Role of DetR in defence is critical for virulence of Xanthomonas oryzae pv. oryzae

Microbial polysaccharides biosynthesis and their regulatory strategies

Microbial polysaccharides hold significant potential for various applications, including food, cosmetics, petroleum, and pharmaceuticals. A deeper understanding of their biosynthetic pathways and regulatory strategies is crucial for enhancing production efficiency and reducing associated costs. To summarize synthetic biological modification strategies for microbial polysaccharides from a hierarchical perspective, this review classifies these polymers into three categories based on the depths of carried out research regarding their biosynthetic pathways and regulatory strategies, i.e., (1) microbial polysaccharides with well-elucidated biosynthetic pathways, (2) microbial polysaccharides with well-elucidated precursor sugar biosynthetic pathways but synthase-encoding genes incompletely understood, and (3) those whose biosynthesis depends on a single synthetic enzyme. We systematically summarize the biosynthetic pathways of these three categories and provide insights into yield-improvement strategies. This review aims to serve as a valuable reference for metabolic regulation of microbial polysaccharides and to facilitate future advances in their production.

Highly efficient genome editing in Xanthomonas oryzae pv. oryzae through repurposing the endogenous type I-C CRISPR-Cas system

Efficient and modular genome editing technologies that manipulate the genome of bacterial pathogens will facilitate the study of pathogenesis mechanisms. However, such methods are yet to be established for Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight. We identified a single type I-C CRISPR-Cas system in the Xoo genome and leveraged this endogenous defence system for high-efficiency genome editing in Xoo. Specifically, we developed plasmid components carrying a mini-CRISPR array, donor DNA, and a phage-derived recombination system to enable the efficient and programmable genome editing of precise deletions, insertions, base substitutions, and gene replacements. Furthermore, the type I-C CRISPR-Cas system of Xoo cleaves target DNA unidirectionally, and this can be harnessed to generate large genomic deletions up to 212 kb efficiently. Therefore, the genome-editing strategy we have developed can serve as an excellent tool for functional genomics of Xoo, and should also be applicable to other CRISPR-harbouring bacterial plant pathogens.

Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen (Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms

Fusarium wilt is caused by the fungus Fusarium oxysporum f. sp. cubense (Foc) and is the most serious disease affecting bananas (Musa spp.). The fungus is classified into Foc race 1 (R1), Foc race 2, and Foc race 4 based on host specificity. As the rate of spread and the ranges of the devastation of the Foc races exceed the centre of the banana’s origin, even in non-targeted cultivars, there is a possibility of variation in virulence-associated genes. Therefore, the present study investigates the genome assembly of Foc races that infect the Cavendish (AAA) banana group in India, specifically those of the vegetative compatibility group (VCG) 0124 (race 1), 0120 (subtropical race 4), and 01213/16 (tropical race 4). While comparing the general features of the genome sequences (e.g., RNAs, GO, SNPs, and InDels), the study also looked at transposable elements, phylogenetic relationships, and virulence-associated effector genes, and sought insights into race-specific molecular mechanisms of infection based on the presence of unique genes. The results of the analyses revealed variations in the organisation of genome assembly and virulence-associated genes, specifically secreted in xylem (SIX) genes, when compared to their respective reference genomes. The findings contributed to a better understanding of Indian Foc genomes, which will aid in the development of effective Fusarium wilt management techniques for various Foc VCGs in India and beyond.

The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System

Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.

