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Xu Z, Ding Z, Shi L, Xie Y, Zhang Y, Wang Z, Liu Q. Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness. THE ISME JOURNAL 2023; 17:2200-2209. [PMID: 37814126 PMCID: PMC10689771 DOI: 10.1038/s41396-023-01529-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023]
Abstract
Coevolution of bacteria and phages is an important host and parasite dynamic in marine ecosystems, contributing to the understanding of bacterial community diversity. On the time scale, questions remain concerning what is the difference between phage resistance patterns in marine bacteria and how advantageous mutations gradually accumulate during coevolution. In this study, marine Aeromonas was co-cultured with its phage for 180 days and their genetic and phenotypic dynamics were measured every 30 days. We identified 11 phage resistance genes and classified them into three categories: lipopolysaccharide (LPS), outer membrane protein (OMP), and two-component system (TCS). LPS shortening and OMP mutations are two distinct modes of complete phage resistance, while TCS mutants mediate incomplete resistance by repressing the transcription of phage genes. The co-mutation of LPS and OMP was a major mode for bacterial resistance at a low cost. The mutations led to significant reductions in the growth and virulence of bacterial populations during the first 60 days of coevolution, with subsequent leveling off. Our findings reveal the marine bacterial community dynamics and evolutionary trade-offs of phage resistance during coevolution, thus granting further understanding of the interaction of marine microbes.
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Affiliation(s)
- Zhenhe Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Zihan Ding
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Lijia Shi
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuzhen Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519000, Zhuhai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China
| | - Zhuang Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China.
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China.
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2
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Ventroux M, Noirot-Gros MF. Prophage-encoded small protein YqaH counteracts the activities of the replication initiator DnaA in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748575 DOI: 10.1099/mic.0.001268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacterial genomes harbour cryptic prophages that are mostly transcriptionally silent with many unannotated genes. Still, cryptic prophages may contribute to their host fitness and phenotypes. In Bacillus subtilis, the yqaF-yqaN operon belongs to the prophage element skin, and is tightly repressed by the Xre-like repressor SknR. This operon contains several small ORFs (smORFs) potentially encoding small-sized proteins. The smORF-encoded peptide YqaH was previously reported to bind to the replication initiator DnaA. Here, using a yeast two-hybrid assay, we found that YqaH binds to the DNA binding domain IV of DnaA and interacts with Spo0A, a master regulator of sporulation. We isolated single amino acid substitutions in YqaH that abolished the interaction with DnaA but not with Spo0A. Then, using a plasmid-based inducible system to overexpress yqaH WT and mutant derivatives, we studied in B. subtilis the phenotypes associated with the specific loss-of-interaction with DnaA (DnaA_LOI). We found that expression of yqaH carrying DnaA_LOI mutations abolished the deleterious effects of yqaH WT expression on chromosome segregation, replication initiation and DnaA-regulated transcription. When YqaH was induced after vegetative growth, DnaA_LOI mutations abolished the drastic effects of YqaH WT on sporulation and biofilm formation. Thus, YqaH inhibits replication, sporulation and biofilm formation mainly by antagonizing DnaA in a manner that is independent of the cell cycle checkpoint Sda.
