1
|
Li H, Zhong W, Zhang X, Rui Z, Yang Y, Xu J, Gao J, Zhou X, Wu J, Xu J. Isolation and Characterization of a Novel Vibrio Phage vB_ValA_R15Z. Curr Microbiol 2024; 81:285. [PMID: 39073500 DOI: 10.1007/s00284-024-03736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/08/2024] [Indexed: 07/30/2024]
Abstract
Vibrio phages have emerged as a potential alternative to antibiotic therapy for treating Vibrio infections. In this study, a lytic Vibrio phage, vB_ValA_R15Z against Vibrio alginolyticus ATCC 17749T, was isolated from an aquatic water sample collected in Xiamen, China. The phage had an icosahedral head (diameter 69 ± 2 nm) and a short, non-contractile tail measuring 16 ± 2 nm. The genome of vB_ValA_R15Z was found to be a double-stranded DNA consisting of 43, 552 bp, containing 54 coding sequences (CDSs) associated with phage packaging, structure, DNA metabolism, lysis and additional functions. The BLASTN results indicated that vB_ValA_R15Z shared less than 90.18% similarity with known phages recorded in the NCBI GenBank database, suggesting that vB_ValA_R15Z was a novel Vibrio phage. Furthermore, phylogenetic analysis revealed that vB_ValA_R15Z belongs to the genus Kaohsiungvirus. In addition, a typical lytic mechanism (holin-endolysim) was found in the genome of vB_ValA_R15Z, while no antibiotic resistance- or virulence factor-related gene was detected. Overall, the study provides valuable insights into the isolation and characterization of vB_ValA_R15Z, highlighting its potential as an effective phage therapy option for combating Vibrio alginolyticus infections.
Collapse
Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China.
| | - Wanxuan Zhong
- State Key Laboratory of Trophic Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xinyu Zhang
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhang Rui
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jie Gao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xing Zhou
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jie Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, 361005, Fujian, China.
| | - Jie Xu
- Centre for Regional Oceans, Department of Ocean Science and Technology, Faculty of Science and Technology, University of Macau, Macau, 999078, China.
| |
Collapse
|
2
|
Bergamo A, Sava G. Lysozyme: A Natural Product with Multiple and Useful Antiviral Properties. Molecules 2024; 29:652. [PMID: 38338396 PMCID: PMC10856218 DOI: 10.3390/molecules29030652] [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: 01/03/2024] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Lysozyme, especially the one obtained from hen's egg white, continues to show new pharmacological properties. The fact that only a few of these properties can be translated into therapeutic applications is due to the lack of suitable clinical studies. However, this lack cannot hide the evidence that is emerging from scientific research. This review for the first time examines, from a pharmacological point of view, all the relevant studies on the antiviral properties of lysozyme, analyzing its possible mechanism of action and its ability to block viral infections and, in some cases, inhibit viral replication. Lysozyme can interact with nucleic acids and alter their function, but this effect is uncoupled from the catalytic activity that determines its antibacterial activity; it is present in intact lysozyme but is equally potent in a heat-degraded lysozyme or in a nonapeptide isolated by proteolytic digestion. An analysis of the literature shows that lysozyme can be used both as a disinfectant for raw and processed foods and as a drug to combat viral infections in animals and humans. To summarize, it can be said that lysozyme has important antiviral properties, as already suspected in the initial studies conducted over 50 years ago, and it should be explored in suitable clinical studies on humans.
Collapse
|
3
|
Mallawaarachchi V, Roach MJ, Decewicz P, Papudeshi B, Giles SK, Grigson SR, Bouras G, Hesse RD, Inglis LK, Hutton ALK, Dinsdale EA, Edwards RA. Phables: from fragmented assemblies to high-quality bacteriophage genomes. Bioinformatics 2023; 39:btad586. [PMID: 37738590 PMCID: PMC10563150 DOI: 10.1093/bioinformatics/btad586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Abstract
MOTIVATION Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery. RESULTS We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. AVAILABILITY AND IMPLEMENTATION Phables is available on GitHub at https://github.com/Vini2/phables.
