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Jakob S, Steinchen W, Hanßmann J, Rosum J, Langenfeld K, Osorio-Valeriano M, Steube N, Giammarinaro PI, Hochberg GKA, Glatter T, Bange G, Diepold A, Thanbichler M. The virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression. Nat Commun 2024; 15:318. [PMID: 38182620 PMCID: PMC10770331 DOI: 10.1038/s41467-023-44509-z] [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: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
The transcriptional antisilencer VirB acts as a master regulator of virulence gene expression in the human pathogen Shigella flexneri. It binds DNA sequences (virS) upstream of VirB-dependent promoters and counteracts their silencing by the nucleoid-organizing protein H-NS. However, its precise mode of action remains unclear. Notably, VirB is not a classical transcription factor but related to ParB-type DNA-partitioning proteins, which have recently been recognized as DNA-sliding clamps using CTP binding and hydrolysis to control their DNA entry gate. Here, we show that VirB binds CTP, embraces DNA in a clamp-like fashion upon its CTP-dependent loading at virS sites and slides laterally on DNA after clamp closure. Mutations that prevent CTP-binding block VirB loading in vitro and abolish the formation of VirB nucleoprotein complexes as well as virulence gene expression in vivo. Thus, VirB represents a CTP-dependent molecular switch that uses a loading-and-sliding mechanism to control transcription during bacterial pathogenesis.
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Affiliation(s)
- Sara Jakob
- Department of Biology, University of Marburg, Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Rosum
- Department of Biology, University of Marburg, Marburg, Germany
| | - Katja Langenfeld
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Niklas Steube
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, Marburg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Georg K A Hochberg
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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2
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Wińska P, Sobiepanek A, Pawlak K, Staniszewska M, Cieśla J. Phosphorylation of Thymidylate Synthase and Dihydrofolate Reductase in Cancer Cells and the Effect of CK2α Silencing. Int J Mol Sci 2023; 24:ijms24033023. [PMID: 36769342 PMCID: PMC9917831 DOI: 10.3390/ijms24033023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Our previous research suggests an important regulatory role of CK2-mediated phosphorylation of enzymes involved in the thymidylate biosynthesis cycle, i.e., thymidylate synthase (TS), dihydrofolate reductase (DHFR), and serine hydroxymethyltransferase (SHMT). The aim of this study was to show whether silencing of the CK2α gene affects TS and DHFR expression in A-549 cells. Additionally, we attempted to identify the endogenous kinases that phosphorylate TS and DHFR in CCRF-CEM and A-549 cells. We used immunodetection, immunofluorescence/confocal analyses, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), in-gel kinase assay, and mass spectrometry analysis. Our results demonstrate that silencing of the CK2α gene in lung adenocarcinoma cells significantly increases both TS and DHFR expression and affects their cellular distribution. Additionally, we show for the first time that both TS and DHFR are very likely phosphorylated by endogenous CK2 in two types of cancer cells, i.e., acute lymphoblastic leukaemia and lung adenocarcinoma. Moreover, our studies indicate that DHFR is phosphorylated intracellularly by CK2 to a greater extent in leukaemia cells than in lung adenocarcinoma cells. Interestingly, in-gel kinase assay results indicate that the CK2α' isoform was more active than the CK2α subunit. Our results confirm the previous studies concerning the physiological relevance of CK2-mediated phosphorylation of TS and DHFR.
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Affiliation(s)
- Patrycja Wińska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
- Correspondence: (P.W.); (M.S.); Tel.: +48-222-345-573 (P.W.); +48-606-438-241 (M.S.)
| | - Anna Sobiepanek
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Katarzyna Pawlak
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - Monika Staniszewska
- Centre for Advanced Materials and Technologies, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Correspondence: (P.W.); (M.S.); Tel.: +48-222-345-573 (P.W.); +48-606-438-241 (M.S.)