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Affiliation(s)
- Magali Ventroux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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3
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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: 7] [Impact Index Per Article: 2.3] [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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4
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Chandy SK, Thapa B, Raghavachari K. Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method. Phys Chem Chem Phys 2020; 22:27781-27799. [PMID: 33244526 DOI: 10.1039/d0cp05064d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an efficient protocol using our two-layer Molecules-in-Molecules (MIM2) fragmentation-based quantum chemical method for the prediction of NMR chemical shifts of large biomolecules. To investigate the performance of our fragmentation approach and demonstrate its applicability, MIM-NMR calculations are first calibrated on a test set of six proteins. The MIM2-NMR method yields a mean absolute deviation (MAD) from unfragmented full molecule calculations of 0.01 ppm for 1H and 0.06 ppm for 13C chemical shifts. Thus, the errors from fragmentation are only about 3% of our target accuracy of ∼0.3 ppm for 1H and 2-3 ppm for 13C chemical shifts. To compare with experimental chemical shifts, a standard protocol is first derived using two smaller proteins 2LHY (176 atoms) and 2LI1 (146 atoms) for obtaining an appropriate protein structure for NMR chemical shift calculations. The effect of the solvent environment on the calculated NMR chemical shifts is incorporated through implicit, explicit, or explicit-implicit solvation models. The expensive first solvation shell calculations are replaced by a micro-solvation model in which only the immediate interaction between the protein and the explicit solvation environment is considered. A single explicit water molecule for each amine and amide proton is found to be sufficient to yield accurate results for 1H chemical shifts. The 1H and 13C NMR chemical shifts calculated using our protocol give excellent agreement with experiments for two larger proteins, 2MC5 (the helical part with 265 atoms) and 3UMK (33 residue slice with 547 atoms). Overall, our target accuracy of ∼0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for the larger proteins. The proposed MIM-NMR method is accurate and computationally cost-effective and should be applicable to study a wide range of large proteins.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
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5
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Vishwakarma RK, Brodolin K. The σ Subunit-Remodeling Factors: An Emerging Paradigms of Transcription Regulation. Front Microbiol 2020; 11:1798. [PMID: 32849409 PMCID: PMC7403470 DOI: 10.3389/fmicb.2020.01798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/09/2020] [Indexed: 11/13/2022] Open
Abstract
Transcription initiation is a key checkpoint and highly regulated step of gene expression. The sigma (σ) subunit of RNA polymerase (RNAP) controls all transcription initiation steps, from recognition of the -10/-35 promoter elements, upon formation of the closed promoter complex (RPc), to stabilization of the open promoter complex (RPo) and stimulation of the primary steps in RNA synthesis. The canonical mechanism to regulate σ activity upon transcription initiation relies on activators that recognize specific DNA motifs and recruit RNAP to promoters. This mini-review describes an emerging group of transcriptional regulators that form a complex with σ or/and RNAP prior to promoter binding, remodel the σ subunit conformation, and thus modify RNAP activity. Such strategy is widely used by bacteriophages to appropriate the host RNAP. Recent findings on RNAP-binding protein A (RbpA) from Mycobacterium tuberculosis and Crl from Escherichia coli suggest that activator-driven changes in σ conformation can be a widespread regulatory mechanism in bacteria.
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Affiliation(s)
- Rishi Kishore Vishwakarma
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, Montpellier, France
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6
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Abril AG, Rama JLR, Sánchez-Pérez A, Villa TG. Prokaryotic sigma factors and their transcriptional counterparts in Archaea and Eukarya. Appl Microbiol Biotechnol 2020; 104:4289-4302. [PMID: 32232532 DOI: 10.1007/s00253-020-10577-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/13/2020] [Accepted: 03/22/2020] [Indexed: 12/18/2022]
Abstract
RNA polymerases (RNAPs) carry out transcription in the three domains of life, Bacteria, Archaea, and Eukarya. Transcription initiation is highly regulated by a variety of transcription factors, whose number and subunit complexity increase during evolution. This process is regulated in Bacteria by the σ factor, while the three eukaryotic RNAPs require a complex set of transcription factors (TFs) and a TATA-binding protein (TBP). The archaeal transcription system appears to be an ancestral version of the eukaryotic RNAPII, requiring transcription factor B (TFB), TBP, and transcription factor E (TFE). The function of the bacterial sigma (σ) factor has been correlated to the roles played by the eukaryotic RNAP II and the archaeal RNAP. In addition, σ factors, TFB, and TFIIB all contain multiple DNA binding helix-turn-helix (HTH) structural motifs; although TFIIB and TFB display two HTH domains, while the bacterial σ factor spans 4 HTH motifs. The sequence similarities and structure alignments of the bacterial σ factor, eukaryotic TFIIB, and archaeal TFB evidence that these three proteins are homologs.Key Points• Transcription initiation is highly regulated by TFs.• Transcription is finely regulated in all domains of life by different sets of TFs.• Specific TFs in Bacteria, Eukarya and Archaea are homologs.
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Affiliation(s)
- Ana G Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Jose Luis R Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - A Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain.
