Comparative study of regulatory mechanisms for pectinase production by Erwinia carotovora subsp. carotovora and Erwinia chrysanthemi

Pectinases as promising green biocatalysts having broad-spectrum applications: Recent trends, scope, and relevance

Pectinases are a collection of multiple enzymes that have a common substrate, that is, pectin. They can act on different parts of pectin due to the structural heterogeneity of pectin. Therefore, they have been placed in different groups, such as protopectinases, polygalacturonases, polymethylesterases, pectin lyases, and pectate lyases. They are naturally present both in multicellular organisms such as higher plants and in unicellular organisms such as microbes. In past decade, it has been witnessed that chemical and mechanical methods employed in industrial processes have led to environmental hazards and serious health disorders, thus increasing the search for eco-friendly approaches with minimal health risks. Hence, microbial enzymes have been extensively used as safer alternative for these environmentally unsafe methods. Among these microbial enzymes, pectinases hold great significance and is one of the principal enzymes that have been used commercially. It is predominantly used as a green biocatalyst for fruit, fiber, oil, textile, beverage, pulp, and paper industry. Thus, this review focuses on the structure of pectin, microbial sources of pectin, and principle industrial applications of pectinases.

Microbially-derived cocktail of carbohydrases as an anti-biofouling agents: a 'green approach'

Enzymes, also known as biocatalysts, display vital properties like high substrate specificity, an eco-friendly nature, low energy inputs, and cost-effectiveness. Among their numerous known applications, enzymes that can target biofilms or their components are increasingly being investigated for their anti-biofouling action, particularly in healthcare, food manufacturing units and environmental applications. Enzymes can target biofilms at different levels like during the attachment of microorganisms, formation of exopolymeric substances (EPS), and their disruption thereafter. In this regard, a consortium of carbohydrases that can target heterogeneous polysaccharides present in the EPS matrix may provide an effective alternative to conventional chemical anti-biofouling methods. Further, for complete annihilation of biofilms, enzymes can be used alone or in conjunction with other antimicrobial agents. Enzymes hold the promise to replace the conventional methods with greener, more economical, and more efficient alternatives. The present article explores the potential and future perspectives of using carbohydrases as effective anti-biofilm agents.

The Bacterial Soft Rot Pathogens, Pectobacterium carotovorum and P. atrosepticum, Respond to Different Classes of Virulence-Inducing Host Chemical Signals

Soft rot bacteria of the Pectobacterium and Dickeya genera are Gram-negative phytopathogens that produce and secrete plant cell wall-degrading enzymes (PCWDE), the actions of which lead to rotting and decay of their hosts in the field and in storage. Host chemical signals are among the factors that induce the bacteria into extracellular enzyme production and virulence. A class of compounds (Class I) made up of intermediate products of cell wall (pectin) degradation induce exoenzyme synthesis through KdgR, a global negative regulator of exoenzyme production. While the KdgR− mutant of P. carotovorum is no longer inducible by Class I inducers, we demonstrated that exoenzyme production is induced in this strain in the presence of extracts from hosts including celery, potato, carrot, and tomato, suggesting that host plants contain another class of compounds (Class II inducers) different from the plant cell wall-degradative products that work through KdgR. The Class II inducers are thermostable, water-soluble, diffusible, and dialysable through 1 kDa molecular weight cut off pore size membranes, and could be a target for soft rot disease management strategies.

Global Regulator PhoP is Necessary for Motility, Biofilm Formation, Exoenzyme Production and Virulence of Xanthomonas citri Subsp. citri on Citrus Plants

