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Delivery of an Rhs-family nuclease effector reveals direct penetration of the gram-positive cell envelope by a type VI secretion system in Acidovorax citrulli

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mLife 2022年第1期1卷 66-78页

作者： Tong-Tong Pei Yumin Kan Zeng-Hang Wang Ming-Xuan Tang Hao Li Shuangquan Yan Yang Cui Hao-Yu Zheng Han Luo Xiaoye Liang Tao Dong State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic&Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina Department of Immunology and Microbiology School of Life SciencesSouthern University of Science and TechnologyGuangdongChina

The type VI secretion system(T6SS)is a double-tubular nanomachine widely found in gram-negative bacteria.Its spear-like Hcp tube is capable of penetrating a neighboring cell for cytosol-to-cytosol protein delivery.However,gram-positive bacteria have been considered impenetrable to such T6SS action.Here we report that the T6SS of a plant pathogen,Acidovorax citrulli(AC),could deliver an Rhsfamily nuclease effector RhsB to kill not only gram-negative but also gram-positive bacteria.Using bioinformatic,biochemical,and genetic assays,we systematically identified T6SS-secreted effectors and determined that RhsB is a crucial antibacterial effector.RhsB contains an N-terminal PAAR domain,a middle Rhs domain,and an unknown C-terminal domain.RhsB is subject to self-cleavage at both its N-and C-terminal domains and its secretion requires the upstream-encoded chaperone EagT2 and VgrG3.The toxic Cterminus of RhsB exhibits DNase activities and such toxicity is neutralized by either of the two downstream immunity proteins,RimB1 and RimB2.Deletion of rhsB significantly impairs the ability of killing Bacillus subtilis while ectopic expression of immunity proteins RimB1 or RimB2 confers protection.We demonstrate that the AC T6SS not only can effectively outcompete Escherichia coli and B.subtilis in planta but also is highly potent in killing other bacterial and fungal species.Collectively,these findings highlight the greatly expanded capabilities of T6SS in modulating microbiome compositions in complex environments.

关键词： cell envelope cell wall interspecies interaction protein secretion

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Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities

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Quantitative Biology 2023年第1期11卷 15-30页

作者： Huan Du Meng Li Yang Liu Archaeal Biology Center Institute for Advanced StudyShenzhen UniversityShenzhen 518060China Shenzhen Key Laboratory of Marine Microbiome Engineering Institute for Advanced StudyShenzhen UniversityShenzhen 18060China

Background:Synthetic microbial communities,with different strains brought together by balancing their nutrition and promoting their interactions,demonstrate great advantages for exploring complex performance of communities and for further biotechnology applications.The potential of such microbial communities has not been explored,due to our limited knowledge of the extremely complex microbial interactions that are involved in designing and controlling effective and stable communities.Results:Genome-scale metabolic models(GEM)have been demonstrated as an effective tool for predicting and guiding the investigation and design of microbial communities,since they can explicitly and efficiently predict the phenotype of organisms from their genotypic data and can be used to explore the molecular mechanisms of microbehabitats and microbe-microbe interactions.In this work,we reviewed two main categories of GEM-based approaches and three uses related to design of synthetic microbial communities:predicting multi-species interactions,exploring environmental impacts on microbial phenotypes,and optimizing community-level performance.Conclusions:Although at the infancy stage,GEM-based approaches exhibit an increasing scope of applications in designing synthetic microbial communities.Compared to other methods,especially the use of laboratory cultures,GEM-based approaches can greatly decrease the trial-and-error cost of various procedures for designing synthetic communities and improving their functionality,such as identifying community members,determining media composition,evaluating microbial interaction potential or selecting the best community configuration.Future efforts should be made to overcome the limitations of the approaches,ranging from quality control of GEM reconstructions to community-level modeling algorithms,so that more applications of GEMs in studying phenotypes of microbial communities can be expected.

关键词： genome-scale metabolic modeling microbial community design interspecies interaction environmental impact community-level performance

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