Collapse
Affiliation(s)
- Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Michael J Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Przemyslaw Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- The Department of Surgery—Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, South Australia 5000, Australia
| | - Ryan D Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Laura K Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Abbey L K Hutton
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| |
Collapse
|
4
|
Mallawaarachchi V, Roach MJ, Decewicz P, Papudeshi B, Giles SK, Grigson SR, Bouras G, Hesse RD, Inglis LK, Hutton ALK, Dinsdale EA, Edwards RA. Phables: from fragmented assemblies to high-quality bacteriophage genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535632. [PMID: 37066369 PMCID: PMC10104058 DOI: 10.1101/2023.04.04.535632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Microbial communities influence both human health and different environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies, and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of genomes can occur, leading to the need for new approaches in viral identification. Therefore, the identification and characterisation of novel phages remain a challenge. We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. Phables is available on GitHub at https://github.com/Vini2/phables.
Collapse
Affiliation(s)
- Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michael J Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, The University of Adelaide, North Tce, Adelaide, SA, 5000, Australia
| | - Ryan D Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Laura K Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Abbey L K Hutton
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| |
Collapse
|
5
|
Lammens EM, Feyaerts N, Kerremans A, Boon M, Lavigne R. Assessing the Orthogonality of Phage-Encoded RNA Polymerases for Tailored Synthetic Biology Applications in Pseudomonas Species. Int J Mol Sci 2023; 24:ijms24087175. [PMID: 37108338 PMCID: PMC10138996 DOI: 10.3390/ijms24087175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
The phage T7 RNA polymerase (RNAP) and lysozyme form the basis of the widely used pET expression system for recombinant expression in the biotechnology field and as a tool in microbial synthetic biology. Attempts to transfer this genetic circuitry from Escherichia coli to non-model bacterial organisms with high potential have been restricted by the cytotoxicity of the T7 RNAP in the receiving hosts. We here explore the diversity of T7-like RNAPs mined directly from Pseudomonas phages for implementation in Pseudomonas species, thus relying on the co-evolution and natural adaptation of the system towards its host. By screening and characterizing different viral transcription machinery using a vector-based system in P. putida., we identified a set of four non-toxic phage RNAPs from phages phi15, PPPL-1, Pf-10, and 67PfluR64PP, showing a broad activity range and orthogonality to each other and the T7 RNAP. In addition, we confirmed the transcription start sites of their predicted promoters and improved the stringency of the phage RNAP expression systems by introducing and optimizing phage lysozymes for RNAP inhibition. This set of viral RNAPs expands the adaption of T7-inspired circuitry towards Pseudomonas species and highlights the potential of mining tailored genetic parts and tools from phages for their non-model host.
Collapse
Affiliation(s)
- Eveline-Marie Lammens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Nathalie Feyaerts
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| |
Collapse
|
6
|
Yuan SS, Gao D, Xie XQ, Ma CY, Su W, Zhang ZY, Zheng Y, Ding H. IBPred: a sequence-based predictor for identifying ion binding protein in phage. Comput Struct Biotechnol J 2022; 20:4942-4951. [PMID: 36147670 PMCID: PMC9474292 DOI: 10.1016/j.csbj.2022.08.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Ion binding proteins (IBPs) can selectively and non-covalently interact with ions. IBPs in phages also play an important role in biological processes. Therefore, accurate identification of IBPs is necessary for understanding their biological functions and molecular mechanisms that involve binding to ions. Since molecular biology experimental methods are still labor-intensive and cost-ineffective in identifying IBPs, it is helpful to develop computational methods to identify IBPs quickly and efficiently. In this work, a random forest (RF)-based model was constructed to quickly identify IBPs. Based on the protein sequence information and residues’ physicochemical properties, the dipeptide composition combined with the physicochemical correlation between two residues were proposed for the extraction of features. A feature selection technique called analysis of variance (ANOVA) was used to exclude redundant information. By comparing with other classified methods, we demonstrated that our method could identify IBPs accurately. Based on the model, a Python package named IBPred was built with the source code which can be accessed at https://github.com/ShishiYuan/IBPred.
