Plant Pathogenic Bacteria: Genomics and Molecular Biology | Book
Caister Academic Press
Robert W. Jackson
School of Biological Sciences, University of Reading, Whiteknights, Reading, UK
xii + 330
GB £219 or US $319Buy book
Bacteria pathogenic for plants are responsible for devastating losses in agriculture. The use of antibiotics to control such infections is restricted in many countries due to worries over the evolution and transmission of antibiotic resistance. The advent of genome sequencing has enabled a better understanding, at the molecular level, of the strategies and mechanisms of pathogenesis, evolution of resistance to plant defence mechanisms, and the conversion of non-pathogenic into pathogenic bacteria.
In this book, internationally acclaimed experts review the most important developments providing an invaluable, up-to-date summary of the molecular biology and genomics of plant pathogenic bacteria. The book opens with two chapters on bacterial evolution, diversity and taxonomy, topics that have been transformed by molecular biology and genomics analyses. The third chapter delves into the crucially understudied area of pathogen adaptation to the plant apoplast environment. The following seven chapters focus on specific plant pathogens: Agrobacterium, Leifsonia, Pectobacterium, Pseudomonas, Ralstonia, Xanthomonas, and Xylella. The next four chapters review specific, intensively studied areas of research in the plant pathogen field: microbe associated molecular patterns (MAMPs) and innate immunity; use of bacterial virulence factors to suppress plant defence; cyclic di-GMP signalling and the regulation of virulence; and plasmids and the spread of virulence. The final chapter covers the critical area of bioinformatics.
With contributions from some of the pioneering bacterial plant pathogen genome sequencers, this book is essential reading for every plant pathogen researcher, from the PhD student to the experienced scientist, as it provides a timely review of the current and most topical areas of research.
"... comprehensive in coverage ... This book is a timely addition to the literature in a rapidly expanding field which provides ample evidence of hypothesis testing on a broad front." from ISPP Newsletter - International Society for Plant Pathology (2008)
"a timely book that is a good reference text appropriate for institutional libraries and, particularly, for researchers working on the molecular biology of bacterial phytopathogens. It is an expert and readable collection of chapters on cutting edge issues ... The book would be an excellent starting point for non-expert readers looking for a fast track route into molecular aspects of bacterial plant pathogens." from Microbiology Today (2009)
"a through up-to-date reviewof the field of the genetics and genomics of plant pathogenic bacteria. The book is a most valuable starting point for researchers new to bacterial plant pathogens, for established researchers to the professor, to get an up to date reviewof the state of art of the field. Themany comparative aspects to human and animal pathogenic bacteria, elaborated on,make the book valuable none the least to the food hygienist or microbiologist." from Int. J. Food. Microbiol. (2009) 128: 521.
Table of contents
1 . Origin and Evolution of Phytopathogenic Bacteria
Plant pathogenic bacteria impact innumerable and valuable agricultural crops, causing hundreds of millions of dollars in damage each year. Understanding their evolution is paramount to establishing and effecting practical disease management strategies to reduce or prevent their reproduction and spread. This chapter provides an overview of the evolution of plant pathogens, considering their phylogenetic distribution, and the genetic and evolutionary factors that have contributed to their emergence. The importance of secretion systems as pathogenicity determinants is considered, with examples from a diverse array of characterized plant pathogens. Also addressed are the evolutionary constraints experienced by generalist and specialist pathogens, the ecological factors that determine their relative success, and the coevolutionary arms race that develops between specialist pathogens and their hosts. Finally, several case studies of recurrently emerging pathogens are presented, which not only illustrate the incredible evolutionary potential of phytopathogenic bacteria, but also the major contributions of anthropogenic factors to emerging infectious diseases.
2 . The Impact of Genomic Approaches on Our Understanding of Diversity and Taxonomy of Plant Pathogenic Bacteria
Boris A. Vinatzer and Carolee T. Bull
Our understanding of the diversity of bacterial plant pathogens has changed dramatically over the past 100 years. Initially, it was thought that each newly described disease was caused by a distinct bacterial species. Later, similarities in the physiology and codification of nomenclature resulted in the consolidation of taxa regardless of demonstrated diversity and host range. We have now entered an era in which genomic approaches can reveal genetic diversity in much finer detail. This has resulted in the development of phylogenetic trees, which identify theoretical evolutionary groupings at ranks below the level of the currently described bacterial species. There are cases in which these groupings coincide with previously defined pathovars or genomospecies while in other cases these groups represent biologically or ecologically relevant groups that still need to be defined taxonomically. In this chapter we give an overview of the history of systematics and of bacterial species concepts, describe current genomics approaches to uncover diversity, and finally discuss the potential consequences of the already uncovered genomic diversity on the taxonomy of plant pathogenic bacteria.
