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Liu L, Luo D, Zhang Y, Liu D, Yin K, Tang Q, Chou SH, He J. Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from Bacillus thuringiensis. Microbiol Spectr 2024; 12:e0045024. [PMID: 38819160 PMCID: PMC11218506 DOI: 10.1128/spectrum.00450-24] [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: 02/19/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
A riboswitch generally regulates the expression of its downstream genes through conformational change in its expression platform (EP) upon ligand binding. The cyclic diguanosine monophosphate (c-di-GMP) class I riboswitch Bc1 is widespread and conserved among Bacillus cereus group species. In this study, we revealed that Bc1 has a long EP with two typical ρ-independent terminator sequences 28 bp apart. The upstream terminator T1 is dominant in vitro, while downstream terminator T2 is more efficient in vivo. Through mutation analysis, we elucidated that Bc1 exerts a rare and incoherent "transcription-translation" dual regulation with T2 playing a crucial role. However, we found that Bc1 did not respond to c-di-GMP under in vitro transcription conditions, and the expressions of downstream genes did not change with fluctuation in intracellular c-di-GMP concentration. To explore this puzzle, we conducted SHAPE-MaP and confirmed the interaction of Bc1 with c-di-GMP. This shows that as c-di-GMP concentration increases, T1 unfolds but T2 remains almost intact and functional. The presence of T2 masks the effect of T1 unwinding, resulting in no response of Bc1 to c-di-GMP. The high Shannon entropy values of EP region imply the potential alternative structures of Bc1. We also found that zinc uptake regulator can specifically bind to the dual terminator coding sequence and slightly trigger the response of Bc1 to c-di-GMP. This work will shed light on the dual-regulation riboswitch and enrich our understanding of the RNA world.IMPORTANCEIn nature, riboswitches are involved in a variety of metabolic regulation, most of which preferentially regulate transcription termination or translation initiation of downstream genes in specific ways. Alternatively, the same or different riboswitches can exist in tandem to enhance regulatory effects or respond to multiple ligands. However, many putative conserved riboswitches have not yet been experimentally validated. Here, we found that the c-di-GMP riboswitch Bc1 with a long EP could form a dual terminator and exhibit non-canonical and incoherent "transcription-translation" dual regulation. Besides, zinc uptake regulator specifically bound to the coding sequence of the Bc1 EP and slightly mediated the action of Bc1. The application of SHAPE-MaP to the dual regulation mechanism of Bc1 may establish the foundation for future studies of such complex untranslated regions in other bacterial genomes.
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Affiliation(s)
- Lu Liu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dehua Luo
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongji Zhang
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dingqi Liu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kang Yin
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Tang
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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2
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Lee-Lopez C, Islam MS, Meléndez AB, Yukl ET. Influence of the Heme Nitric Oxide/Oxygen Binding Protein (H-NOX) on Cell Cycle Regulation in Caulobacter crescentus. Mol Cell Proteomics 2023; 22:100679. [PMID: 37979947 PMCID: PMC10746521 DOI: 10.1016/j.mcpro.2023.100679] [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: 06/13/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023] Open
Abstract
The ability of an organism to respond to environmental changes is paramount to survival across a range of conditions. The bacterial heme nitric oxide/oxygen binding proteins (H-NOX) are a family of biofilm-regulating gas sensors that enable bacteria to respond accordingly to the cytotoxic molecule nitric oxide. By interacting with downstream signaling partners, H-NOX regulates the production of the bacterial secondary messenger cyclic diguanylate monophosphate (c-di-GMP) to influence biofilm formation. The aquatic organism Caulobacter crescentus has the propensity to attach to surfaces as part of its transition into the stalked S-phase of its life cycle. This behavior is heavily influenced by intracellular c-di-GMP and thus poses H-NOX as a potential influencer of C. crescentus surface attachment and cell cycle. By generating a strain of C. crescentus lacking hnox, our laboratory has demonstrated that this strain exhibits a considerable growth deficit, an increase in biofilm formation, and an elevation in c-di-GMP. Furthermore, in our comprehensive proteome study of 2779 proteins, 236 proteins were identified that exhibited differential expression in Δhnox C. crescentus, with 132 being downregulated and 104 being upregulated, as determined by a fold change of ≥1.5 or ≤0.66 and a p value ≤0.05. Our systematic analysis unveiled several regulated candidates including GcrA, PopA, RsaA, FtsL, DipM, FlgC, and CpaE that are associated with the regulation of the cellular division process, surface proteins, flagellum, and pili assembly. Further examination of Gene Ontology and pathways indicated that the key differences could be attributed to several metabolic processes. Taken together, our data indicate a role for the HNOX protein in C. crescentus cell cycle progression.
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Affiliation(s)
- Cameron Lee-Lopez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
| | - Md Shariful Islam
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA; Department of Mathematics and Physics, North South University, Dhaka, Bangladesh
| | - Ady B Meléndez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA
| | - Erik T Yukl
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico, USA.
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Ahmed YM, Bowman GR. Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain in C. crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553945. [PMID: 37645878 PMCID: PMC10462113 DOI: 10.1101/2023.08.19.553945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Asymmetric cell division in bacteria is achieved through cell polarization, where regulatory proteins are directed to specific cell poles. Curiously, both poles contain a membraneless microdomain, established by the polar assembly hub PopZ, through most of the cell cycle, yet many PopZ clients are unipolar and transiently localized. We find that PopZ's interaction with the response regulator CpdR is controlled by phosphorylation, via the histidine kinase CckA. Phosphorylated CpdR does not interact with PopZ and is not localized to cell poles. At poles where CckA acts as a phosphatase, de-phosphorylated CpdR binds directly with PopZ and subsequently recruits ClpX, substrates, and other members of a protease complex to the cell pole. We also find that co-recruitment of protease components and substrates to polar microdomains enhances their coordinated activity. This study connects phosphosignaling with polar assembly and the activity of a protease that triggers cell cycle progression and cell differentiation.