Citrus canker caused by Xanthomonas citri subsp. citri is one of the most important bacterial diseases of citrus, impacting both plant growth and fruit quality. Identifying and elucidating the roles of genes associated with pathogenesis has aided our understanding of the molecular basis of citrus-bacteria interactions. However, the complex virulence mechanisms of X. citri subsp. citri are still not well understood. In this study, we characterized the role of PhoP in X. citri subsp. citri using a phoP deletion mutant, ΔphoP. Compared with wild-type strain XHG3, ΔphoP showed reduced motility, biofilm formation, as well as decreased production of cellulase, amylase, and polygalacturonase. In addition, the virulence of ΔphoP on citrus leaves was significantly decreased. To further understand the virulence mechanisms of X. citri subsp. citri, high-throughput RNA sequencing technology (RNA-Seq) was used to compare the transcriptomes of the wild-type and mutant strains. Analysis revealed 1017 differentially-expressed genes (DEGs), of which 614 were up-regulated and 403 were down-regulated in ΔphoP. Gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggested that the DEGs were enriched in flagellar assembly, two-component systems, histidine metabolism, bacterial chemotaxis, ABC transporters, and bacterial secretion systems. Our results showed that PhoP activates the expression of a large set of virulence genes, including 22 type III secretion system genes and 15 type III secretion system effector genes, as well as several genes involved in chemotaxis, and flagellar and histidine biosynthesis. Two-step reverse-transcription polymerase chain reaction analysis targeting 17 genes was used to validate the RNA-seq data, and confirmed that the expression of all 17 genes, except for that of virB1, decreased significantly. Our results suggest that PhoP interacts with a global signaling network to co-ordinate the expression of multiple virulence factors involved in modification and adaption to the host environment during infection.

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Dickeya is a genus of phytopathogenic enterobacterales causing soft rot in a variety of plants (e.g. potato, chicory, maize). Among the species affiliated to this genus, Dickeya aquatica, described in 2014, remained particularly mysterious because it had no known host. Furthermore, while D. aquatica was proposed to represent a deep-branching species among Dickeya genus, its precise phylogenetic position remained elusive. Here, we report the complete genome sequence of the D. aquatica type strain 174/2. We demonstrate the affinity of D. aquatica strain 174/2 for acidic fruits such as tomato and cucumber and show that exposure of this bacterium to acidic pH induces twitching motility. An in-depth phylogenomic analysis of all available Dickeya proteomes pinpoints D. aquatica as the second deepest branching lineage within this genus and reclassifies two lineages that likely correspond to new genomospecies (gs.): Dickeya gs. poaceaephila (Dickeya sp NCPPB 569) and Dickeya gs. undicola (Dickeya sp 2B12), together with a new putative genus, tentatively named Prodigiosinella. Finally, from comparative analyses of Dickeya proteomes, we infer the complex evolutionary history of this genus, paving the way to study the adaptive patterns and processes of Dickeya to different environmental niches and hosts. In particular, we hypothesize that the lack of xylanases and xylose degradation pathways in D. aquatica could reflect adaptation to aquatic charophyte hosts which, in contrast to land plants, do not contain xyloglucans.

Integration Host Factor Is Essential for Biofilm Formation, Extracellular Enzyme, Zeamine Production, and Virulence in Dickeya zeae

Dickeya zeae is a globally important pathogenic bacterium that infects many crops, including rice, maize, potato, and banana. Bacterial foot rot of rice caused by D. zeae is one of the most important bacterial diseases of rice in China and some Southeast Asian countries. To investigate the functions of integration host factor (IHF) in D. zeae, we generated knockout mutants of ihfA and ihfB. Phenotypic assays showed that both the ΔihfA and ΔihfB strains had greatly reduced mobility, biofilm formation, extracellular protease, and pectinase activities, and toxin production compared with the wild-type strain. In addition, the mutants did not inhibit the germination of rice seeds, failed to cause soft rot in potatoes and a hypersensitive response in tobacco, and were avirulent in rice. Quantitative reverse-transcription polymerase chain reaction analysis demonstrated that IHF positively regulates the expression of zmsA, hrpN/Y, pelA/B/C, pehX, celZ, prtG, fliC, and DGC (diguanylate cyclase). Electrophoretic mobility shift assays further confirmed that IhfA binds to the promoter region of the DGC gene and may alter the levels of a second bacterial messenger, c-di-GMP, to regulate the pathogenicity or other physiological functions of D. zeae. In summary, IHF is an important integrated regulator of pathogenicity in D. zeae.

