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Chen M, Shang Y, Cui W, Wang X, Zhu J, Dong H, Wang H, Su T, Wang W, Zhang K, Li B, Xu S, Hu W, Zhang F, Gu L. Molecular mechanism of proteolytic cleavage-dependent activation of CadC-mediated response to acid in E. coli. Commun Biol 2024; 7:1335. [PMID: 39415060 DOI: 10.1038/s42003-024-06931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 09/20/2024] [Indexed: 10/18/2024] Open
Abstract
Colonizing in the gastrointestinal tract, Escherichia coli confronts diverse acidic challenges and evolves intricate acid resistance strategies for its survival. The lysine-mediated decarboxylation (Cad) system, featuring lysine decarboxylase CadA, lysine/cadaverine antiporter CadB, and transcriptional activator CadC, plays a crucial role in E. coli's adaptation to moderate acidic stress. While the activation of the one-component system CadC and subsequent upregulation of cadBA operon in response to acid and lysine presence have been proposed, the molecular mechanisms governing the transition of CadC from an inactive to an active state remain elusive. Under neutral conditions, CadC is inhibited by forming a complex with lysine-specific permease LysP, stabilized in this inactive state by a disulfide bond. Our study unveils that, in an acidic environment, the disulfide bond in CadC is reduced by the disulfide bond isomerase DsbC, exposing R184 to periplasmic proteases, namely DegQ and DegP. Cleavage at R184 by DegQ and DegP generates an active N-terminal DNA-binding domain of CadC, which binds to the cadBA promoter, resulting in the upregulated transcription of the cadA and cadB genes. Upon activation, CadA decarboxylates lysine, producing cadaverine, subsequently transported extracellularly by CadB. We propose that accumulating cadaverine gradually binds to the CadC pH-sensing domain, preventing cleavage and activation of CadC as a feedback mechanism. The identification of DegP, DegQ, and DsbC completes a comprehensive roadmap for the activation and regulation of the Cad system in response to moderate acidic stress in E. coli.
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Affiliation(s)
- Min Chen
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Ye Shang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Wenhao Cui
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Xiaomeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Jiakun Zhu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Hongjie Dong
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Hongwei Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Tiantian Su
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Weiwei Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwuweiqi Road, jinan, China
| | - Kundi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Bingqing Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwuweiqi Road, jinan, China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China.
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, China.
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Yin M, Liu Z, Sun Z, Qu X, Chen Z, Diao Y, Cheng Y, Shen S, Wang X, Cai Z, Lu B, Tan S, Wang Y, Zhao X, Chen F. Biomimetic Scaffolds Regulating the Iron Homeostasis for Remolding Infected Osteogenic Microenvironment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407251. [PMID: 39373362 DOI: 10.1002/advs.202407251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 09/12/2024] [Indexed: 10/08/2024]
Abstract
The treatment of infected bone defects (IBDs) needs simultaneous elimination of infection and acceleration of bone regeneration. One mechanism that hinders the regeneration of IBDs is the iron competition between pathogens and host cells, leading to an iron deficient microenvironment that impairs the innate immune responses. In this work, an in situ modification strategy is proposed for printing iron-active multifunctional scaffolds with iron homeostasis regulation ability for treating IBDs. As a proof-of-concept, ultralong hydroxyapatite (HA) nanowires are modified through in situ growth of a layer of iron gallate (FeGA) followed by incorporation in the poly(lactic-co-glycolic acid) (PLGA) matrix to print biomimetic PLGA based composite scaffolds containing FeGA modified HA nanowires (FeGA-HA@PLGA). The photothermal effect of FeGA endows the scaffolds with excellent antibacterial activity. The released iron ions from the FeGA-HA@PLGA help restore the iron homeostasis microenvironment, thereby promoting anti-inflammatory, angiogenesis and osteogenic differentiation. The transcriptomic analysis shows that FeGA-HA@PLGA scaffolds exert anti-inflammatory and pro-osteogenic differentiation by activating NF-κB, MAPK and PI3K-AKT signaling pathways. Animal experiments confirm the excellent bone repair performance of FeGA-HA@PLGA scaffolds for IBDs, suggesting the promising prospect of iron homeostasis regulation therapy in future clinical applications.
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Affiliation(s)
- Mengting Yin
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Zhiqing Liu
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Zhongyi Sun
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, 201102, P. R. China
- Suzhou First People's Hospital, School of Medicine, Anhui University of Science and Technology, Anhui, 232001, P.R. China
| | - Xinyu Qu
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Ziyan Chen
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Yuying Diao
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, 201102, P. R. China
| | - Yuxuan Cheng
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Sisi Shen
- Department of Plastic and Reconstructive Surgery, Shanghai Key Laboratory of Tissue Engineering, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
| | - Xiansong Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Key Laboratory of Tissue Engineering, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China
| | - Zhuyun Cai
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Bingqiang Lu
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Shuo Tan
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Yan Wang
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, 201102, P. R. China
| | - Xinyu Zhao
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
| | - Feng Chen
- Center for Orthopaedic Science and Translational Medicine, Department of Orthopaedics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R China
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, 201102, P. R. China
- Suzhou First People's Hospital, School of Medicine, Anhui University of Science and Technology, Anhui, 232001, P.R. China
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Zhao J, Sun H, Wang G, Wang Q, Wang Y, Li Q, Bi S, Qi Q, Wang Q. Engineering Chimeric Chemoreceptors and Two-Component Systems for Orthogonal and Leakless Biosensing of Extracellular γ-Aminobutyric Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14216-14228. [PMID: 38860925 DOI: 10.1021/acs.jafc.4c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Two-component systems (TCSs) sensing and responding to various stimuli outside and inside cells are valuable resources for developing biosensors with synthetic biology applications. However, the use of TCS-based biosensors suffers from a limited effector spectrum, hypersensitivity, low dynamic range, and unwanted signal crosstalk. Here, we developed a tailor-made Escherichia coli whole-cell γ-aminobutyric acid (GABA) biosensor by engineering a chimeric GABA chemoreceptor PctC and TCS. By testing different TCSs, the chimeric PctC/PhoQ showed the response to GABA. Chimera-directed evolution and introduction of the insulated chimeric pair PctC/PhoQ*PhoP* produced biosensors with up to 3.50-fold dynamic range and good orthogonality. To further enhance the dynamic range and lower the basal leakage, three strategies, engineering of PhoP DNA binding sites, fine-tuning reporter expression by optimizing transcription/translation components, and a tobacco etch virus protease-controlled protein degradation, were integrated. This chimeric biosensor displayed a low basal leakage, a large dynamic range (15.8-fold), and a high threshold level (22.7 g L-1). Finally, the optimized biosensor was successfully applied in the high-throughput microdroplet screening of GABA-overproducing Corynebacterium glutamicum, demonstrating its desired properties for extracellular signal biosensing.