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7
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Antitermination protein P7 of bacteriophage Xp10 distinguishes different types of transcriptional pausing by bacterial RNA polymerase. Biochimie 2020; 170:57-64. [DOI: 10.1016/j.biochi.2019.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022]
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8
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Abstract
Bacteriophages employ small proteins to usurp host molecular machinery, thereby interfering with central metabolic processes in infected bacteria. Generally, phages inhibit or redirect host transcription to favor transcription of their own genomes. Mechanistic and structural studies of phage-modulated host transcription may provide inspirations for the development of novel antibacterial substances.
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Affiliation(s)
- Markus C Wahl
- Freie Universität Berlin, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Ranjan Sen
- Laboratory of Transcription, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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9
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Tabib-Salazar A, Mulvenna N, Severinov K, Matthews SJ, Wigneshweraraj S. Xenogeneic Regulation of the Bacterial Transcription Machinery. J Mol Biol 2019; 431:4078-4092. [DOI: 10.1016/j.jmb.2019.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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10
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Structural basis for transcription antitermination at bacterial intrinsic terminator. Nat Commun 2019; 10:3048. [PMID: 31296855 PMCID: PMC6624301 DOI: 10.1038/s41467-019-10955-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/29/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation—in particular transcription antitermination—is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation. Bacteriophages reprogram the host transcriptional machinery. Here the authors provide insights into the mechanism of how bacteriophages regulate host transcription by determining the cryo-EM structures of two bacterial transcription elongation complexes bound with the bacteriophage master host-transcription regulator protein P7.
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11
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van Tol N, Flores Andaluz G, Leeggangers HACF, Roushan MR, Hooykaas PJJ, van der Zaal BJ. Zinc Finger Artificial Transcription Factor-Mediated Chloroplast Genome Interrogation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:393-406. [PMID: 30398644 PMCID: PMC6375250 DOI: 10.1093/pcp/pcy216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/01/2018] [Indexed: 06/08/2023]
Abstract
The large majority of core photosynthesis proteins in plants are encoded by nuclear genes, but a small portion have been retained in the plastid genome. These plastid-encoded chloroplast proteins fulfill essential roles in the process of photochemistry. Here, we report the use of nuclear-encoded, chloroplast-targeted zinc finger artificial transcription factors (ZF-ATFs) with effector domains of prokaryotic origin to modulate the expression of chloroplast genes, and to enhance the photochemical activity and growth characteristics of Arabidopsis thaliana plants. This technique was named chloroplast genome interrogation. Using this novel approach, we obtained evidence that ZF-ATFs can indeed be translocated to chloroplasts of Arabidopsis plants, can modulate their growth and operating light use efficiency of PSII, and finally can induce statistically significant changes in the expression levels of several chloroplast genes. Our data suggest that the distortion of chloroplast gene expression might be a feasible approach to manipulate the efficiency of photosynthesis in plants.
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Affiliation(s)
- Niels van Tol
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Gema Flores Andaluz
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Hendrika A C F Leeggangers
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - M Reza Roushan
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Paul J J Hooykaas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Bert J van der Zaal
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
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12
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Liu B, Wang Z, Lan L, Yang Q, Zhang P, Shi L, Lang Y, Tabib-Salazar A, Wigneshweraraj S, Zhang J, Wang Y, Tang Y, Matthews S, Zhang X. A Rapid Colorimetric Method to Visualize Protein Interactions. Chemistry 2018; 24:6727-6731. [DOI: 10.1002/chem.201800401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Indexed: 01/30/2023]
Affiliation(s)
- Bing Liu
- BioBank; First Affiliated Hospital; School of medicine; Xi'an Jiaotong University; Xi'an 710049 P. R. China
- Department of Life Sciences; Imperial College London; London UK
| | - Zhihao Wang
- Department of Life Sciences; Imperial College London; London UK
| | - Ling Lan
- Beijing National Laboratory for Molecular Science; State Key Laboratory for Structural Chemistry of Unstable, and Stable Species; Institute of Chemistry Chinese Academy of Science; Beijing 100190 P. R. China
| | - Qianfan Yang
- College of Chemistry; Sichuan University; Chengdu 610065 P. R. China
| | - Peipei Zhang
- BioBank; First Affiliated Hospital; School of medicine; Xi'an Jiaotong University; Xi'an 710049 P. R. China
| | - Lei Shi
