Dickeya Manipulates Multiple Quorum Sensing Systems to Control Virulence and Collective Behaviors

Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia

Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.

Pseudomonas chlororaphis L5 and Enterobacter asburiae L95 biocontrol Dickeya soft rot diseases by quenching virulence factor modulating quorum sensing signal

Virulence factor modulating (VFM) is a quorum sensing (QS) signal shared by and specific to Dickeya bacteria, regulating the production of plant cell wall degrading enzymes (PCWDEs) and virulence of Dickeya. High polarity and trace of VFM signal increase the difficulty of signal separation and structure identification, and thus limit the development of quorum quenching strategy to biocontrol bacterial soft rot diseases caused by Dickeya. In order to high-throughput screen VFM quenching bacteria, a vfmE-gfp biosensor VR2 (VFM Reporter) sensitive to VFM signal was first constructed. Subsequently, two bacterial strains with high quenching efficiency were screened out by fluorescence intensity measurement and identified as Pseudomonas chlororaphis L5 and Enterobacter asburiae L95 using multilocus sequence analysis (MLSA). L5 and L95 supernatants reduced the expression of vfm genes, and both strains also decreased the production of PCWDEs of D. zeae MS2 and significantly reduced the virulence of D. oryzae EC1 on rice seedlings, D. zeae MS2 on banana seedlings, D. dadantii 3937 on potato and D. fangzhongdai CL3 on taro. Findings in this study provide a method to high-throughput screen VFM quenching bacteria and characterize novel functions of P. chlororaphis and E. asburiae in biocontrolling plant diseases through quenching VFM QS signal.

The phc Quorum-Sensing System in Ralstonia solanacearum Species Complex

Ralstonia solanacearum species complex (RSSC) strains are devastating plant pathogens distributed worldwide. The primary cell density-dependent gene expression system in RSSC strains is phc quorum sensing (QS). It regulates the expression of about 30% of all genes, including those related to cellular activity, primary and secondary metabolism, pathogenicity, and more. The phc regulatory elements encoded by the phcBSRQ operon and phcA gene play vital roles. RSSC strains use methyl 3-hydroxymyristate (3-OH MAME) or methyl 3-hydroxypalmitate (3-OH PAME) as the QS signal. Each type of RSSC strain has specificity in generating and receiving its QS signal, but their signaling pathways might not differ significantly. In this review, I describe the genetic and biochemical factors involved in QS signal input and the regulatory network and summarize control of the phc QS system, new cell-cell communications, and QS-dependent interactions with soil fungi.

Quorum-quenching enzymes: Promising bioresources and their opportunities and challenges as alternative bacteriostatic agents in food industry

The problems of spoilage, disease, and biofilm caused by bacterial quorum-sensing (QS) systems have posed a significant challenge to the development of the food industry. Quorum-quenching (QQ) enzymes can block QS by hydrolyzing or modifying the signal molecule, making these enzymes promising new candidates for use as antimicrobials. With many recent studies of QQ enzymes and their potential to target foodborne bacteria, an updated and systematic review is necessary. Thus, the goals of this review were to summarize what is known about the effects of bacterial QS on the food industry; discuss the current understanding of the catalytic mechanisms of QQ enzymes, including lactonase, acylase, and oxidoreductase; and describe strategies for the engineering and evolution of QQ enzymes for practical use. In particular, this review focuses on the latest progress in the application of QQ enzymes in the field of food. Finally, the current challenges limiting the systematic application of QQ enzymes in the food industry are discussed to help guide the future development of these important enzymes.

Disruption of the metC Gene Affects Methionine Biosynthesis in Pectobacterium carotovorum subsp. carotovorum Pcc21 and Reduces Soft-Rot Disease

Plant pathogenic Pectobacterium species cause severe soft rot/blackleg diseases in many economically important crops worldwide. Pectobacterium utilizes plant cell wall degrading enzymes (PCWDEs) as the main virulence determinants for its pathogenicity. In this study, we screened a random mutant, M29 is a transposon insertion mutation in the metC gene encoding cystathionine β-lyase that catalyzes cystathionine to homocysteine at the penultimate step in methionine biosynthesis. M29 became a methionine auxotroph and resulted in growth defects in methionine-limited conditions. Impaired growth was restored with exogenous methionine or homocysteine rather than cystathionine. The mutant exhibited reduced soft rot symptoms in Chinese cabbages and potato tubers, maintaining activities of PCWDEs and swimming motility. The mutant was unable to proliferate in both Chinese cabbages and potato tubers. The reduced virulence was partially restored by a complemented strain or 100 µM of methionine, whereas it was fully restored by the extremely high concentration (1 mM). Our transcriptomic analysis showed that genes involved in methionine biosynthesis or transporter were downregulated in the mutant. Our results demonstrate that MetC is important for methionine biosynthesis and transporter and influences its virulence through Pcc21 multiplication in plant hosts.

