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Chen S, Hu M, Hu A, Xue Y, Wang S, Liu F, Li C, Zhou X, Zhou J. The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2. MOLECULAR PLANT PATHOLOGY 2022; 23:1487-1507. [PMID: 35819797 PMCID: PMC9452768 DOI: 10.1111/mpp.13244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
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.
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Affiliation(s)
- Shanshan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Anqun Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Si Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Fan Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Chuhao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
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Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States. Microorganisms 2021; 9:microorganisms9081733. [PMID: 34442812 PMCID: PMC8401272 DOI: 10.3390/microorganisms9081733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato production over the past decade in the Northeastern and North Central United States. To clarify the pathogen present at the outset of the epidemic in 2015 and 2016, a phylogenetic study was made of 121 pectolytic soft rot bacteria isolated from symptomatic potato; also included were 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed the epidemic isolates to cluster with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains was low, with one sequence type (ST1) identified in 17 of 19 strains. Pectobacterium parmentieri was more diverse, with ten sequence types detected among 37 of the 2015–2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management.
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Feng L, Schaefer AL, Hu M, Chen R, Greenberg EP, Zhou J. Virulence Factor Identification in the Banana Pathogen Dickeya zeae MS2. Appl Environ Microbiol 2019; 85:e01611-19. [PMID: 31540986 PMCID: PMC6856320 DOI: 10.1128/aem.01611-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/16/2019] [Indexed: 11/20/2022] Open
Abstract
The phytopathogen Dickeya zeae MS2 is a particularly virulent agent of banana soft rot disease. To begin to understand this banana disease and to understand the role of quorum sensing and quorum-sensing-related regulatory elements in D. zeae MS2, we sequenced its genome and queried the sequence for genes encoding LuxR homologs. We identified a canonical LuxR-LuxI homolog pair similar to those in other members of the genus Dickeya The quorum-sensing signal for this pair was N-3-oxo-hexanoyl-homoserine lactone, and the circuit affected motility, cell clumping, and production of the pigment indigoidine, but it did not affect infections of banana seedlings in our experiments. We also identified a luxR homolog linked to a gene annotated as encoding a proline iminopeptidase. Similar linked pairs have been associated with virulence in other plant pathogens. We show that mutants with deletions in the proline iminopeptidase gene are attenuated for virulence. Surprisingly, a mutant with a deletion in the gene encoding the LuxR homolog shows normal virulence.IMPORTANCEDickeya zeae is an emerging banana soft rot pathogen in China. We used genome sequencing and annotation to create an inventory of potential virulence factors and virulence gene regulators encoded in Dickeya zeae MS2, a particularly virulent strain. We created mutations in several genes and tested these mutants in a banana seedling infection model. A strain with a mutated proline iminopeptidase gene, homologs of which are important for disease in the Xanthomonas species phytopathogens, was attenuated for soft rot symptoms in our model. Understanding how the proline iminopeptidase functions as a virulence factor may lead to insights about how to control the disease, and it is of general importance as homologs of the proline iminopeptidase occur in dozens of plant-associated bacteria.
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Affiliation(s)
- Luwen Feng
- Guangdong Province Sociomicrobiology Basic Science and Frontier Technology Research Team & Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, People's Republic of China
| | - Amy L Schaefer
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Ming Hu
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People's Republic of China
| | - Ruiyi Chen
- Guangdong Province Sociomicrobiology Basic Science and Frontier Technology Research Team & Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, People's Republic of China
| | - E Peter Greenberg
- Guangdong Province Sociomicrobiology Basic Science and Frontier Technology Research Team & Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, People's Republic of China
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jianuan Zhou
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People's Republic of China
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Shi Z, Wang Q, Li Y, Liang Z, Xu L, Zhou J, Cui Z, Zhang LH. Putrescine Is an Intraspecies and Interkingdom Cell-Cell Communication Signal Modulating the Virulence of Dickeya zeae. Front Microbiol 2019; 10:1950. [PMID: 31497009 PMCID: PMC6712546 DOI: 10.3389/fmicb.2019.01950] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/08/2019] [Indexed: 11/13/2022] Open
Abstract
The infections caused by Dickeya zeae become a severe problem in recent years, but the regulatory mechanisms that govern the bacterial virulence remain to be fragmental. Here we report the investigation of potential involvement of polyamines in regulation of D. zeae virulence. We showed that null mutation of speA encoding arginine decarboxylase dramatically decreased the bacterial swimming motility, swarming motility and biofilm formation, and exogenous addition of putrescine effectively rescues the defective phenotypes of D. zeae. HPLC and mass spectrometry analysis validated that speA was essential for production of putrescine in D. zeae. In addition, we demonstrated that D. zeae EC1 could detect and response to putrescine molecules produced by itself or from host plant through specific transporters. Among the two transporters identified, the one represented by PotF played a dominated role over the other represented by PlaP in modulation of putrescine-dependent biological functions. Furthermore, we provided evidence that putrescine signal is critical for D. zeae EC1 bacterial invasion and virulence against rice seeds. Our data depict a novel function of putrescine signal in pathogen-host communication and in modulation of the virulence of an important plant bacterial pathogen.