3 . Adaptation to the Plant Apoplast by Plant Pathogenic Bacteria
Arantza Rico, Rachel Jones, and Gail M. Preston
Many plant pathogenic bacteria spend most of their parasitic life in the apoplast, which is the intercellular space of the plants. The apoplast is a nutrient-limited environment that is guarded by plant defences, so plant pathogenic bacteria have evolved several strategies to succesfully colonize this niche, which include the type III secretion system and its effectors, toxins and cell wall degrading enzymes, among others. Genomic and nutritional assays suggest that some apoplast-colonising pathogens show nutritional specialization to the plant host and it is possible that some of the keys to apoplast colonisation reside in bacterial adaptation to, and modulation of the nutritional and physiological characteristics of the plant apoplast. In this chapter, we offer a review of bacterial strategies for the adaptation to the apoplast in plant pathogenic bacteria, and of the evolutionary processes that may have affected the evolution of these strategies. We also discuss evidence for the hypothesis that successful pathogens modulate plant metabolism for their benefit. Finally we propose strategies and avenues for research that will promote further understanding of the complex picture of apoplast physiology during disease development.
4 . The Genomics of Agrobacterium: Insights into its Pathogenicity, Biocontrol, and Evolution
Joao C. Setubal, Derek Wood, Thomas Burr, Stephen K. Farrand, Barry S. Goldman, Brad Goodner, Leon Otten, and Steven Slater
The genus Agrobacterium belongs to the Rhizobiaceae family of α-Proteobacteria and includes widely found plant pathogens that cause the crown gall and hairy root diseases. A. tumefaciens is also well-known as a natural biotechnological tool thanks to its ability to transfer part of its DNA into plant cells. In this chapter we review current genomic knowledge about three species in this genus: A. tumefaciens C58, A. vitis S4, and A. radiobacter K84, focusing on the genomic basis for virulence determinants, and symbiotic interactions. These organisms have a relatively complex genome architecture, with each genome containing several replicons, and this provides an interesting view into bacterial evolution. In the second half of the chapter we describe this architecture as well as the syntenic relationships between these three species and closely related Rhizobium genomes. An analysis of the secondary large replicons and the smaller plasmids concludes the chapter.
5 . Common Genes and Genomic Breaks: A Detailed Case Study of the Xylella fastidiosa Genome Backbone and Evolutionary Insights
Alessandro M. Varani, Wanessa C. Lima, Leandro M. Moreira, Mariana C. de Oliveira, Rangel de Souza, Edwin Civerolo, Ana Tereza R. de Vasconcelos and Marie-Anne Van Sluys
It has been more than seven years since the first genome sequence of a plant pathogen, Xylella fastidiosa strain 9a5c, was published. At present, more than 10 genomes of the γ-Proteobacteria Xanthomonadales group are available for comparative genomics, and several studies related to functional genomics have been conducted, resulting in insights about the evolution, virulence and pathogenicity of this group of plant pathogens. The subject of this review is to explore the history of the chromosome backbone evolution and differentiation among four X. fastidiosa strains, and address the question of how and when those organisms became pathogenically competent. To address this question, three main lines of discussion are developed: (a) correlation of the bacterial life style with their genes involved in virulence and pathogenicity; (b) definition of the minimal core genome using a comparative approach; and (c) looking at the disruptions and rearrangements caused by mobile genetic elements. The discussion raised here allowed us to assess the differential evolutionary profiles inside the Xanthomonadales.
6 . Genome Sequence-based Insights into the Biology of the Sugarcane Pathogen Leifsonia xyli subsp. xyli
Claudia B. Monteiro-Vitorello, Marcelo Marques Zerillo, Marie-Anne Van Sluys, and Luis Eduardo Aranha Camargo
Leifsonia xyli subsp. xyli (Lxx) causes ratoon stunting disease (RSD), a major worldwide disease of sugarcane. Formerly classified as Clavibacter xyli subsp. xyli, Lxx is a fastidious member of the GC-rich Actinomycetales., a taxonomic order that comprises two other genera of plant pathogens of great agricultural impact. In this review we present some interesting features of the genome of Lxx with emphasis on pathogenicity. Most striking is the observation that Lxx has a relatively large number of pseudogenes suggestive of an ongoing process of genome decay. It has been proposed that Lxx was once a free-living bacterium that is now restricted to the xylem as a consequence or cause of the accumulation of pseudogenes. This point stems from the observation that although Lxx has only been detected inhabiting the xylem of sugar cane, it carries several genes typical of free-living organism. In this review we also discuss the relevance of lateral gene transfer in the acquisition of a few genes associated with pathogenicity and the contribution of mobile genetic elements.