Identification of an Extracellular Endoglucanase That Is Required for Full Virulence in Xanthomonas citri subsp. citri

Xanthomonas citri subsp. citri causes citrus canker disease, which is characterized by the formation of water-soaked lesions, white or yellow spongy pustules and brown corky canker. In this work, we report the contribution of extracellular endoglucanase to canker development during infection. The ectopic expression of nine putative cellulases in Escherichia coli indicated that two endoglucanases, BglC3 and EngXCA, show carboxymethyl cellulase activity. Both bglC3 and engXCA genes were transcribed in X. citri subsp. citri, however, only BglC3 protein was detected outside the cell in western blot analysis. The deletion of bglC3 gene resulted in complete loss of extracellular carboxymethyl cellulase activity and delayed the onset of canker symptoms in both infiltration- and wound-inoculation assays. When growing in plant tissue, the cell density of bglC3 mutant was lower than that of the wild type. Our data demonstrated that BglC3 is an extracellular endoglucanase required for the full virulence of X. citri subsp. citri.

Characterization of Cell-Death-Inducing Members of the Pectate Lyase Gene Family in Phytophthora capsici and Their Contributions to Infection of Pepper

Pectate lyases (PL) play a critical role in pectin degradation. PL have been extensively studied in major bacterial and fungal pathogens of a wide range of plant species. However, the contribution of PL to infection by oomycete pathogens remains largely unknown. Here, we cloned 22 full-length pectate lyase (PcPL) genes from a highly aggressive strain of Phytophthora capsici SD33. Of these, PVX agroinfiltration revealed that 12 PcPL genes were found to be highly induced during infection of pepper by SD33 but the induction level was twofold less in a mildly aggressive strain, YN07. The four genes with the highest transcript levels as measured by by quantitative reverse-transcription polymerase chain reaction (PcPL1, PcPL15, PcPL16, and PcPL20) also produced a severe cell death response following transient expression in pepper leaves but the other eight PcPL genes did not. Overexpression of these four genes increased the virulence of SD33 on pepper slightly, and increased it more substantially during infection of tobacco. Overexpression of the genes in YN07 restored its aggressiveness to near that of SD33. Gene silencing experiments with the 12 PcPL genes produced diverse patterns of silencing of PcPL genes, from which it could be inferred from regression analysis that PcPL1, PcPL16, and PcPL20 could account for nearly all of the contributions of the PcPL genes to virulence.

Nitrogen metabolism meets phytopathology

Nitrogen (N) is essential for life and is a major limiting factor of plant growth. Because soils frequently lack sufficient N, large quantities of inorganic N fertilizers are added to soils for crop production. However, nitrate, urea, and ammonium are a major source of global pollution, because much of the N that is not taken up by plants enters streams, groundwater, and lakes, where it affects algal production and causes an imbalance in aquatic food webs. Many agronomical data indicate that the higher use of N fertilizers during the green revolution had an impact on the incidence of crop diseases. In contrast, examples in which a decrease in N fertilization increases disease severity are also reported, indicating that there is a complex relationship linking N uptake and metabolism and the disease infection processes. Thus, although it is clear that N availability affects disease, the underlying mechanisms remain unclear. The aim of this review is to describe current knowledge of the mechanisms that link plant N status to the plant's response to pathogen infection and to the virulence and nutritional status of phytopathogens.

Comparison of expression, purification and characterization of a new pectate lyase from Phytophthora capsici using two different methods

BACKGROUND

Pectate lyases (PELs) play an important role in the infection process of plant pathogens and also have a commercial significance in industrial applications. Most of the PELs were expressed as soluble recombinant proteins, while a few recombinant proteins were insoluble. The production of a large-scale soluble recombinant PEL would allow not only a more detailed structural and functional characterization of this enzyme but also may have important applications in the food industry.