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Affiliation(s)
- Jingyu Zhao
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Huanhuan Sun
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Gege Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Qi Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingbin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, P. R. China
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Lindemeier D, Graubner W, Mehner-Breitfeld D, Malešević M, Brüser T. Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli. PLoS One 2024; 19:e0305823. [PMID: 38917203 PMCID: PMC11198818 DOI: 10.1371/journal.pone.0305823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
SlyD is a widely-occurring prokaryotic FKBP-family prolyl isomerase with an additional chaperone domain. Often, such as in Escherichia coli, a third domain is found at its C-terminus that binds nickel and provides it for nickel-enzyme biogenesis. SlyD has been found to bind signal peptides of proteins that are translocated by the Tat pathway, a system for the transport of folded proteins across membranes. Using peptide arrays to analyze these signal peptide interactions, we found that SlyD interacted only with positively charged peptides, with a preference for arginines over lysines, and large hydrophobic residues enhanced binding. Especially a twin-arginine motif was recognized, a pair of highly conserved arginines adjacent to a stretch of hydrophobic residues. Using isothermal titration calorimetry (ITC) with purified SlyD and a signal peptide-containing model Tat substrate, we could show that the wild type twin-arginine signal peptide was bound with higher affinity than an RR>KK mutated variant, confirming that positive charges are recognized by SlyD, with a preference of arginines over lysines. The specific role of negative charges of the chaperone domain surface and of hydrophobic residues in the chaperone active site was further analyzed by ITC of mutated SlyD variants. Our data show that the supposed key hydrophobic residues of the active site are indeed crucial for binding, and that binding is influenced by negative charges on the chaperone domain. Recognition of positive charges is likely achieved by a large negatively charged surface region of the chaperone domain, which is highly conserved although individual positions are variable.
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Affiliation(s)
- Daniel Lindemeier
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | - Wenke Graubner
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
| | | | - Miroslav Malešević
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Hanover, Germany
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5
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Zhao X, Guo M, Wang Y, Jin M, Hou N, Wu H. Toxic effects of nanoplastics on biological nitrogen removal in constructed wetlands: Evidence from iron utilization and metabolism. WATER RESEARCH 2024; 256:121577. [PMID: 38593605 DOI: 10.1016/j.watres.2024.121577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Abstract
Nanoplastics (NPs) in wastewaters may present a potential threat to biological nitrogen removal in constructed wetlands (CWs). Iron ions are pivotal in microbially mediated nitrogen metabolism, however, explicit evidence demonstrating the impact of NPs on nitrogen removal regulated by iron utilization and metabolism remains unclear. Here, we investigated how NPs disturb intracellular iron homeostasis, consequently interfering with the coupling mechanism between iron utilization and nitrogen metabolism in CWs. Results indicated that microorganisms affected by NPs developed a siderophore-mediated iron acquisition mechanism to compensate for iron loss. This deficiency resulted from NPs internalization limited the activity of the electron transport system and key enzymes involved in nitrogen metabolism. Microbial network analysis further suggested that NPs exposure could potentially trigger destabilization in microbial networks and impair effective microbial communication, and ultimately inhibit nitrogen metabolism. These adverse effects, accompanied by the dominance of Fe3+ over certain electron acceptors engaged in nitrogen metabolism under NPs exposure, were potentially responsible for the observed significant deterioration in nitrogen removal (decreased by 30 %). This study sheds light on the potential impact of NPs on intracellular iron utilization and offers a substantial understanding of the iron-nitrogen coupling mechanisms in CWs.
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Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yunan Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ming Jin
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ning Hou
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Haiming Wu
- School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China.
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6
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Kion-Crosby W, Barquist L. Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders. BIOINFORMATICS ADVANCES 2024; 4:vbae066. [PMID: 39027639 PMCID: PMC11256956 DOI: 10.1093/bioadv/vbae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 05/02/2024] [Indexed: 07/20/2024]
Abstract
Summary The increasing number of publicly available bacterial gene expression data sets provides an unprecedented resource for the study of gene regulation in diverse conditions, but emphasizes the need for self-supervised methods for the automated generation of new hypotheses. One approach for inferring coordinated regulation from bacterial expression data is through neural networks known as denoising autoencoders (DAEs) which encode large datasets in a reduced bottleneck layer. We have generalized this application of DAEs to include deep networks and explore the effects of network architecture on gene set inference using deep learning. We developed a DAE-based pipeline to extract gene sets from transcriptomic data in Escherichia coli, validate our method by comparing inferred gene sets with known pathways, and have used this pipeline to explore how the choice of network architecture impacts gene set recovery. We find that increasing network depth leads the DAEs to explain gene expression in terms of fewer, more concisely defined gene sets, and that adjusting the width results in a tradeoff between generalizability and biological inference. Finally, leveraging our understanding of the impact of DAE architecture, we apply our pipeline to an independent uropathogenic E.coli dataset to identify genes uniquely induced during human colonization. Availability and implementation https://github.com/BarquistLab/DAE_architecture_exploration.
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Affiliation(s)
- Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
- Department of Biology, University of Toronto, Mississauga, ON L5L 1C6, Canada
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Su R, Fu H, Ding L, Fu B, He S, Ma H, Hu H, Ren H. Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system. BIORESOURCE TECHNOLOGY 2024; 393:130028. [PMID: 37977494 DOI: 10.1016/j.biortech.2023.130028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.
