic bacteria. T3SSs are highly conserved, complex molecular injection machines that translocate bacterial effector proteins directly into eukaryotic cells. Recent genetic, biochemical and structural studies revealed that the activity of the T3SS is regulated by common mechanisms in different bacterial species. In many cases, type III secretion is activated upon host cell contact and depends on specific control proteins, including transcriptional regulators and type III secretion chaperones.

Bacterial phytopathogens and genome science

There are now fourteen completed genomes of bacterial phytopathogens, all of which have been generated in the past six years. These genomes come from a phylogenetically diverse set of organisms, and range in size from 870 kb to more than 6Mb. The publication of these annotated genomes has significantly helped our understanding of bacterial plant disease. These genomes have also provided important information about bacterial evolution. Examples of recently completed genomes include: Pseudomonas syringae pv tomato, which is notable for its large repertoire of effector proteins; Leifsonia xyli subsp. xyli, the first Gram-positive bacterial genome to be sequenced; and Phytoplasma asteris, the small genome that lacks important functions previously thought to be essential in a bacterium.

Diverse AvrPtoB homologs from several Pseudomonas syringae pathovars elicit Pto-dependent resistance and have similar virulence activities

AvrPtoB is a type III effector protein from Pseudomonas syringae pv. tomato that physically interacts with the tomato Pto kinase and, depending on the host genotype, either elicits or suppresses programmed cell death associated with plant immunity. We reported previously that avrPtoB-related sequences are present in diverse gram-negative phytopathogenic bacteria. Here we describe characterization of avrPtoB homologs from P. syringae pv. tomato T1, PT23, and JL1065, P. syringae pv. syringae B728a, and P. syringae pv. maculicola ES4326. The avrPtoB homolog from P. syringae pv. maculicola, hopPmaL, was identified previously. The four new genes identified in this study are designated avrPtoB(T1), avrPtoB(PT23), avrPtoB(JL1065), and avrPtoB(B728a). The AvrPtoB homologs exhibit 52 to 66% amino acid identity with AvrPtoB. Transcripts of each of the avrPtoB homologs were detected in the Pseudomonas strains from which they were isolated. Proteins encoded by the homologs were detected in all strains except P. syringae pv. tomato T1, suggesting that T1 suppresses accumulation of AvrPtoB(T1). All of the homologs interacted with the Pto kinase in a yeast two-hybrid system and elicited a Pto-dependent defense response when they were delivered into leaf cells by DC3000DeltaavrPtoDeltaavrPtoB, a P. syringae pv. tomato strain with a deletion of both avrPto and avrPtoB. Like AvrPtoB, all of the homologs enhanced the ability of DC3000DeltaavrPtoDeltaavrPtoB to form lesions on leaves of two susceptible tomato lines. With the exception of HopPmaL which lacks the C-terminal domain, all AvrPtoB homologs suppressed programmed cell death elicited by the AvrPto-Pto interaction in an Agrobacterium-mediated transient assay. Thus, despite their divergent sequences, AvrPtoB homologs from diverse P. syringae pathovars have conserved avirulence and virulence activities similar to AvrPtoB activity.

Targeting of two effector protein classes to the type III secretion system by a HpaC- and HpaB-dependent protein complex fromXanthomonas campestrispv.vesicatoria

The Gram-negative plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria translocates effector proteins via a specialized type III secretion (TTS) system into the host cell cytosol. The efficient secretion of many effector proteins depends on the global TTS chaperone HpaB. Here, we identified a novel export control protein, HpaC, which significantly contributes to bacterial pathogenicity. Deletion of hpaC leads to a severe reduction in secretion of effector proteins and the putative type III translocon proteins HrpF and XopA. By contrast, secretion of the TTS pilus protein HrpE is not affected. We provide experimental evidence that HpaC differentiates between two classes of effector proteins. Using an in vivo reporter assay, we found that HpaC specifically promotes the translocation of the effector proteins XopJ and XopF1 into the plant cell, whereas AvrBs3 and XopC are efficiently translocated even in the absence of HpaC. Similar findings were obtained for HpaB. Inhibition of protein synthesis suggests that HpaB is involved in the secretion of stored effector proteins. Furthermore, protein-protein interaction studies revealed that HpaB and HpaC form an oligomeric protein complex and that they interact with members of both effector protein classes and the conserved TTS system component HrcV. Taken together, our data indicate that HpaB and HpaC play a central role in recruiting TTS substrates to the secretion apparatus.