7 . Genomics-driven Advances in Xanthomonas Biology
Damien F. Meyer and Adam J. Bogdanove
The genus Xanthomonas consists of 20 plant-associated species, many of which cause important diseases of crops and ornamentals. Individual species comprise multiple pathovars, characterized by distinctive host specificity or mode of infection. Genomics is at the center of a revolution in Xanthomonas biology. Complete genome sequences are available for nine Xanthomonas strains, representing three species and five pathovars, including vascular and non-vascular pathogens of the important models for plant biology, Arabidopsis thaliana and rice. With the diversity of complete and pending Xanthomonas genome sequences, the genus has become a superb model for understanding functional, regulatory, epidemiological, and evolutionary aspects of host- and tissue-specific plant pathogenesis. In this chapter, we review structural, functional, and comparative genomics studies that are driving rapid advances in our understanding of this important group of bacteria.
8 . Genomics of the Enterobacterial Plant Pathogens
Ian Toth, Leighton Pritchard, Paul Birch and Hui Liu
The enterobacterial plant pathogens are an important group of bacteria responsible for disease on a wide range of plant species in geographically diverse regions. The enterobacterial plant pathogens entered the postgenomics age in 2004, with the completion of the Pectobacterium atrosepticum SCRI1043 genome sequence. Since then, other enterobacterial plant pathogens have been sequenced, and an array of computational and functional genomics tools have been developed in conjunction with these sequences. Genomic analyses are helping to identify many shared pathogenicity and lifestyle mechanisms among plant (and animal) pathogens, helping to forge new collaborations between scientists working on different pathosystems. These analyses are also uncovering pathogen-specific features, often acquired through horizontal gene transfer, which offer new insights into how individual pathogens infect particular hosts, their modes of pathogenesis or their life in the wider environment. This chapter describes current progress in genomic and post-genomic research on enterobacterial plant pathogens, together with some of the most recent findings.
9 . Ralstonia solanacearum and Bacterial Wilt in the Postgenomics Era
The first Ralstonia solanacearum GMI1000 genome sequence was completed in 2002. This work paved the way for an enhanced understanding of the molecular genetics of this important plant pathogen. The availability of a fully annotated genome sequence made it possible to further our understanding of gene expression in planta and led to the discovery of important nuances in virulence gene regulatory cascades. Moreover, analysis of the more recently sequenced Race 3 biovar 2 strain, UW551, made comparative genomics possible. Other recent advances stemming from the genomic profile of R. solanacearum has led to an appreciation of this pathogen as a species complex, with a rich evolutionary history as well as the discovery and molecular dissection of a lysogenic bacteriophage that contributed to virulence on tobacco. Now that the genome is available, progress towards a more comprehensive study of the life cycle of this successful soil inhabitant and deadly plant pathogen can be made.
10 . Pseudomonas syringae Genomics Provides Important Insights to Secretion Systems, Effector Genes and the Evolution of Virulence
D.L. Arnold, S.A.C. Godfrey and R. W. Jackson
The start of the 21st Century was a watershed for Pseudomonas syringae genomics, with the completion of three genome sequences for different P. syringae pathovars. The release of these sequences permitted a series of investigations designed at unraveling the biology of this group of plant pathogens. One area that has benefited has been the identification of different secretion systems and their substrate effectors; some of these secretion systems can deliver proteins into the plant environment to subvert the plants' resistance machinery and to gain access to plant nutrients. The most investigated secretion system in P. syringae is the type III system which delivers effector proteins into the plant cytoplasm to disrupt the plantsŐ cellular pathways, including signaling mechanisms that would otherwise trigger defence mechanisms. The genome sequences have been analysed to predict the number of effector genes present in the different strains, gain insights into the function of these proteins and examine how the bacteria can evolve and change its effector repertoire in order to overcome plant resistance. There is still much scope for further analysis, particularly of poorly understood secretion systems. For example, very little is known about the role of non-type III secretion systems in P. syringae. Indeed, the genome sequences have allowed us to identify putative orthologues of the vas-vgr type VI system in P. syringae and intriguingly there appears to be some variation in gene content and synteny between the pathovars.
