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Yang Y, Hu Z, Kang Y, Gao J, Chen H, Liu H, Wang Y, Liu B. Phage SPO1 Protein Gp49 Is a Novel RNA Binding Protein That Is Involved in Host Iron Metabolism. Int J Mol Sci 2023; 24:14318. [PMID: 37762620 PMCID: PMC10531801 DOI: 10.3390/ijms241814318] [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: 08/28/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillus subtilis is a model organism for studying Gram-positive bacteria and serves as a cell factory in the industry for enzyme and chemical production. Additionally, it functions as a probiotic in the gastrointestinal tract, modulating the gut microbiota. Its lytic phage SPO1 is also the most studied phage among the genus Okubovrius, including Bacillus phage SPO1 and Camphawk. One of the notable features of SPO1 is the existence of a "host-takeover module", a cluster of 24 genes which occupies most of the terminal redundancy. Some of the gene products from the module have been characterized, revealing their ability to disrupt host metabolism by inhibiting DNA replication, RNA transcription, cell division, and glycolysis. However, many of the gene products which share limited similarity to known proteins remain under researched. In this study, we highlight the involvement of Gp49, a gene product from the module, in host RNA binding and heme metabolism-no observation has been reported in other phages. Gp49 folds into a structure that does not resemble any protein in the database and has a new putative RNA binding motif. The transcriptome study reveals that Gp49 primarily upregulates host heme synthesis which captures cytosolic iron to facilitate phage development.
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Affiliation(s)
- Yanan Yang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yue Kang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Juanjuan Gao
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Hui Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
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2
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Liu W, Bi J, Ren Y, Chen H, Zhang J, Wang T, Wang M, Zhang L, Zhao J, Wu Z, Lv Y, Liu B, Wu R. Targeting extracellular CIRP with an X-aptamer shows therapeutic potential in acute pancreatitis. iScience 2023; 26:107043. [PMID: 37360693 PMCID: PMC10285643 DOI: 10.1016/j.isci.2023.107043] [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: 11/07/2022] [Revised: 03/02/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Severe acute pancreatitis (AP) is associated with a high mortality rate. Cold-inducible RNA binding protein (CIRP) can be released from cells in inflammatory conditions and extracellular CIRP acts as a damage-associated molecular pattern. This study aims to explore the role of CIRP in the pathogenesis of AP and evaluate the therapeutic potential of targeting extracellular CIRP with X-aptamers. Our results showed that serum CIRP concentrations were significantly increased in AP mice. Recombinant CIRP triggered mitochondrial injury and ER stress in pancreatic acinar cells. CIRP-/- mice suffered less severe pancreatic injury and inflammatory responses. Using a bead-based X-aptamer library, we identified an X-aptamer that specifically binds to CIRP (XA-CIRP). Structurally, XA-CIRP blocked the interaction between CIRP and TLR4. Functionally, it reduced CIRP-induced pancreatic acinar cell injury in vitro and L-arginine-induced pancreatic injury and inflammation in vivo. Thus, targeting extracellular CIRP with X-aptamers may be a promising strategy to treat AP.
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Affiliation(s)
- Wuming Liu
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jianbin Bi
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yifan Ren
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of General Surgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jia Zhang
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Gastroenterology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tao Wang
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mengzhou Wang
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Lin Zhang
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Junzhou Zhao
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zheng Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yi Lv
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Rongqian Wu
- National Local Joint Engineering Research Center for Precision Surgery and Regenerative Medicine, Shaanxi Provincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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3
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Macorano L, Binny TM, Spiegl T, Klimenko V, Singer A, Oberleitner L, Applegate V, Seyffert S, Stefanski A, Gremer L, Gertzen CGW, Höppner A, Smits SHJ, Nowack ECM. DNA-binding and protein structure of nuclear factors likely acting in genetic information processing in the Paulinella chromatophore. Proc Natl Acad Sci U S A 2023; 120:e2221595120. [PMID: 37364116 PMCID: PMC10319021 DOI: 10.1073/pnas.2221595120] [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: 12/20/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The chromatophores in Paulinella are evolutionary-early-stage photosynthetic organelles. Biological processes in chromatophores depend on a combination of chromatophore and nucleus-encoded proteins. Interestingly, besides proteins carrying chromatophore-targeting signals, a large arsenal of short chromatophore-targeted proteins (sCTPs; <90 amino acids) without recognizable targeting signals were found in chromatophores. This situation resembles endosymbionts in plants and insects that are manipulated by host-derived antimicrobial peptides. Previously, we identified an expanded family of sCTPs of unknown function, named here "DNA-binding (DB)-sCTPs". DB-sCTPs contain a ~45 amino acid motif that is conserved in some bacterial proteins with predicted functions in DNA processing. Here, we explored antimicrobial activity, DNA-binding capacity, and structures of three purified recombinant DB-sCTPs. All three proteins exhibited antimicrobial activity against bacteria involving membrane permeabilization, and bound to bacterial lipids in vitro. A combination of in vitro assays demonstrated binding of recombinant DB-sCTPs to chromatophore-derived genomic DNA sequences with an affinity in the low nM range. Additionally, we report the 1.2 Å crystal structure of one DB-sCTP. In silico docking studies suggest that helix α2 inserts into the DNA major grove and the exposed residues, that are highly variable between different DB-sCTPs, confer interaction with the DNA bases. Identification of photosystem II subunit CP43 as a potential interaction partner of one DB-sCTP, suggests DB-sCTPs to be involved in more complex regulatory mechanisms. We hypothesize that membrane binding of DB-sCTPs is related to their import into chromatophores. Once inside, they interact with the chromatophore genome potentially providing nuclear control over genetic information processing.