Bioinformatics correctly identifies many type III secretion substrates in the plant pathogen Pseudomonas syringae and the biocontrol isolate P. fluorescens SBW25

The plant pathogen Pseudomonas syringae causes disease by secreting a potentially large set of virulence proteins called effectors directly into host cells, their environment, or both, using a type III secretion system (T3SS). Most P. syringae effectors have a common upstream element called the hrp box, and their N-terminal regions have amino acids biases, features that permit their bioinformatic prediction. One of the most prominent biases is a positive serine bias. We previously used the truncated AvrRpt2(81-255) effector containing a serine-rich stretch from amino acids 81 to 100 as a T3SS reporter. Region 81 to 100 of this reporter does not contribute to the secretion or translocation of AvrRpt2 or to putative effector protein chimeras. Rather, the serine-rich region from the N-terminus of AvrRpt2 is important for protein accumulation in bacteria. Most of the N-terminal region (amino acids 15 to 100) is not essential for secretion in culture or delivery to plants. However, portions of this sequence may increase the efficiency of AvrRpt2 secretion, delivery to plants, or both. Two effectors previously identified with the AvrRpt2(81-255) reporter were secreted in culture independently of AvrRpt2, validating the use of the C terminus of AvrRpt2 as a T3SS reporter. Finally, using the reduced AvrRpt2(101-255) reporter, we confirmed seven predicted effectors from P. syringae pv. tomato DC3000, four from P. syringae pv. syringae B728a, and two from P. fluorescens SBW25.

Pseudomonas syringae type III chaperones ShcO1, ShcS1, and ShcS2 facilitate translocation of their cognate effectors and can substitute for each other in the secretion of HopO1-1

The Pseudomonas syringae type III secretion system (TTSS) translocates effector proteins into plant cells. Several P. syringae effectors require accessory proteins called type III chaperones (TTCs) to be secreted via the TTSS. We characterized the hopO1-1, hopS1, and hopS2 operons in P. syringae pv. tomato DC3000; these operons encode three homologous TTCs, ShcO1, ShcS1, and ShcS2. ShcO1, ShcS1, and ShcS2 facilitated the type III secretion and/or translocation of their cognate effectors HopO1-1, HopS1, and HopS2, respectively. ShcO1 and HopO1-1 interacted with each other in yeast two-hybrid and coimmunoprecipitation assays. Interestingly, ShcS1 and ShcS2 were capable of substituting for ShcO1 in facilitating HopO1-1 secretion and translocation and each TTC was able to bind the other's cognate effectors in yeast two-hybrid assays. Moreover, ShcO1, ShcS1, and ShcS2 all bound to the middle-third region of HopO1-1. The HopS2 effector possessed atypical P. syringae TTSS N-terminal characteristics and was translocated in low amounts. A site-directed HopS2 mutation that introduced a common N-terminal characteristic from other P. syringae type III secreted substrates increased HopS2 translocation, supporting the idea that this characteristic functions as a secretion signal. Additionally, hopO1-2 and hopT1-2 were shown to encode effectors secreted via the DC3000 TTSS. Finally, a DC3000 hopO1-1 operon deletion mutant produced disease symptoms similar to those seen with wild-type DC3000 but was reduced in its ability to multiply in Arabidopsis thaliana. The existence of TTCs that can bind to dissimilar effectors and that can substitute for each other in effector secretion provides insights into the nature of how TTCs function.