RESULTS

We cloned a new pectate lyase gene (Pcpel2) from Phytophthora capsici. Pcpel2 was constructed by pET system and pMAL system, and both constructs were used to express the PCPEL2 in Escherichia coli BL21 (DE3) pLysS. The expressed products were purified using affinity chromatography and gel filtration chromatography. The purity, specific activity and pathogenicity of the purified PCPEL2 expressed by the pMAL system were higher than the purified PCPEL2 expressed by the pET system. In addition, some other characteristics of the purified PCPEL2 differed from the two systems, such as crystallographic features. Purified PCPEL2 expressed by the pMAL system was crystallized by the hanging-drop vapour-diffusion method at 289 K, and initial crystals were grown.

CONCLUSION

The two different methods and comparison presented here would be highly valuable in obtaining an ideal enzyme for the downstream experiments, and supply an useful alternative to purify some insoluble recombinant proteins.

Commensal effect of pectate lyases secreted from Dickeya dadantii on proliferation of Escherichia coli O157:H7 EDL933 on lettuce leaves

The outbreaks caused by enterohemorrhagic Escherichia coli O157:H7 on leafy greens have raised serious and immediate food safety concerns. It has been suggested that several phytopathogens aid in the persistence and proliferation of the human enteropathogens in the phyllosphere. In this work, we examined the influence of virulence mechanisms of Dickeya dadantii 3937, a broad-host-range phytopathogen, on the proliferation of the human pathogen E. coli O157:H7 EDL933 (EDL933) on postharvest lettuce by coinoculation of EDL933 with D. dadantii 3937 derivatives that have mutations in virulence-related genes. A type II secretion system (T2SS)-deficient mutant of D. dadantii 3937, A1919 (ΔoutC), lost the capability to promote the multiplication of EDL933, whereas Ech159 (ΔrpoS), a stress-responsive σ factor RpoS-deficient mutant, increased EDL933 proliferation on lettuce leaves. A spectrophotometric enzyme activity assay revealed that A1919 (ΔoutC) was completely deficient in the secretion of pectate lyases (Pels), which play a major role in plant tissue maceration. In contrast to A1919 (ΔoutC), Ech159 (ΔrpoS) showed more than 2-fold-greater Pel activity than the wild-type D. dadantii 3937. Increased expression of pelD (encodes an endo-pectate lyase) was observed in Ech159 (ΔrpoS) in planta. These results suggest that the pectinolytic activity of D. dadantii 3937 is the dominant determinant of enhanced EDL933 proliferation on the lettuce leaves. In addition, RpoS, the general stress response σ factor involved in cell survival in suboptimal conditions, plays a role in EDL933 proliferation by controlling the production of pectate lyases in D. dadantii 3937.

Gluconate metabolism is required for virulence of the soft-rot pathogen Pectobacterium carotovorum

Pectobacterium carotovorum is a ubiquitous soft rot pathogen that uses global virulence regulators to coordinate pathogenesis in response to undefined environmental conditions. We characterize an operon in P. carotovorum required for gluconate metabolism and virulence. The operon contains four genes that are highly conserved among proteobacteria (initially annotated ygbJKLM), one of which was misassigned as a type III secreted effector, (ygbK, originally known as hopAN1). A mutant with a deletion-insertion within this operon is unable to metabolize gluconate, a precursor for the pentose phosphate pathway. The mutant exhibits attenuated growth on the leaves of its host of isolation, potato, and those of Arabidopsis thaliana. Notably, the mutant hypermacerates potato tubers and is deficient in motility. Global virulence regulators that are responsive to cell wall pectin breakdown products and other undefined environmental signals, KdgR and FlhD, respectively, are misregulated in the mutant. The alteration of virulence mediated via changes in transcription of known global virulence regulators in our ygbJ-M operon mutant suggests a role for host-derived catabolic intermediates in P. carotovorum pathogenesis. Thus, we rename this operon in P. carotovorum vguABCD for virulence and gluconate metabolism.

