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Genes and Genomes of Plant Pathogenic Bacteria
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Genes and Genomes of Plant Pathogenic Bacteria

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (31 August 2011) | Viewed by 112613

Special Issue Editors

Dr. Gail M. Preston

E-Mail Website
Guest Editor
Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
Interests: molecular plant-microbe interactions
Dr. Magdalen Lindeberg

E-Mail Website
Guest Editor
Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
Interests: microbial genomics ; pseudomonas syringe ; gene ontology
Dr. Robert W. Jackson

E-Mail Website
Guest Editor
School of Biological Sciences, University of Reading, READING, Berkshire RG6 6AH, UK
Interests: microbiology; plant pathology; bacterial pathogenesis
Dr. Dawn Arnold

E-Mail Website
Guest Editor
Centre for Research in Plant Science, University of The West of England, Frenchay Campus, Bristol BS16 1QY, UK
Interests: molecular plant pathology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacterial plant pathogens are a diverse group of organisms that infect a wide range of host plants and cause a variety of economically important diseases. Pioneering studies of pathogenicity mechanisms have led to certain bacterial plant pathogens, such as Pseudomonas syringae, being
recognised as major models for unravelling the genetics of pathogen-host interactions. Others, such as Agrobacterium tumefaciens, have important applications in genetic engineering and biotechnology. Many plant pathogenic bacteria share common features with animal pathogenic bacteria, such as the ability to use protein secretion systems to deliver effector proteins into plant cells. However, they have distinctive metabolic and biosynthetic pathways that allow them to assimilate plant metabolites and to produce hormones and toxins that modulate plant physiology and development.

Our understanding of the pathogenicity mechanisms used by bacterial plant pathogens has been greatly enhanced by the availability of complete genome sequences, which have begun to be coupled with draft genome sequence data and transcriptomic data generated by next generation sequencing. With such a depth of genetic data available, the genes and genomes of plant pathogenic bacteria are key resources that have a major impact in understanding the biology and evolution of plant pathogenesis. This issue will highlight the diversity and impact of research in this area by bringing together cutting edge research papers and review articles from leading phytobacteriologists.

Dr. Gail M. Preston
Dr. Magdalen Lindeberg
Dr. Robert W. Jackson
Dr. Dawn Arnold
Guest Editors

Keywords

  • effector
  • type III secretion
  • type VI secretion
  • regulatory network
  • next generation sequencing
  • comparative genomics
  • toxin
  • extracellular polysaccharides (EPS)
  • cell wall degrading enzymes (CWDE)
  • quorum sensing

Published Papers (12 papers)

