Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, the expression of which is regulated by quorum sensing (QS). The QS systems of B. glumae rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate the genes for toxoflavin bi...
Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, the expression of which is regulated by quorum sensing (QS). The QS systems of B. glumae rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate the genes for toxoflavin biosynthesis and an IclR-type transcriptional regulator gene, qsmR. To understand genome-wide transcriptional profiling of QS signaling, we employed RNAseq of the wild-type B. glumae BGR1 with QS-defective mutant, BGS2 (BGR1 tofI::${\Omega}$) and QS-dependent transcriptional regulator mutant, BGS9 (BGR1 qsmR::${\Omega}$). A comparison of gene expression profiling among the wild-type BGR1 and the two mutants before and after QS onset as well as gene ontology (GO) enrichment analysis from differential expressed genes (DEGs) revealed that genes involved in motility were highly enriched in TofI-dependent DEGs, whereas genes for transport and DNA polymerase were highly enriched in QsmR-dependent DEGs. Further, a combination of pathways with these DEGs and phenotype analysis of mutants pointed to a couple of metabolic processes, which are dependent on QS in B. glumae, that were directly or indirectly related with bacterial motility. The consistency of observed bacterial phenotypes with GOs or metabolic pathways in QS-regulated genes implied that integration RNAseq with GO enrichment or pathways would be useful to study bacterial physiology and phenotypes.
Burkholderia glumae causes rice grain rot and sheath rot by producing toxoflavin, the expression of which is regulated by quorum sensing (QS). The QS systems of B. glumae rely on N-octanoyl homoserine lactone, synthesized by TofI and its cognate receptor TofR, to activate the genes for toxoflavin biosynthesis and an IclR-type transcriptional regulator gene, qsmR. To understand genome-wide transcriptional profiling of QS signaling, we employed RNAseq of the wild-type B. glumae BGR1 with QS-defective mutant, BGS2 (BGR1 tofI::${\Omega}$) and QS-dependent transcriptional regulator mutant, BGS9 (BGR1 qsmR::${\Omega}$). A comparison of gene expression profiling among the wild-type BGR1 and the two mutants before and after QS onset as well as gene ontology (GO) enrichment analysis from differential expressed genes (DEGs) revealed that genes involved in motility were highly enriched in TofI-dependent DEGs, whereas genes for transport and DNA polymerase were highly enriched in QsmR-dependent DEGs. Further, a combination of pathways with these DEGs and phenotype analysis of mutants pointed to a couple of metabolic processes, which are dependent on QS in B. glumae, that were directly or indirectly related with bacterial motility. The consistency of observed bacterial phenotypes with GOs or metabolic pathways in QS-regulated genes implied that integration RNAseq with GO enrichment or pathways would be useful to study bacterial physiology and phenotypes.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
제안 방법
glumae, QS-dependent phenotypes were demonstrated by several groups and most of them are well-known characteristics in other bacteria such as toxoflavin production, virulence, detoxification of oxidative stress, and motility. In this study, we analyzed the profiling of QS-dependent gene expression using two QS mutants at two different time points (before and after the onset of QS) to understand QS-dependent phenotypes and signaling pathways through a combination of RNAseqbased differential expressed genes (DEGs) with GO enrichment and pathway analyses. Through this approach, we found that QS-regulated genes are not only involved in several metabolic pathways but also our results are consistent with QS-dependent phenotypes such as motility.
The genes involved in flagellar motility and ribosome pathways were up-regulated and down-regulated in a QS-dependent manner, particularly by TofI. The reported phenotypes as well as phenotypic validation from this study were consistent with the QS-dependent pathways and GO enrichments. Integration of GO enrichment or metabolic pathways is useful in application of generated DEGs from B.
, 2008). To identify TofI- and QsmRregulated genes, differential expressed genes (DEGs) were selected using twofold changes of log2 ratio of (BGR1/ BGS2) and (BGR1/BGS9) RPKM values, respectively, as the criterion. Based on this criterion, 735 TofI- and 442 QsmR-dependent genes were identified.
이론/모형
The significance of enrichment for total of GO terms was calculated by Fisher’s exact test, and the obtained p-values were adjusted for multiple hypothesis testing by q-value (Storey and Tibshirani, 2003).
성능/효과
2). According to the results from 24 qPCR sets including the reference gene (blgu_1g13500), the trends of expression patterns of QS-regulated genes from RNAseq analysis were in good accordance with the expression levels by qPCR although the altitude of fold change is different due to sensitivity of each technique (Fig. 2).
glumae BGR1 with QS-defective mutant, BGS2 (BGR1 tofI::Ω) and QS-dependent transcriptional regulator mutant, BGS9 (BGR1 qsmR::Ω). By comparing the gene expression profiling among the wild-type BGR1 and the two mutants before (6 h LB liquid culture) and after (10 h LB liquid culture) the onset of QS, 1133 TofI-dependent and 840 QsmR-dependent genes were identified. Enrichment of gene ontology (GO) revealed the unique and shared signaling cascades between TofI- and QsmR-dependent QS.
