JIA-2021-1010 水平转移转录因子通过调控细胞色素bd氧化酶基因参与Xoc氧胁迫适应性和毒力机制的研究

doi:10.1016/S2095-3119(21)63801-7

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (6): 1673-1682.DOI: 10.1016/S2095-3119(21)63801-7

JIA-2021-1010 水平转移转录因子通过调控细胞色素bd氧化酶基因参与Xoc氧胁迫适应性和毒力机制的研究

收稿日期:2021-06-09 接受日期:2021-07-07 出版日期:2022-06-01 发布日期:2021-07-07

A transferred regulator that contributes to Xanthomonas oryzae pv. oryzicola oxidative stress adaptation and virulence by regulating the expression of cytochrome bd oxidase genes

WANG Pei-hong^1*, WANG Sai^1*, NIE Wen-han¹, WU Yan¹, Iftikhar AHMAD^{1, 2}, Ayizekeranmu YIMING¹, HUANG Jin¹, CHEN Gong-you¹, ZHU Bo¹

¹ Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education/Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, P.R.China
² Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari 61100, Pakistan

Received:2021-06-09 Accepted:2021-07-07 Online:2022-06-01 Published:2021-07-07
About author:WANG Pei-hong, E-mail: wangpeihong@sjtu.edu.cn; Correspondence ZHU Bo, Tel: +86-21-34205873, E-mail: bzhu1981@sjtu.edu.cn * These authors contributed equally to this study.
Supported by:
This work was supported by the National Key R&D Program of China (2018YFD0201202 and 2017YFD0201108), the Agri-X Interdisciplinary Fund of Shanghai Jiao Tong University, China (Agri-X2017010), the Shanghai Committee of Science and Technology, China (19390743300), and the National Natural Science Foundation of China (31200003).

摘要/Abstract

摘要：

早在2011年，研究者已对其进行了全基因组测序，并发现此基因组中有超过30%的编码基因是假定基因。另外，水平基因转移(horizontal gene transfer，HGT)已被认为是细菌基因组创新和进化的驱动力之一。前人在Xoc应对氧化应激的分子机制研究中，鉴定到了一个参与BLS256响应氧化胁迫并对毒性有贡献的水平转移基因(xoc_2868)。然而，xoc_2868作为一个转录因子的未知编码基因，其调控机制尚未被揭示。本研究基于BLAST序列比对和系统发育分析，初步判断其下游基因(xoc_2866和xoc_2867)与xoc_2868一样，均可能是BLS256在长期进化过程中通过水平转移从伯克氏菌科(Burkholderiaceae)获得的。为探索xoc_2868在BLS256响应氧胁迫过程中的潜在作用，我们分别对野生型(BLS256)和突变株(Δxoc_2868)在氧胁迫处理后进行了转录组测序。RNA-seq数据分析表明，在氧胁迫条件下，突变株中几个参与胞外多糖(EPS)和黄原胶(xanthan)生物合成基因的表达相较野生型显著下调，但未检测到其下游基因(xoc_2866和xoc_2867)的表达。为进一步鉴定受XOC_2868直接调控的基因，我们在野生型xoc_2868 C端融合了His6标签，并对此重组菌株进行了染色质免疫共沉淀 (ChIP-seq)分析。结合转录组分析发现，XOC_2868直接调控一个编码细胞色素bd氧化酶的两个亚基并参与氧化还原平衡的操纵子(cydAB)。与野生型菌株相比，cydA和cydAB缺失突变菌株与Δxoc_2868菌株一致出现对外源H₂O₂敏感性增强和细菌毒力减弱的表型。综上所述，本研究探讨了一种HGT形成和选择驱动的调控回路进化的可能性，xoc_2868与其两个下游基因可能是作为一个基因簇转移的，但它们在BLS256中各自进化，并在外界选择压下得以保留，XOC_2868通过结合新的调控位点直接调控了细胞色素bd氧化酶表达的通路，通过清除H₂O₂和其他ROS保护细胞免受氧化应激。此外，对胞外多糖和黄原胶合成相关基因的间接激活，也促进了其在宿主体内的定植和传播，从而参与了BLS256的致病力。本研究结果强调了在BLS256进化过程中，HGT现象对其毒力和适应性影响的可能性。