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Affiliation(s)
- Luis Macorano
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Taniya M. Binny
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Tobias Spiegl
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Victoria Klimenko
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Anna Singer
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Linda Oberleitner
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Violetta Applegate
- Center for Structural Studies, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Sarah Seyffert
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Medical Faculty and University Hospital, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7 Structural Biochemistry) and JuStruct Jülich Center of Structural Biology, Forschungszentrum Jülich, 52428Jülich, Germany
- Institute of Physical Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Christoph G. W. Gertzen
- Center for Structural Studies, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Pharmacy, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Sander H. J. Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
- Institute of Biochemistry, Department of Chemistry, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
| | - Eva C. M. Nowack
- Institute of Microbial Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225Düsseldorf, Germany
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4
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Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res 2023; 51:1674-1686. [PMID: 36660822 PMCID: PMC9976917 DOI: 10.1093/nar/gkac1274] [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: 08/16/2022] [Revised: 12/19/2022] [Accepted: 12/27/2022] [Indexed: 01/21/2023] Open
Abstract
ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.
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Affiliation(s)
- Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu Cao
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chenxi He
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xianjiang Lan
- Department of Systems Biology for Medicine, School of Basic Medical Sciences; Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Division of Hematology, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gerd A Blobel
- Division of Hematology, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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5
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Zhang K, Li S, Wang Y, Wang Z, Mulvenna N, Yang H, Zhang P, Chen H, Li Y, Wang H, Gao Y, Wigneshweraraj S, Matthews S, Zhang K, Liu B. Bacteriophage protein PEIP is a potent Bacillus subtilis enolase inhibitor. Cell Rep 2022; 40:111026. [PMID: 35793626 DOI: 10.1016/j.celrep.2022.111026] [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: 11/04/2021] [Revised: 04/26/2022] [Accepted: 06/09/2022] [Indexed: 11/03/2022] Open
Abstract
Enolase is a highly conserved enzyme that presents in all organisms capable of glycolysis or fermentation. Its immediate product phosphoenolpyruvate is essential for other important processes like peptidoglycan synthesis and the phosphotransferase system in bacteria. Therefore, enolase inhibitors are of great interest. Here, we report that Gp60, a phage-encoded enolase inhibitor protein (PEIP) of bacteriophage SPO1 for Bacillus subtilis, is an enolase inhibitor. PEIP-expressing bacteria exhibit growth attenuation, thinner cell walls, and safranin color in Gram staining owing to impaired peptidoglycan synthesis. We solve the structure of PEIP-enolase tetramer and show that PEIP disassembles enolase by disrupting the basic dimer unit. The structure reveals that PEIP does not compete for substrate binding but induces a cascade of conformational changes that limit accessibility to the enolase catalytic site. This phage-inspired disassembly of enolase represents an alternative strategy for the development of anti-microbial drugs.
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Affiliation(s)
- Kaining Zhang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhihao Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Nancy Mulvenna
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Hang Yang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Peipei Zhang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, China
| | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Yongxiang Gao
- MOE Key Laboratory for Cellular Dynamics and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | | | - Steve Matthews
- Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Institute for Protein Science and Phage Research, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China; Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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6
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Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins. Proc Natl Acad Sci U S A 2022; 119:2116278119. [PMID: 35193978 PMCID: PMC8892312 DOI: 10.1073/pnas.2116278119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
Histone-like protein from Escherichia coli strain U93 (HU) protein is the most abundant nucleoid-associated protein in bacteria, which plays a fundamental role in chromosomal compaction and organization. It is essential for most bacteria as well as Apicomplexans, thus an important target for the development of antimicrobial and antimalaria drugs. We report Gp46 as a phage protein HU inhibitor. It inhibits HU of Bacillus subtilis by occupying its DNA binding site, thus preventing chromosome segregation during cell division. As key residues for the interaction are highly conserved, Gp46 interacts with HUs of a broad range of pathogens, including many pathogenic bacteria and Apicomplexan parasites like Plasmodium falciparum. Thus, this cross-species property could benefit antibiotic and antimalaria drug development that targets HU. The architectural protein histone-like protein from Escherichia coli strain U93 (HU) is the most abundant bacterial DNA binding protein and highly conserved among bacteria and Apicomplexan parasites. It not only binds to double-stranded DNA (dsDNA) to maintain DNA stability but also, interacts with RNAs to regulate transcription and translation. Importantly, HU is essential to cell viability for many bacteria; hence, it is an important antibiotic target. Here, we report that Gp46 from bacteriophage SPO1 of Bacillus subtilis is an HU inhibitor whose expression prevents nucleoid segregation and causes filamentous morphology and growth defects in bacteria. We determined the solution structure of Gp46 and revealed a striking negatively charged surface. An NMR-derived structural model for the Gp46–HU complex shows that Gp46 occupies the DNA binding motif of the HU and therefore, occludes DNA binding, revealing a distinct strategy for HU inhibition. We identified the key residues responsible for the interaction that are conserved among HUs of bacteria and Apicomplexans, including clinically significant Mycobacterium tuberculosis, Acinetobacter baumannii, and Plasmodium falciparum, and confirm that Gp46 can also interact with these HUs. Our findings provide detailed insight into a mode of HU inhibition that provides a useful foundation for the development of antibacteria and antimalaria drugs.
