The Role of Prophage in Plant-Pathogenic Bacteria

Varani, Alessandro de Mello; Monteiro-Vitorello, Cláudia Barros; Nakaya, Hidehiko; Sluys, Marie‐Anne Van

doi:10.1146/annurev-phyto-081211-173010

Cited by 62 publications

(74 citation statements)

References 147 publications

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“…X. fastidiosa has the largest ratio of phage genes to genome size (7 to 9%) in a set of 37 phytopathogenic bacterial genomes (65). Various phage species, including Xfas53, were predicted in the sequenced genomes.…”

Section: Discussionmentioning

confidence: 99%

“…multiplex), and Ann-1 (X. fastidiosa subsp. sandyi) (15,46,55,57,65), none of these were identified in CFBP 8072 or CFBP 8073 by PHAST but were identified, at least partially and/or fragmented, in the genome sequences of CFBP 8072 or CFBP 8073, based on a blast search. The prophage Xfp6 shared by the 9a5c and 6c strains (55) was also found in strains CFBP 8072 and CFBP 8073 with a very high level of conservation.…”

Section: Discussionmentioning

confidence: 99%

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New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

Jacques

Denancé

Legendre³

et al. 2016

Appl Environ Microbiol

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Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although this bacterium is classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and Coffea canephora) with leaf scorch symptoms growing in a confined greenhouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary identification based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/X. fastidiosa subsp. sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and CFBP 8074, isolated from Coffea arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provide genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee plant adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee plants.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

Jacques

Denancé

Legendre³

et al. 2016

Appl Environ Microbiol

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“…Several studies suggested that transpositional activity and recombination of HTEs might represent an important driving force of chromosomal evolution amongst X. fastidiosa strains Van Sluys et al, 2003;de Mello Varani et al, 2008, Varani et al, 2013. Thus, we decided to verify the presence of such elements in the draft genomes of the two CLS-associated strains.…”

Section: Resultsmentioning

confidence: 99%

“…However, most of the genomic information available for X. fastidiosa has been obtained from North American strains (Varani et al, 2013) and the relative lack of sequence information from South American strains may have introduced biases to some of the conclusions drawn from recent genomic studies within the group (Doddapaneni et al, 2006(Doddapaneni et al, , 2007. So far, there is only one work that attempted to perform a genomic survey of South American X. fastidiosa strains (da Silva et al, 2007) and this study did not involve whole-genomic sequencing, but microarraybased comparisons, followed by suppressive subtractive hybridization.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil

et al. 2015

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Strains of Xylella fastidiosa constitute a complex group of bacteria that develop within the xylem of many plant hosts, causing diseases of significant economic importance, such as Pierce's disease in North American grapevines and citrus variegated chlorosis in Brazil. X. fastidiosa has also been obtained from other host plants, in direct correlation with the development of diseases, as in the case of coffee leaf scorch (CLS) -a disease with potential to cause severe economic losses to the Brazilian coffee industry. This paper describes a thorough genomic characterization of coffeeinfecting X. fastidiosa strains, initially performed through a microarray-based approach, which demonstrated that CLS strains could be subdivided in two phylogenetically distinct subgroups. Whole-genomic sequencing of two of these bacteria (one from each subgroup) allowed identification of ORFs and horizontally transferred elements (HTEs) that were specific to CLSrelated X. fastidiosa strains. Such analyses confirmed the size and importance of HTEs as major mediators of chromosomal evolution amongst these bacteria, and allowed identification of differences in gene content, after comparisons were made with previously sequenced X. fastidiosa strains, isolated from alternative hosts. Although direct experimentation still needs to be performed to elucidate the biological consequences associated with such differences, it was interesting to verify that CLS-related bacteria display variations in genes that produce toxins, as well as surface-related factors (such as fimbrial adhesins and LPS) that have been shown to be involved with recognition of specific host factors in different pathogenic bacteria.

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“…Moreover, the matter of whether or not xanthan functions as a physical barrier against bacteriophage attack has been discussed [62,63]. The presence of clustered, regularly interspaced, short palindromic repeat (CRISPR)/Cas systems [64], as reported for Xanthomonas genomes [65][66][67][68], may be an indication of the viral threat for these bacteria besides the frequent identification of prophages or genes of viral origin in Xanthomonas genomes [69,70].…”

Section: Initial Systems Analysis Of Plant-pathogenic Xanthomonas Cammentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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The Role of Prophage in Plant-Pathogenic Bacteria

Cited by 62 publications

References 147 publications

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

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