Collapse
|
7
|
Li Z, Wang W, Ma B, Yin J, Hu C, Luo P, Wang Y. Genomic and biological characteristics of a newly isolated lytic bacteriophage PZJ0206 infecting the Enterobacter cloacae. Virus Res 2022; 316:198800. [DOI: 10.1016/j.virusres.2022.198800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
|
8
|
Pantoja Angles A, Valle-Pérez AU, Hauser C, Mahfouz MM. Microbial Biocontainment Systems for Clinical, Agricultural, and Industrial Applications. Front Bioeng Biotechnol 2022; 10:830200. [PMID: 35186907 PMCID: PMC8847691 DOI: 10.3389/fbioe.2022.830200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Many applications of synthetic biology require biological systems in engineered microbes to be delivered into diverse environments, such as for in situ bioremediation, biosensing, and applications in medicine and agriculture. To avoid harming the target system (whether that is a farm field or the human gut), such applications require microbial biocontainment systems (MBSs) that inhibit the proliferation of engineered microbes. In the past decade, diverse molecular strategies have been implemented to develop MBSs that tightly control the proliferation of engineered microbes; this has enabled medical, industrial, and agricultural applications in which biological processes can be executed in situ. The customization of MBSs also facilitate the integration of sensing modules for which different compounds can be produced and delivered upon changes in environmental conditions. These achievements have accelerated the generation of novel microbial systems capable of responding to external stimuli with limited interference from the environment. In this review, we provide an overview of the current approaches used for MBSs, with a specific focus on applications that have an immediate impact on multiple fields.
Collapse
Affiliation(s)
- Aaron Pantoja Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Charlotte Hauser
- Laboratory for Nanomedicine, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz, ; Charlotte Hauser,
| |
Collapse
|
9
|
Rahimi-Midani A, Lee SW, Choi TJ. Potential Solutions Using Bacteriophages against Antimicrobial Resistant Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10121496. [PMID: 34943708 PMCID: PMC8698741 DOI: 10.3390/antibiotics10121496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages are viruses that specifically infect a bacterial host. They play a great role in the modern biotechnology and antibiotic-resistant microbe era. Since the discovery of phages, their application as a control agent has faced challenges that made antibiotics a better fit for combating pathogenic bacteria. Recently, with the novel sequencing technologies providing new insight into the nature of bacteriophages, their application has a second chance to be used. However, novel challenges need to be addressed to provide proper strategies for their practical application. This review focuses on addressing these challenges by initially introducing the nature of bacteriophages and describing the phage-host-dependent strategies for phage application. We also describe the effect of the long-term application of phages in natural environments and other bacterial communities. Overall, this review gathered crucial information for the future application of phages. We predict the use of phages will not be the only control strategy against pathogenic bacteria. Therefore, more studies must be done for low-risk control methods against antimicrobial-resistant bacteria.
Collapse
Affiliation(s)
- Aryan Rahimi-Midani
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
| | - Tae-Jin Choi
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
- Correspondence:
| |
Collapse
|
10
|
Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
Collapse
Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
| |
Collapse
|
11
|
Becker K, Meyer A, Roberts TM, Panke S. Plasmid replication based on the T7 origin of replication requires a T7 RNAP variant and inactivation of ribonuclease H. Nucleic Acids Res 2021; 49:8189-8198. [PMID: 34255845 PMCID: PMC8373140 DOI: 10.1093/nar/gkab596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/22/2021] [Accepted: 07/09/2021] [Indexed: 01/09/2023] Open
Abstract
T7 RNA polymerase (RNAP) is a valuable tool in biotechnology, basic research and synthetic biology due to its robust, efficient and selective transcription of genes. Here, we expand the scope of T7 RNAP to include plasmid replication. We present a novel type of plasmid, termed T7 ori plasmids that replicate, in an engineered Escherichia coli, with a T7 phage origin as the sole origin of replication. We find that while the T7 replication proteins; T7 DNA polymerase, T7 single-stranded binding proteins and T7 helicase-primase are dispensable for replication, T7 RNAP is required, although dependent on a T7 RNAP variant with reduced activity. We also find that T7 RNAP-dependent replication of T7 ori plasmids requires the inactivation of cellular ribonuclease H. We show that the system is portable among different plasmid architectures and ribonuclease H-inactivated E. coli strains. Finally, we find that the copy number of T7 ori plasmids can be tuned based on the induction level of RNAP. Altogether, this study assists in the choice of an optimal genetic tool by providing a novel plasmid that requires T7 RNAP for replication.