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Affiliation(s)
- Runhua Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Huimin Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Lili Ding
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Su He
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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Zhang N, Li T, Pan H, Wang Y, Li Q, Luan J, He X, Shi W, Li Y, Wang C, Zhang F, Hu W. Genetic components of Escherichia coli involved in its complex prey-predator interaction with Myxococcus xanthus. Front Microbiol 2023; 14:1304874. [PMID: 38116529 PMCID: PMC10728724 DOI: 10.3389/fmicb.2023.1304874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Myxococcus xanthus and Escherichia coli represent a well-studied microbial predator-prey pair frequently examined in laboratory settings. While significant progress has been made in comprehending the mechanisms governing M. xanthus predation, various aspects of the response and defensive mechanisms of E. coli as prey remain elusive. In this study, the E. coli MG1655 large-scale chromosome deletion library was screened, and a mutant designated as ME5012 was identified to possess significantly reduced susceptibility to predation by M. xanthus. Within the deleted region of ME5012 encompassing seven genes, the significance of dusB and fis genes in driving the observed phenotype became apparent. Specifically, the deletion of fis resulted in a notable reduction in flagellum production in E. coli, contributing to a certain level of resistance against predation by M. xanthus. Meanwhile, the removal of dusB in E. coli led to diminished inducibility of myxovirescin A production by M. xanthus, accompanied by a slight decrease in susceptibility to myxovirescin A. These findings shed light on the molecular mechanisms underlying the complex interaction between M. xanthus and E. coli in a predatory context.
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Affiliation(s)
- Ning Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Tingyi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Hongwei Pan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Qi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Jia Luan
- Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, United States
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
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9
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Denic M, Turlin E, Zamble DB, Betton JM, Vinella D, De Reuse H. The SlyD metallochaperone targets iron-sulfur biogenesis pathways and the TCA cycle. mBio 2023; 14:e0096723. [PMID: 37584558 PMCID: PMC10653786 DOI: 10.1128/mbio.00967-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
IMPORTANCE Correct folding of proteins represents a crucial step for their functions. Among the chaperones that control protein folding, the ubiquitous PPIases catalyze the cis/trans-isomerization of peptidyl-prolyl bonds. Only few protein targets of PPIases have been reported in bacteria. To fill this knowledge gap, we performed a large-scale two-hybrid screen to search for targets of the Escherichia coli and Helicobacter pylori SlyD PPIase-metallochaperone. SlyD from both organisms interacts with enzymes (i) containing metal cofactors, (ii) from the central metabolism tricarboxylic acid (TCA) cycle, and (iii) involved in the formation of the essential and ancestral Fe-S cluster cofactor. E. coli and H. pylori ∆slyD mutants present similar phenotypes of diminished susceptibility to antibiotics and to oxidative stress. In H. pylori, measurements of the intracellular ATP content, proton motive force, and activity of TCA cycle proteins suggest that SlyD regulates TCA cycle enzymes by controlling the formation of their indispensable Fe-S clusters.
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Affiliation(s)
- Milica Denic
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Evelyne Turlin
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Deborah B. Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Michel Betton
- Unité Adaptation au stress et Métabolisme chez les entérobactéries, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Daniel Vinella
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hilde De Reuse
- Unité Pathogenèse de Helicobacter, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
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Tang B, Wang B, Xu Z, Hou R, Zhang M, Chen X, Liu Y, Liu F. Iron ions regulate antifungal HSAF biosynthesis in Lysobacter enzymogenes by manipulating the DNA-binding affinity of the ferric uptake regulator (Fur). Microbiol Spectr 2023; 11:e0061723. [PMID: 37737630 PMCID: PMC10581043 DOI: 10.1128/spectrum.00617-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/05/2023] [Indexed: 09/23/2023] Open
Abstract
Heat-stable antifungal factor (HSAF), produced by Lysobacter enzymogenes OH11, is regarded as a potential biological pesticide due to its broad-spectrum antifungal activity and novel mode of action. However, the current production of HSAF is low and cannot meet the requirements for large-scale production. Herein, we discovered that iron ions greatly promoted HSAF production, and the ferric uptake regulator (Fur) was involved in this regulatory process. Fur was also found to participate in the regulation of iron homeostasis in OH11 via the classic inhibition mechanism of Holo-Fur. Furthermore, Fur was collectively observed to directly bind to the promoter of the HSAF biosynthesis gene, and its DNA-binding affinity was attenuated by the addition of iron ions in vitro and in vivo. Its regulatory mechanism followed the uncommon inhibition mechanism of Apo-Fur. In summary, Fur exhibited a bidirectional regulatory mechanism in OH11. This study reveals a novel regulatory mechanism whereby Fur upregulates the biosynthesis of secondary metabolites. These findings contribute to the improvement of HSAF production and may guide its development into biological pesticides. IMPORTANCE HSAF possesses potent and broad antifungal activity with a novel mode of action. The HSAF yield is critical for fermentation production. In this study, iron ions were found to increase HSAF production, and the specific mechanism was elaborated. These results provide theoretical support for genetic transformation to improve HSAF yield, supporting its development into biological pesticides.
