Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin

Hussain, Annam; Shahbaz, Maham; Tariq, Muhammad Ilyas; Ibrahim, Muhammad; Hong, Xianxian; Naeem, Farooq; Khalid, Zunera; Raza, Hafiz Muhammad Zeeshan; Zhu, Bao‐Ku; Li, Bin

doi:10.1016/j.compbiolchem.2020.107245

Cited by 7 publications

(7 citation statements)

References 40 publications

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“…Once detected and characterized using the above approaches, six strains (60BGCRMSO1-5, 60BGCRMSO3-5, 60BGCRMSO3-9, 60BGCRMSO3-11, 60BGCRPA10-1, and 60BGCRWC8-5) were selected and subjected to whole-genome sequencing, characterization, and phylogenetic analysis. The genome characteristics of the sequenced strains were consistent with the previously sequenced strains of this pathogen (e.g., [20,21,32,33]), with a high level of completeness (Table 2). The toxoflavin gene cluster of the six genomes was identified and compared with the other publicly available B. glumae genomes.…”

Section: Discussionsupporting

confidence: 77%

“…As expected, this gene cluster is present in all the strains; however, a significant variation between the tofR, toxG, and toxI genes among some strains was observed (Table S2), which may reflect the different levels of virulence of these strains. In this regard, when compared with the other B. glumae strains, the high rice virulent strain 411gr-6 [5,32] has a significant difference in the aminoacid sequence of the toxG (55.2%), while the other strains showed ≥99.6% of identity (Table S2). Similarly, a significant difference was observed in the aminoacid sequence of the LysR-type regulator toxR of the FDAARGOS_346, FDAAR-GOS_921, FDAARGOS_949, and LMG 2196 strains.…”

Section: Discussionmentioning

confidence: 99%

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Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

et al. 2022

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Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice were initially identified as B. glumae by polymerase chain reaction (PCR) using species-specific primers. Among them, six selected strains isolated from the susceptible japonica rice cultivar DOA2 were characterized in terms of morpho-physiology, pathology, phylogenetics, and genomics. Our genome sequence analysis of the six selected strains revealed the presence of multiple prophages, which may reflect the high level of diversity in this bacterial species through dynamic horizontal gene transfer processes, including phage infection. This notion was supported by the results of phylogenetic and phylogenomic analyses, which showed the formation of several subgroups not related to the years of isolation or the geographical origins. This study reports the isolation of B. glumae as the causal pathogen of BPB disease in japonica rice in Thailand and provides genomic resources to better understand the biology and diversity of this plant pathogenic bacterium. Further studies with a vast collection of B. glumae strains from various rice-growing regions around the world are needed to elucidate the evolution, variability, and lifestyle of the pathogen.

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Section: Discussionsupporting

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

et al. 2022

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“…Although B. glumae is known as a plant pathogen, the clinical isolate B. glumae strain AU6208 has been reported from patients with chronic infections (Weinberg et al, 2007). The sequenced genomes of plantassociated B. glumae strains, including 336gr-1, LMG2196, and PG1, and the clinical isolate AU6208, were compared with that of B. glumae BGR1 isolated from an infected rice plant in South Korea (Francis et al, 2013;Lee et al, 2016;Hussain et al, 2020). These comparative studies revealed that while the isolates share common characteristics, such as toxoflavin biosynthesis genes, unique genomic regions and large-scale genome rearrangement and inversion were observed in each strain (Francis et al, 2013;Lee et al, 2016;Hussain et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…The sequenced genomes of plantassociated B. glumae strains, including 336gr-1, LMG2196, and PG1, and the clinical isolate AU6208, were compared with that of B. glumae BGR1 isolated from an infected rice plant in South Korea (Francis et al, 2013;Lee et al, 2016;Hussain et al, 2020). These comparative studies revealed that while the isolates share common characteristics, such as toxoflavin biosynthesis genes, unique genomic regions and large-scale genome rearrangement and inversion were observed in each strain (Francis et al, 2013;Lee et al, 2016;Hussain et al, 2020). However, whether the genotypically distinct isolates of B. glumae have distinctive physiological traits and evolutionary routes for environmental adaptation is unknown.…”

