1
|
Chen Y, Guo R, Liang Y, Luo L, Han Y, Wang H, Zhang H, Liu Y, Zheng K, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus. Virus Res 2023; 334:199183. [PMID: 37499764 PMCID: PMC10404802 DOI: 10.1016/j.virusres.2023.199183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.
Collapse
Affiliation(s)
- Ying Chen
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China.
| | - Lin Luo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ying Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
| |
Collapse
|
2
|
Chechik M, Greive SJ, Antson AA, Jenkins HT. Structure of HK97 small terminase:DNA complex unveils a novel DNA binding mechanism by a circular protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549218. [PMID: 37503206 PMCID: PMC10370121 DOI: 10.1101/2023.07.17.549218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA recognition is critical for assembly of double-stranded DNA viruses, in particular for the initiation of packaging the viral genome into the capsid. DNA packaging has been extensively studied for three archetypal bacteriophage systems: cos, pac and phi29. We identified the minimal site within the cos region of bacteriophage HK97 specifically recognised by the small terminase and determined a cryoEM structure for the small terminase:DNA complex. This nonameric circular protein utilizes a previously unknown mechanism of DNA binding. While DNA threads through the central tunnel, unexpectedly, DNA-recognition is generated at its exit by a substructure formed by the N- and C-terminal segments of two adjacent protomers of the terminase which are unstructured in the absence of DNA. Such interaction ensures continuous engagement of the small terminase with DNA, allowing sliding along DNA while simultaneously checking the DNA sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the cos site.
Collapse
Affiliation(s)
- Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | | | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| |
Collapse
|
3
|
Lokareddy RK, Hou CFD, Li F, Yang R, Cingolani G. Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function. Viruses 2022; 14:v14102215. [PMID: 36298770 PMCID: PMC9611059 DOI: 10.3390/v14102215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent DNA packaging, have been studied in depth, shedding light on the chemo-mechanical coupling between ATP hydrolysis and DNA translocation. Instead, significantly less is known about the small terminase subunit, TerS, which is dispensable or even inhibitory in vitro, but essential in vivo. By taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of phage TerSs, in this review, we take an inventory of known TerSs studied to date. Our analysis suggests that TerS evolved and diversified into a flexible molecular framework that can conserve biological function with minimal sequence and quaternary structure conservation to fit different packaging strategies and environmental conditions.
Collapse
|
4
|
Fung HKH, Grimes S, Huet A, Duda RL, Chechik M, Gault J, Robinson C, Hendrix R, Jardine P, Conway J, Baumann C, Antson A. Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system. Nucleic Acids Res 2022; 50:8719-8732. [PMID: 35947691 PMCID: PMC9410871 DOI: 10.1093/nar/gkac647] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/06/2022] [Accepted: 07/24/2022] [Indexed: 12/24/2022] Open
Abstract
Many essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and herpes viruses, use a homomeric ring ATPase to processively translocate viral genomic DNA into procapsids during assembly. Our current understanding of viral DNA packaging comes from three archetypal bacteriophage systems: cos, pac and phi29. Detailed mechanistic understanding exists for pac and phi29, but not for cos. Here, we reconstituted in vitro a cos packaging system based on bacteriophage HK97 and provided a detailed biochemical and structural description. We used a photobleaching-based, single-molecule assay to determine the stoichiometry of the DNA-translocating ATPase large terminase. Crystal structures of the large terminase and DNA-recruiting small terminase, a first for a biochemically defined cos system, reveal mechanistic similarities between cos and pac systems. At the same time, mutational and biochemical analyses indicate a new regulatory mechanism for ATPase multimerization and coordination in the HK97 system. This work therefore establishes a framework for studying the evolutionary relationships between ATP-dependent DNA translocation machineries in double-stranded DNA viruses.