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Affiliation(s)
- Bao Tang
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
- School of Life Sciences, Jiangsu University, Zhengjiang, Jiangsu, China
| | - Bo Wang
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
| | - Zhizhou Xu
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Rouxian Hou
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Min Zhang
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
| | - Xian Chen
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
| | - Youzhou Liu
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
| | - Fengquan Liu
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Institute of Plant Protection, Nanjing, Jiangsu, China
- College of Plant Protection, Hainan University, Haikou, China
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11
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Siddiq A, Dong G, Balan B, Harrison LG, Jex A, Olivier M, Allain T, Buret AG. A thermo-resistant and RNase-sensitive cargo from Giardia duodenalis extracellular vesicles modifies the behaviour of enterobacteria. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e109. [PMID: 38938375 PMCID: PMC11080815 DOI: 10.1002/jex2.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) recently emerged as important players in the pathophysiology of parasitic infections. While the protist parasite Giardia duodenalis can produce EVs, their role in giardiasis remains obscure. Giardia can disrupt gut microbiota biofilms and transform commensal bacteria into invasive pathobionts at sites devoid of colonizing trophozoites via unknown mechanisms. We hypothesized that Giardia EVs could modify gut bacterial behaviour via a novel mode of trans-kingdom communication. Our findings indicate that Giardia EVs exert bacteriostatic effects on Escherichia coli HB101 and Enterobacter cloacae TW1, increasing their swimming motility. Giardia EVs also decreased the biofilm-forming ability of E. coli HB101 but not by E. cloacae TW1, supporting the hypothesis that these effects are, at least in part, bacteria-selective. E. coli HB101 and E. cloacae TW1 exhibited increased adhesion/invasion onto small intestine epithelial cells when exposed to Giardia EVs. EVs labelled with PKH67 revealed colocalization with E. coli HB101 and E. cloacae TW1 bacterial cells. Small RNA sequencing revealed a high abundance of ribosomal RNA (rRNA)- and transfer RNA (tRNA)-derived small RNAs, short-interfering RNAs (siRNAs) and micro-RNAs (miRNAs) within Giardia EVs. Proteomic analysis of EVs uncovered the presence of RNA chaperones and heat shock proteins that can facilitate the thermal stability of EVs and its sRNA cargo, as well as protein-modifying enzymes. In vitro, RNase heat-treatment assays showed that total RNAs in EVs, but not proteins, are responsible for modulating bacterial swimming motility and biofilm formation. G. duodenalis small RNAs of EVs, but not proteins, were responsible for the increased bacterial adhesion to intestinal epithelial cells induced upon exposure to Giardia EVs. Together, the findings indicate that Giardia EVs contain a heat-stable, RNase-sensitive cargo that can trigger the development of pathobiont characteristics in Enterobacteria, depicting a novel trans-kingdom cross-talk in the gut.
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Affiliation(s)
- Affan Siddiq
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
| | - George Dong
- Department of Microbiology and Immunology, The Research Institute of the McGill University Health Centre, Program in Infectious Diseases and Immunology in Global HeathMontréalQCCanada
| | - Balu Balan
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneAustralia
- The University of MelbourneMelbourneAustralia
| | - Luke G. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
| | - Aaron Jex
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneAustralia
- The University of MelbourneMelbourneAustralia
| | - Martin Olivier
- Department of Microbiology and Immunology, The Research Institute of the McGill University Health Centre, Program in Infectious Diseases and Immunology in Global HeathMontréalQCCanada
| | - Thibault Allain
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
| | - Andre G. Buret
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
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12
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Mezcord V, Escalante J, Nishimura B, Traglia GM, Sharma R, Vallé Q, Tuttobene MR, Subils T, Marin I, Pasteran F, Actis LA, Tolmasky ME, Bonomo RA, Rao G, Ramirez MS. Induced Heteroresistance in Carbapenem-Resistant Acinetobacter baumannii (CRAB) via Exposure to Human Pleural Fluid (HPF) and Its Impact on Cefiderocol Susceptibility. Int J Mol Sci 2023; 24:11752. [PMID: 37511511 PMCID: PMC10380697 DOI: 10.3390/ijms241411752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Infections caused by Carbapenem-resistant Acinetobacter baumannii (CRAB) isolates, such as hospital-acquired pneumonia (HAP), bacteremia, and skin and soft tissue infections, among others, are particularly challenging to treat. Cefiderocol, a chlorocatechol-substituted siderophore antibiotic, was approved by the U.S. Food and Drug Administration (FDA) in 2019 and prescribed for the treatment of CRAB infections. Despite the initial positive treatment outcomes with this antimicrobial, recent studies reported a higher-than-average all-cause mortality rate in patients treated with cefiderocol compared to the best available therapy. The cause(s) behind these outcomes remains unconfirmed. A plausible hypothesis is heteroresistance, a phenotype characterized by the survival of a small proportion of cells in a population that is seemingly isogenic. Recent results have demonstrated that the addition of human fluids to CRAB cultures leads to cefiderocol heteroresistance. Here, we describe the molecular and phenotypic analyses of CRAB heteroresistant bacterial subpopulations to better understand the nature of the less-than-expected successful outcomes after cefiderocol treatment. Isolation of heteroresistant variants of the CRAB strain AMA40 was carried out in cultures supplemented with cefiderocol and human pleural fluid (HPF). Two AMA40 variants, AMA40 IHC1 and IHC2, were resistant to cefiderocol. To identify mutations and gene expression changes associated with cefiderocol heteroresistance, we subjected these variants to whole genome sequencing and global transcriptional analysis. We then assessed the impact of these mutations on the pharmacodynamic activity of cefiderocol via susceptibility testing, EDTA and boronic acid inhibition analysis, biofilm formation, and static time-kill assays. Heteroresistant variants AMA40 IHC1 and AMA40 IHC2 have 53 chromosomal mutations, of which 40 are common to both strains. None of the mutations occurred in genes associated with high affinity iron-uptake systems or β-lactam resistance. However, transcriptional analyses demonstrated significant modifications in levels of expression of genes associated with iron-uptake systems or β-lactam resistance. The blaNDM-1 and blaADC-2, as well as various iron-uptake system genes, were expressed at higher levels than the parental strain. On the other hand, the carO and ompA genes' expression was reduced. One of the mutations common to both heteroresistant strains was mapped within ppiA, a gene associated with iron homeostasis in other species. Static time-kill assays demonstrated that supplementing cation-adjusted Mueller-Hinton broth with human serum albumin (HAS), the main protein component of HPF, considerably reduced cefiderocol killing activity for all three strains tested. Notably, collateral resistance to amikacin was observed in both variants. We conclude that exposing CRAB to fluids with high HSA concentrations facilitates the rise of heteroresistance associated with point mutations and transcriptional upregulation of genes coding for β-lactamases and biofilm formation. The findings from this study hold significant implications for understanding the emergence of CRAB resistance mechanisms against cefiderocol treatment. This understanding is vital for the development of treatment guidelines that can effectively address the challenges posed by CRAB infections.