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Affiliation(s)
- Zurong Shi
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,College of Agriculture and Biology, Zhongkai University of Agricluture and Engineering, Guangzhou, China
| | - Qingwei Wang
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yasheng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zhibing Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Zining Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China.,Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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In Vitro Formation of Dickeya zeae MS1 Biofilm. Curr Microbiol 2018; 76:100-107. [PMID: 30390102 DOI: 10.1007/s00284-018-1593-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
Abstract
Bacterial soft rot caused by Dickeya zeae MS1 (Erwinia chrysanthemi) is one of the most devastating banana diseases worldwide. However, knowledge of the development and ecological interactions of D. zeae MS1 biofilm is limited. Here, we visualized the development and architecture of D. zeae MS1 biofilm using confocal laser scanning microscopy, and we evaluated the ability of D. zeae MS1 to form biofilms under different environmental conditions (carbon sources, temperatures, pH levels and mineral elements) using a microtiter plate assay. We found that the development of D. zeae MS1 biofilm could be categorized into four phases and that mature biofilm consisted of a highly organized architecture of both bacterial cells and a self-produced matrix of extracellular polysaccharides. Furthermore, sucrose was the most suitable carbon source for supporting the growth of biofilm cells and that 32 °C and pH 7.0 were the most favorable of the temperatures and pH levels examined. Meanwhile, the addition of Ca2+, Fe2+, K+ and Na+ enhanced the formation of biofilm in minimal medium cultures, whereas 2.5 mM Cu2+ and Mn2+ was inhibitory. A better understanding of biofilm formation under different environmental parameters will improve our knowledge of the growth kinetics of D. zeae MS1 biofilm.
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Hu M, Li J, Chen R, Li W, Feng L, Shi L, Xue Y, Feng X, Zhang L, Zhou J. Dickeya zeae strains isolated from rice, banana and clivia rot plants show great virulence differentials. BMC Microbiol 2018; 18:136. [PMID: 30336787 PMCID: PMC6194671 DOI: 10.1186/s12866-018-1300-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/01/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Dickeya zeae is the causal agent of maize and rice foot rot diseases, but recently it was also found to infect banana and cause severe losses in China. Strains from different sources showed significant diversity in nature, implying complicated evolution history and pathogenic mechanisms. RESULTS D. zeae strains were isolated from soft rot banana plants and ornamental monocotyledonous Clivia miniata. Compared with D. zeae strain EC1 isolated from rice, clivia isolates did not show any antimicrobial activity, produced less extracellular enzymes, had a much narrow host ranges, but released higher amount of extracellular polysaccharides (EPS). In contrast, the banana isolates in general produced more extracellular enzymes and EPS than strain EC1. Furthermore, we provided evidence that the banana D. zeae isolate MS2 produces a new antibiotic/phytotoxin(s), which differs from the zeamine toxins produced by rice pathogen D. zeae strain EC1 genetically and in its antimicrobial potency. CONCLUSIONS The findings from this study expanded the natural host range of D. zeae and highlighted the genetic and phenotypic divergence of D. zeae strains. Conclusions can be drawn from a series of tests that at least two types of D. zeae strains could cause the soft rot disease of banana, with one producing antimicrobial compound while the other producing none, and the D. zeae clivia strains could only infect monocot hosts. D. zeae strains isolated from different sources have diverse virulence characteristics.