Collapse
Affiliation(s)
- Herman K H Fung
- Department of Biology, University of York, York, YO10 5DD, UK
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Shelley Grimes
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alexis Huet
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Robert L Duda
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Roger W Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| |
Collapse
|
5
|
Mondal P, Mallick B, Dutta M, Dutta S. Isolation, characterization, and application of a novel polyvalent lytic phage STWB21 against typhoidal and nontyphoidal Salmonella spp. Front Microbiol 2022; 13:980025. [PMID: 36071966 PMCID: PMC9441917 DOI: 10.3389/fmicb.2022.980025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella is one of the common causal agents of bacterial gastroenteritis-related morbidity and mortality among children below 5 years and the elderly populations. Salmonellosis in humans is caused mainly by consuming contaminated food originating from animals. The genus Salmonella has several serovars, and many of them are recently reported to be resistant to multiple drugs. Therefore, isolation of lytic Salmonella bacteriophages in search of bactericidal activity has received importance. In this study, a Salmonella phage STWB21 was isolated from a lake water sample and found to be a novel lytic phage with promising potential against the host bacteria Salmonella typhi. However, some polyvalence was observed in their broad host range. In addition to S. typhi, the phage STWB21 was able to infect S. paratyphi, S. typhimurium, S. enteritidis, and a few other bacterial species such as Sh. flexneri 2a, Sh. flexneri 3a, and ETEC. The newly isolated phage STWB21 belongs to the Siphoviridae family with an icosahedral head and a long flexible non-contractile tail. Phage STWB21 is relatively stable under a wide range of pH (4–11) and temperatures (4°C–50°C) for different Salmonella serovars. The latent period and burst size of phage STWB21 against S. typhi were 25 min and 161 plaque-forming units per cell. Since Salmonella is a foodborne pathogen, the phage STWB21 was applied to treat a 24 h biofilm formed in onion and milk under laboratory conditions. A significant reduction was observed in the bacterial population of S. typhi biofilm in both cases. Phage STWB21 contained a dsDNA of 112,834 bp in length, and the GC content was 40.37%. Also, genomic analysis confirmed the presence of lytic genes and the absence of any lysogeny or toxin genes. Overall, the present study reveals phage STWB21 has a promising ability to be used as a biocontrol agent of Salmonella spp. and proposes its application in food industries.
Collapse
Affiliation(s)
- Payel Mondal
- Division of Electron Microscopy, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Bani Mallick
- Division of Electron Microscopy, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Moumita Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
- *Correspondence: Moumita Dutta, ;
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| |
Collapse
|
6
|
Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
Collapse
Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
7
|
Stevenson CEM, Lawson DM. Analysis of Protein-DNA Interactions Using Surface Plasmon Resonance and a ReDCaT Chip. Methods Mol Biol 2021; 2263:369-379. [PMID: 33877608 DOI: 10.1007/978-1-0716-1197-5_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The recognition of specific DNA sequences by proteins is crucial to fundamental biological processes such as DNA replication, transcription, and gene regulation. The technique of surface plasmon resonance (SPR) is ideally suited for the measurement of these interactions because it is quantitative, simple to implement, reproducible, can be automated, and requires very little sample. This typically involves the direct capture of biotinylated DNA to a streptavidin (SA) chip before flowing over the protein of interest and monitoring the interaction. However, once the DNA has been immobilized on the chip, it cannot be removed without damaging the chip surface. Moreover, if the protein-DNA interaction is strong, then it may not be possible to remove the protein from the DNA without damaging the chip surface. Given that the chips are costly, this will limit the number of samples that can be tested. Therefore, we have developed a Reusable DNA Capture Technology, or ReDCaT chip, that enables a single streptavidin chip to be used multiple times making the technique simple, quick, and cost effective. The general steps to prepare the ReDCaT chip, run a simple binding experiment, and analysis of data will be described in detail. Some additional applications will also be introduced.