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Affiliation(s)
- Vyanka Mezcord
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (V.M.)
| | - Jenny Escalante
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (V.M.)
| | - Brent Nishimura
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (V.M.)
| | - German M. Traglia
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Salto 50000, Uruguay
| | - Rajnikant Sharma
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA (Q.V.)
| | - Quentin Vallé
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA (Q.V.)
| | - Marisel R. Tuttobene
- Área Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario 2000, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario 2000, Argentina
| | - Tomás Subils
- Instituto de Procesos Biotecnológicos y Químicos de Rosario (IPROBYQ, CONICET-UNR), Rosario 2000, Argentina
| | - Ingrid Marin
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (V.M.)
| | - Fernando Pasteran
- National Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas, ANLIS Dr. Carlos G. Malbrán, Buenos Aires 1282, Argentina
| | - Luis A. Actis
- Department of Microbiology, Miami University, Oxford, OH 45056, USA
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (V.M.)
| | - Robert A. Bonomo
- Research Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Gauri Rao
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA (Q.V.)
| | - María S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92831, USA; (V.M.)
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13
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Römling U, Cao LY, Bai FW. Evolution of cyclic di-GMP signalling on a short and long term time scale. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001354. [PMID: 37384391 PMCID: PMC10333796 DOI: 10.1099/mic.0.001354] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Lian-Ying Cao
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
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14
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Abstract
The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIANtr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.
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Affiliation(s)
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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15
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Zhang F, Wang Y, Wang X, Dong H, Chen M, Du N, Wang H, Hu W, Zhang K, Gu L. RT-IVT method allows multiplex real-time quantification of in vitro transcriptional mRNA production. Commun Biol 2023; 6:453. [PMID: 37095292 PMCID: PMC10124930 DOI: 10.1038/s42003-023-04830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/11/2023] [Indexed: 04/26/2023] Open
Abstract
For the past 30 years, in vitro transcription (IVT) technology has been extensively used for RNA production or for basic transcriptional mechanism research. However, methods for mRNA quantification still need to be improved. In this study, we designed a RT-IVT method using binary fluorescence quencher (BFQ) probes and the PBCV-1 DNA ligase to quantify mRNA production in real-time by fluorescence resonance energy transfer (FRET) and RNA-splinted DNA ligation. Compared with existing methods, the RT-IVT method is inexpensive and non-radioactive, and can detect mRNA production in unpurified systems in real-time and shows high sensitivity and selectivity. The activity of T7 RNA polymerase and Escherichia coli RNA polymerase holoenzyme was then characterized with this method. We then multiplexed the real-time mRNA quantification for three T7 promoters on a RT-PCR thermocycler by using BFQ probes with different colored fluorophores that were specific for each target. Ultimately, we created an inexpensive multiplexed method to quantify mRNA production in real-time, and future research could use these methods to measure the affinity of transcriptional repressors to their target DNA sequence.
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Affiliation(s)
- Fengyu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Xiaomeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Hongjie Dong
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibaizhong Road, 272033, Jining, China
| | - Min Chen
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Ning Du
- Institute of Ecology and Biodiversity, School of Life Sciences, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Hongwei Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China
| | - Kundi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China.
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237, Qingdao, China.
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16
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Wang W, Yue Y, Zhang M, Song N, Jia H, Dai Y, Zhang F, Li C, Li B. Host acid signal controls Salmonella flagella biogenesis through CadC-YdiV axis. Gut Microbes 2022; 14:2146979. [PMID: 36456534 PMCID: PMC9728131 DOI: 10.1080/19490976.2022.2146979] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Upon entering host cells, Salmonella quickly turns off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control. Here, we demonstrate that the acid signal can suppress flagella synthesis and motility of Salmonella, and this occurs after the transcription of master flagellar gene flhDC and depends on the anti-FlhDC factor YdiV. YdiV expression is activated after acid treatment. A global screen with ydiV promoter DNA and total protein from acid-treated Salmonella revealed a novel regulator of YdiV, the acid-related transcription factor CadC. Further studies showed that CadCC, the DNA binding domain of CadC, directly binds to a 33 nt region of the ydiV promoter with a 0.2 μM KD affinity. Furthermore, CadC could separate H-NS-ydiV promoter DNA complex to form CadC-DNA complex at a low concentration. Structural simulation and mutagenesis assays revealed that H43 and W106 of CadC are essential for ydiV promoter binding. No acid-induced flagellum control phenotype was observed in cadC mutant or ydiV mutant strains, suggesting that flagellum control during acid adaption is dependent on CadC and YdiV. The intracellular survival ability of cadC mutant strain decreased significantly compared with WT strain while the flagellin expression could not be effectively controlled in the cadC mutant strain when surviving within host cells. Together, our results demonstrated that acid stress acts as an important host signal to trigger Salmonella flagellum control through the CadC-YdiV-FlhDC axis, allowing Salmonella to sense a hostile environment and regulate flagellar synthesis during infection.
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Affiliation(s)
- Weiwei Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yingying Yue
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Min Zhang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Nannan Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Haihong Jia
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuanji Dai
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, China
| | - Cuiling Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Bingqing Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China,Shandong First Medical University, Key Lab for Biotech-Drugs of National Health Commission, Jinan, China,KeyLaboratory for Rare & Uncommon Diseases of Shandong Province, Jinan, China,CONTACT Bingqing Li Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan250021Shandong, China
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17
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Song Y, Zhang S, Ye Z, Song Y, Chen L, Tong A, He Y, Bao R. The novel type II toxin-antitoxin PacTA modulates Pseudomonas aeruginosa iron homeostasis by obstructing the DNA-binding activity of Fur. Nucleic Acids Res 2022; 50:10586-10600. [PMID: 36200834 PMCID: PMC9561280 DOI: 10.1093/nar/gkac867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
Type II toxin–antitoxin (TA) systems are widely distributed in bacterial and archaeal genomes and are involved in diverse critical cellular functions such as defense against phages, biofilm formation, persistence, and virulence. GCN5-related N-acetyltransferase (GNAT) toxin, with an acetyltransferase activity-dependent mechanism of translation inhibition, represents a relatively new and expanding family of type II TA toxins. We here describe a group of GNAT-Xre TA modules widely distributed among Pseudomonas species. We investigated PacTA (one of its members encoded by PA3270/PA3269) from Pseudomonas aeruginosa and demonstrated that the PacT toxin positively regulates iron acquisition in P. aeruginosa. Notably, other than arresting translation through acetylating aminoacyl-tRNAs, PacT can directly bind to Fur, a key ferric uptake regulator, to attenuate its DNA-binding affinity and thus permit the expression of downstream iron-acquisition-related genes. We further showed that the expression of the pacTA locus is upregulated in response to iron starvation and the absence of PacT causes biofilm formation defect, thereby attenuating pathogenesis. Overall, these findings reveal a novel regulatory mechanism of GNAT toxin that controls iron-uptake-related genes and contributes to bacterial virulence.