Collapse
Affiliation(s)
- Katja Becker
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Andreas Meyer
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland.,FGen GmbH, Basel 4057, Switzerland
| | | | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| |
Collapse
|
12
|
Isolation and characterization of a novel Escherichia coli Kayfunavirus phage DY1. Virus Res 2020; 293:198274. [PMID: 33359502 DOI: 10.1016/j.virusres.2020.198274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/20/2022]
Abstract
Phage therapy has been revitalized since antibiotic resistance in bacteria is increasing. Compared with antibiotics, phages can target specific bacteria precisely, which requires more understanding of phage-host interactions by investigating different phages. Escherichia coli is a common pathogen with very high diversity. Based on the O antigens, E. coli can be classified into at least 183 serotypes and existing phages are far from being able to lyse all E. coli. Therefore, a novel phage specific to E. coli, named DY1, was identified and characterized to enhance our understanding of the phages of E. coli and expand the phage library. Phage DY1 belongs to the family Autographiviridae which is derived from Podoviridae. The genome of DY1 was determined to be 39,817 bp and comprises 54 putative open reading frames. Comparative genome and phylogenetic analysis demonstrated that DY1 was highly similar to phages belonging to the genus Kayfunavirus; however, the highest average nucleotide identity (ANI) values of DY1 with known phages was 0.82 suggesting that DY1 was a novel phage. Through stability tests, DY1 was very stable at temperatures ranging from 20 to 50 °C and pH levels from 5 to 11. Taken together, we report that phage DY1 is a novel Kayfunavirus phage with the potential for phage therapy.
Collapse
|
13
|
Brungardt J, Govind R, Trick HN. A simplified method for producing laboratory grade recombinant TEV protease from E. coli. Protein Expr Purif 2020; 174:105662. [PMID: 32387144 DOI: 10.1016/j.pep.2020.105662] [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: 02/26/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 11/28/2022]
Abstract
The tobacco etch virus (TEV) protease has become a popular choice for cleaving fusion proteins because of its high stringency in sequence recognition. Procedures for isolating recombinant protein from the cytoplasm of E. coli require rupturing of the cell wall via enzymatic treatment combined with sonication or French press. Here we present an expedited method for producing laboratory-grade TEV protease in E. coli using a freeze-thaw method, followed by purification with immobilized metal affinity chromatography. Protease is obtained by expression from the pDZ2087 plasmid in BL21 (DE3) cells. Proteolysis resulting from this product, cleaves a maltose-binding protein fusion to completion at a fusion-to-protease molar ratio of 50:1.
Collapse
Affiliation(s)
- Jordan Brungardt
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS 66502, USA
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA.
| |
Collapse
|
14
|
Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, Du S, Rensing C. Pelagiphages in thePodoviridaefamily integrate into host genomes. Environ Microbiol 2018; 21:1989-2001. [DOI: 10.1111/1462-2920.14487] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental ScienceCollege of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen Fujian China
| | | | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Jing Sun
- Department of MicrobiologyOregon State University Corvallis OR USA
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry University Fuzhou Fujian China
| |
Collapse
|
15
|
Zeng H, He W, Li C, Zhang J, Ling N, Ding Y, Xue L, Chen M, Wu H, Wu Q. Complete genome analysis of a novel phage GW1 lysing Cronobacter. Arch Virol 2018; 164:625-628. [PMID: 30426215 DOI: 10.1007/s00705-018-4084-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/05/2018] [Indexed: 01/31/2023]
Abstract
A newly identified lytic Cronobacter phage, GW1, was isolated from the Pearl River of Guangzhou, China. GW1 had a double-stranded DNA genome of 39,695 nucleotides with an average GC content of 53.18 %. Among the 49 open reading frames (ORFs) identified, genes for rRNA, tRNA, antibiotic resistance, and virulence factors were not found in the phage genome. The morphology, genomic features, and phylogenetic position of GW1 revealed that it represents a new species in the genus T7virus. This novel lytic Cronobacter phage may provide an alternative for phage therapy and biocontrol against Cronobacter.