- College of Chemical Engineering; North China University of Science and Technology; Tangshan 063210 P. R. China
| | - Yunhe Lang
- College of Chemical Engineering; North China University of Science and Technology; Tangshan 063210 P. R. China
| | | | | | - Jiye Zhang
- BioBank; First Affiliated Hospital; School of medicine; Xi'an Jiaotong University; Xi'an 710049 P. R. China
| | - Yawen Wang
- BioBank; First Affiliated Hospital; School of medicine; Xi'an Jiaotong University; Xi'an 710049 P. R. China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Science; State Key Laboratory for Structural Chemistry of Unstable, and Stable Species; Institute of Chemistry Chinese Academy of Science; Beijing 100190 P. R. China
| | - Steve Matthews
- Department of Life Sciences; Imperial College London; London UK
| | - Xiufeng Zhang
- College of Chemical Engineering; North China University of Science and Technology; Tangshan 063210 P. R. China
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13
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Wang Erickson AF, Deighan P, Chen S, Barrasso K, Garcia CP, Martínez-Lumbreras S, Alfano C, Krysztofinska EM, Thapaliya A, Camp AH, Isaacson RL, Hochschild A, Losick R. A novel RNA polymerase-binding protein that interacts with a sigma-factor docking site. Mol Microbiol 2017; 105:652-662. [PMID: 28598017 PMCID: PMC5558796 DOI: 10.1111/mmi.13724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2017] [Indexed: 11/30/2022]
Abstract
Sporulation in Bacillus subtilis is governed by a cascade of alternative RNA polymerase sigma factors. We previously identified a small protein Fin that is produced under the control of the sporulation sigma factor σF to create a negative feedback loop that inhibits σF -directed gene transcription. Cells deleted for fin are defective for spore formation and exhibit increased levels of σF -directed gene transcription. Based on pull-down experiments, chemical crosslinking, bacterial two-hybrid experiments and nuclear magnetic resonance chemical shift analysis, we now report that Fin binds to RNA polymerase and specifically to the coiled-coil region of the β' subunit. The coiled-coil is a docking site for sigma factors on RNA polymerase, and evidence is presented that the binding of Fin and σF to RNA polymerase is mutually exclusive. We propose that Fin functions by a mechanism distinct from that of classic sigma factor antagonists (anti-σ factors), which bind directly to a target sigma factor to prevent its association with RNA polymerase, and instead functions to inhibit σF by competing for binding to the β' coiled-coil.
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Affiliation(s)
- Anna F. Wang Erickson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Padraig Deighan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115
| | - Shanshan Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Kelsey Barrasso
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115
| | - Cinthia P. Garcia
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115
| | | | - Caterina Alfano
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, United Kingdom
| | - Ewelina M. Krysztofinska
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, United Kingdom
| | - Arjun Thapaliya
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, United Kingdom
| | - Amy H. Camp
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075
| | - Rivka L. Isaacson
- Department of Chemistry, King's College London, Britannia House, Trinity Street, London, United Kingdom
| | - Ann Hochschild
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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14
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15
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Brown DR, Sheppard CM, Burchell L, Matthews S, Wigneshweraraj S. The Xp10 Bacteriophage Protein P7 Inhibits Transcription by the Major and Major Variant Forms of the Host RNA Polymerase via a Common Mechanism. J Mol Biol 2016; 428:3911-3919. [PMID: 27515396 PMCID: PMC5053324 DOI: 10.1016/j.jmb.2016.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 01/24/2023]
Abstract
The σ factor is a functionally obligatory subunit of the bacterial transcription machinery, the RNA polymerase. Bacteriophage-encoded small proteins that either modulate or inhibit the bacterial RNAP to allow the temporal regulation of bacteriophage gene expression often target the activity of the major bacterial σ factor, σ70. Previously, we showed that during Xanthomonas oryzae phage Xp10 infection, the phage protein P7 inhibits the host RNAP by preventing the productive engagement with the promoter and simultaneously displaces the σ70 factor from the RNAP. In this study, we demonstrate that P7 also inhibits the productive engagement of the bacterial RNAP containing the major variant bacterial σ factor, σ54, with its cognate promoter. The results suggest for the first time that the major variant form of the host RNAP can also be targeted by bacteriophage-encoded transcription regulatory proteins. Since the major and major variant σ factor interacting surfaces in the RNAP substantially overlap, but different regions of σ70 and σ54 are used for binding to the RNAP, our results further underscore the importance of the σ–RNAP interface in bacterial RNAP function and regulation and potentially for intervention by antibacterials. Xp10 phage transcription regulator P7 inhibits transcription by RNAP containing σ54. P7 prevents the productive engagement of the σ54–RNAP with the promoter DNA. • P7 disrupts preformed σ54–RNAP-promoter complexes.