PXO_RS20535, Encoding a Novel Response Regulator, Is Required for Chemotactic Motility, Biofilm Formation, and Tolerance to Oxidative Stress in Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of bacterial leaf blight of rice, possesses two-component regulatory systems (TCSs) as an intracellular signaling pathway. In this study, we observed changes in virulence, biofilm formation, motility, chemotaxis, and tolerance against oxidative stress of a knockout mutant strain for the PXO_RS20535 gene, encoding an orphan response regulator (RR). The mutant strain lost virulence, produced significantly less biofilm, and showed remarkably reduced motility in swimming, swarming, and twitching. Furthermore, the mutant strain lost glucose-guided movement and showed clear diminution of growth and survival in the presence of H₂O₂. These results indicate that the RR protein encoded in the PXO_RS20535 gene (or a TCS mediated by the protein) is closely involved in regulation of biofilm formation, all types of motility, chemotaxis, and tolerance against reactive oxygen species (ROS) in Xoo. Moreover we found that the expression of most genes required for a type six secretion system (T6SS) was decreased in the mutant, suggesting that lack of the RR gene most likely leads to defect of T6SS in Xoo.

Contribution of the cold shock protein CspA to virulence in Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) causes a damaging bacterial leaf blight disease in rice. Cold shock proteins (Csps) are highly conserved nucleic acid-binding proteins present in various bacterial genera, but relatively little is known about their functions in Xanthomonas. Herein, we identified four Csps (CspA-CspD) in the Xoo PXO99^A strain. Deletion of cspA decreased cold adaptation and a few known pathogenic factors, including bacterial pathogenicity, biofilm formation and polysaccharide production. Furthermore, we performed transcriptomic and chromosome immunoprecipitation (ChIP) experiments to identify direct targets of CspA and to determine its DNA-binding sequence. Integrative data analysis revealed that CspA directly regulates two genes, PXO_RS11830 and PXO_RS01060, by binding to a conserved CCAAT sequence in the promoter region. We generated single-deletion mutants of each gene and the results indicate that both are responsible for Xanthomonas pathogenicity. In addition, quantitative real-time polymerase chain reaction and western blotting showed that CspA suppressed the expression of its direct targets. In summary, our study clarifies the characteristics of Csps in Xanthomonas and greatly advances our understanding of the mechanisms underlying the contribution of CspA to bacterial virulence.

Genome-wide Screening to Identify Responsive Regulators Involved in the Virulence of Xanthomonas oryzae pv. oryzae

Two-component systems (TCSs) are critical to the pathogenesis of Xanthomonas oryzae pv. oryzae (Xoo). We mutated 55 of 62 genes annotated as responsive regulators (RRs) of TCSs in the genome of Xoo strain PXO99A and identified 9 genes involved in Xoo virulence. Four (rpfG, hrpG, stoS, and detR) of the 9 genes were previously reported as key regulators of Xoo virulence and the other 5 have not been characterized. Lesion lengths on rice leaves inoculated with the mutants were shorter than those of the wild type and were significantly restored with gene complementation. The population density of the 5 mutants in planta was smaller than that of PXO99A at 14 days after inoculation, but the growth curves of the mutants in rich medium were similar to those of the wild type. These newly reported RR genes will facilitate studies on the function of TCSs and of the integrated regulation of TCSs for Xoo pathogenesis.

Deciphering the functions of the outer membrane porin OprBXo involved in virulence, motility, exopolysaccharide production, biofilm formation and stress tolerance in Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) is a Gram-negative bacterium causing bacterial leaf blight disease in rice. Previously, proteomic analysis has shown that the outer membrane protein B in Xoo (OprBXo) is more abundant in the wildtype strain than is the outer membrane protein 1 in the Xoo (Omp1X) knockout mutant. OprBXo shows high homology with OprB, which has been well characterized as a carbohydrate-selective porin in X. citri ssp. citri and Pseudomonas species. However, the functions of OprBXo in Xoo have not yet been documented. To elucidate the functions of OprBXo, we generated the OprBXo-overexpressing mutant, Xoo(OprBXo), and the knockout mutant, XooΔoprBXo(EV). We found that the virulence and migration of Xoo(OprBXo), but not XooΔoprBXo(EV), were markedly reduced in rice. To postulate the mechanisms affected by OprBXo, comparative proteomic analysis was performed. Based on the results of proteomics, we employed diverse phenotypic assays to characterize the functions of OprBXo. Abnormal twitching motility and reduction in swarming motility were observed in Xoo(OprBXo). Moreover, Xoo(OprBXo) decreased, but XooΔoprBXo(EV) enhanced, exopolysaccharide production and biofilm formation. The chemotactic ability of XooΔoprBXo(EV) was dramatically lower than that of Xoo(EV) in the presence of glucose and xylose. Xoo(OprBXo) was resistant to sodium dodecylsulphate and hydrogen peroxide, but XooΔoprBXo(EV) was highly sensitive compared with Xoo(EV). Thus, OprBXo is not only essential for chemotaxis and stress tolerance, but also for motility, biofilm formation and exopolysaccharide production, which may contribute to the virulence of Xoo. These results will lead to new insights into the functions of a sugar-selective porin in Xoo.