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Affiliation(s)
- Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610093, China.,Central Laboratory, Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu 610081, China
| | - Siping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zirui Ye
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongyan Song
- Central Laboratory, Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu 610081, China
| | - Lin Chen
- Central Laboratory, Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu 610081, China
| | - Aiping Tong
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610093, China
| | - Yongxing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610093, China
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18
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Fu D, Shao Y, Li J, Wu J, Wu X, Song X, Tu J, Qi K. LuxR family transcriptional repressor YjjQ modulates the biofilm formation and motility of avian pathogenic Escherichia coli. Res Vet Sci 2022; 152:10-19. [PMID: 35901637 DOI: 10.1016/j.rvsc.2022.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/09/2022] [Accepted: 07/17/2022] [Indexed: 11/27/2022]
Abstract
Avian pathogenic Escherichia coli (APEC) can cause the acute and sudden death of poultry, which leads to serious economic losses in the poultry industry. Biofilm formation contributes to the persistence of bacterial infection, drug resistance, and resistance to diverse environmental stress. Many transcription regulators in APEC play an essential role in the formation of biofilm and could provide further insights into APEC pathogenesis. YjjQ has an important role in the pathogenicity of bacteria by regulating the expression of virulence factors, such as flagellar and iron uptake. However, YjjQ regulates other virulence factors, and their role in the overall regulatory network is unclear. Here, we further evaluate the function of YjjQ on APEC biofilm formation and motility. In this study, we successfully constructed mutant (AE27∆yjjQ) and complement (AE27ΔyjjQ-comp) strains of the wild-type strain AE27. Inactivation of the yjjQ gene significantly increased biofilm-forming ability in APEC. Scanning electron microscopy showed that the biofilm formation of the AE27 was single-layered and flat, whereas that of the AE27∆yjjQ had a porous three-dimensional structure. Moreover, the deletion of the yjjQ gene inhibited the motility of APEC. RNA-sequencing was used to further investigate the regulatory mechanism of YjjQ in APEC. The results indicate that YjjQ regulates biofilm formation and flagellar genes in AE27∆yjjQ. RT-qPCR shows that YjjQ affects the transcriptional levels of genes, including flagella genes (flhD, flhC and flgE), and biofilm formation genes (pstA, uhpC, nikD, and ygcS). These results confirm that the transcription regulator YjjQ is involved in APEC biofilm formation and motility, and provide new evidence for the prevention and control of APEC.
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Affiliation(s)
- Dandan Fu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jiaxuan Li
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jianmei Wu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Xiaoyan Wu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, PR China.
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Antibiotic resistance and siderophores production by clinical Escherichia coli strains. BIOTECHNOLOGIA 2022; 103:169-184. [PMID: 36606072 PMCID: PMC9642952 DOI: 10.5114/bta.2022.116211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/17/2022] [Accepted: 03/01/2022] [Indexed: 01/09/2023] Open
Abstract
The phenomenon of antibiotic resistance has dramatically increased in the last few decades, especially in enterobacterial pathogens. Different strains of Escherichia coli have been reported to produce a variety of structurally different siderophores. In the present study, 32 E. coli strains were collected from different clinical settings in Cairo, Egypt and subjected to the antibiotic susceptibility test by using 19 antibiotics belonging to 7 classes of chemical groups. The results indicated that 31 strains could be considered as extensively drug-resistant and only one strain as pan drug-resistant. Siderophores production by all the tested E. coli strains was determined qualitatively and quantitatively. Two E. coli strains coded 21 and 49 were found to be the most potent siderophores producers, with 79.9 and 46.62%, respectively. Bacterial colonies with cured plasmids derived from strain 49 showed susceptibility to all the tested antibiotics. Furthermore, E. coli DH5α cells transformed with the plasmid isolated from E. coli strain 21 or E. coli strain 49 were found to be susceptible to ansamycins, quinolones, and sulfonamide groups of antibiotics. In contrast, both plasmid-cured and plasmid-transformed strains did not produce siderophores, indicating that the genes responsible for siderophores production were located on plasmids and regulated by genes located on the chromosome. On the basis of the obtained results, it could be concluded that there is a positive correlation between antibiotic resistance, especially to quinolones and sulfonamide groups, and siderophores production by E. coli strains used in this study.