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7
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Liu B, Li S, Liu Y, Chen H, Hu Z, Wang Z, Zhao Y, Zhang L, Ma B, Wang H, Matthews S, Wang Y, Zhang K. Bacteriophage Twort protein Gp168 is a β-clamp inhibitor by occupying the DNA sliding channel. Nucleic Acids Res 2021; 49:11367-11378. [PMID: 34614154 PMCID: PMC8565349 DOI: 10.1093/nar/gkab875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial chromosome replication is mainly catalyzed by DNA polymerase III, whose beta subunits enable rapid processive DNA replication. Enabled by the clamp-loading complex, the two beta subunits form a ring-like clamp around DNA and keep the polymerase sliding along. Given the essential role of β-clamp, its inhibitors have been explored for antibacterial purposes. Similarly, β-clamp is an ideal target for bacteriophages to shut off host DNA synthesis during host takeover. The Gp168 protein of phage Twort is such an example, which binds to the β-clamp of Staphylococcus aureus and prevents it from loading onto DNA causing replication arrest. Here, we report a cryo-EM structure of the clamp–Gp168 complex at 3.2-Å resolution. In the structure of the complex, the Gp168 dimer occupies the DNA sliding channel of β-clamp and blocks its loading onto DNA, which represents a new inhibitory mechanism against β-clamp function. Interestingly, the key residues responsible for this interaction on the β-clamp are well conserved among bacteria. We therefore demonstrate that Gp168 is potentially a cross-species β-clamp inhibitor, as it forms complex with the Bacillus subtilis β-clamp. Our findings reveal an alternative mechanism for bacteriophages to inhibit β-clamp and provide a new strategy to combat bacterial drug resistance.
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Affiliation(s)
- Bing Liu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Shanshan Li
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yang Liu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Zhihao Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Biyun Ma
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Steve Matthews
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710061, China
| | - Kaiming Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
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Łubkowska B, Jeżewska-Frąckowiak J, Sobolewski I, Skowron PM. Bacteriophages of Thermophilic ' Bacillus Group' Bacteria-A Review. Microorganisms 2021; 9:1522. [PMID: 34361957 PMCID: PMC8303945 DOI: 10.3390/microorganisms9071522] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/03/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages of thermophiles are of increasing interest owing to their important roles in many biogeochemical, ecological processes and in biotechnology applications, including emerging bionanotechnology. However, due to lack of in-depth investigation, they are underrepresented in the known prokaryotic virosphere. Therefore, there is a considerable potential for the discovery of novel bacteriophage-host systems in various environments: marine and terrestrial hot springs, compost piles, soil, industrial hot waters, among others. This review aims at providing a reference compendium of thermophages characterized thus far, which infect the species of thermophilic 'Bacillus group' bacteria, mostly from Geobacillus sp. We have listed 56 thermophages, out of which the majority belong to the Siphoviridae family, others belong to the Myoviridae and Podoviridae families and, apparently, a few belong to the Sphaerolipoviridae, Tectiviridae or Corticoviridae families. All of their genomes are composed of dsDNA, either linear, circular or circularly permuted. Fourteen genomes have been sequenced; their sizes vary greatly from 35,055 bp to an exceptionally large genome of 160,590 bp. We have also included our unpublished data on TP-84, which infects Geobacillus stearothermophilus (G. stearothermophilus). Since the TP-84 genome sequence shows essentially no similarity to any previously characterized bacteriophage, we have defined TP-84 as a new species in the newly proposed genus Tp84virus within the Siphoviridae family. The information summary presented here may be helpful in comparative deciphering of the molecular basis of the thermophages' biology, biotechnology and in analyzing the environmental aspects of the thermophages' effect on the thermophile community.
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Affiliation(s)
- Beata Łubkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
- The High School of Health in Gdansk, Pelplinska 7, 80-335 Gdansk, Poland
| | - Joanna Jeżewska-Frąckowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
| | - Ireneusz Sobolewski
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
| | - Piotr M. Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (J.J.-F.); (I.S.); (P.M.S.)
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