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Affiliation(s)
- D R Brown
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK.
| | - C M Sheppard
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
| | - L Burchell
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
| | - S Matthews
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK
| | - S Wigneshweraraj
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK.
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16
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Zhou Z, Leake MC. Force Spectroscopy in Studying Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:307-27. [PMID: 27193551 DOI: 10.1007/978-3-319-32189-9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biophysical force spectroscopy tools-for example, optical tweezers, magnetic tweezers, atomic force microscopy-have been used to study elastic, mechanical, conformational and dynamic properties of single biological specimens from single proteins to whole cells to reveal information not accessible by ensemble average methods such as X-ray crystallography, mass spectroscopy, gel electrophoresis and so on. Here, we review the application of these tools on a range of infection-related questions from antibody-inhibited protein processivity to virus-cell adhesion. In each case, we focus on how the instrumental design tailored to the biological system in question translates into the functionality suitable for that particular study. The unique insights that force spectroscopy has gained to complement knowledge learned through population averaging techniques in interrogating biomolecular details prove to be instrumental in therapeutic innovations such as those in structure-based drug design.
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Affiliation(s)
- Zhaokun Zhou
- Departments of Physics and Biology, Biological Physical Sciences Institute, University of York, York, YO10 5DD, UK.
| | - Mark C Leake
- Departments of Physics and Biology, Biological Physical Sciences Institute, University of York, York, YO10 5DD, UK
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17
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Swails J, Zhu T, He X, Case DA. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. JOURNAL OF BIOMOLECULAR NMR 2015; 63:125-39. [PMID: 26232926 PMCID: PMC6556433 DOI: 10.1007/s10858-015-9970-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/20/2015] [Indexed: 05/08/2023]
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.
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Affiliation(s)
- Jason Swails
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA.
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18
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Yang H, Ma Y, Wang Y, Yang H, Shen W, Chen X. Transcription regulation mechanisms of bacteriophages: recent advances and future prospects. Bioengineered 2015; 5:300-4. [PMID: 25482231 DOI: 10.4161/bioe.32110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. Therefore, it is essential to understand the mechanisms underlying phage-host interactions. After initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. This review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. Through this review, we aim to broaden the understanding of phage-host interactions while providing a reference source for researchers studying the regulation of phage transcription.
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Affiliation(s)
- Haiquan Yang
- a Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Jiangnan University; Wuxi, China
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19
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Zenkin N, Severinov K, Yuzenkova Y. Bacteriophage Xp10 anti-termination factor p7 induces forward translocation by host RNA polymerase. Nucleic Acids Res 2015; 43:6299-308. [PMID: 26038312 PMCID: PMC4513864 DOI: 10.1093/nar/gkv586] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/05/2015] [Accepted: 05/22/2015] [Indexed: 11/12/2022] Open
Abstract
Regulation of transcription elongation is based on response of RNA polymerase (RNAP) to various pause signals and is modulated by various accessory factors. Here we report that a 7 kDa protein p7 encoded by bacteriophage Xp10 acts as an elongation processivity factor of RNAP of host bacterium Xanthomonas oryzae, a major rice pathogen. Our data suggest that p7 stabilizes the upstream DNA duplex of the elongation complex thus disfavouring backtracking and promoting forward translocated states of the elongation complex. The p7-induced 'pushing' of RNAP and modification of RNAP contacts with the upstream edge of the transcription bubble lead to read-through of various types of pauses and termination signals and generally increase transcription processivity and elongation rate, contributing for transcription of an extremely long late genes operon of Xp10. Forward translocation was observed earlier upon the binding of unrelated bacterial elongation factor NusG, suggesting that this may be a general pathway of regulation of transcription elongation.
