Understanding the genomics and specialised metabolites of the biopesticidal bacterium Burkholderia ambifaria

了解生物农药细菌伯克霍尔德氏菌的基因组学和专门代谢物

• 批准号: 1646512
• 金额: --
• 依托单位: CARDIFF UNIVERSITY
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-1646512
• 关键词: Understanding; genomics; specialised; metabolites; biopesticidal

Harnessing beneficial interactions between microorganisms and plants can provide multiple solutions to food security by reducing chemical pesticide and fertilizer use, and improving crop yields. Burkholderia are Gram-negative, environmental bacteria that have been used as natural biotechnological agents for pollutant bioremediation and biological control of plant pathogens. They occur in high numbers at the roots of major crop species including maize and rice. Burkholderia encode pathways that can fix atmospheric nitrogen and produce antimicrobial metabolites that kill a range of plant pathogens (bacteria, fungi and nematodes). However, the pathways that are most beneficial in plant interactions have not been systematically defined. The Burkholderia genome (8+ Mb) contains multiple large chromosomal replicons. The smallest, third chromosome (> 1Mb; c3) can be deleted, attenuating virulence but leaving rhizosphere fitness intact, opening up chromosome engineering as a means to harness Burkholderia's biotechnological potential. Aim. The PhD will define the Burkholderia and plant genetic pathways involved in protective and growth promoting rhizosphere interactions, with an overall goal to engineer the most beneficial bacterial pathways onto a synthetic c3. Objective 1 (Year 1). Screening Burkholderia strains for growth promotion and plant protection using Arabidopsis models. Multiple Burkholderia biocontrol strains are being genome sequenced as part of BBSRC antibiotic discovery genome mining (EM, 2014-17). The PhD will genetically characterise these strains (EM rotation) and establish Arabidopsis growth promotion assays (JM rotation), to identify the most bioactive Burkholderia. An Arabidopsis protection assay will be established (MG rotation) to determine how the bacterial pathogen, Xanthomonas is killed at the rhizosphere by Burkholderia, using a range of defence and hormone mutants to provide mechanistic insight. Objective 2 (Year 2-3). Exploring the molecular basis for growth promotion and plant protection using post-genomic approaches. Global gene expression occurring in both Burkholderia and Arabidopsis during beneficial interactions will be determined using RNA-seq, defining the underlying transcriptional networks engaged in these processes (interdisciplinary rotations between EM and JM labs). Objective 3 (Year 3-4). Synthetically engineer the Burkholderia c3 to encode specific growth promotion and pathogen control functions. Selected pathways identified from the global gene expression analysis will be engineered onto a synthetic third chromosome. They will be re-tested in a c3 mutant background, establishing which beneficial pathways remain effective in isolation, ultimately working towards the goal of producing a composite Burkholderia replicon for crop protection and plant growth promotion that can be utilized in environmentally adapted Burkholderia's.

利用微生物和植物之间的有益相互作用，可以通过减少化学农药和化肥的使用，提高作物产量，为粮食安全提供多种解决方案。伯克霍尔德氏菌属是革兰氏阴性的环境细菌，已被用作污染物生物修复和植物病原体生物防治的天然生物技术剂。它们大量出现在包括玉米和水稻在内的主要作物物种的根部。伯克霍尔德氏菌编码的途径可以固定大气中的氮，并产生抗菌代谢物，杀死一系列植物病原体（细菌，真菌和线虫）。然而，在植物相互作用中最有益的途径尚未系统地定义。伯克霍尔德氏菌基因组（8+ Mb）含有多个大的染色体复制子。最小的第三条染色体（> 1 Mb; c3）可以被删除，减弱毒力但保持根际适应性完整，开辟了染色体工程作为利用伯克霍尔德氏菌生物技术潜力的手段。瞄准博士将定义伯克霍尔德菌和植物遗传途径参与保护和促进生长的根际相互作用，总体目标是将最有益的细菌途径工程化到合成的c3上。目标1（第1年）。使用拟南芥模型筛选用于生长促进和植物保护的伯克霍尔德菌菌株。作为BBSRC抗生素发现基因组挖掘（EM，2014-17）的一部分，正在对多种伯克霍尔德菌生物控制菌株进行基因组测序。博士将对这些菌株进行遗传鉴定（EM旋转），并建立拟南芥生长促进试验（JM旋转），以确定最具生物活性的伯克霍尔德氏菌。将建立拟南芥保护测定（MG旋转）以确定细菌病原体黄单胞菌如何在根际被伯克霍尔德氏菌杀死，使用一系列防御和激素突变体以提供机制见解。目标2（第2-3年）。利用后基因组方法探索促进生长和植物保护的分子基础。在有益的相互作用期间，伯克霍尔德氏菌和拟南芥中发生的全球基因表达将使用RNA-seq来确定，定义参与这些过程的潜在转录网络（EM和JM实验室之间的跨学科旋转）。目标3（第3-4年）。合成工程伯克霍尔德氏菌c3编码特定的生长促进和病原体控制功能。从全局基因表达分析中鉴定的选定途径将被工程化到合成的第三染色体上。它们将在c3突变体背景下重新测试，确定哪些有益途径在隔离中仍然有效，最终致力于生产用于作物保护和植物生长促进的复合伯克霍尔德氏菌复制子的目标，该复制子可用于环境适应的伯克霍尔德氏菌。

项目成果

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity.

• DOI: 10.1128/mbio.00715-21
• 发表时间: 2021-08-31
• 期刊: mBio
• 影响因子: 6.4
• 作者: Mullins AJ;Webster G;Kim HJ;Zhao J;Petrova YD;Ramming CE;Jenner M;Murray JAH;Connor TR;Hertweck C;Challis GL;Mahenthiralingam E
• 通讯作者: Mahenthiralingam E

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.

• DOI: 10.1093/femsle/fny069
• 发表时间: 2018-05-01
• 期刊: FEMS microbiology letters
• 影响因子: 2.1
• 作者: Beaton A;Lood C;Cunningham-Oakes E;MacFadyen A;Mullins AJ;Bestawy WE;Botelho J;Chevalier S;Coleman S;Dalzell C;Dolan SK;Faccenda A;Ghequire MGK;Higgins S;Kutschera A;Murray J;Redway M;Salih T;da Silva AC;Smith BA;Smits N;Thomson R;Woodcock S;Welch M;Cornelis P;Lavigne R;van Noort V;Tucker NP
• 通讯作者: Tucker NP

Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments.

从海洋沉积物中分离出的两种利用胆碱的产甲烷古菌（Methanococcoides spp.）的基因组序列。

• DOI: 10.1128/mra.00342-19
• 发表时间: 2019
• 期刊: Microbiology resource announcements
• 影响因子: 0.8
• 作者: Webster G

Exploration of polyyne biosynthetic gene cluster diversity in bacteria leads to the discovery of the Pseudomonas polyyne protegencin

对细菌中多炔生物合成基因簇多样性的探索导致了假单胞菌多炔保护蛋白的发现

• DOI: 10.1101/2021.03.05.433886
• 发表时间: 2021
• 作者: Mullins A

Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.

• DOI: 10.1128/mra.00485-20
• 发表时间: 2020-10-15
• 期刊: Microbiology resource announcements
• 影响因子: 0.8
• 作者: Mullins AJ;Jones C;Bull MJ;Webster G;Parkhill J;Connor TR;Murray JAH;Challis GL;Mahenthiralingam E
• 通讯作者: Mahenthiralingam E