Abstract: Horizontal gene transfer (HGT) has been well documented as a driving force in the evolution of bacteria. It has been shown that a horizontally acquired gene, xoc_2868, involved in the global response against oxidative stress and pathogenicity of Xanthomonas oryzae pv. oryzicola strain BLS256. However, as a transcriptional factor (TF), the regulatory mechanism of XOC_2868 has not yet been revealed. Here, evolutionary analysis suggested XOC_2868 might be co-transferred with its physically proximate downstream genes from a Burkholderiaceae ancestor. Interestingly, RNA-seq data of wild-type (BLS256) and Δxoc_2868 strains under oxidative stress showed that XOC_2868 did not regulate the expression of its adjacent genes, but remarkably influenced the expression of several genes involved in the extracellular polysaccharide (EPS) production and xanthan biosynthesis. Chromatin immunoprecipitation-sequence (ChIP-seq) combined with transcriptome analysis revealed that XOC_2868 directly regulates a cydAB operon, encoding two subunits of cytochrome bd oxidase and involved in redox balance. Consistent with Δxoc_2868 strain, cydA- and cydAB-knockout mutants also showed a higher sensitivity to H₂O₂ along with a reduced bacterial virulence compared with the wild-type strain. Overall, our findings raise the possibility of regulatory circuit evolution shaped by HGT and driven by selection and reveal a novel regulatory pathway that regulates the expression of cytochrome bd oxidase and thus contributes to the virulence of BLS256.

Key words: HGT , transcriptional factor , Xanthomonas oryzae pv. oryzicola , oxidative stress adaptation and virulence

. JIA-2021-1010 水平转移转录因子通过调控细胞色素bd氧化酶基因参与Xoc氧胁迫适应性和毒力机制的研究[J]. Journal of Integrative Agriculture, 2022, 21(6): 1673-1682.

WANG Pei-hong, WANG Sai, NIE Wen-han, WU Yan, Iftikhar AHMAD, Ayizekeranmu YIMING, HUANG Jin, CHEN Gong-you, ZHU Bo. A transferred regulator that contributes to Xanthomonas oryzae pv. oryzicola oxidative stress adaptation and virulence by regulating the expression of cytochrome bd oxidase genes[J]. Journal of Integrative Agriculture, 2022, 21(6): 1673-1682.