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Wang XP, Huang Z, Li YL, Jin KY, Dong DJ, Wang JX, Zhao XF. Krüppel-like factor 15 integrated autophagy and gluconeogenesis to maintain glucose homeostasis under 20-hydroxyecdysone regulation. PLoS Genet 2022; 18:e1010229. [PMID: 35696369 PMCID: PMC9191741 DOI: 10.1371/journal.pgen.1010229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/02/2022] [Indexed: 01/18/2023] Open
Abstract
The regulation of glycometabolism homeostasis is vital to maintain health and development of animal and humans; however, the molecular mechanisms by which organisms regulate the glucose metabolism homeostasis from a feeding state switching to a non-feeding state are not fully understood. Using the holometabolous lepidopteran insect Helicoverpa armigera, cotton bollworm, as a model, we revealed that the steroid hormone 20-hydroxyecdysone (20E) upregulated the expression of transcription factor Krüppel-like factor (identified as Klf15) to promote macroautophagy/autophagy, apoptosis and gluconeogenesis during metamorphosis. 20E via its nuclear receptor EcR upregulated Klf15 transcription in the fat body during metamorphosis. Knockdown of Klf15 using RNA interference delayed pupation and repressed autophagy and apoptosis of larval fat body during metamorphosis. KLF15 promoted autophagic flux and transiting to apoptosis. KLF15 bound to the KLF binding site (KLF bs) in the promoter of Atg8 (autophagy-related gene 8/LC3) to upregulate Atg8 expression. Knockdown Atg8 reduced free fatty acids (FFAs), glycerol, free amino acids (FAAs) and glucose levels. However, knockdown of Klf15 accumulated FFAs, glycerol, and FAAs. Glycolysis was switched to gluconeogenesis, trehalose and glycogen synthesis were changed to degradation during metamorphosis, which were accompanied by the variation of the related genes expression. KLF15 upregulated phosphoenolpyruvate carboxykinase (Pepck) expression by binding to KLF bs in the Pepck promoter for gluconeogenesis, which utilised FFAs, glycerol, and FAAs directly or indirectly to increase glucose in the hemolymph. Taken together, 20E via KLF15 integrated autophagy and gluconeogenesis by promoting autophagy-related and gluconeogenesis-related genes expression. Glucose is the direct substrate for energy production in animal and humans. Autophagy and gluconeogenesis are known to help organisms maintaining energy substrates; however, the mechanism of integration of autophagy and gluconeogenesis is unclear. Holometabolous insects stop feeding during metamorphosis under steroid hormone 20-hydroxyecdysone (20E) regulation, providing a good model for the study. Using lepidopteran insect Helicoverpa armigera, cotton bollworm, as a model, we revealed that Krüppel-like factor 15 (KLF15) integrated autophagy and gluconeogenesis to maintain glucose homeostasis under 20E regulation. 20E increased Klf15 expression, and KLF15 in turn promoted autophagy-related and gluconeogenesis-related genes expression during metamorphosis. Autophagy and apoptosis of the fat body provided substrates for gluconeogenesis. This work clarified the important functions and mechanisms of KLF15 in autophagy and glycometabolism reprogramming for glucose homeostasis after feeding stop during insect metamorphosis.
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Affiliation(s)
- Xiao-Pei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhen Huang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Yan-Li Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Ke-Yan Jin
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Du-Juan Dong
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
- * E-mail:
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Switching off Bacterial Flagellar Biogenesis by YdiU-Mediated UMPylation of FlhDC. mBio 2022; 13:e0024922. [PMID: 35532215 PMCID: PMC9239255 DOI: 10.1128/mbio.00249-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Bacterial flagellin activates the host immune system and triggers pyroptosis. Salmonella reduces flagellin expression when it survives within host cells. Here, we found that the UMPylator YdiU significantly altered the Salmonella flagellar biogenesis process upon host cell entry. The expression levels of class II and class III flagellar genes, but not the class I flagellar genes flhDC, were dramatically increased in a ΔydiU strain compared to wild-type (WT) Salmonella in a host-simulating environment. A direct interaction between YdiU and FlhDC was detected by bacterial two-hybrid assay. Furthermore, YdiU efficiently catalyzed the UMPylation of FlhC but not FlhD, FliA, or FliC. UMPylation of FlhC completely eliminated its DNA-binding activity. In vivo experiments showed that YdiU was required and sufficient for Salmonella flagellar control within host cells. Mice infected with the ΔydiU strain died much earlier than WT strain-infected mice and developed much more severe inflammation and injury in organs and much higher levels of cytokines in blood, demonstrating that early host death induced by the ΔydiU strain is probably due to excessive inflammation. Our results indicate that YdiU acts as an essential factor of Salmonella to mediate host immune escape.
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Abstract
Iron limitation is a universal strategy of host immunity during bacterial infection. However, the mechanisms by which pathogens antagonize host nutritional immunity have not been fully elucidated. Here, we identified a requirement for the UMPylator YdiU for this process in Salmonella. The expression of YdiU was dramatically induced by the metal starvation signal. The intracellular iron content was much lower in the ΔydiU strain than in wild-type Salmonella, and the ΔydiU strain exhibited severe growth defect under metal deficiency environments. Genome-wide expression analyses revealed significantly decreased expression of iron uptake genes in ΔydiU strain compared with the wild-type strain. Interestingly, YdiU did not affect the expression level of the major iron uptake regulator Fur but directly UMPylated Fur on its H118 residue in vivo and in vitro. UMPylation destroyed the Fur dimer, promoted Fur aggregation, and eliminated the DNA-binding activity of Fur, thus abolishing the ability of Fur to inhibit iron uptake. Restricting Fur to the deUMPylated state dramatically eliminates Salmonella iron uptake in iron deficiency environments. In parallel, YdiU facilitates Salmonella survival within host cells by regulating the iron uptake pathway.
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Sulfane Sulfur Posttranslationally Modifies the Global Regulator AdpA to Influence Actinorhodin Production and Morphological Differentiation of Streptomyces coelicolor. mBio 2022; 13:e0386221. [PMID: 35467418 PMCID: PMC9239190 DOI: 10.1128/mbio.03862-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factor AdpA is a key regulator controlling both secondary metabolism and morphological differentiation in Streptomyces. Due to its critical functions, its expression undergoes multilevel regulations at transcriptional, posttranscriptional, and translational levels, yet no posttranslational regulation has been reported. Sulfane sulfur, such as hydro polysulfide (HSnH, n ≥ 2) and organic polysulfide (RSnH, n ≥ 2), is common inside microorganisms, but its physiological functions are largely unclear. Here, we discovered that sulfane sulfur posttranslationally modifies AdpA in Streptomyces coelicolor via specifically reacting with Cys62 of AdpA to form a persulfide (Cys62-SSH). This modification decreases the affinity of AdpA to its self-promoter PadpA, allowing increased expression of adpA, further promoting the expression of its target genes actII-4 and wblA. ActII-4 activates actinorhodin biosynthesis, and WblA regulates morphological development. Bioinformatics analyses indicated that AdpA-Cys62 is highly conserved in Streptomyces, suggesting the prevalence of such modification in this genus. Thus, our study unveils a new type of regulation on the AdpA activity and sheds a light on how sulfane sulfur stimulates the production of antibiotics in Streptomyces.
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Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. Int J Mol Sci 2022; 23:ijms23042179. [PMID: 35216300 PMCID: PMC8879271 DOI: 10.3390/ijms23042179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.
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25
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Wang W, Yue Y, Zhang M, Song N, Jia H, Dai Y, Zhang F, Li C, Li B. Host acid signal controls Salmonella flagella biogenesis through CadC-YdiV axis. Gut Microbes 2022. [PMID: 36456534 DOI: 10.1080/194909762125747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Upon entering host cells, Salmonella quickly turns off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control. Here, we demonstrate that the acid signal can suppress flagella synthesis and motility of Salmonella, and this occurs after the transcription of master flagellar gene flhDC and depends on the anti-FlhDC factor YdiV. YdiV expression is activated after acid treatment. A global screen with ydiV promoter DNA and total protein from acid-treated Salmonella revealed a novel regulator of YdiV, the acid-related transcription factor CadC. Further studies showed that CadCC, the DNA binding domain of CadC, directly binds to a 33 nt region of the ydiV promoter with a 0.2 μM KD affinity. Furthermore, CadC could separate H-NS-ydiV promoter DNA complex to form CadC-DNA complex at a low concentration. Structural simulation and mutagenesis assays revealed that H43 and W106 of CadC are essential for ydiV promoter binding. No acid-induced flagellum control phenotype was observed in cadC mutant or ydiV mutant strains, suggesting that flagellum control during acid adaption is dependent on CadC and YdiV. The intracellular survival ability of cadC mutant strain decreased significantly compared with WT strain while the flagellin expression could not be effectively controlled in the cadC mutant strain when surviving within host cells. Together, our results demonstrated that acid stress acts as an important host signal to trigger Salmonella flagellum control through the CadC-YdiV-FlhDC axis, allowing Salmonella to sense a hostile environment and regulate flagellar synthesis during infection.
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Affiliation(s)
- Weiwei Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yingying Yue
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Min Zhang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Nannan Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Haihong Jia
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuanji Dai
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, China
| | - Cuiling Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Bingqing Li
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Shandong First Medical University, Key Lab for Biotech-Drugs of National Health Commission, Jinan, China
- KeyLaboratory for Rare & Uncommon Diseases of Shandong Province, Jinan, China
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Shao S, Li C, Zhao L, Zhang Y, Yin K, Wang Q. Interplay between ferric uptake regulator Fur and horizontally acquired virulence regulator EsrB coordinates virulence gene expression in Edwardsiella piscicida. Microbiol Res 2021; 253:126892. [PMID: 34673373 DOI: 10.1016/j.micres.2021.126892] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 12/23/2022]
Abstract
Edwardsiella piscicida mediates hemorrhagic septicemia and is a leading pathogen of fish. E. piscicida invades and colonizes macrophages using type III and VI secretion systems (T3/T6SS) that are controlled by a two-component system (TCS) EsrA-EsrB. Iron acquisition is essential for E. piscicida pathogenesis and coordination between iron and TCS signaling in modulating bacterial virulence is not well understood. Here, we show that iron uptake systems are co-regulated by ferric uptake regulator (Fur) in E. piscicida. Fur bound to 98 genes that harbored conserved Fur-box to globally control the expression of ∼755 genes, including those encoding iron uptake systems, T3/T6SS, and Icc, cAMP phosphodiesterase that represses biofilm formation. Additionally, Fur, in complex with iron, bound to the esrB promoter to repress expression and ultimately attenuated virulence. Conversely, EsrB activated the expression of T3/T6SS and iron uptake systems to mitigate a shortage of intracellular iron during iron scarcity. Furthermore, EsrB directly bound to and activated the fur promoter, leading to Fur-ferrous ion-dependent esrB repression in the presence of iron. Finally, Fur-EsrB interplay was essential for bacterial fitness during in vivo infection and survival in seawater environments. Collectively, we highlight the mechanisms that underlie the reciprocal regulatory networks of iron homeostasis and virulence systems in E. piscicida.
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Affiliation(s)
- Shuai Shao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Chunli Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Luyao Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519000, Zhuhai, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China
| | - Kaiyu Yin
- School of Hospitality Management, Shanghai Business School, Shanghai, 200235, China.
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China.
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27
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Zhang Y, Liu Z, Tang Y, Ma X, Tang H, Li H, Liu Z. Cbl upregulates cysH for hydrogen sulfide production in Aeromonas veronii. PeerJ 2021; 9:e12058. [PMID: 34589297 PMCID: PMC8435198 DOI: 10.7717/peerj.12058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/04/2021] [Indexed: 11/20/2022] Open
Abstract
Endogenous hydrogen sulfide (H2S) is generated in many metabolism pathways, and has been recognized as a second messenger against antibiotics and reactive oxygen species (ROS). In Aeromonas veronii, Small Protein B (SmpB) plays an important role in resisting stress. The absence of smpB could trigger sulfate assimilation pathway to adapt the nutrient deficiency, of which was mediated by up-regulation of cbl and cys genes and followed with enhancing H2S production. To figure out the mutual regulations of cbl and cys genes, a series of experiments were performed. Compared with the wild type, cysH was down-regulated significantly in cbl deletion by qRT-PCR. The fluorescence analysis further manifested that Cbl had a positive regulatory effect on the promoter of cysJIH. Bacterial one-hybrid analysis and electrophoretic mobility shift assay (EMSA) verified that Cbl bound with the promoter of cysJIH. Collectively, the tolerance to adversity could be maintained by the production of H2S when SmpB was malfunctioned, of which the activity of cysJIH promoter was positively regulated by upstream Cbl protein. The outcomes also suggested the enormous potentials of Aeromonas veronii in environmental adaptability.
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Affiliation(s)
| | | | | | - Xiang Ma
- Hainan University, Haikou, China
| | | | - Hong Li
- Hainan University, Haikou, China
| | - Zhu Liu
- Hainan University, Haikou, China
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