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Research

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854 KiB  
Article
Genomic Distribution and Divergence of Levansucrase-Coding Genes in Pseudomonas syringae
by Abhishek Srivastava, Nehaya Al-Karablieh, Shaunak Khandekar, Arifa Sharmin, Helge Weingart and Matthias S. Ullrich
Genes 2012, 3(1), 115-137; https://doi.org/10.3390/genes3010115 - 10 Feb 2012
Cited by 12 | Viewed by 8659
Abstract
In the plant pathogenic bacterium, Pseudomonas syringae, the exopolysaccharide levan is synthesized by extracellular levansucrase (Lsc), which is encoded by two conserved 1,296-bp genes termed lscB and lscC in P. syringae strain PG4180. A third gene, lscA, is homologous to the [...] Read more.
In the plant pathogenic bacterium, Pseudomonas syringae, the exopolysaccharide levan is synthesized by extracellular levansucrase (Lsc), which is encoded by two conserved 1,296-bp genes termed lscB and lscC in P. syringae strain PG4180. A third gene, lscA, is homologous to the 1,248-bp lsc gene of the bacterium Erwinia amylovora, causing fire blight. However, lscA is not expressed in P. syringae strain PG4180. Herein, PG4180 lscA was shown to be expressed from its native promoter in the Lsc-deficient E. amylovora mutant, Ea7/74-LS6, suggesting that lscA might be closely related to the E. amylovora lsc gene. Nucleotide sequence analysis revealed that lscB and lscC homologs in several P. syringae strains are part of a highly conserved 1.8-kb region containing the ORF, flanked by 450-452-bp and 49-51-bp up- and downstream sequences, respectively. Interestingly, the 450-452-bp upstream sequence, along with the initial 48-bp ORF sequence encoding for the N-terminal 16 amino acid residues of Lsc, were found to be highly similar to the respective sequence of a putatively prophage-borne glycosyl hydrolase-encoding gene in several P. syringae genomes. Minimal promoter regions of lscB and lscC were mapped in PG4180 by deletion analysis and were found to be located in similar positions upstream of lsc genes in three P. syringae genomes. Thus, a putative 498-500-bp promoter element was identified, which possesses the prophage-associated com gene and DNA encoding common N-terminal sequences of all 1,296-bp Lsc and two glycosyl hydrolases. Since the gene product of the non-expressed 1,248-bp lscA is lacking this conserved N-terminal region but is otherwise highly homologous to those of lscB and lscC, it was concluded that lscA might have been the ancestral lsc gene in E. amylovora and P. syringae. Our data indicated that its highly expressed paralogs in P. syringae are probably derived from subsequent recombination events initiated by insertion of the 498-500-bp promoter element, described herein, containing a translational start site. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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469 KiB  
Article
Implication of an Aldehyde Dehydrogenase Gene and a Phosphinothricin N-Acetyltransferase Gene in the Diversity of Pseudomonas cichorii Virulence
by Masayuki Tanaka, Ullah Md Wali, Hitoshi Nakayashiki, Tatsuya Fukuda, Hiroyuki Mizumoto, Kouhei Ohnishi, Akinori Kiba and Yasufumi Hikichi
Genes 2012, 3(1), 62-80; https://doi.org/10.3390/genes3010062 - 27 Dec 2011
Cited by 7 | Viewed by 8194
Abstract
Pseudomonas cichorii harbors the hrp genes. hrp-mutants lose their virulence on eggplant but not on lettuce. A phosphinothricin N-acetyltransferase gene (pat) is located between hrpL and an aldehyde dehydrogenase gene (aldH) in the genome of P. cichorii [...] Read more.
Pseudomonas cichorii harbors the hrp genes. hrp-mutants lose their virulence on eggplant but not on lettuce. A phosphinothricin N-acetyltransferase gene (pat) is located between hrpL and an aldehyde dehydrogenase gene (aldH) in the genome of P. cichorii. Comparison of nucleotide sequences and composition of the genes among pseudomonads suggests a common ancestor of hrp and pat between P. cichorii strains and P. viridiflava strains harboring the single hrp pathogenicity island. In contrast, phylogenetic diversification of aldH corresponded to species diversification amongst pseudomonads. In this study, the involvement of aldH and pat in P. cichorii virulence was analyzed. An aldH-deleted mutant (ΔaldH) and a pat-deleted mutant (Δpat) lost their virulence on eggplant but not on lettuce. P. cichorii expressed both genes in eggplant leaves, independent of HrpL, the transcriptional activator for the hrp. Inoculation into Asteraceae species susceptible to P. cichorii showed that the involvement of hrp, pat and aldH in P. cichorii virulence is independent of each other and has no relationship with the phylogeny of Asteraceae species based on the nucleotide sequences of ndhF and rbcL. It is thus thought that not only the hrp genes but also pat and aldH are implicated in the diversity of P. cichorii virulence on susceptible host plant species. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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1424 KiB  