Collapse
Affiliation(s)
- Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| |
Collapse
|
8
|
Niazi M, Florio TJ, Yang R, Lokareddy RK, Swanson NA, Gillilan RE, Cingolani G. Biophysical analysis of Pseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation. Nucleic Acids Res 2020; 48:11721-11736. [PMID: 33125059 PMCID: PMC7672466 DOI: 10.1093/nar/gkaa866] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/19/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022] Open
Abstract
The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
Collapse
Affiliation(s)
- Marzia Niazi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Tyler J Florio
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Nicholas A Swanson
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| |
Collapse
|
9
|
Grabarczyk DB. Crystal structure and interactions of the Tof1-Csm3 (Timeless-Tipin) fork protection complex. Nucleic Acids Res 2020; 48:6996-7004. [PMID: 32469068 PMCID: PMC7337906 DOI: 10.1093/nar/gkaa456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/13/2022] Open
Abstract
The Tof1-Csm3 fork protection complex has a central role in the replisome-it promotes the progression of DNA replication forks and protects them when they stall, while also enabling cohesion establishment and checkpoint responses. Here, I present the crystal structure of the Tof1-Csm3 complex from Chaetomium thermophilum at 3.1 Å resolution. The structure reveals that both proteins together form an extended alpha helical repeat structure, which suggests a mechanical or scaffolding role for the complex. Expanding on this idea, I characterize a DNA interacting region and a cancer-associated Mrc1 binding site. This study provides the molecular basis for understanding the functions of the Tof1-Csm3 complex, its human orthologue the Timeless-Tipin complex and additionally the Drosophila circadian rhythm protein Timeless.
Collapse
Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg, Germany
| |
Collapse
|
10
|
Yazdi M, Bouzari M, Ghaemi EA, Shahin K. Isolation, Characterization and Genomic Analysis of a Novel Bacteriophage VB_EcoS-Golestan Infecting Multidrug-Resistant Escherichia coli Isolated from Urinary Tract Infection. Sci Rep 2020; 10:7690. [PMID: 32376832 PMCID: PMC7203180 DOI: 10.1038/s41598-020-63048-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Escherichia coli (E. coli) is one of the most common uropathogenic bacteria. The emergence of multi-drug resistance among these bacteria resulted in a worldwide public health problem which requires alternative treatment approaches such as phage therapy. In this study, phage VB_EcoS-Golestan, a member of Siphoviridae family, with high lytic ability against E. coli isolates, was isolated from wastewater. Its burst size was large and about 100 plaque-forming units/infected cell, rapid adsorption time, and high resistance to a broad range of pH and temperatures. Bioinformatics analysis of the genomic sequence suggests that VB_EcoS-Golestan is a new phage closely related to Escherichia phages in the Kagunavirus genus, Guernseyvirinae subfamily of Siphoviridae. The genome size was 44829 bp bp that encodes 78 putative ORFs, no tRNAs, 7 potential promoter sequences and 13 Rho-factor-independent terminators. No lysogenic mediated genes were detected in VB_EcoS-Golestan genome. Overall VB_EcoS-Golestan might be used as a potential treatment approach for controlling E. coli mediated urinary tract infection, however, further studies are essential to ensure its safety.
Collapse
Affiliation(s)
- Mahsa Yazdi
- Department of Biology, Faculty of Sciences, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Majid Bouzari
- Department of Biology, Faculty of Sciences, University of Isfahan, 81746-73441, Isfahan, Iran.
| | - Ezzat Allah Ghaemi
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, 4934174515, Gorgan, Iran.
| | - Khashayar Shahin
- Department of Biology, Faculty of Sciences, University of Isfahan, 81746-73441, Isfahan, Iran
| |
Collapse
|
11
|
Hayes JA, Hilbert BJ, Gaubitz C, Stone NP, Kelch BA. A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry. J Biol Chem 2020; 295:3783-3793. [PMID: 32014998 DOI: 10.1074/jbc.ra119.012224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/30/2020] [Indexed: 11/06/2022] Open
Abstract
Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerSP76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerSP76-26 revealed that it forms a ring with a wide central pore and radially arrayed helix-turn-helix domains. The structure further showed that these helix-turn-helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerSP76-26 can bind DNA. Finally, the TerSP76-26 structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerSP76-26 to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerSP76-26, revealing key differences between this thermophilic phage and its mesophilic counterparts.