| | - Joanna Cieśla
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
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3
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Pang K, Wang W, Qin J, Shi Z, Hao L, Ma Y, Xu H, Wu Z, Pan D, Chen Z, Han C. Role of protein phosphorylation in cell signaling, disease, and the intervention therapy. MedComm (Beijing) 2022; 3:e175. [PMID: 36349142 PMCID: PMC9632491 DOI: 10.1002/mco2.175] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is an important post-transcriptional modification involving an extremely wide range of intracellular signaling transduction pathways, making it an important therapeutic target for disease intervention. At present, numerous drugs targeting protein phosphorylation have been developed for the treatment of various diseases including malignant tumors, neurological diseases, infectious diseases, and immune diseases. In this review article, we analyzed 303 small-molecule protein phosphorylation kinase inhibitors (PKIs) registered and participated in clinical research obtained in a database named Protein Kinase Inhibitor Database (PKIDB), including 68 drugs approved by the Food and Drug Administration of the United States. Based on previous classifications of kinases, we divided these human protein phosphorylation kinases into eight groups and nearly 50 families, and delineated their main regulatory pathways, upstream and downstream targets. These groups include: protein kinase A, G, and C (AGC) and receptor guanylate cyclase (RGC) group, calmodulin-dependent protein kinase (CaMK) group, CMGC [Cyclin-dependent kinases (CDKs), Mitogen-activated protein kinases (MAPKs), Glycogen synthase kinases (GSKs), and Cdc2-like kinases (CLKs)] group, sterile (STE)-MAPKs group, tyrosine kinases (TK) group, tyrosine kinase-like (TKL) group, atypical group, and other groups. Different groups and families of inhibitors stimulate or inhibit others, forming an intricate molecular signaling regulatory network. This review takes newly developed new PKIs as breakthrough point, aiming to clarify the regulatory network and relationship of each pathway, as well as their roles in disease intervention, and provide a direction for future drug development.
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Affiliation(s)
- Kun Pang
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Wei Wang
- Department of Medical CollegeSoutheast UniversityNanjingJiangsuChina
| | - Jia‐Xin Qin
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Zhen‐Duo Shi
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
| | - Yu‐Yang Ma
- Graduate SchoolBengbu Medical CollegeBengbuAnhuiChina
| | - Hao Xu
- Graduate SchoolBengbu Medical CollegeBengbuAnhuiChina
| | - Zhuo‐Xun Wu
- Department of Pharmaceutical SciencesCollege of Pharmacy and Health SciencesSt. John's University, QueensNew YorkNew YorkUSA
| | - Deng Pan
- Graduate SchoolBengbu Medical CollegeBengbuAnhuiChina
| | - Zhe‐Sheng Chen
- Department of Pharmaceutical SciencesCollege of Pharmacy and Health SciencesSt. John's University, QueensNew YorkNew YorkUSA
| | - Cong‐Hui Han
- Department of Urology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical CollegeThe Affiliated Xuzhou Hospital of Medical College of Southeast UniversityThe Affiliated Xuzhou Center Hospital of Nanjing University of Chinese MedicineXuzhouJiangsuChina
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4
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Sato T, Utashima S(H, Yoshii Y, Hirata K, Kanda S, Onoda Y, Jin JQ, Xiao S, Minami R, Fukushima H, Noguchi A, Manabe Y, Fukase K, Atomi H. A non-carboxylating pentose bisphosphate pathway in halophilic archaea. Commun Biol 2022; 5:1290. [PMID: 36434094 PMCID: PMC9700705 DOI: 10.1038/s42003-022-04247-2] [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: 07/28/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.
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Affiliation(s)
- Takaaki Sato
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
| | - Sanae (Hodo) Utashima
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Yoshii
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kosuke Hirata
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shuichiro Kanda
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yushi Onoda
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Jian-qiang Jin
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Suyi Xiao
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryoko Minami
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hikaru Fukushima
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ayako Noguchi
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yoshiyuki Manabe
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Forefront Research Center, Osaka University, Osaka, Japan
| | - Koichi Fukase
- grid.136593.b0000 0004 0373 3971Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Forefront Research Center, Osaka University, Osaka, Japan
| | - Haruyuki Atomi
- grid.258799.80000 0004 0372 2033Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan ,grid.258799.80000 0004 0372 2033Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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