A novel bacterial strain Burkholderia sp. F25 capable of degrading diffusible signal factor signal shows strong biocontrol potential

Vast quantities of synthetic pesticides have been widely applied in various fields to kill plant pathogens, resulting in increased pathogen resistance and decreased effectiveness of such chemicals. In addition, the increased presence of pesticide residues affects living organisms and the environment largely on a global scale. To mitigate the impact of crop diseases more sustainably on plant health and productivity, there is a need for more safe and more eco-friendly strategies as compared to chemical prevention. Quorum sensing (QS) is an intercellular communication mechanism in a bacterial population, through which bacteria adjust their population density and behavior upon sensing the levels of signaling molecules in the environment. As an alternative, quorum quenching (QQ) is a promising new strategy for disease control, which interferes with QS by blocking intercellular communication between pathogenic bacteria to suppress the expression of disease-causing genes. Black rot caused by Xanthomonas campestris pv. campestris (Xcc) is associated with the diffusible signal factor (DSF). As detailed in this study, a new QQ strain F25, identified as Burkholderia sp., displayed a superior ability to completely degrade 2 mM of DSF within 72 h. The main intermediate product in the biodegradation of DSF was identified as n-decanoic acid, based on gas chromatography-mass spectrometry (GC-MS). A metabolic pathway for DSF by strain F25 is proposed, based on the chemical structure of DSF and its intermediates, demonstrating the possible degradation of DSF via oxidation-reduction. The application of strain F25 and its crude enzyme as biocontrol agents significantly attenuated black rot caused by Xcc, and inhibited tissue maceration in the host plant Raphanus sativus L., without affecting the host plant. This suggests that agents produced from strain F25 and its crude enzyme have promising applications in controlling infectious diseases caused by DSF-dependent bacterial pathogens. These findings are expected to provide a new therapeutic strategy for controlling QS-mediated plant diseases.

Genomic and phenotypic biology of a novel Dickeya zeae WH1 isolated from rice in China: Insights into pathogenicity and virulence factors

Soft rot caused by Dickeya zeae is an important bacterial disease affecting rice and other plants worldwide. In this study, Nanopore and Illumina sequencing platforms were used to sequence the high-quality complete genome of a novel D. zeae strain WH1 (size: 4.68 Mb; depth: 322.37x for Nanopore, 243.51x for Illumina; GC content: 53.59%), which was isolated from healthy rice root surface together with Paenibacillus polymyxa, a potential biocontrol bacterium against D. zeae strain WH1. However, the pure WH1 culture presented severe pathogenicity. Multilocus sequence analysis (MLSA) indicated that strains WH1, EC1, and EC2 isolated from rice were grouped into a clade differentiated from other D. zeae strains. The average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) analyses demonstrated that WH1 was phylogenetically closest to EC2. Furthermore, the pathogenicity determinants and virulence factors of WH1 were mainly analyzed through genomic comparison with complete genomes of other D. zeae strains with high virulence (EC1, EC2, MS1, and MS2). The results revealed that plant cell wall-degrading extracellular enzymes (PCWDEs), flagellar and chemotaxis, and quorum sensing were highly conserved in all analyzed genomes, which were confirmed through phenotypic assays. Besides, WH1 harbored type I, II, III, and VI secretion systems (T1SS, T2SS, T3SS, and T6SS), but lost T4SS and T5SS. Like strains MS1 and MS2 isolated from bananas, WH1 harbored genes encoding both capsule polysaccharide (CPS) and exopolysaccharide (EPS) biosynthesis. The results of pathogenicity assays demonstrated that WH1 produced severe soft rot symptoms on potato tubers, carrots, radishes, and Chinese cabbage. Meanwhile, WH1 also produced phytotoxin(s) to inhibit rice seed germination with an 87% inhibitory rate in laboratory conditions. More importantly, we confirmed that phytotoxin(s) produced by WH1 are different from zeamines produced by EC1. Comparative genomics analyses and phenotypic and pathogenicity assays suggested that WH1 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings highlight the emergence of a new type of D. zeae strain with high virulence, causing soft rot in rice and other plants.