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Affiliation(s)
- Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Konstantin Severinov
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854-8020, USA Skolkovo Institute of Science and Technology, Skolkovo,143025, Russia Institute of Molecular Genetics, Russian Academy of Sciences, Moscow,123182, Russia Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Yulia Yuzenkova
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
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20
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Lenneman BR, Rothman-Denes LB. Structural and biochemical investigation of bacteriophage N4-encoded RNA polymerases. Biomolecules 2015; 5:647-67. [PMID: 25924224 PMCID: PMC4496689 DOI: 10.3390/biom5020647] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/01/2015] [Accepted: 04/13/2015] [Indexed: 11/16/2022] Open
Abstract
Bacteriophage N4 regulates the temporal expression of its genome through the activity of three distinct RNA polymerases (RNAP). Expression of the early genes is carried out by a phage-encoded, virion-encapsidated RNAP (vRNAP) that is injected into the host at the onset of infection and transcribes the early genes. These encode the components of new transcriptional machinery (N4 RNAPII and cofactors) responsible for the synthesis of middle RNAs. Both N4 RNAPs belong to the T7-like "single-subunit" family of polymerases. Herein, we describe their mechanisms of promoter recognition, regulation, and roles in the phage life cycle.
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Affiliation(s)
- Bryan R Lenneman
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | - Lucia B Rothman-Denes
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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21
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Distinct pathways of RNA polymerase regulation by a phage-encoded factor. Proc Natl Acad Sci U S A 2015; 112:2017-22. [PMID: 25646468 DOI: 10.1073/pnas.1416330112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. Here, we dissect the transcription antitermination mechanism of Xanthomonas oryzae virus Xp10 protein p7, which binds host RNA polymerase (RNAP) and regulates both transcription initiation and termination. We show that p7 suppresses intrinsic termination by decreasing RNAP pausing and increasing the transcription complex stability, in cooperation with host-encoded factor NusA. Uniquely, the antitermination activity of p7 depends on the ω subunit of the RNAP core and is modulated by ppGpp. In contrast, the inhibition of transcription initiation by p7 does not require ω but depends on other RNAP sites. Our results suggest that p7, a bifunctional transcription factor, uses distinct mechanisms to control different steps of transcription. We propose that regulatory functions of the ω subunit revealed by our analysis may extend to its homologs in eukaryotic RNAPs.
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22
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Liu B, Shadrin A, Sheppard C, Mekler V, Xu Y, Severinov K, Matthews S, Wigneshweraraj S. The sabotage of the bacterial transcription machinery by a small bacteriophage protein. BACTERIOPHAGE 2014; 4:e28520. [PMID: 24701369 DOI: 10.4161/bact.28520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 11/19/2022]
Abstract
Many bacteriophages produce small proteins that specifically interfere with the bacterial host transcription machinery and thus contribute to the acquisition of the bacterial cell by the bacteriophage. We recently described how a small protein, called P7, produced by the Xp10 bacteriophage inhibits bacterial transcription initiation by causing the dissociation of the promoter specificity sigma factor subunit from the host RNA polymerase holoenzyme. In this addendum to the original publication, we present the highlights of that research.
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Affiliation(s)
- Bing Liu
- MRC Centre for Molecular Bacteriology and Infection; Imperial College London; London, UK
| | - Andrey Shadrin
- MRC Centre for Molecular Bacteriology and Infection; Imperial College London; London, UK
| | - Carol Sheppard
- MRC Centre for Molecular Bacteriology and Infection; Imperial College London; London, UK
| | - Vladimir Mekler
- Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry; Rutgers, The State University of New Jersey; Piscataway, NJ USA
| | - Yingqi Xu
- MRC Centre for Molecular Bacteriology and Infection; Imperial College London; London, UK
| | - Konstantin Severinov
- Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry; Rutgers, The State University of New Jersey; Piscataway, NJ USA ; St. Petersburg State Polytechnical University; St. Petersburg, Russia
| | - Steve Matthews
- MRC Centre for Molecular Bacteriology and Infection; Imperial College London; London, UK
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