Mutation in the xpsD gene of Xanthomonas axonopodis pv. citri affects cellulose degradation and virulence

The Gram-negative bacterium Xanthomonas axonopodis pv. citri, the causal agent of citrus canker, is a major threat to the citrus industry worldwide. Although this is a leaf spot pathogen, it bears genes highly related to degradation of plant cell walls, which are typically found in plant pathogens that cause symptoms of tissue maceration. Little is known on Xac capacity to cause disease and hydrolyze cellulose. We investigated the contribution of various open reading frames on degradation of a cellulose compound by means of a global mutational assay to selectively screen for a defect in carboxymethyl cellulase (CMCase) secretion in X. axonopodis pv. citri. Screening on CMC agar revealed one mutant clone defective in extracellular glycanase activity, out of nearly 3,000 clones. The insertion was located in the xpsD gene, a component of the type II secretion system (T2SS) showing an influence in the ability of Xac to colonize tissues and hydrolyze cellulose. In summary, these data show for the first time, that X. axonopodis pv. citri is capable of hydrolyzing cellulose in a T2SS-dependent process. Furthermore, it was demonstrated that the ability to degrade cellulose contributes to the infection process as a whole.

The role of pectate lyase and the jasmonic acid defense response in Pseudomonas viridiflava virulence

Pseudomonas viridiflava is a common pathogen of Arabidopsis thaliana in wild populations, yet very little is known about mechanisms of resistance and virulence in this interaction. We examined the induced defense response of A. thaliana to several strains of P. viridiflava collected from this host by quantifying the expression of PR-1 and LOX2/PDF1.2, which serve as markers for induction of the salicylic and jasmonic acid (JA) pathways, respectively. Growth of these strains then was assessed on Col-0, the fad3/7/8 and coil-1 mutants deficient in JA- and ethylene (ET)-induced defense responses, and the sid2-1 mutant deficient in salicylic acid-induced defense responses. All strains of P. viridiflava induced high expression of LOX2 and PDF1.2 on Col-0. In contrast, PR-1 expression was delayed and reduced relative to PDF1.2 expression. Additionally, three of four P. viridiflava strains were more virulent on fad3/7/8 relative to Col-0, whereas all strains were more virulent on coil-1 relative to Col-0, indicating that P. viridiflava generally may be suppressed by JA/ET-mediated defense responses. In contrast, no increase in the growth of P. viridiflava strains was observed in the sid2-1 mutant relative to Col-0. Parallel experiments were performed with the closely related P. syringae pv. tomato for comparative purposes. In addition, we assessed the role of pectate lyase and the alternative sigma factor HrpL in P. viridiflava virulence on A. thaliana and found that pectate lyase activity is correlated with virulence, whereas the removal of pectate lyase or HrpL significantly reduced virulence.

PecS and PecT coregulate the synthesis of HrpN and pectate lyases, two virulence determinants in Erwinia chrysanthemi 3937

Erwinia chrysanthemi strain 3937 is a necrotrophic bacterial plant pathogen. Pectinolytic enzymes and, in particular, pectate lyases play a key role in soft rot symptoms; however, the efficient colonization of plants by E. chrysanthemi requires additional factors. These factors include HrpN (harpin), a heat-stable, glycine-rich hydrophilic protein, which is secreted by the type III secretion system. We investigated the expression of hrpN in E. chrysanthemi 3937 in various environmental conditions and different regulatory backgrounds. Using lacZ fusions, hrpN expression was markedly influenced by the carbon source, osmolarity, growth phase, and growth substrate. hrpN was repressed when pectinolysis started and negatively regulated by the repressors of pectate lyase synthesis, PecS and PecT. Primer extension data and in vitro DNA-protein interaction experiments support a model whereby PecS represses hrpN expression by binding to the hrpN regulatory region and inhibiting transcript elongation. The results suggest coordinated regulation of HrpN and pectate lyases by PecS and PecT. A putative model of the synthesis of these two virulence factors in E. chrysanthemi during pathogenesis is presented.

Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described.