Collapse
Affiliation(s)
- Janelle A Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Brendan J Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Christl Gaubitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Nicholas P Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| |
Collapse
|
12
|
Identification of the First Gene Transfer Agent (GTA) Small Terminase in Rhodobacter capsulatus and Its Role in GTA Production and Packaging of DNA. J Virol 2019; 93:JVI.01328-19. [PMID: 31534034 PMCID: PMC6854486 DOI: 10.1128/jvi.01328-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Genetic exchange mediated by viruses of bacteria (bacteriophages) is the primary driver of rapid bacterial evolution. The priority of viruses is usually to propagate themselves. Most bacteriophages use the small terminase protein to identify their own genome and direct its inclusion into phage capsids. Gene transfer agents (GTAs) are descended from bacteriophages, but they instead package fragments of the entire bacterial genome without preference for their own genes. GTAs do not selectively target specific DNA, and no GTA small terminases are known. Here, we identified the small terminase from the model Rhodobacter capsulatus GTA, which then allowed prediction of analogues in other species. We examined the role of the small terminase in GTA production and propose a structural basis for random DNA packaging.IMPORTANCE Random transfer of any and all genes between bacteria could be influential in the spread of virulence or antimicrobial resistance genes. Discovery of the true prevalence of GTAs in sequenced genomes is hampered by their apparent similarity to bacteriophages. Our data allowed the prediction of small terminases in diverse GTA producer species, and defining the characteristics of a "GTA-type" terminase could be an important step toward novel GTA identification. Importantly, the GTA small terminase shares many features with its phage counterpart. We propose that the GTA terminase complex could become a streamlined model system to answer fundamental questions about double-stranded DNA (dsDNA) packaging by viruses that have not been forthcoming to date.
Collapse
|
13
|
Arens JS, Duffy C, Feiss M. Acidic residues and a predicted, highly conserved α-helix are critical for the endonuclease/strand separation functions of bacteriophage λ's TerL. Mol Microbiol 2019; 112:1483-1498. [PMID: 31430408 DOI: 10.1111/mmi.14373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2019] [Indexed: 01/10/2023]
Abstract
Complementation, endonuclease, strand separation, and packaging assays using mutant TerLλ 's, coupled with bioinformatic information and modeling of its endonuclease, identified five residues, D401, E408, D465, E563, and E586, as critical acidic residues of TerLλ 's endonuclease. Studies of phage and viral TerL nucleases indicate acidic residues participate in metal ion-binding, part of a two-ion metal catalysis mechanism, where metal ion A activates a water for DNA backbone hydrolysis. Modeling places D401, D465, and E586 in locations analogous to those of the metal-binding residues of many phage and viral TerLs. Our work leads to a model of TerLλ 's endonuclease domain where at least three acidic residues from a ~185 residue segment (D401 to E586) are near each other in the structure, forming the endonuclease catalytic center at cosN, the nicking site. DNA interactions required to bring the rotationally symmetric cosN precisely to the catalytic center are proposed to rely on an ~60 residue region that includes a conserved α-helix for dimerization. Metal ion A, positioned by TerLλ 's acidic D401 and E586, would be placed at cosN for water activation, ensuring high accuracy for DNA backbone hydrolysis.
Collapse
Affiliation(s)
- Jean Sippy Arens
- Department of Microbiology and Immunology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Carol Duffy
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Michael Feiss
- Department of Microbiology and Immunology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| |
Collapse
|
14
|
The Revisited Genome of Bacillus subtilis Bacteriophage SPP1. Viruses 2018; 10:v10120705. [PMID: 30544981 PMCID: PMC6316719 DOI: 10.3390/v10120705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 02/05/2023] Open
Abstract
Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago [1]. Its complete DNA sequence was reported in 1997 [2]. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.