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Affiliation(s)
- Ming Hu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Jieling Li
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Ruiting Chen
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Wenjun Li
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Luwen Feng
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Lei Shi
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Yang Xue
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Xiaoyin Feng
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Lianhui Zhang
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
| | - Jianuan Zhou
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642 China
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Zhou J, Zhang H, Lv M, Chen Y, Liao L, Cheng Y, Liu S, Chen S, He F, Cui Z, Jiang Z, Chang C, Zhang L. SlyA regulates phytotoxin production and virulence in Dickeya zeae EC1. MOLECULAR PLANT PATHOLOGY 2016; 17:1398-1408. [PMID: 26814706 PMCID: PMC6638372 DOI: 10.1111/mpp.12376] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/23/2016] [Accepted: 01/24/2016] [Indexed: 06/05/2023]
Abstract
Dickeya zeae is a causal agent of rice root rot disease. The pathogen is known to produce a range of virulence factors, including phytotoxic zeamines and extracellular enzymes, but the mechanisms of virulence regulation remain vague. In this study, we identified a SlyA/MarR family transcription factor SlyA in D. zeae strain EC1. Disruption of slyA significantly decreased zeamine production, enhanced swimming and swarming motility, reduced biofilm formation and significantly decreased pathogenicity on rice. Quantitative polymerase chain reaction (qPCR) analysis confirmed the role of SlyA in transcriptional modulation of a range of genes associated with bacterial virulence. In trans expression of slyA in expI mutants recovered the phenotypes of motility and biofilm formation, suggesting that SlyA is downstream of the acylhomoserine lactone-mediated quorum sensing pathway. Taken together, the findings from this study unveil a key transcriptional regulatory factor involved in the modulation of virulence factor production and overall pathogenicity of D. zeae EC1.
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Affiliation(s)
- Jia‐Nuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Hai‐Bao Zhang
- Institute of Molecular and Cell Biology 61 Biopolis DriveSingapore138673
| | - Ming‐Fa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Yu‐Fan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Li‐Sheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Ying‐Ying Cheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Shi‐Yin Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Shao‐Hua Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Fei He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Zi‐Ning Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Zi‐De Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Chang‐Qing Chang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
| | - Lian‐Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant PathologySouth China Agricultural UniversityGuangzhou510642China
- Institute of Molecular and Cell Biology 61 Biopolis DriveSingapore138673
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Zhou J, Cheng Y, Lv M, Liao L, Chen Y, Gu Y, Liu S, Jiang Z, Xiong Y, Zhang L. The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species. BMC Genomics 2015; 16:571. [PMID: 26239726 PMCID: PMC4522980 DOI: 10.1186/s12864-015-1545-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/17/2015] [Indexed: 12/26/2022] Open
Abstract
Background Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular mechanisms of host specificity and pathogenesis are hardly known. Results The complete genome of D. zeae strain EC1 isolated from diseased rice plants was sequenced, annotated, and compared with the genomes of other Dickeya spp.. The pathogen contains a chromosome of 4,532,364 bp with 4,154 predicted protein-coding genes. Comparative genomics analysis indicates that D. zeae EC1 is most co-linear with D. chrysanthemi Ech1591, most conserved with D. zeae Ech586 and least similar to D. paradisiaca Ech703. Substantial genomic rearrangement was revealed by comparing EC1 with Ech586 and Ech703. Most virulence genes were well-conserved in Dickeya strains except Ech703. Significantly, the zms gene cluster involved in biosynthesis of zeamines, which were shown previously as key virulence determinants, is present in D. zeae strains isolated from rice, and some D. solani strains, but absent in other Dickeya species and the D. zeae strains isolated from other plants or sources. In addition, a DNA fragment containing 9 genes associated with fatty acid biosynthesis was found inserted in the fli gene cluster encoding flagellar biosynthesis of strain EC1 and other two rice isolates but not in other strains. This gene cluster shares a high protein similarity to the fatty acid genes from Pantoea ananatis. Conlusion Our findings delineate the genetic background of D. zeae EC1, which infects both dicotyledons and monocotyledons, and suggest that D. zeae strains isolated from rice could be grouped into a distinct pathovar, i.e., D. zeae subsp. oryzae. In addition, the results of this study also unveiled that the zms gene cluster presented in the genomes of D. zeae rice isolates and D. solani strains, and the fatty acid genes inserted in the fli gene cluster of strain EC1 were likely derived from horizontal gene transfer during later stage of bacterial evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1545-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yingying Cheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Mingfa Lv
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Lisheng Liao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yufan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yanfang Gu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Shiyin Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Zide Jiang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Yuanyan Xiong
- State Key laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore.
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