Section: Introductionmentioning

confidence: 99%

Influence of genomic structural variations and nutritional conditions on the emergence of quorum sensing-dependent gene regulation defects in Burkholderia glumae

et al. 2022

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Bacteria often change their genetic and physiological traits to survive in harsh environments. To determine whether, in various strains of Burkholderia glumae, genomic diversity is associated with the ability to adapt to ever-changing environments, whole genomes of 44 isolates from different hosts and regions were analyzed. Whole-genome phylogenetic analysis of the 44 isolates revealed six clusters and two divisions. While all isolates possessed chromosomes 1 and 2, strains BGR80S and BGR81S had one chromosome resulting from the merging of the two chromosomes. Upon comparison of genomic structures to the prototype BGR1, inversions, deletions, and rearrangements were found within or between chromosomes 1 and/or 2 in the other isolates. When three isolates—BGR80S, BGR15S, and BGR21S, representing clusters III, IV, and VI, respectively—were grown in Luria-Bertani medium, spontaneous null mutations were identified in qsmR encoding a quorum-sensing master regulator. Six days after subculture, qsmR mutants were found at detectable frequencies in BGR15S and BGR21S, and reached approximately 40% at 8 days after subculture. However, the qsmR mutants appeared 2 days after subculture in BGR80S and dominated the population, reaching almost 80%. No qsmR mutant was detected at detectable frequency in BGR1 or BGR13S. The spontaneous qsmR mutants outcompeted their parental strains in the co-culture. Daily addition of glucose or casamino acids to the batch cultures of BGR80S delayed emergence of qsmR mutants and significantly reduced their incidence. These results indicate that spontaneous qsmR mutations are correlated with genomic structures and nutritional conditions.

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“…We noticed that B. gladioli strain KACC11889 and ATCC 10,248 were reported as not producing toxoflavin, although they possess a complete Tox gene cluster (Table 1). It has been reported that the loss of toxoflavin production in the KACC11889 strain is due to the lack of quorum-sensing (QS) system Tof I-M-R, which functions as an on/off switch for toxoflavin biosynthesis via regulation of ToxJ regulator [24,38,39]. We also searched for the Tof I-M-R cluster in the selected B. glidioli and B. glumae strains.…”

Section: Identification Of Quorum-sensing Genes In Cgb10mentioning

confidence: 99%

Burkholderia gladioli CGB10: A Novel Strain Biocontrolling the Sugarcane Smut Disease

et al. 2020

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In this study, we isolated an endophytic Burkholderia gladioli strain, named CGB10, from sugarcane leaves. B. gladioli CGB10 displayed strong inhibitory activity against filamentous growth of fungal pathogens, one of which is Sporisorium scitamineum that causes sugarcane smut, a major disease affecting the quality and production of sugarcane in tropical and subtropical regions. CGB10 could effectively suppress sugarcane smut under field conditions, without itself causing any obvious damage or disease, thus underscoring a great potential as a biocontrol agent (BCA) for the management of sugarcane smut. A toxoflavin biosynthesis and transport gene cluster potentially responsible for such antifungal activity was identified in the CGB10 genome. Additionally, a quorum-sensing gene cluster was identified too and compared with two close Burkholderia species, thus supporting an overall connection to the regulation of toxoflavin synthesis therein. Overall, this work describes the in vitro and field Sporisorium scitamineum biocontrol by a new B. gladioli strain, and reports genes and molecular mechanisms potentially involved.

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Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin

Cited by 7 publications

References 40 publications

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight

Influence of genomic structural variations and nutritional conditions on the emergence of quorum sensing-dependent gene regulation defects in Burkholderia glumae

Burkholderia gladioli CGB10: A Novel Strain Biocontrolling the Sugarcane Smut Disease

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