Comparative Pathogenomic Analysis of Two Banana Pathogenic Dickeya Strains Isolated from China and the Philippines

Dickeya is a major and typical member of soft rot Pectobacteriaceae (SRP) with a wide range of plant hosts worldwide. Previous studies have identified D. zeae as the causal agent of banana soft rot disease in China. In 2017, we obtained banana soft rot pathogen strain FZ06 from the Philippines. Genome sequencing and analysis indicated that FZ06 can be classified as D. dadantii and represents a novel subspecies of D. dadantii, which we propose to name as subsp. paradisiaca. Compared with Chinese banana soft rot pathogenic strain D. zeae MS2, strain FZ06 has a similar host range but different virulence; FZ06 is significantly less virulent to banana and potato but more virulent to Chinese cabbage and onion. Characterization of virulence factors revealed obviously less production of pectate lyases (Pels), polygalacturonases (Pehs), proteases (Prts), and extrapolysaccharides (EPSs), as well as lower swimming and swarming motility and biofilm formation in strain FZ06. Genomic comparison of the two strains revealed five extra gene clusters in FZ06, including one Stt-type T2SS, three T4SSs, and one T4P. Expression of cell wall degrading enzyme (CWDE)-encoding genes is significantly lower in FZ06 than in MS2.

The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2

Dickeya zeae is an aggressive bacterial phytopathogen that infects a wide range of host plants. It has been reported that integration host factor (IHF), a nucleoid-associated protein consisting of IHFα and IHFβ subunits, regulates gene expression by influencing nucleoid structure and DNA bending. To define the role of IHF in the pathogenesis of D. zeae MS2, we deleted either and both of the IHF subunit encoding genes ihfA and ihfB, which significantly reduced the production of cell wall-degrading enzymes (CWDEs), an unknown novel phytotoxin and the virulence factor-modulating (VFM) quorum-sensing (QS) signal, cell motility, biofilm formation, and thereafter the infection ability towards both potato slices and banana seedlings. To characterize the regulatory pathways of IHF protein associated with virulence, IHF binding sites (consensus sequence 5'-WATCAANNNNTTR-3') were predicted and 272 binding sites were found throughout the genome. The expression of 110 tested genes was affected by IHF. Electrophoretic mobility shift assay (EMSA) showed direct interaction of IhfA protein with the promoters of vfmE, speA, pipR, fis, slyA, prtD, hrpL, hecB, hcp, indA, hdaA, flhD, pilT, gcpJ, arcA, arcB, and lysR. This study clarified the contribution of IHF in the pathogenic process of D. zeae by controlling the production of VFM and putrescine QS signals, phytotoxin, and indigoidine, the luxR-solo system, Fis, SlyA, and FlhD transcriptional regulators, and secretion systems from type I to type VI. Characterization of the regulatory networks of IHF in D. zeae provides a target for prevention and control of plant soft rot disease.

Isolation and Genome Analysis of Pectobacterium colocasium sp. nov. and Pectobacterium aroidearum, Two New Pathogens of Taro

Bacterial soft rot is one of the most destructive diseases of taro (Colocasia esculenta) worldwide. In recent years, frequent outbreaks of soft rot disease have seriously affected taro production and became a major constraint to the development of taro planting in China. However, little is known about the causal agents of this disease, and the only reported pathogens are two Dickeya species and P. carotovorum. In this study, we report taro soft rot caused by two novel Pectobacterium strains, LJ1 and LJ2, isolated from taro corms in Ruyuan County, Shaoguan City, Guangdong Province, China. We showed that LJ1 and LJ2 fulfill Koch's postulates for taro soft rot. The two pathogens can infect taro both individually and simultaneously, and neither synergistic nor antagonistic interaction was observed between the two pathogens. Genome sequencing of the two strains indicated that LJ1 represents a novel species of the genus Pectobacterium, for which the name "Pectobacterium colocasium sp. nov." is proposed, while LJ2 belongs to Pectobacterium aroidearum. Pan-genome analysis revealed multiple pathogenicity-related differences between LJ1, LJ2, and other Pectobacterium species, including unique virulence factors, variation in the copy number and organization of Type III, IV, and VI secretion systems, and differential production of plant cell wall degrading enzymes. This study identifies two new soft rot Pectobacteriaceae (SRP) pathogens causing taro soft rot in China, reports a new case of co-infection of plant pathogens, and provides valuable resources for further investigation of the pathogenic mechanisms of SRP.