1
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Xu G, Yang S. Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity. Int J Biol Macromol 2024; 275:133635. [PMID: 38964677 DOI: 10.1016/j.ijbiomac.2024.133635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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2
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Meier SSM, Multamäki E, Ranzani AT, Takala H, Möglich A. Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling. Nat Commun 2024; 15:4876. [PMID: 38858359 PMCID: PMC11164954 DOI: 10.1038/s41467-024-49251-8] [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: 02/07/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Bacteria must constantly probe their environment for rapid adaptation, a crucial need most frequently served by two-component systems (TCS). As one component, sensor histidine kinases (SHK) control the phosphorylation of the second component, the response regulator (RR). Downstream responses hinge on RR phosphorylation and can be highly stringent, acute, and sensitive because SHKs commonly exert both kinase and phosphatase activity. With a bacteriophytochrome TCS as a paradigm, we here interrogate how this catalytic duality underlies signal responses. Derivative systems exhibit tenfold higher red-light sensitivity, owing to an altered kinase-phosphatase balance. Modifications of the linker intervening the SHK sensor and catalytic entities likewise tilt this balance and provide TCSs with inverted output that increases under red light. These TCSs expand synthetic biology and showcase how deliberate perturbations of the kinase-phosphatase duality unlock altered signal-response regimes. Arguably, these aspects equally pertain to the engineering and the natural evolution of TCSs.
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Affiliation(s)
| | - Elina Multamäki
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- Department of Anatomy, University of Helsinki, Helsinki, Finland.
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany.
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
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3
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Kaczmarczyk A, van Vliet S, Jakob RP, Teixeira RD, Scheidat I, Reinders A, Klotz A, Maier T, Jenal U. A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution. Nat Commun 2024; 15:3920. [PMID: 38724508 PMCID: PMC11082216 DOI: 10.1038/s41467-024-48295-0] [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: 01/18/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Monitoring changes of signaling molecules and metabolites with high temporal resolution is key to understanding dynamic biological systems. Here, we use directed evolution to develop a genetically encoded ratiometric biosensor for c-di-GMP, a ubiquitous bacterial second messenger regulating important biological processes like motility, surface attachment, virulence and persistence. The resulting biosensor, cdGreen2, faithfully tracks c-di-GMP in single cells and with high temporal resolution over extended imaging times, making it possible to resolve regulatory networks driving bimodal developmental programs in different bacterial model organisms. We further adopt cdGreen2 as a simple tool for in vitro studies, facilitating high-throughput screens for compounds interfering with c-di-GMP signaling and biofilm formation. The sensitivity and versatility of cdGreen2 could help reveal c-di-GMP dynamics in a broad range of microorganisms with high temporal resolution. Its design principles could also serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites and antibiotics.
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Affiliation(s)
- Andreas Kaczmarczyk
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| | - Simon van Vliet
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Roman Peter Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | | | - Inga Scheidat
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alberto Reinders
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alexander Klotz
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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4
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Arkhipov DV, Lomin SN, Romanov GA. A Model of the Full-Length Cytokinin Receptor: New Insights and Prospects. Int J Mol Sci 2023; 25:73. [PMID: 38203244 PMCID: PMC10779265 DOI: 10.3390/ijms25010073] [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: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Cytokinins (CK) are one of the most important classes of phytohormones that regulate a wide range of processes in plants. A CK receptor, a sensor hybrid histidine kinase, was discovered more than 20 years ago, but the structural basis for its signaling is still a challenge for plant biologists. To date, only two fragments of the CK receptor structure, the sensory module and the receiver domain, were experimentally resolved. Some other regions were built up by molecular modeling based on structures of proteins homologous to CK receptors. However, in the long term, these data have proven insufficient for solving the structure of the full-sized CK receptor. The functional unit of CK receptor is the receptor dimer. In this article, a molecular structure of the dimeric form of the full-length CK receptor based on AlphaFold Multimer and ColabFold modeling is presented for the first time. Structural changes of the receptor upon interacting with phosphotransfer protein are visualized. According to mathematical simulation and available data, both types of dimeric receptor complexes with hormones, either half- or fully liganded, appear to be active in triggering signals. In addition, the prospects of using this and similar models to address remaining fundamental problems of CK signaling were outlined.