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Affiliation(s)
- Yasin M Ahmed
- Department of Molecular Biology, University of Wyoming, Laramie Wyoming 82071
| | - Grant R Bowman
- Department of Molecular Biology, University of Wyoming, Laramie Wyoming 82071
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4
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Lu N, Duvall SW, Zhao G, Kowallis KA, Zhang C, Tan W, Sun J, Petitjean HN, Tomares DT, Zhao GP, Childers WS, Zhao W. Scaffold-Scaffold Interaction Facilitates Cell Polarity Development in Caulobacter crescentus. mBio 2023; 14:e0321822. [PMID: 36971555 PMCID: PMC10127582 DOI: 10.1128/mbio.03218-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Caulobacter crescentus
is a well-established bacterial model to study asymmetric cell division for decades. During cell development, the polarization of scaffold protein PopZ from monopolar to bipolar plays a central role in
C. crescentus
asymmetric cell division.
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5
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Goodsell DS, Lasker K. Integrative visualization of the molecular structure of a cellular microdomain. Protein Sci 2023; 32:e4577. [PMID: 36700303 PMCID: PMC9926476 DOI: 10.1002/pro.4577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus. The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well-studied example of a cellular condensate.
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Affiliation(s)
- David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.,Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Keren Lasker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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6
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Tan W, Cheng S, Li Y, Li XY, Lu N, Sun J, Tang G, Yang Y, Cai K, Li X, Ou X, Gao X, Zhao GP, Childers WS, Zhao W. Phase separation modulates the assembly and dynamics of a polarity-related scaffold-signaling hub. Nat Commun 2022; 13:7181. [PMID: 36418326 PMCID: PMC9684454 DOI: 10.1038/s41467-022-35000-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Asymmetric cell division (ACD) produces morphologically and behaviorally distinct cells and is the primary way to generate cell diversity. In the model bacterium Caulobacter crescentus, the polarization of distinct scaffold-signaling hubs at the swarmer and stalked cell poles constitutes the basis of ACD. However, mechanisms involved in the formation of these hubs remain elusive. Here, we show that a swarmer-cell-pole scaffold, PodJ, forms biomolecular condensates both in vitro and in living cells via phase separation. The coiled-coil 4-6 and the intrinsically disordered regions are the primary domains that contribute to biomolecular condensate generation and signaling protein recruitment in PodJ. Moreover, a negative regulation of PodJ phase separation by the stalked-cell-pole scaffold protein SpmX is revealed. SpmX impedes PodJ cell-pole accumulation and affects its recruitment ability. Together, by modulating the assembly and dynamics of scaffold-signaling hubs, phase separation may serve as a general biophysical mechanism that underlies the regulation of ACD in bacteria and other organisms.
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Affiliation(s)
- Wei Tan
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Sihua Cheng
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Yingying Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Xiao-Yang Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.256922.80000 0000 9139 560XDepartment of Pharmacy, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - Ning Lu
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Jingxian Sun
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Guiyue Tang
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Yujiao Yang
- grid.9227.e0000000119573309CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kezhu Cai
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.263817.90000 0004 1773 1790Department of Materials Science and Engineering, School of Engineering, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xuefei Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Xijun Ou
- grid.263817.90000 0004 1773 1790Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xiang Gao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Guo-Ping Zhao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.9227.e0000000119573309CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443State Key Lab of Genetic Engineering & Institutes of Biomedical Sciences, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - W. Seth Childers
- grid.21925.3d0000 0004 1936 9000Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Wei Zhao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
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7
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Fatima NI, Fazili KM, Bhat NH. Proteolysis dependent cell cycle regulation in Caulobacter crescentus. Cell Div 2022; 17:3. [PMID: 35365160 PMCID: PMC8973945 DOI: 10.1186/s13008-022-00078-z] [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: 08/21/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
Caulobacter crescentus, a Gram-negative alpha-proteobacterium, has surfaced as a powerful model system for unraveling molecular networks that control the bacterial cell cycle. A straightforward synchronization protocol and existence of many well-defined developmental markers has allowed the identification of various molecular circuits that control the underlying differentiation processes executed at the level of transcription, translation, protein localization and dynamic proteolysis. The oligomeric AAA+ protease ClpXP is a well-characterized example of an enzyme that exerts post-translational control over a number of pathways. Also, the proteolytic pathways of its candidate proteins are reported to play significant roles in regulating cell cycle and protein quality control. A detailed evaluation of the impact of its proteolysis on various regulatory networks of the cell has uncovered various significant cellular roles of this protease in C. crescentus. A deeper insight into the effects of regulatory proteolysis with emphasis on cell cycle progression could shed light on how cells respond to environmental cues and implement developmental switches. Perturbation of this network of molecular machines is also associated with diseases such as bacterial infections. Thus, research holds immense implications in clinical translation and health, representing a promising area for clinical advances in the diagnosis, therapeutics and prognosis.
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Affiliation(s)
- Nida I Fatima
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Khalid Majid Fazili
- Department of Biotechnology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Nowsheen Hamid Bhat
- Department of Biotechnology, Central University of Kashmir, Ganderbal, Jammu and Kashmir, 191201, India.
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