Collapse
|
15
|
Amorim AR, Neves LA, Valêncio CR, Roberto GF, Zafalon GFD. An approach for COFFEE objective function to global DNA multiple sequence alignment. Comput Biol Chem 2018; 75:39-44. [PMID: 29738913 DOI: 10.1016/j.compbiolchem.2018.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/29/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can be used to prediction of structures or functions of unknown proteins and to phylogenetic tree reconstruction. There are many heuristics to perform multiple sequence alignment, as Progressive Alignment, Ant Colony, Genetic Algorithms, among others. Along the years, some tools were proposed to perform MSA and MSA-GA is one of them. The MSA-GA is a tool based on Genetic Algorithm to perform multiple sequence alignment and its results are generally better than other well-known tools in bioinformatics, as Clustal W. The COFFEE objective function was implemented in the MSA-GA in order to allow it to produce better alignments to less similar sequence sets of proteins. Nonetheless, the COFFEE objective function is not suited do perform multiple sequence alignment of nucleotides. Thus, we have modified the COFFEE objective function, previously implemented in the MSA-GA, to allow it to obtain better results also to sequences of nucleotides. Our results have shown that our approach has achieved better results in all cases when compared with standard COFFEE and most of cases when compared with WSP for all test cases from BAliBase and BRAliBase. Moreover, our results are more reliable because their standard deviations have less variation.
Collapse
Affiliation(s)
- Anderson Rici Amorim
- Department of Computer Science and Statistics, São Paulo State University, Rua Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil
| | - Leandro Alves Neves
- Department of Computer Science and Statistics, São Paulo State University, Rua Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil
| | - Carlos Roberto Valêncio
- Department of Computer Science and Statistics, São Paulo State University, Rua Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil
| | - Guilherme Freire Roberto
- Department of Computer Science and Statistics, São Paulo State University, Rua Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil
| | - Geraldo Francisco Donegá Zafalon
- Department of Computer Science and Statistics, São Paulo State University, Rua Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil.
| |
Collapse
|
16
|
Misawa T, Kanda Y, Demizu Y. Rational Design and Synthesis of Post-Functionalizable Peptide Foldamers as Helical Templates. Bioconjug Chem 2017; 28:3029-3035. [DOI: 10.1021/acs.bioconjchem.7b00621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Takashi Misawa
- Division of Organic Chemistry and ‡Division of Pharmacology, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yasunari Kanda
- Division of Organic Chemistry and ‡Division of Pharmacology, National Institute of Health Sciences, Tokyo 158-8501, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry and ‡Division of Pharmacology, National Institute of Health Sciences, Tokyo 158-8501, Japan
| |
Collapse
|
17
|
Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA. Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism. Nucleic Acids Res 2017; 45:3580-3590. [PMID: 28100693 PMCID: PMC5389553 DOI: 10.1093/nar/gkw1354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+. High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism.
Collapse
Affiliation(s)
- Rui-Gang Xu
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Elena V Blagova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Anna Lopatina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Evgeny Klimuk
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| |
Collapse
|
18
|
Djacem K, Tavares P, Oliveira L. Bacteriophage SPP1 pac Cleavage: A Precise Cut without Sequence Specificity Requirement. J Mol Biol 2017; 429:1381-1395. [PMID: 28082080 DOI: 10.1016/j.jmb.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 01/23/2023]
Abstract
In many tailed bacteriophages, DNA packaging is initiated by recognition and cleavage of a specific sequence pac by the small (TerS) and large (TerL) terminase subunits. It was previously shown that the SPP1 pac region has two sequences where TerS binds (pacR and pacL), flanking the segment where TerL cleaves the SPP1 DNA (pacC). However, the pac-specific sequences required to achieve this endonucleolytic cut were not established. Their characterization is essential to understand the underlying mechanism. We show that the pacR sequence localized within 35bp downstream of the pac cut can be extensively degenerated, including its c1 and c2 repeats, and that only a disruption of a 5-bp polyadenine tract impairs the pac cleavage. This result together with deletion analysis of pacL shows that the specific DNA sequences required for targeting the terminase for pac cleavage are considerably shorter than the large region bound by TerS. Furthermore, extensive degeneration of the 6-bp target sequence within pacC where pac cleavage occurs reveals that TerL maintains, remarkably, its precise position of cleavage. Studies with SPP1-related phages show the conservation of the cut position, irrespective of the sequence variation in pacC and in pacR or the changes in pacL-pacC distance. Mechanistically, our data are compatible with a model in which TerS interactions with part of the pacL sequence and a poly-A tract in pacR are sufficient to orient very accurately the TerL nuclease to a defined pacC position. They also demonstrate that the resulting precise cut at pacC is independent of the targeted DNA sequence.