参考文献

Ali F, Seshasayee A S N. 2020. Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in bacteria. Nucleic Acids Research, 48, 4100–4114.
André A, Maucourt M, Moing A, Rolin D, Renaudin J. 2005. Sugar import and phytopathogenicity of Spiroplasma citri: glucose and fructose play distinct roles. Molecular Plant–Microbe Interactions, 18, 33–42.
Babu M M, Luscombe N M, Aravind L, Gerstein M, Teichmann S A. 2004. Structure and evolution of transcriptional regulatory networks. Current Opinion in Structural Biology, 14, 283–291.
Babu M M, Teichmann S A. 2003. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Research, 31, 1234–1244.
Babu M M, Teichmann S A, Aravind L. 2006. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. Journal of Molecular Biology, 358, 614–633.
Bacciu D, Falchi G, Spazziani A, Bossi L, Marogna G, Leori G S, Rubino S, Uzzau S. 2004. Transposition of the heat-stable toxin astA gene into a gifsy-2-related prophage of Salmonella enterica serovar Abortusovis. Journal of Bacteriology, 186, 4568–4574.
Bae N, Park H J, Park H, Kim M, Han S W. 2018. Deciphering the functions of the outer membrane porin OprBXo involved in virulence, motility, exopolysaccharide production, biofilm formation and stress tolerance in Xanthomonas oryzae pv. oryzae. Molecular Plant Pathology, 19, 2527–2542.
Baughn A D, Malamy M H. 2004. The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen. Nature, 427, 441–444.
Borisov V B, Davletshin A I, Konstantinov A A. 2010. Peroxidase activity of cytochrome bd from Escherichia coli. Biochemistry (Mosc), 75, 428–436.
Borisov V B, Gennis R B, Hemp J, Verkhovsky M I. 2011. The cytochrome bd respiratory oxygen reductases. Biochimica et Biophysica Acta, 1807, 1398–1413.
Chevalier S, Bouffartigues E, Bodilis J, Maillot O, Lesouhaitier O, Feuilloley M G J, Orange N, Dufour A, Cornelis P. 2017. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiology Reviews, 41, 698–722.
Degli Esposti M, Rosas-Pérez T, Servín-Garcidueñas L E, Bolaños L M, Rosenblueth M, Martínez-Romero E. 2015. Molecular evolution of cytochrome bd oxidases across proteobacterial genomes. Genome Biology and Evolution, 7, 801–820.
Edwards S E, Loder C S, Wu G, Corker H, Bainbridge B W, Hill S, Poole R K. 2000. Mutation of cytochrome bd quinol oxidase results in reduced stationary phase survival, iron deprivation, metal toxicity and oxidative stress in Azotobacter vinelandii. FEMS Microbiology Letters, 185, 71–77.
Endley S, McMurray D, Ficht T A. 2001. Interruption of the cydB locus in Brucella abortus attenuates intracellular survival and virulence in the mouse model of infection. Journal of Bacteriology, 183, 2454–2462.
Fang Y, Wang H, Liu X, Xin D, Rao Y, Zhu B. 2019. Transcriptome analysis of Xanthomonas oryzae pv. oryzicola exposed to H2O2 reveals horizontal gene transfer contributes to its oxidative stress response. PLoS ONE, 14, e0218844.
Ficarra F A, Grandellis C, Galván E M, Ielpi L, Feil R, Lunn J E, Gottig N, Ottado J. 2017. Xanthomonas citri ssp. citri requires the outer membrane porin OprB for maximal virulence and biofilm formation. Molecular Plant Pathology, 18, 720–733.
Gelfand M S. 2006. Evolution of transcriptional regulatory networks in microbial genomes. Current Opinion in Structural Biology, 16, 420–429.
Goyal A. 2019. Horizontal gene transfer drives the evolution of dependencies in bacteria. bioRxiv, doi: 10.1101/836403.
Guo W, Cai L L, Zou H S, Ma W X, Liu X L, Zou L F, Li Y R, Chen X B, Chen G Y. 2012. Ketoglutarate transport protein KgtP is secreted through the type III secretion system and contributes to virulence in Xanthomonas oryzae pv. oryzae. Applied and Environmental Microbiology, 78, 5672–5681.
Hershberg R, Yeger-Lotem E, Margalit H. 2005. Chromosomal organization is shaped by the transcription regulatory network. Trends in Genetics, 21, 138–142.
de Hoon M J, Imoto S, Nolan J, Miyano S. 2004. Open source clustering software. Bioinformatics, 20, 1453–1454.
Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho P Y, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, et al. 2007. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science, 316, 593–597.