11 . MAMPs/PAMPs - Elicitors of Innate Immunity in Plants
Gitte Erbs and Mari-Anne Newman
Plants perceive several general elicitors from both host and non-host pathogens. These elicitors are essential structures for pathogen survival and are for that reason conserved among pathogens. These conserved microbe-specific molecules, also referred to as Microbe or Pathogen Associated Molecular Patterns (MAMPs or PAMPs), are recognised by the plant innate immune systems Pattern Recognition Receptors (PRRs). General bacterial elicitors, like lipopolysaccharides (LPS), flagellin (Flg), elongation factor Tu (EF-Tu), cold shock protein (CSP), peptidoglycan (PGN) and the enzyme superoxide dismutase (SodM) are known to act as MAMPs and induce immune responses in plants or plant cells (G—mez-G—mez and Boller, 2000; Erbs and Newman, 2003; Felix and Boller, 2003; Kunze et al., 2004; Watt et al., 2006, Gust et al., 2007; Erbs et al., unpublished). The corresponding PRRs for some of these bacterial elicitors have, in recent years, been identified. Here, the current knowledge regarding bacterial elicitors of innate immunity in plants is presented.
12 . The Art of Manipulation: Bacterial Type III Effectors and Their Plant Targets
A successful plant pathogen has to accomplish several tasks during infection of a plant host. It has to gain entry into the tissue, acquire nutrients, multiply, and spread to uninfected tissues or neighbouring plants. Pathogens have evolved different virulence factors to accomplish this. Key to this are bacterial effector proteins that are directly translocated into plant cells via a type III protein secretion system. These effectors are potent devices to manipulate the eukaryotic cell from within. Bacterial infections are antagonised by the plant which carries a sophisticated surveillance system to detect invading microbes and respond with defence reactions to prevent pathogen proliferation. The conflicting interests have spawned a complex pathogen-plant interaction network between effectors in pathogenic bacteria and protective plant defence systems. The net outcome is of grave importance for both interaction partners and the evolutionary pressure has led to the development of a large set of effectors in plant pathogenic bacteria which accomplish diverse virulence activities.
13 . Cyclic di-GMP Signalling and the Regulation of Virulence in Bacterial Plant Pathogens
J. Maxwell Dow, Yvonne Fouhy, BelŽn Fernandez Garcia and Robert P. Ryan
Cyclic di-GMP is a novel second messenger that regulates a range of functions including developmental transitions, adhesion, biofilm formation and virulence in diverse bacteria including plant pathogens. Cellular levels of cyclic di-GMP are influenced by both synthesis and degradation. The GGDEF protein domain synthesises cyclic di-GMP, whereas EAL and HD-GYP domains are involved in cyclic di-GMP hydrolysis. The majority of proteins with GGDEF, EAL and HD-GYP domains contain additional signal input domains, suggesting that their activities (and consequently cyclic di-GMP levels) are responsive to environmental cues. Cyclic di-GMP exerts its effects on certain cellular functions by binding to proteins containing a PilZ domain. This domain may occur either as a stand-alone domain, which may act as an "adaptor" to bind other proteins, or as part of a larger protein as is found in the BcsA subunit of cellulose synthase. Some details of the organisation and function of cyclic di-GMP signalling systems have emerged, where both networks of systems regulating the same functions and systems apparently dedicated to specific other tasks occur together in bacterial cells. This has lead to the controversial concept of discrete pools of cyclic di-GMP that are generated and act in a highly localised fashion.
14 . Gene Traders: Characteristics of Native Plasmids from Plant Pathogenic Bacteria
George W. Sundin and Jesús Murillo
The concept of bacterial plasmids as gene traders is illustrative of the role of these elements in horizontal gene transfer, and specifically in the acquisition and distribution of sequences that enable rapid evolution. Plasmids are components of the horizontal gene pool and, as such, their genetic content is potentially accessible by a wide range of organisms. Most plasmids appear to ameliorate any potential negative effect on host fitness by encoding determinants of virulence and ecological fitness that can enhance adaptation to a specific niche or can influence niche expansion. The availability of multiple complete genome sequences of bacterial phytopathogens has shown the importance of horizontally-acquired gene sequences in pathogen evolution. We suspect that plasmids have played a significant role in this gene mobility and also in the delivery of acquired genes to bacterial chromosomes through plasmid integration events. The versatility of plasmids plays a critical role in the evolutionary arms race of bacterial pathogens and plants.
15 . Bioinformatics Aspects of High-Throughput Sequencing Technology
Dan MacLean and David J. Studholme
Recently developed massively high throughput sequencing technologies look set to revolutionise the way that we practise research in microbial and plant sciences, and will necessitate greater investment in data management and analysis than in the past. In this manuscript, we describe some of the informatics issues and solutions that we have come across in the early stages of using these new technologies both for resequencing and de novo
sequencing. As well as issues directly connected with the infrastructure and technology of high throughput sequencing, we present a brief tour of many more traditional sequence analysis tools that will continue to be relevant in the context of larger datasets.
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(EAN: 9781904455370 Subjects: [bacteriology] [microbiology] [molecular microbiology] [genomics] [environmental microbiology] [molecular biology] )