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Affiliation(s)
| | | | - Georgy A. Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia; (D.V.A.); (S.N.L.)
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5
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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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6
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Structural features discriminating hybrid histidine kinase Rec domains from response regulator homologs. Nat Commun 2023; 14:1002. [PMID: 36864019 PMCID: PMC9981736 DOI: 10.1038/s41467-023-36597-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/07/2023] [Indexed: 03/04/2023] Open
Abstract
In two-component systems, the information gathered by histidine kinases (HKs) are relayed to cognate response regulators (RRs). Thereby, the phosphoryl group of the auto-phosphorylated HK is transferred to the receiver (Rec) domain of the RR to allosterically activate its effector domain. In contrast, multi-step phosphorelays comprise at least one additional Rec (Recinter) domain that is typically part of the HK and acts as an intermediary for phosphoryl-shuttling. While RR Rec domains have been studied extensively, little is known about discriminating features of Recinter domains. Here we study the Recinter domain of the hybrid HK CckA by X-ray crystallography and NMR spectroscopy. Strikingly, all active site residues of the canonical Rec-fold are pre-arranged for phosphoryl-binding and BeF3- binding does not alter secondary or quaternary structure, indicating the absence of allosteric changes, the hallmark of RRs. Based on sequence-covariation and modeling, we analyze the intra-molecular DHp/Rec association in hybrid HKs.
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7
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Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization. Sci Rep 2023; 13:2727. [PMID: 36810577 PMCID: PMC9944927 DOI: 10.1038/s41598-023-29110-0] [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: 07/31/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Bacterial second messengers c-di-GMP and (p)ppGpp have broad functional repertoires ranging from growth and cell cycle control to the regulation of biofilm formation and virulence. The recent identification of SmbA, an effector protein from Caulobacter crescentus that is jointly targeted by both signaling molecules, has opened up studies on how these global bacterial networks interact. C-di-GMP and (p)ppGpp compete for the same SmbA binding site, with a dimer of c-di-GMP inducing a conformational change that involves loop 7 of the protein that leads to downstream signaling. Here, we report a crystal structure of a partial loop 7 deletion mutant, SmbA∆loop in complex with c-di-GMP determined at 1.4 Å resolution. SmbA∆loop binds monomeric c-di-GMP indicating that loop 7 is required for c-di-GMP dimerization. Thus the complex probably represents the first step of consecutive c-di-GMP binding to form an intercalated dimer as has been observed in wild-type SmbA. Considering the prevalence of intercalated c-di-GMP molecules observed bound to proteins, the proposed mechanism may be generally applicable to protein-mediated c-di-GMP dimerization. Notably, in the crystal, SmbA∆loop forms a 2-fold symmetric dimer via isologous interactions with the two symmetric halves of c-di-GMP. Structural comparisons of SmbA∆loop with wild-type SmbA in complex with dimeric c-di-GMP or ppGpp support the idea that loop 7 is critical for SmbA function by interacting with downstream partners. Our results also underscore the flexibility of c-di-GMP, to allow binding to the symmetric SmbA∆loop dimer interface. It is envisaged that such isologous interactions of c-di-GMP could be observed in hitherto unrecognized targets.
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8
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The role of sensory kinase proteins in two-component signal transduction. Biochem Soc Trans 2022; 50:1859-1873. [DOI: 10.1042/bst20220848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Two-component systems (TCSs) are modular signaling circuits that regulate diverse aspects of microbial physiology in response to environmental cues. These molecular circuits comprise a sensor histidine kinase (HK) protein that contains a conserved histidine residue, and an effector response regulator (RR) protein with a conserved aspartate residue. HKs play a major role in bacterial signaling, since they perceive specific stimuli, transmit the message across the cytoplasmic membrane, and catalyze their own phosphorylation, and the trans-phosphorylation and dephosphorylation of their cognate response regulator. The molecular mechanisms by which HKs co-ordinate these functions have been extensively analyzed by genetic, biochemical, and structural approaches. Here, we describe the most common modular architectures found in bacterial HKs, and address the operation mode of the individual functional domains. Finally, we discuss the use of these signaling proteins as drug targets or as sensing devices in whole-cell biosensors with medical and biotechnological applications.
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9
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Wang L, Fan R, Li Z, Wang L, Bai X, Bu T, Dong Y, Xu Y, Quan C. Insights into the structure and function of the histidine kinase ComP from Bacillus amyloliquefaciens based on molecular modeling. Biosci Rep 2022; 42:BSR20220352. [PMID: 36052710 PMCID: PMC9620489 DOI: 10.1042/bsr20220352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/01/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
The ComPA two-component signal transduction system (TCS) is essential in Bacillus spp. However, the molecular mechanism of the histidine kinase ComP remains unclear. Here, we predicted the structure of ComP from Bacillus amyloliquefaciens Q-426 (BaComP) using an artificial intelligence approach, analyzed the structural characteristics based on the molecular docking results and compared homologous proteins, and then investigated the biochemical properties of BaComP. We obtained a truncated ComPS protein with high purity and correct folding in solution based on the predicted structures. The expression and purification of BaComP proteins suggested that the subdomains in the cytoplasmic region influenced the expression and stability of the recombinant proteins. ComPS is a bifunctional enzyme that exhibits the activity of both histidine kinase and phosphotransferase. We found that His571 played an obligatory role in the autophosphorylation of BaComP based on the analysis of the structures and mutagenesis studies. The molecular docking results suggested that the HATPase_c domain contained an ATP-binding pocket, and the ATP molecule was coordinated by eight conserved residues from the N, G1, and G2 boxes. Our study provides novel insight into the histidine kinase BaComP and its homologous proteins.
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Affiliation(s)
- Lulu Wang
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Ruochen Fan
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
| | - Zhuting Li
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Lina Wang
- Institute of Cancer Stem Cell, Dalian Medical University, 9 Western Lvshun Road, Dalian 116044, Liaoning, China
| | - Xue Bai
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Tingting Bu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Yuesheng Dong
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, Liaoning, China
| | - Yongbin Xu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
| | - Chunshan Quan
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, Liaoning, China
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10
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Dual Regulatory Role Exerted by Cyclic Dimeric GMP To Control FsnR-Mediated Bacterial Swimming. mBio 2022; 13:e0141422. [PMID: 36069448 DOI: 10.1128/mbio.01414-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial motility has great medical and ecological significance because of its essential role in bacterial survival and pathogenesis. Cyclic dimeric GMP (c-di-GMP), a second messenger in bacteria, is the predominant regulator of flagellar synthesis and motility and possesses turnover mechanisms that have been thoroughly investigated. Therefore, much attention has been focused on identifying the upstream stimulatory signals and downstream modules that respond to altered c-di-GMP levels. Here, we systematically analyzed c-di-GMP cyclases and phosphodiesterases in Stenotrophomonas maltophilia to screen for motility regulators. Of these enzymes, we identified and characterized a new phosphodiesterase named SisP, which was found to facilitate bacterial swimming upon stimulation with ferrous iron. SisP-mediated degradation of c-di-GMP leads to FsnR-dependent transcription of flagellar genes. Remarkably, c-di-GMP controls FsnR via two independent mechanisms: by direct binding and indirectly by modulating its phosphorylation state. In this study, we deciphered a novel "one stone, two birds" regulatory strategy of c-di-GMP and uncovered the signal that stimulates c-di-GMP hydrolysis. Facilitation of bacterial swimming motility by ferrous iron might contribute to the higher risk of bacterial infection in acutely ill patients. IMPORTANCE Stenotrophomonas maltophilia has become a great threat to human health because of the high mortality of infected patients. Swimming motility plays a crucial role in regulating bacterial virulence and adaptation. However, limited progress has been made in cyclic dimeric GMP (c-di-GMP) controlling swimming motility of S. maltophilia. Here, we characterized c-di-GMP turnover enzymes encoded by S. maltophilia and dissected the regulatory details of a phosphodiesterase named SisP. We demonstrated that SisP degrades c-di-GMP to fully activate FsnR through directly releasing FsnR from the FsnR-c-di-GMP complex and indirectly increasing its phosphorylation level. This finding uncovered a quantitative, rather than an on-off, regulatory manner employed by c-di-GMP to regulate activities of its effectors. Identification of the specific activation of SisP by ferrous iron proposes SisP as a putative drug-target for controlling bacterial infection and ferrous iron at the wounds or cuts as a putative factor contributing to the higher risk of bacterial infection.
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11
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Insights into the atypical autokinase activity of the Pseudomonas aeruginosa GacS histidine kinase and its interaction with RetS. Structure 2022; 30:1285-1297.e5. [PMID: 35767996 DOI: 10.1016/j.str.2022.06.002] [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: 12/05/2021] [Revised: 03/30/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022]
Abstract
Virulence in Pseudomonas aeruginosa (PA) depends on complex regulatory networks, involving phosphorelay systems based on two-component systems (TCSs). The GacS/GacA TCS is a master regulator of biofilm formation, swarming motility, and virulence. GacS is a membrane-associated unorthodox histidine kinase (HK) whose phosphorelay signaling pathway is inhibited by the RetS hybrid HK. Here we provide structural and functional insights into the interaction of GacS with RetS. The structure of the GacS-HAMP-H1 cytoplasmic regions reveals an unusually elongated homodimer marked by a 135 Å long helical bundle formed by the HAMP, the signaling helix (S helix) and the DHp subdomain. The HAMP and S helix regions are essential for GacS signaling and contribute to the GacS/RetS binding interface. The structure of the GacS D1 domain together with the discovery of an unidentified functional ND domain, essential for GacS full autokinase activity, unveils signature motifs in GacS required for its atypical autokinase mechanism.
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12
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Tan C, Xu P, Tao F. Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism. RESEARCH 2022. [DOI: 10.34133/research.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rationally controlling cellular metabolism is of great importance but challenging owing to its highly complex and chaotic nature. Natural existing sensory proteins like histidine kinases (HKs) are understood as “sensitive nodes” of biological networks that can trigger disruptive metabolic reprogramming (MRP) upon perceiving environmental fluctuation. Here, the “sensitive node” genes were adopted to devise a global MRP platform consisting of a CRISPR interference-mediated dual-gene combinational knockdown toolbox and survivorship-based metabolic interaction decoding algorithm. The platform allows users to decode the interfering effects of
n
×
n
gene pairs while only requiring the synthesis of
n
pairs of primers. A total of 35 HK genes and 24 glycine metabolic genes were selected as the targets to determine the effectiveness of our platform in a
Vibrio
sp. FA2. The platform was applied to decode the interfering impact of HKs on antibiotic resistance in strain FA2. A pattern of combined knockdown of HK genes (
sasA_8
and
04288
) was demonstrated to be capable of reducing antibiotic resistance of
Vibrio
by 108-fold. Patterns of combined knockdown of glycine pathway genes (e.g.,
gcvT
and
ltaE
) and several HK genes (e.g.,
cpxA
and
btsS
) were also revealed to increase glycine production. Our platform may enable an efficient and rational approach for global MRP based on the elucidation of high-order gene interactions. A web-based 1-stop service (
https://smrp.sjtu.edu.cn
) is also provided to simplify the implementation of this smart strategy in a broad range of cells.
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Affiliation(s)
- Chunlin Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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13
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Acquisition of enzymatic progress curves in real time by quenching-free ion exchange chromatography. Anal Biochem 2021; 639:114523. [PMID: 34906539 DOI: 10.1016/j.ab.2021.114523] [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: 09/29/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022]
Abstract
We describe a quenching-free, 'online' ion exchange chromatography (oIEC) method for the quantitative analysis of enzymatic reactions in real-time. We show that separate quenching of the ongoing reaction performed conventionally is not required, since enzymatic reactions are interrupted upon immobilization of the reaction compounds by binding to the stationary phase of the ion exchange column. The reaction mix samples are directly injected into the column, thereby improving data consistency and allowing automation of the process. The method allows reliable and efficient acquisition of enzymatic progress curves by automatic loading of aliquots of an ongoing reaction at predefined timepoints. We demonstrate the applicability of this method for a variety of enzymatic reactions. SUBJECT: Enzymatic assays and analysis.
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14
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Jensen BC, Vaney P, Flaspohler J, Coppens I, Parsons M. Unusual features and localization of the membrane kinome of Trypanosoma brucei. PLoS One 2021; 16:e0258814. [PMID: 34653230 PMCID: PMC8519429 DOI: 10.1371/journal.pone.0258814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
In many eukaryotes, multiple protein kinases are situated in the plasma membrane where they respond to extracellular ligands. Ligand binding elicits a signal that is transmitted across the membrane, leading to activation of the cytosolic kinase domain. Humans have over 100 receptor protein kinases. In contrast, our search of the Trypanosoma brucei kinome showed that there were only ten protein kinases with predicted transmembrane domains, and unlike other eukaryotic transmembrane kinases, seven are predicted to bear multiple transmembrane domains. Most of the ten kinases, including their transmembrane domains, are conserved in both Trypanosoma cruzi and Leishmania species. Several possess accessory domains, such as Kelch, nucleotide cyclase, and forkhead-associated domains. Surprisingly, two contain multiple regions with predicted structural similarity to domains in bacterial signaling proteins. A few of the protein kinases have previously been localized to subcellular structures such as endosomes or lipid bodies. We examined the localization of epitope-tagged versions of seven of the predicted transmembrane kinases in T. brucei bloodstream forms and show that five localized to the endoplasmic reticulum. The last two kinases are enzymatically active, integral membrane proteins associated with the flagellum, flagellar pocket, or adjacent structures as shown by both fluorescence and immunoelectron microscopy. Thus, these kinases are positioned in structures suggesting participation in signal transduction from the external environment.
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Affiliation(s)
- Bryan C. Jensen
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- * E-mail:
| | - Pashmi Vaney
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - John Flaspohler
- Biology Department, Concordia College, Moorhead, Minnesota, United States of America
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Marilyn Parsons
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Departments of Pediatrics and Global Health, University of Washington, Seattle, Washington, United States of America
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15
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Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases. Biomolecules 2021; 11:biom11101524. [PMID: 34680156 PMCID: PMC8534201 DOI: 10.3390/biom11101524] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
Two-component signal transduction systems (TCSs) are widely conserved in bacteria to respond to and adapt to the changing environment. Since TCSs are also involved in controlling the expression of virulence, biofilm formation, quorum sensing, and antimicrobial resistance in pathogens, they serve as candidates for novel drug targets. TCSs consist of a sensor histidine kinase (HK) and its cognate response regulator (RR). Upon perception of a signal, HKs autophosphorylate their conserved histidine residues, followed by phosphotransfer to their partner RRs. The phosphorylated RRs mostly function as transcriptional regulators and control the expression of genes necessary for stress response. HKs sense their specific signals not only in their extracytoplasmic sensor domain but also in their cytoplasmic and transmembrane domains. The signals are sensed either directly or indirectly via cofactors and accessory proteins. Accumulating evidence shows that a single HK can sense and respond to multiple signals in different domains. The underlying molecular mechanisms of how HK activity is controlled by these signals have been extensively studied both biochemically and structurally. In this article, we introduce the wide diversity of signal perception in different domains of HKs, together with their recently clarified structures and molecular mechanisms.
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16
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Bersching K, Jacob S. The Molecular Mechanism of Fludioxonil Action Is Different to Osmotic Stress Sensing. J Fungi (Basel) 2021; 7:jof7050393. [PMID: 34067802 PMCID: PMC8156855 DOI: 10.3390/jof7050393] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
The group III two-component hybrid histidine kinase MoHik1p in the filamentous fungus Magnaporthe oryzae is known to be a sensor for external osmotic stress and essential for the fungicidal activity of the phenylpyrrole fludioxonil. The mode of action of fludioxonil has not yet been completely clarified but rather assumed to hyperactivate the high osmolarity glycerol (HOG) signaling pathway. To date, not much is known about the detailed molecular mechanism of how osmotic stress is detected or fungicidal activity is initiated within the HOG pathway. The molecular mechanism of signaling was studied using a mutant strain in which the HisKA signaling domain was modified by an amino acid change of histidine H736 to alanine A736. We found that MoHik1pH736A is as resistant to fludioxonil but not as sensitive to osmotic stress as the null mutant ∆Mohik1. H736 is required for fludioxonil action but is not essential for sensing sorbitol stress. Consequently, this report provides evidence of the difference in the molecular mechanism of fludioxonil action and the perception of osmotic stress. This is an excellent basis to understand the successful phenylpyrrole-fungicides’ mode of action better and will give new ideas to decipher cellular signaling mechanisms.
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The upcycled roles of pseudoenzymes in two-component signal transduction. Curr Opin Microbiol 2021; 61:82-90. [PMID: 33872991 DOI: 10.1016/j.mib.2021.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022]
Abstract
Upon first glance at a bacterial genome, pseudoenzymes appear unremarkable due to their lack of critical motifs that facilitate catalysis. These pseudoenzymes exist within signal transduction enzymes including histidine kinases, response regulators, diguanylate cyclases, and phosphodiesterases. Here, we summarize recent studies of bacterial pseudo-histidine kinases and pseudo-response regulators that regulate cell division, capsule formation, and the circadian rhythm. These examples illuminate the mechanistic potential of catalytically dead signaling enzymes and their impact upon bacterial signal transduction. Moreover, proteins lacking characteristic catalytic features of two-component systems reveal the sophisticated underlying potential of canonical two-component systems.
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Vandelle E, Colombo T, Regaiolo A, Maurizio V, Libardi T, Puttilli MR, Danzi D, Polverari A. Transcriptional Profiling of Three Pseudomonas syringae pv. actinidiae Biovars Reveals Different Responses to Apoplast-Like Conditions Related to Strain Virulence on the Host. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:376-396. [PMID: 33356409 DOI: 10.1094/mpmi-09-20-0248-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pseudomonas syringae pv. actinidiae is a phytopathogen that causes devastating bacterial canker in kiwifruit. Among five biovars defined by genetic, biochemical, and virulence traits, P. syringae pv. actinidiae biovar 3 (Psa3) is the most aggressive and is responsible for the most recent reported outbreaks; however, the molecular basis of its heightened virulence is unclear. Therefore, we designed the first P. syringae multistrain whole-genome microarray, encompassing biovars Psa1, Psa2, and Psa3 and the well-established model P. syringae pv. tomato, and analyzed early bacterial responses to an apoplast-like minimal medium. Transcriptomic profiling revealed i) the strong activation in Psa3 of all hypersensitive reaction and pathogenicity (hrp) and hrp conserved (hrc) cluster genes, encoding components of the type III secretion system required for bacterial pathogenicity and involved in responses to environmental signals; ii) potential repression of the hrp/hrc cluster in Psa2; and iii) activation of flagellum-dependent cell motility and chemotaxis genes in Psa1. The detailed investigation of three gene families encoding upstream regulatory proteins (histidine kinases, their cognate response regulators, and proteins with diguanylate cyclase or phosphodiesterase domains) indicated that cyclic di-GMP may be a key regulator of virulence in P. syringae pv. actinidiae biovars. The gene expression data were supported by the quantification of biofilm formation. Our findings suggest that diverse early responses to the host apoplast, even among bacteria belonging to the same pathovar, can lead to different virulence strategies and may explain the differing outcomes of infections. Based on our detailed structural analysis of hrp operons, we also propose a revision of hrp cluster organization and operon regulation in P. syringae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Elodie Vandelle
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Teresa Colombo
- National Research Council of Italy (CNR), Institute of Molecular Biology and Pathology (IBPM) c/o Department of Biochemical Sciences "A. Rossi Fanelli", "Sapienza" University of Rome, Rome, 00185, Italy
| | - Alice Regaiolo
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Vanessa Maurizio
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Tommaso Libardi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | | | - Davide Danzi
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
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The CckA-ChpT-CtrA Phosphorelay Controlling Rhodobacter capsulatus Gene Transfer Agent Production Is Bidirectional and Regulated by Cyclic di-GMP. J Bacteriol 2021; 203:JB.00525-20. [PMID: 33288624 DOI: 10.1128/jb.00525-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
Protein phosphorylation is a universal mechanism for transducing cellular signals in prokaryotes and eukaryotes. The histidine kinase CckA, the histidine phosphotransferase ChpT, and the response regulator CtrA are conserved throughout the alphaproteobacteria. In Rhodobacter capsulatus, these proteins are key regulators of the gene transfer agent (RcGTA), which is present in several alphaproteobacteria. Using purified recombinant R. capsulatus proteins, we show in vitro autophosphorylation of CckA protein, and phosphotransfer to ChpT and thence to CtrA, to demonstrate biochemically that they form a phosphorelay. The secondary messenger cyclic di-GMP changed CckA from a kinase to a phosphatase, resulting in reversal of the phosphotransfer flow in the relay. The substitutions of two residues in CckA greatly affected the kinase or phosphatase activity of the protein in vitro, and production of mutant CckA proteins in vivo confirmed the importance of kinase but not phosphatase activity for the lytic release of RcGTA. However, phosphatase activity was needed to produce functional RcGTA particles. The binding of cyclic di-GMP to the wild-type and mutant CckA proteins was evaluated directly using a pulldown assay based on biotinylated cyclic di-GMP and streptavidin-linked beads.IMPORTANCE The CckA, ChpT, and CtrA phosphorelay proteins are widespread in the alphaproteobacteria, and there are two groups of organisms that differ in terms of whether this pathway is essential for cell viability. Little is known about the biochemical function of these proteins in organisms where the pathway is not essential, a group that includes Rhodobacter capsulatus This work demonstrates biochemically that CckA, ChpT, and CtrA also form a functional phosphorelay in the latter group and that the direction of phosphotransfer is reversed by cyclic di-GMP. It is important to improve understanding of more representatives of this pathway in order to obtain deeper insight into the function, composition, and evolutionary significance of a wider range of bacterial regulatory networks.
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20
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Aline Dias da P, Nathalia Marins de A, Gabriel Guarany de A, Robson Francisco de S, Cristiane Rodrigues G. The World of Cyclic Dinucleotides in Bacterial Behavior. Molecules 2020; 25:molecules25102462. [PMID: 32466317 PMCID: PMC7288161 DOI: 10.3390/molecules25102462] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
The regulation of multiple bacterial phenotypes was found to depend on different cyclic dinucleotides (CDNs) that constitute intracellular signaling second messenger systems. Most notably, c-di-GMP, along with proteins related to its synthesis, sensing, and degradation, was identified as playing a central role in the switching from biofilm to planktonic modes of growth. Recently, this research topic has been under expansion, with the discoveries of new CDNs, novel classes of CDN receptors, and the numerous functions regulated by these molecules. In this review, we comprehensively describe the three main bacterial enzymes involved in the synthesis of c-di-GMP, c-di-AMP, and cGAMP focusing on description of their three-dimensional structures and their structural similarities with other protein families, as well as the essential residues for catalysis. The diversity of CDN receptors is described in detail along with the residues important for the interaction with the ligand. Interestingly, genomic data strongly suggest that there is a tendency for bacterial cells to use both c-di-AMP and c-di-GMP signaling networks simultaneously, raising the question of whether there is crosstalk between different signaling systems. In summary, the large amount of sequence and structural data available allows a broad view of the complexity and the importance of these CDNs in the regulation of different bacterial behaviors. Nevertheless, how cells coordinate the different CDN signaling networks to ensure adaptation to changing environmental conditions is still open for much further exploration.
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21
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Del Medico L, Cerletti D, Schächle P, Christen M, Christen B. The type IV pilin PilA couples surface attachment and cell-cycle initiation in Caulobacter crescentus. Proc Natl Acad Sci U S A 2020; 117:9546-9553. [PMID: 32295877 PMCID: PMC7196804 DOI: 10.1073/pnas.1920143117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding how bacteria colonize surfaces and regulate cell-cycle progression in response to cellular adhesion is of fundamental importance. Here, we use transposon sequencing in conjunction with fluorescence resonance energy transfer (FRET) microscopy to uncover the molecular mechanism for how surface sensing drives cell-cycle initiation in Caulobacter crescentus We identify the type IV pilin protein PilA as the primary signaling input that couples surface contact to cell-cycle initiation via the second messenger cyclic di-GMP (c-di-GMP). Upon retraction of pili filaments, the monomeric pilin reservoir in the inner membrane is sensed by the 17-amino acid transmembrane helix of PilA to activate the PleC-PleD two-component signaling system, increase cellular c-di-GMP levels, and signal the onset of the cell cycle. We termed the PilA signaling sequence CIP for "cell-cycle initiating pilin" peptide. Addition of the chemically synthesized CIP peptide initiates cell-cycle progression and simultaneously inhibits surface attachment. The broad conservation of the type IV pili and their importance in pathogens for host colonization suggests that CIP peptide mimetics offer strategies to inhibit surface sensing, prevent biofilm formation and control persistent infections.
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Affiliation(s)
- Luca Del Medico
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Dario Cerletti
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Philipp Schächle
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Matthias Christen
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
| | - Beat Christen
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische HochschuleZürich, Zürich 8093, Switzerland
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22
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Bouillet S, Wu T, Chen S, Stock AM, Gao R. Structural asymmetry does not indicate hemiphosphorylation in the bacterial histidine kinase CpxA. J Biol Chem 2020; 295:8106-8117. [PMID: 32094228 DOI: 10.1074/jbc.ra120.012757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/19/2020] [Indexed: 11/06/2022] Open
Abstract
Histidine protein kinases (HKs) are prevalent prokaryotic sensor kinases that are central to phosphotransfer in two-component signal transduction systems, regulating phosphorylation of response regulator proteins that determine the output responses. HKs typically exist as dimers and can potentially autophosphorylate at each conserved histidine residue in the individual protomers, leading to diphosphorylation. However, analyses of HK phosphorylation in biochemical assays in vitro suggest negative cooperativity, whereby phosphorylation in one protomer of the dimer inhibits phosphorylation in the second protomer, leading to ∼50% phosphorylation of the available sites in dimers. This negative cooperativity is often correlated with an asymmetric domain arrangement, a common structural characteristic of autophosphorylation states in many HK structures. In this study, we engineered covalent dimers of the cytoplasmic domains of Escherichia coli CpxA, enabling us to quantify individual species: unphosphorylated, monophosphorylated, and diphosphorylated dimers. Together with mathematical modeling, we unambiguously demonstrate no cooperativity in autophosphorylation of CpxA despite its asymmetric structures, indicating that these asymmetric domain arrangements are not linked to negative cooperativity and hemiphosphorylation. Furthermore, the modeling indicated that many parameters, most notably minor amounts of ADP generated during autophosphorylation reactions or present in ATP preparations, can produce ∼50% total phosphorylation that may be mistakenly attributed to negative cooperativity. This study also establishes that the engineered covalent heterodimer provides a robust experimental system for investigating cooperativity in HK autophosphorylation and offers a useful tool for testing how symmetric or asymmetric structural features influence HK functions.
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Affiliation(s)
- Sophie Bouillet
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Ti Wu
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Shaoxing Chen
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
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23
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Precise timing of transcription by c-di-GMP coordinates cell cycle and morphogenesis in Caulobacter. Nat Commun 2020; 11:816. [PMID: 32041947 PMCID: PMC7010744 DOI: 10.1038/s41467-020-14585-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/13/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their G1 period. Here we demonstrate that a gradual increase in the concentration of the second messenger c-di-GMP determines precise gene expression during G1/S transition in Caulobacter crescentus. We show that c-di-GMP stimulates the kinase ShkA by binding to its central pseudo-receiver domain, activates the TacA transcription factor, and initiates a G1/S-specific transcription program leading to cell morphogenesis and S-phase entry. Activation of the ShkA-dependent genetic program causes c-di-GMP to reach peak levels, which triggers S-phase entry and promotes proteolysis of ShkA and TacA. Thus, a gradual increase of c-di-GMP results in precise control of ShkA-TacA activity, enabling G1/S-specific gene expression that coordinates cell cycle and morphogenesis. Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their G1 period. Here the authors show that an increase in c-di-GMP concentration modulates the activity of kinase ShkA and transcription factor TacA, thus enabling G1/S transition in Caulobacter.
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