Collapse
Affiliation(s)
- Haiyan Zeng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Wenjing He
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Chengsi Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Na Ling
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Liang Xue
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Moutong Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Haoming Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China.
| |
Collapse
|
16
|
Orlov MA, Ryasik AA, Sorokin AA. Destabilization of the DNA Duplex of Actively Replicating Promoters of T7-Like Bacteriophages. Mol Biol 2018. [DOI: 10.1134/s0026893318050114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Wang Q, Zeng X, Yang Q, Yang C. Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:617-623. [PMID: 29803035 DOI: 10.1016/j.scitotenv.2018.05.213] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 103 copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.
Collapse
Affiliation(s)
- Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China
| | - Xiangpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China.
| | - Chuanzhen Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| |
Collapse
|
18
|
Borkotoky S, Murali A. The highly efficient T7 RNA polymerase: A wonder macromolecule in biological realm. Int J Biol Macromol 2018; 118:49-56. [DOI: 10.1016/j.ijbiomac.2018.05.198] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 12/01/2022]
|
19
|
Garry DJ, Ellington AD, Molineux IJ, Bull JJ. Viral attenuation by engineered protein fragmentation. Virus Evol 2018; 4:vey017. [PMID: 29942657 PMCID: PMC6009699 DOI: 10.1093/ve/vey017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A possible but untested method of viral attenuation is protein fragmentation, engineering wild-type proteins as two or more peptides that self-assemble after translation. Here, the bacteriophage T7 was engineered to encode its essential RNA polymerase as two peptides. Initial fitness was profoundly suppressed. Subjecting the engineered virus to over 100 generations of adaptation by serial transfer resulted in a large fitness increase, still remaining below that of evolved wild-type. The fitness increase was accompanied by three substitutions in the fragmented peptides as well as six mutations in other parts of the genome, but the fragmentation was retained. This study thereby demonstrates the feasibility of using gene fragmentation as a possibly permanent method of attenuation, but the initial fitness of the engineered genome may be a poor measure of its fitness on extended adaptation.
Collapse
Affiliation(s)
- Daniel J Garry
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA
| | - Ian J Molineux
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - James J Bull
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| |
Collapse
|
20
|
Borysowski J, Weber-Dabrowska B, Górski A. Bacteriophage Endolysins as a Novel Class of Antibacterial Agents. Exp Biol Med (Maywood) 2016; 231:366-77. [PMID: 16565432 DOI: 10.1177/153537020623100402] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Endolysins are double-stranded DNA bacteriophage-encoded peptidoglycan hydrolases produced in phage-infected bacterial cells toward the end of the lytic cycle. They reach the peptidoglycan through membrane lesions formed by holins and cleave it, thus, inducing lysis of the bacterial cell and enabling progeny virions to be released. Endolysins are also capable of degrading peptidoglycan when applied externally (as purified recombinant proteins) to the bacterial cell wall, which also results in a rapid lysis of the bacterial cell. The unique ability of endolysins to rapidly cleave peptidoglycan in a generally species-specific manner renders them promising potential antibacterial agents. Originally developed with a view to killing bacteria colonizing mucous membranes (with the first report published in 2001), endolysins also hold promise for the treatment of systemic infections. As potential antibacterials, endolysins possess several important features, for instance, a novel mode of action, a narrow antibacterial spectrum, activity against bacteria regardless of their antibiotic sensitivity, and a low probability of developing resistance. However, there is only one report directly comparing the activity of an endolysin with that of an antibiotic, and no general conclusions can be drawn regarding whether lysins are more effective than traditional antibiotics. The results of the first preclinical studies indicate that the most apparent potential problems associated with endolysin therapy (e.g., their immunogenicity, the release of proinflammatory components during bacteriolysis, or the development of resistance), in fact, may not seriously hinder their use. However, all data regarding the safety and therapeutic effectiveness of endolysins obtained from preclinical studies must be ultimately verified by clinical trials. This review discusses the prophylactic and therapeutic applications of endolysins, especially with respect to their potential use in human medicine. Additionally, we outline current knowledge regarding the structure and natural function of the enzymes in phage biology, including the most recent findings.