Collapse
Affiliation(s)
- Karima Djacem
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Paulo Tavares
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Leonor Oliveira
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
| |
Collapse
|
19
|
Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela
De Souza L, Cuskin F, Gilbert H, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ. A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism. ACS CENTRAL SCIENCE 2016; 2:896-903. [PMID: 28058278 PMCID: PMC5200933 DOI: 10.1021/acscentsci.6b00232] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 06/06/2023]
Abstract
The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.
Collapse
Affiliation(s)
- Yi Jin
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Marija Petricevic
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Huw Jenkins
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Leticia Portela
De Souza
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Fiona Cuskin
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Harry
J. Gilbert
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Ethan D. Goddard-Borger
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| |
Collapse
|
20
|
Zhang J, Gao B, Chai H, Ma Z, Yang G. Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm. BMC Bioinformatics 2016; 17:323. [PMID: 27565741 PMCID: PMC5002159 DOI: 10.1186/s12859-016-1201-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/24/2016] [Indexed: 11/13/2022] Open
Abstract
Background DNA-binding proteins (DBPs) play fundamental roles in many biological processes. Therefore, the developing of effective computational tools for identifying DBPs is becoming highly desirable. Results In this study, we proposed an accurate method for the prediction of DBPs. Firstly, we focused on the challenge of improving DBP prediction accuracy with information solely from the sequence. Secondly, we used multiple informative features to encode the protein. These features included evolutionary conservation profile, secondary structure motifs, and physicochemical properties. Thirdly, we introduced a novel improved Binary Firefly Algorithm (BFA) to remove redundant or noisy features as well as select optimal parameters for the classifier. The experimental results of our predictor on two benchmark datasets outperformed many state-of-the-art predictors, which revealed the effectiveness of our method. The promising prediction performance on a new-compiled independent testing dataset from PDB and a large-scale dataset from UniProt proved the good generalization ability of our method. In addition, the BFA forged in this research would be of great potential in practical applications in optimization fields, especially in feature selection problems. Conclusions A highly accurate method was proposed for the identification of DBPs. A user-friendly web-server named iDbP (identification of DNA-binding Proteins) was constructed and provided for academic use. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1201-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jian Zhang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China
| | - Bo Gao
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China
| | - Haiting Chai
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China
| | - Zhiqiang Ma
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China
| | - Guifu Yang
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130117, People's Republic of China. .,Office of Informatization Management and Planning, Northeast Normal University, Changchun, 130117, People's Republic of China.
| |
Collapse
|
21
|
Abstract
During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase’s small subunit (TerS). The large terminase subunit (TerL) contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in cosB, the recognition site. TerS binding to cosB positions TerL to cut the concatemeric DNA at the adjacent nicking site, cosN. TerL introduces staggered nicks in cosN, generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the cosB-containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead’s portal vertex and translocation ensues. DNA topology plays a role in the TerSλ-cosBλ interaction. Here we show that a site, I2, located between cosN and cosB, is critically important for an early DNA packaging step. I2 contains a complex static bend. I2 mutations block DNA packaging. I2 mutant DNA is cut by terminase at cosN in vitro, but in vivo, no cos cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by I2 mutations are presented.
Collapse
|