FlhDC in turn activated the expression of genes involved in flagellum biosynthesis and motor functions. However, in this study we found that TofI strongly controlled the up-regulation of genes involved in flagellum biosynthesis and motor functions but QsmR did not (Table 2). In addition, swarming motility assays showed complete defects in BGS2, whereas in BGS9 slight swarming defects showed up a few times whenever these two mutants were used as controls for swarming tests of other mutants.
In conclusion, we observed QS-dependent GO enrichment or pathway including DNA modification in both TofI- and QsmR-dependent genes. The genes involved in flagellar motility and ribosome pathways were up-regulated and down-regulated in a QS-dependent manner, particularly by TofI.
참고문헌 (21)
Cother EJ Noble DH de Ven RJ van Lanoiselet V Ash G Vuthy N Visarto P Stodart B 2010 Bacterial pathogens of rice in the Kingdom of Cambodia and description of a new pathogen causing a serious sheath rot disease Plant Pathol 5 944 953
Chun H Choi O Goo E Kim N Kim H Kang Y Kim J Moon JS Hwang I 2009 The quorum sensing-dependent gene katG of Burkholderia glumae is important for protection from visible light J. Bacteriol 191 4152 4157 19395481
Deng Y Wu J Tao F Zhang LH 2011 Listening to a new language: DSF-based quorum sensing in Gram-negative bacteria Chem. Rev 111 160 173 21166386
Devescovi G Bigirimana J Degrassi G Cabrio L LiPuma JJ Kim J Hwang I Venturi V 2007 Involvement of a quorum-sensing-regulated lipase secreted by a clinical isolate of Burkholderia glumae in severe disease symptoms in rice Appl. Environ. Microbiol 73 4950 4958 17557855
Fuqua WC Winans SC Greenberg EP 1994 Quorum sensing in bacteria: The LuxR-LuxI family of cell density-responsive transcriptional regulators J. Bacteriol 176 269 275 8288518
Goo E Majerczyk CD An JH Chandler JR Seo YS Ham H Lim JY Kim H Lee B Jang MS Greenberg EP Hwang I 2012 Bacterial quorum sensing, cooperativity, and anticipation of stationary-phase stress Proc. Natl. Acad. Sci. USA 109 19775 19780 23150539
Jimenez PN Koch G Thompson JA Xavier KB Cool RH Quax WJ 2012 The multiple signaling systems regulating virulence in Pseudomonas aeruginosa Microbiol. Mol. Biol. Rev 76 46 65 22390972
Kapatral V Campbell JW Minnich SA Thomson NR Matsumura P Prüss BM 2004 Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate Microbiology 150 2289 2300 15256571
Kim J Kim JG Kang Y Jang JY Jog GJ Lim JY Kim S Suga H Nagamatsu T Hwang I 2004 Quorum sensing and the LysR-type transcriptional activator ToxR regulate toxoflavin biosynthesis and transport in Burkholderia glumae Mol. Microbiol 54 921 934 15522077
Kim J Kang Y Choi O Jeong Y Jeong JE Lim JY Kim M Moon JS Suga H Hwang I 2007 Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in Burkholderia glumae Mol. Microbiol 64 165 179 17376080
Kim J Oh J Choi O Kang Y Kim H Goo E Ma J Nagamatsu T Moon JS Hwang I 2009 Biochemical evidence for ToxR and ToxJ binding to the tox operons of Burkholderia glumae and mutational analysis of ToxR J. Bac-teriol 191 4870 4878
Kim J Kang Y Kim JG Choi O Hwang I 2010 Occurrence of Burkholderia glumae on rice and field crops in Korea Plant Pathol. J 26 271 272
Labbate M Queck SY Koh KS Rice SA Givskov M Kjelleberg S 2004 Quorum sensing-controlled biofilm development in Serratia liquefaciens MG1 J. Bacteriol 186 692 698 14729694
Milton DL 2006 Quorum sensing in vibrios: complexity for diversification Int. J. Med. Microbiol 296 61 71 16487746
Moreira CG Weinshenker D Sperandio V 2010 QseC mediates Salmonella enterica serovar typhimurium virulence in vitro and in vivo Infect. Immun 78 914 926 20028809
Nandakumar R Shahjahan AKM Yuan XL Dickstein ER Groth DE Clark CA Cartwright RD Rush MC 2009 Burkholderia glumae and B. gladioli cause bacterial panicle blight in rice in the southern United States Plant Dis 93 896 905
Pai A Tanouchi Y You L 2012 Optimality and robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme Proc. Natl. Acad. Sci. USA 109 19810 19815 23144221
※ AI-Helper는 부적절한 답변을 할 수 있습니다.