Communication
Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade
by David J. Studholme, Arthur Wasukira, Konrad Paszkiewicz, Valente Aritua, Richard Thwaites, Julian Smith and Murray Grant
Genes 2011, 2(4), 1050-1065; https://doi.org/10.3390/genes2041050 - 02 Dec 2011
Cited by 43 | Viewed by 10490 | Correction
Abstract
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as [...] Read more.
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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927 KiB  
Article
Type Three Secretion System in Pseudomonas savastanoi Pathovars: Does Timing Matter?
by Stefania Tegli, Andrea Gori, Matteo Cerboneschi, Maria Grazia Cipriani and Angelo Sisto
Genes 2011, 2(4), 957-979; https://doi.org/10.3390/genes2040957 - 25 Nov 2011
Cited by 18 | Viewed by 8295
Abstract
Pseudomonas savastanoi pv. savastanoi is the causal agent of Olive knot disease, relying on the Type Three Secretion System (TTSS) for its pathogenicity. In this regard, nothing was known about the two other pathovars belonging to this species, pv. nerii and pv. fraxini [...] Read more.
Pseudomonas savastanoi pv. savastanoi is the causal agent of Olive knot disease, relying on the Type Three Secretion System (TTSS) for its pathogenicity. In this regard, nothing was known about the two other pathovars belonging to this species, pv. nerii and pv. fraxini, characterized by a different host range. Here we report on the organization of the entire TTSS cluster on the three pathovars, and a phylogenetic analysis including the TTSS of those bacteria belonging to the P. syringae complex sequenced so far, highlighting the evolution of each operon (hrpC, hrpJ, hrpRS, hrpU and hrpZ). Moreover, by Real-Time PCR we analyzed the in vitro expression of four main TTSS genes, revealing different activation patterns in the three pathovars, hypothetically related to their diverse virulence behaviors. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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1476 KiB  
Article
Identification of Genes Involved in the Glycosylation of Modified Viosamine of Flagellins in Pseudomonas syringae by Mass Spectrometry
by Masanobu Yamamoto, Mayumi Ohnishi-Kameyama, Chi L. Nguyen, Fumiko Taguchi, Kazuhiro Chiku, Tadashi Ishii, Hiroshi Ono, Mitsuru Yoshida and Yuki Ichinose
Genes 2011, 2(4), 788-803; https://doi.org/10.3390/genes2040788 - 28 Oct 2011
Cited by 24 | Viewed by 7098
Abstract
Previously we revealed that flagellin proteins in Pseudomonas syringae pv. tabaci 6605 (Pta 6605) were glycosylated with a trisaccharide, modified viosamine (mVio)-rhamnose-rhamnose and that glycosylation was required for virulence. We further identified some glycosylation-related genes, including vioA, vioB, vioT, fgt1 [...] Read more.
Previously we revealed that flagellin proteins in Pseudomonas syringae pv. tabaci 6605 (Pta 6605) were glycosylated with a trisaccharide, modified viosamine (mVio)-rhamnose-rhamnose and that glycosylation was required for virulence. We further identified some glycosylation-related genes, including vioA, vioB, vioT, fgt1, and fgt2. In this study, we newly identified vioR and vioM in a so-called viosamine island as biosynthetic genes for glycosylation of mVio in Pta 6605 by the mass spectrometry (MS) of flagellin glycan in the respective mutants. Furthermore, characterization of the mVio-related genes and MS analyses of flagellin glycans in other pathovars of P. syringae revealed that mVio-related genes were essential for mVio biosynthesis in flagellin glycans, and that P. syringae pv. syringae B728a, which does not possess a viosamine island, has a different structure of glycan in its flagellin protein. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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Review