Katzen F, Ferreiro D U, Oddo C G, Ielmini M V, Becker A, Pühler A, Ielpi L. 1998. Xanthomonas campestris pv. campestris gum mutants: Effects on xanthan biosynthesis and plant virulence. Journal of Bacteriology, 180, 1607–1617.
Kim S, Cho Y J, Song E S, Lee S H, Kim J G, Kang L W. 2016. Time-resolved pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae. BMC Genomics, 17, 345.
Landova B, Silhan J. 2020. Conformational changes of DNA repair glycosylase MutM triggered by DNA binding. FEBS Letters, 594, 3032–3044.
Landt S G, Marinov G K, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein B E, Bickel P, Brown J B, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor K I, Euskirchen G, Gerstein M, Gertz J, Hartemink A J, Hoffman M M, Iyer V R, et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research, 22, 1813–1831.
Lawrence J G, Roth J R. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics, 143, 1843–1860.
Leclerc J, Rosenfeld E, Trainini M, Martin B, Meuric V, Bonnaure-Mallet M, Baysse C. 2015. The cytochrome bd oxidase of Porphyromonas gingivalis contributes to oxidative stress resistance and dioxygen tolerance. PLoS ONE, 10, e0143808.
Lindqvist A, Membrillo-Hernańdez J, Poole R K, Cook G M. 2000. Roles of respiratory oxidases in protecting Escherichia coli K12 from oxidative stress. Antonie Van Leeuwenhoek, 78, 23–31.
Lindsay J A. 2010. Genomic variation and evolution of Staphylococcus aureus. International Journal of Medical Microbiology, 300, 98–103.
Liu H, Yang C L, Ge M Y, Ibrahim M, Li B, Zhao W J, Chen G Y, Zhu B, Xie G L. 2014. Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress. Frontiers in Microbiology, 5, 547.
Lozada-Chávez I, Janga S C, Collado-Vides J. 2006. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Research, 34, 3434–3445.
Ochman H, Lawrence J G, Groisman E A. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299–304.
Perez J C, Groisman E A. 2009. Evolution of transcriptional regulatory circuits in bacteria. Cell, 138, 233–244.
Poole R K, Hill S. 1997. Respiratory protection of nitrogenase activity in Azotobacter vinelandii - Roles of the terminal oxidases. Bioscience Reports, 17, 303–317.
Price M N, Dehal P S, Arkin A P. 2008. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biology, 9, R4.
Safarian S, Rajendran C, Müller H, Preu J, Langer J D, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, Michel H. 2016. Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Science, 352, 583–586.
Saldanha A J. 2004. Java Treeview - Extensible visualization of microarray data. Bioinformatics, 20, 3246–3248.
Shi L, Sohaskey C D, Kana B D, Dawes S, North R J, Mizrahi V, Gennaro M L. 2005. Changes in energy metabolism of Mycobacterium tuberculosis in mouse lung and under in vitro conditions affecting aerobic respiration. Proceedings of the National Academy of Sciences of the United States of America, 102, 15629–15634.
Slater H, Alvarez-Morales A, Barber C E, Daniels M J, Dow J M. 2000. A two-component system involving an HD-GYP domain protein links cell–cell signalling to pathogenicity gene expression in Xanthomonas campestris. Molecular Microbiology, 38, 986–1003.
Small J L, Park S W, Kana B D, Ioerger T R, Sacchettini J C, Ehrt S. 2013. Perturbation of cytochrome c maturation reveals adaptability of the respiratory chain in Mycobacterium tuberculosis. mBio, 4, e00475-13.
Trapnell C, Pachter L, Salzberg S L. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105–1111.
Upadhya R, Campbell L T, Donlin M J, Aurora R, Lodge J K. 2013. Global transcriptome profile of Cryptococcus neoformans during exposure to hydrogen peroxide induced oxidative stress. PLoS ONE, 8, e55110.
Vojnov A A, Slater H, Daniels M J, Dow J M. 2001. Expression of the gum operon directing xanthan biosynthesis in Xanthomonas campestris and its regulation in planta. Molecular Plant–Microbe Interactions, 14, 768–774.
Wylie J L, Worobec E A. 1995. The OprB porin plays a central role in carbohydrate uptake in Pseudomonas aeruginosa. Journal of Bacteriology, 177, 3021–3026.

JIA-2021-1010 水平转移转录因子通过调控细胞色素bd氧化酶基因参与Xoc氧胁迫适应性和毒力机制的研究

A transferred regulator that contributes to Xanthomonas oryzae pv. oryzicola oxidative stress adaptation and virulence by regulating the expression of cytochrome bd oxidase genes

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics