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Li H, Li R, Yu H, Zhang Y, Feng H. Evolution and classification of Ser/Thr phosphatase PP2C family in bacteria: Sequence conservation, structures, domain distribution. PLoS One 2025; 20:e0322880. [PMID: 40388423 PMCID: PMC12088040 DOI: 10.1371/journal.pone.0322880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 03/28/2025] [Indexed: 05/21/2025] Open
Abstract
Serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) are widely present across various organisms and play crucial roles in regulating cellular processes such as growth, proliferation, signal transduction, and other physiological functions. Recent research has increasingly focused on the regulation of STKs and STPs in bacteria. STKs have been well studied, identified and characterized in a variety of bacterial species. However, the role of STPs in bacteria remains less understood, and the number of proteins characterized is limited. It has been found that most of the STPs characterized in bacteria were Mg2+/Mn2+ dependent 2C protein phosphatases (PP2Cs), but the evolutionary relationship and taxonomic distribution of bacterial PP2C phosphatases were still not fully elucidated. In this study, we utilized bacterial PP2C phosphatase sequences from the InterPro database to perform a phylogenetic analysis, categorizing the family into five groups. Based on this classification, we examined the evolutionary relationships, species distribution, sequence and structural variations, and domain distribution characteristics of bacterial PP2C phosphatases. Our analysis uncovered evidence of a common evolutionary origin for bacterial PP2C phosphatases. These findings advance the understanding of PP2C phosphatases, offering valuable insights for future functional studies of bacterial serine/threonine phosphatases and aiding in the design of targeted therapeutics for pathogenic bacteria.
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Affiliation(s)
- Hang Li
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Rui Li
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyue Yu
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Youhuan Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Hong Feng
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
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Zhu D, Fan Y, Wang X, Li P, Huang Y, Jiao J, Zhao C, Li Y, Wang S, Du X. Characterization of Molecular Chaperone GroEL as a Potential Virulence Factor in Cronobacter sakazakii. Foods 2023; 12:3404. [PMID: 37761113 PMCID: PMC10528849 DOI: 10.3390/foods12183404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The molecular chaperone GroEL of C. sakazakii, a highly conserved protein encoded by the gene grol, has the basic function of responding to heat shock, thus enhancing the bacterium's adaptation to dry and high-temperature environments, which poses a threat to food safety and human health. Our previous study demonstrated that GroEL was found in the bacterial membrane fraction and caused a strong immune response in C. sakazakii. In this study, we tried to elucidate the subcellular location and virulent effects of GroEL. In live C. sakazakii cells, GroEL existed in both the soluble and insoluble fractions. To study the secretory mechanism of GroEL protein, a non-reduced Western immunoblot was used to analyze the form of the protein, and the result showed that the exported GroEL protein was mainly in monomeric form. The exported GroEL could also be located on bacterial surface. To further research the virulent effect of C. sakazakii GroEL, an indirect immunofluorescence assay was used to detect the adhesion of recombinant GroEL protein to HCT-8 cells. The results indicated that the recombinant GroEL protein could adhere to HCT-8 cells in a short period of time. The recombinant GroEL protein could activate the NF-κB signaling pathway to release more pro-inflammatory cytokines (TNF-α, IL-6 and IL-8), downregulating the expression of tight-junction proteins (claudin-1, occluding, ZO-1 and ZO-2), which collectively resulted in dose-dependent virulent effects on host cells. Inhibition of the grol gene expression resulted in a significant decrease in bacterial adhesion to and invasion of HCT-8 cells. Moreover, the deficient GroEL also caused slow growth, decreased biofilm formation, defective motility and abnormal filamentation of the bacteria. In brief, C. sakazakii GroEL was an important virulence factor. This protein was not only crucial for the physiological activity of C. sakazakii but could also be secreted to enhance the bacterium's adhesion and invasion capabilities.
