Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp

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Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight of rice. For the virulence of the bacterium, the hrp genes, encoding components of the type III secretion system, are indispensable. The expression of hrp genes is regulated by two key hrp regulators, HrpG and HrpX: HrpG regulates hrpX, and HrpX regulates other hrp genes. Several other regulators have been shown to be involved in the regulation of hrp genes. Here, we found that a LysR-type transcriptional regulator that we named GamR, encoded by XOO_2767 of X. oryzae pv. oryzae strain MAFF311018, positively regulated the transcription of both hrpG and hrpX, which are adjacent to each other but have opposite orientations, with an intergenic upstream region in common. In a gel electrophoresis mobility shift assay, GamR bound directly to the middle of the upstream region common to hrpG and hrpX. The loss of either GamR or its binding sites decreased hrpG and hrpX expression. Also, GamR bound to the upstream region of either a galactose metabolism-related gene (XOO_2768) or a galactose metabolism-related operon (XOO_2768 to XOO_2771) located next to gamR itself and positively regulated the genes. The deletion of the regulator gene resulted in less bacterial growth in a synthetic medium with galactose as a sole sugar source. Interestingly, induction of the galactose metabolismrelated gene was dependent on galactose, while that of the hrp regulator genes was galactose independent. Our results indicate that the LysR-type transcriptional regulator that regulates the galactose metabolism-related gene(s) also acts in positive regulation of two key hrp regulators and the following hrp genes in X. oryzae pv. oryzae. IMPORTANCEThe expression of hrp genes encoding components of the type III secretion system is essential for the virulence of many plantpathogenic bacteria, including Xanthomonas oryzae pv. oryzae. It is specifically induced during infection. Research has revealed that in this bacterium, hrp gene expression is controlled by two key hrp regulators, HrpG and HrpX, along with several other regulators in the complex regulatory network, but the details remain unclear. Here, we found that a novel LysR-type transcriptional activator, named GamR, functions as an hrp regulator by directly activating the transcription of both hrpG and hrpX. Interestingly, GamR also regulates a galactose metabolism-related gene (or operon) in a galactose-dependent manner, while the regulation of hrpG and hrpX is independent of the sugar. Our finding of a novel hrp regulator that directly and simultaneously regulates two key hrp regulators provides new insights into an important and complex regulation system of X. oryzae pv. oryzae hrp genes. In several plant-pathogenic bacteria, hrp genes are essential for bacterial pathogenicity (1). The hrp genes generally comprise more than 20 genes and are clustered in the genome of each bacterium. The genes mainly encode components of a type III secretion apparatus, through which the bacteria secrete numerous proteins, s...

Section: Figmentioning

confidence: 99%

GamR, the LysR-Type Galactose Metabolism Regulator, Regulates hrp Gene Expression via Transcriptional Activation of Two Key hrp Regulators, HrpG and HrpX, in Xanthomonas oryzae pv. oryzae

Rashid

Ikawa

Tsuge

2016

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“…oryzae and strain BLS256 for X. oryzae pv. oryzicola (11,12,14,32). Nontarget bacterial DNAs were pooled in equimolar concentrations, with the DNA from 10 strains included in each pool.…”

Section: Methodsmentioning

confidence: 99%

“…oryzae and two strains of X. oryzae pv. oryzicola are publicly available (GenBank accession numbers AYSX00000000 and AYSY00000000, respectively) (11)(12)(13)(14). These resources, along with draft genome sequences of another nine X. oryzae strains, provided insights into the genetic diversity among strains within this species, including a unique group of weakly pathogenic X. oryzae strains isolated in the United States (13; V. Verdier, unpublished).…”

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confidence: 99%

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

Lang

Langlois

Nguyen

et al. 2014

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dMolecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 10 4 to 10 5 CFU ml ؊1 , while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens.

“…Genome comparison among species and pathovars of Xanthomonas suggest specificity is determined by a complex set of genetic differences involving both gene content and gene sequence (11). Of these two kinds of difference, content and sequence, gene content differences are more easily studied, since it can be done by correlating the presence of genes with particular pathovars (e.g., in Pseudomonas syringae [12]); however, more subtle sequence-based host adaptations may be equally important.…”

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confidence: 99%

Recent Evolutionary Radiation and Host Plant Specialization in the Xylella fastidiosa Subspecies Native to the United States

Nunney

Vickerman

Bromley

et al. 2013

112

The bacterial pathogen, Xylella fastidiosa, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 "non-IHR" isolates, 2 minimally recombinant "intermediate" ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp. multiplex showed no host overlap with the introduced subspecies (subspecies fastidiosa and sandyi). MLST sequences revealed that subsp. multiplex underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (/ ‫؍‬ 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): "almond," "peach," and "oak" types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity.T he genetic typing of bacterial isolates is an increasingly important tool for understanding the epidemiology of pathogenic bacteria. It permits us to track biogeographical patterns, host specificity, and the evolutionary changes occurring within taxa. To achieve these goals, one of the most useful and widely used typing methodologies is multilocus sequence typing (MLST), introduced in 1998 (1, 2). The spread of this methodology has been rapid in the study of human bacterial pathogens; however, MLST schemes are equally important in the study of plant pathogens (3), and schemes for plant bacteria are beginning to become established, e.g., Pseudomonas syringae (4), Xylella fastidiosa (5, 6), fruit tree phytoplasmas (7), Ralstonia solanacearum (8), Xanthomonas spp. (9), and Acidovorax citrulli (10).The genetic typing of plant pathogens provides a critical first step in answering the important question of what genetic factors determine host specificity. Genome comparison among species and pathovars of Xanthomonas suggest specificity is determined by a complex set of genetic differences involving both gene content and gene sequence (11). Of these two kinds of difference, content and sequence, gene content differences are more easily studied, since it...