Elucidating Functions of FleQ in Xanthomonas oryzae pv. oryzae by Comparative Proteomic and Phenotypic Analyses

To acclimate to different environments, gene expression has to be controlled using diverse transcriptional activators. FleQ activates σ⁵⁴-dependent transcription initiation and regulates flagellar biosynthesis and other mechanisms in several bacteria. Xanthomonas oryzae pv. oryzae (Xoo), which is a causal agent of bacterial leaf blight on rice, lacking FleQ loses swimming motility and virulence is not altered. However, other biological mechanisms related with FleQ in Xoo are unknown. In this study, we generated the FleQ-overexpressing strain, Xoo(FleQ), and knockout mutant, XooΔfleQ. To predict the mechanisms affected by FleQ, label-free shotgun comparative proteomics was carried out. Based on proteomic results, we performed diverse phenotypic assays. Xoo(FleQ) had reduced ability to elicit disease symptoms and exopolysaccharide production. Additionally, the ability of XooΔfleQ(EV) (empty vector) and Xoo(FleQ) to form biofilm was decreased. Swarming motility of XooΔfleQ(EV) was abolished, but was only reduced for Xoo(FleQ). Additionally, abnormal twitching motility was observed in both strains. Siderophore production of Xoo(FleQ) was enhanced in iron-rich conditions. The proteomic and phenotypic analyses revealed that FleQ is involved in flagellar-dependent motility and other mechanisms, including symptom development, twitching motility, exopolysaccharide production, biofilm formation, and siderophore production. Thus, this study provides fundamental information about a σ⁵⁴-dependent transcription activator in Xoo.

Dissecting the virulence-related functionality and cellular transcription mechanism of a conserved hypothetical protein in Xanthomonas oryzae pv. oryzae

Hypothetical proteins without defined functions are largely distributed in all sequenced bacterial genomes. Understanding their potent functionalities is a basic demand for bacteriologists. Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight of rice, is one of the model systems for the study of molecular plant pathology. One-quarter of proteins in the genome of this bacterium are defined as hypothetical proteins, but their roles in Xoo pathogenicity are unknown. Here, we generated in-frame deletions for six hypothetical proteins selected from strain PXO99A and found that one of them (PXO_03177) is required for the full virulence of this strain. PXO_03177 is conserved in Xanthomonas, and is predicted to contain two domains relating to polysaccharide synthesis. However, we found that mutation of this gene did not affect the production or modification of extracellular polysaccharides (EPSs) and lipopolysaccharides (LPSs), two major polysaccharides produced by Xoo relating to its infection. Interestingly, we found that inactivation of PXO_03177 significantly impaired biofilm formation and tolerance to sodium dodecyl sulfate (SDS), both of which are considered to play key roles during Xoo infection in rice leaves. These findings thus enable us to define a function for PXO_03177 in the virulence of Xoo. Furthermore, we also found that the global regulator Clp controls the transcription of PXO_03177 by direct binding to its promoter region, presenting the first cellular regulatory pathway for the modulation of expression of this hypothetical protein gene. Our results provide reference information for PXO_03177 homologues in Xanthomonas.