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Affiliation(s)
- Dongdong Zhu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Yufei Fan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Xiaoyi Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Ping Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Yaping Huang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Jingbo Jiao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Chumin Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Yue Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
| | - Shuo Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xinjun Du
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China; (D.Z.); (Y.F.); (X.W.); (P.L.); (Y.H.); (J.J.); (C.Z.); (Y.L.); (S.W.)
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Role of serine/threonine protein phosphatase PrpN in the life cycle of Bacillus anthracis. PLoS Pathog 2022; 18:e1010729. [PMID: 35913993 PMCID: PMC9371265 DOI: 10.1371/journal.ppat.1010729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 08/11/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Reversible protein phosphorylation at serine/threonine residues is one of the most common protein modifications, widely observed in all kingdoms of life. The catalysts controlling this modification are specific serine/threonine kinases and phosphatases that modulate various cellular pathways ranging from growth to cellular death. Genome sequencing and various omics studies have led to the identification of numerous serine/threonine kinases and cognate phosphatases, yet the physiological relevance of many of these proteins remain enigmatic. In Bacillus anthracis, only one ser/thr phosphatase, PrpC, has been functionally characterized; it was reported to be non-essential for bacterial growth and survival. In the present study, we characterized another ser/thr phosphatase (PrpN) of B. anthracis by various structural and functional approaches. To examine its physiological relevance in B. anthracis, a null mutant strain of prpN was generated and shown to have defects in sporulation and reduced synthesis of toxins (PA and LF) and the toxin activator protein AtxA. We also identified CodY, a global transcriptional regulator, as a target of PrpN and ser/thr kinase PrkC. CodY phosphorylation strongly controlled its binding to the promoter region of atxA, as shown using phosphomimetic and phosphoablative mutants. In nutshell, the present study reports phosphorylation-mediated regulation of CodY activity in the context of anthrax toxin synthesis in B. anthracis by a previously uncharacterized ser/thr protein phosphatase–PrpN. Reversible protein phosphorylation at specific ser/thr residues causes conformational changes in the protein structure, thereby modulating its cellular activity. In B. anthracis, though the role of ser/thr phosphorylation is implicated in various cellular pathways including pathogenesis, till date only one STP (PrpC) has been functionally characterized. This manuscript reports functional characterization of another STP (PrpN) in B. anthracis and with the aid of a null mutant strain (BAS ΔprpN) we provide important insight regarding the role of PrpN in the life cycle of B. anthracis. We have also identified the global transcriptional regulator, CodY as a target of PrpN and PrkC, and for the first time showed the physiological relevance of CodY phosphorylation status in the regulation of anthrax toxin synthesis.
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Abstract
Temperature is one of the ubiquitous signals that control both the development as well as virulence of various microbial species. Therefore their survival is dependent upon initiating appropriate response upon temperature fluctuations. In particular, pathogenic microbes exploit host-temperature sensing mechanisms for triggering the expression of virulence genes. Many studies have revealed that the biomolecules within a cell such as DNA, RNA, lipids and proteins help in sensing change in temperature, thereby acting as thermosensors. This review shall provide an insight into the different mechanisms of thermosensing and how they aid pathogenic microbes in host invasion.
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ClpC-Mediated Sporulation Regulation at Engulfment Stage in Bacillus anthracis. Indian J Microbiol 2021; 61:170-179. [PMID: 33927458 DOI: 10.1007/s12088-021-00927-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Bacterial sporulation is a conserved process utilized by members of Bacillus genus and Clostridium in response to stress such as nutrient or temperature. Sporulation initiation is triggered by stress signals perceived by bacterial cell that leads to shutdown of metabolic pathways of bacterial cells. The mechanism of sporulation involves a complex network that is regulated at various checkpoints to form the viable bacterial spore. Engulfment is one such check point that drives the required cellular rearrangement necessary for the spore assembly and is mediated by bacterial proteolytic machinery that involves association of various Clp ATPases and ClpP protease. The present study highlights the importance of degradation of an anti-sigma factor F, SpoIIAB by ClpCP proteolytic machinery playing a crucial role in culmination of engulfment process during the sporulation in Bacillus anthracis.
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