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240 KiB  
Review
Insights into Cross-Kingdom Plant Pathogenic Bacteria
by Morgan W.B. Kirzinger, Geetanchaly Nadarasah and John Stavrinides
Genes 2011, 2(4), 980-997; https://doi.org/10.3390/genes2040980 - 28 Nov 2011
Cited by 36 | Viewed by 10769
Abstract
Plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. Phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology [...] Read more.
Plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. Phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology and overcoming highly developed adaptive immune responses. Emerging research, however, has highlighted the ability of seemingly dedicated human pathogens to cause plant disease, and specialized plant pathogens to cause human disease. Such microbes represent interesting systems for studying the evolution of cross-kingdom pathogenicity, and the benefits and tradeoffs of exploiting multiple hosts with drastically different morphologies and physiologies. This review will explore cross-kingdom pathogenicity, where plants and humans are common hosts. We illustrate that while cross-kingdom pathogenicity appears to be maintained, the directionality of host association (plant to human, or human to plant) is difficult to determine. Cross-kingdom human pathogens, and their potential plant reservoirs, have important implications for the emergence of infectious diseases. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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457 KiB  
Review
Information Management of Genome Enabled Data Streams for Pseudomonas syringae on the Pseudomonas-Plant Interaction (PPI) Website
by Magdalen Lindeberg
Genes 2011, 2(4), 841-852; https://doi.org/10.3390/genes2040841 - 02 Nov 2011
Cited by 1 | Viewed by 6860
Abstract
Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include [...] Read more.
Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization. To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively. The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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877 KiB  
Review
Involvement of Type IV Pili in Pathogenicity of Plant Pathogenic Bacteria
by Saul Burdman, Ofir Bahar, Jennifer K. Parker and Leonardo De La Fuente
Genes 2011, 2(4), 706-735; https://doi.org/10.3390/genes2040706 - 18 Oct 2011
Cited by 51 | Viewed by 17364
Abstract
Type IV pili (T4P) are hair-like appendages found on the surface of a wide range of bacteria belonging to the β-, γ-, and δ-Proteobacteria, Cyanobacteria and Firmicutes. They constitute an efficient device for a particular type of bacterial surface motility, named twitching, and [...] Read more.
Type IV pili (T4P) are hair-like appendages found on the surface of a wide range of bacteria belonging to the β-, γ-, and δ-Proteobacteria, Cyanobacteria and Firmicutes. They constitute an efficient device for a particular type of bacterial surface motility, named twitching, and are involved in several other bacterial activities and functions, including surface adherence, colonization, biofilm formation, genetic material uptake and virulence. Tens of genes are involved in T4P synthesis and regulation, with the majority of them being generally named pil/fim genes. Despite the multiple functionality of T4P and their well-established role in pathogenicity of animal pathogenic bacteria, relatively little attention has been given to the role of T4P in plant pathogenic bacteria. Only in recent years studies have begun to examine with more attention the relevance of these surface appendages for virulence of plant bacterial pathogens. The aim of this review is to summarize the current knowledge about T4P genetic machinery and its role in the interactions between phytopathogenic bacteria and their plant hosts. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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265 KiB  
Review
RNA-Seq for Plant Pathogenic Bacteria
by Jeffrey A. Kimbrel, Yanming Di, Jason S. Cumbie and Jeff H. Chang
Genes 2011, 2(4), 689-705; https://doi.org/10.3390/genes2040689 - 13 Oct 2011
Cited by 9 | Viewed by 11006
Abstract
The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but [...] Read more.
The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknowns that need to be considered. Here, we review some new developments for RNA-Seq and highlight recent findings for host-associated bacteria. We also discuss the technical and statistical challenges in the practical application of RNA-Seq for studying bacterial transcriptomes and describe some of the currently available solutions. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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408 KiB  
Review
Genes Involved in the Production of Antimetabolite Toxins by Pseudomonas syringae Pathovars
by Eva Arrebola, Francisco M Cazorla, Alejandro Pérez-García and Antonio de Vicente
Genes 2011, 2(3), 640-660; https://doi.org/10.3390/genes2030640 - 15 Sep 2011
Cited by 13 | Viewed by 8108
Abstract
Pseudomonas syringae is pathogenic in a wide variety of plants, causing diseases with economic impacts. Pseudomonas syringae pathovars produce several toxins that can function as virulence factors and contribute to disease symptoms. These virulence factors include antimetabolite toxins, such as tabtoxin, phaseolotoxin and [...] Read more.
Pseudomonas syringae is pathogenic in a wide variety of plants, causing diseases with economic impacts. Pseudomonas syringae pathovars produce several toxins that can function as virulence factors and contribute to disease symptoms. These virulence factors include antimetabolite toxins, such as tabtoxin, phaseolotoxin and mangotoxin, which target enzymes in the pathways of amino acid metabolism. The antimetabolite toxins are generally located in gene clusters present in the flexible genomes of specific strains. These gene clusters are typically present in blocks of genes that appear to be integrated into specific sites in the P. syringae core genome. A general overview of the genetic organization and biosynthetic and regulatory functions of these genetic traits of the antimetabolite toxins will be given in the present work. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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177 KiB  
Review
Comparative Genomics of Erwinia amylovora and Related Erwinia Species—What do We Learn?
by Youfu Zhao and Mingsheng Qi
Genes 2011, 2(3), 627-639; https://doi.org/10.3390/genes2030627 - 15 Sep 2011
Cited by 35 | Viewed by 8231
Abstract
Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia [...] Read more.
Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia, including E. amylovora, E. pyrifoliae, E. tasmaniensis, and E. billingiae, have provided us near complete genetic information about this pathogen and its closely-related species. This review describes in silico subtractive hybridization-based comparative genomic analyses of eight genomes currently available, and highlights what we have learned from these comparative analyses, as well as genetic and functional genomic studies. Sequence analyses reinforce the assumption that E. amylovora is a relatively homogeneous species and support the current classification scheme of E. amylovora and its related species. The potential evolutionary origin of these Erwinia species is also proposed. The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized. Future research directions are also suggested. Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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Other

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145 KiB  
Correction
Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050–1065.
by David J Studholme, Arthur Wasukira, Konrad Paszkiewicz, Valente Aritua, Richard Thwaites, Julian Smith and Murray Grant
Genes 2012, 3(1), 88-89; https://doi.org/10.3390/genes3010088 - 11 Jan 2012
Cited by 4 | Viewed by 6038
Abstract
Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported [...] Read more.
Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the Group 1 Xanthomonas species are unaffected. However, we wish to apologize to the authors of a previous work [2] for creating any negative impression on the quality of their phylogenetic analyses and to take this opportunity to rectify the errors. [...] Full article
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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