Collapse
Affiliation(s)
- Jan Borysowski
- Department of Clinical Immunology, Institute of Transplantology, the Medical University of Warsaw, 02-006 Warsaw, Poland.
| | | | | |
Collapse
|
21
|
Borkotoky S, Meena CK, Murali A. Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach. Bioinform Biol Insights 2016; 10:155-66. [PMID: 27594785 PMCID: PMC5004996 DOI: 10.4137/bbi.s40427] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/31/2016] [Accepted: 08/07/2016] [Indexed: 12/26/2022] Open
Abstract
The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and post-docking molecular mechanics/generalized Born surface area analysis. Evaluation of the simulation trajectories and binding free energies of the complexes after simulation showed enoxaparin to be the best among low molecular weight heparins. Binding free energy analysis revealed that van der Waals interactions and polar solvation energy provided the substantial driving force for the binding process. Furthermore, per-residue free energy decomposition analysis revealed that the residues Asp 471, Asp 506, Asp 537, Tyr 571, Met 635, Asp 653, Pro 780, and Asp 812 are important for heparin interaction. Apart from these residues, most favorable contribution in all the three complexes came from Asp 506, Tyr 571, Met 635, Glu 652, and Asp 653, which can be essential for binding of heparin-like structures with T7RNAP. The results obtained from this study will be valuable for the future rational design of novel and potent inhibitors against T7RNAP and related proteins.
Collapse
Affiliation(s)
- Subhomoi Borkotoky
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Chetan Kumar Meena
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ayaluru Murali
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| |
Collapse
|
22
|
Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies. BMC Genomics 2016; 17:679. [PMID: 27561606 PMCID: PMC5000459 DOI: 10.1186/s12864-016-3018-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/13/2016] [Indexed: 11/17/2022] Open
Abstract
Background Phage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes. Results The original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome. Conclusions Using available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3018-2) contains supplementary material, which is available to authorized users.
Collapse
|
23
|
Hamdi S, Rousseau GM, Labrie SJ, Kourda RS, Tremblay DM, Moineau S, Slama KB. Characterization of Five Podoviridae Phages Infecting Citrobacter freundii. Front Microbiol 2016; 7:1023. [PMID: 27446058 PMCID: PMC4925675 DOI: 10.3389/fmicb.2016.01023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Citrobacter freundii causes opportunistic infections in humans and animals, which are becoming difficult to treat due to increased antibiotic resistance. The aim of this study was to explore phages as potential antimicrobial agents against this opportunistic pathogen. We isolated and characterized five new virulent phages, SH1, SH2, SH3, SH4, and SH5 from sewage samples in Tunisia. Morphological and genomic analyses revealed that the five C. freundii phages belong to the Caudovirales order, Podoviridae family, and Autographivirinae subfamily. Their linear double-stranded DNA genomes range from 39,158 to 39,832 bp and are terminally redundant with direct repeats between 183 and 242 bp. The five genomes share the same organization as coliphage T7. Based on genomic comparisons and on the phylogeny of the DNA polymerases, we assigned the five phages to the T7virus genus but separated them into two different groups. Phages SH1 and SH2 are very similar to previously characterized phages phiYeO3-12 and phiSG-JL2, infecting, respectively, Yersinia enterocolitica and Salmonella enterica, as well as sharing more than 80% identity with most genes of coliphage T7. Phages SH3, SH4, and SH5 are very similar to phages K1F and Dev2, infecting, respectively, Escherichia coli and Cronobacter turicensis. Several structural proteins of phages SH1, SH3, and SH4 were detected by mass spectrometry. The five phages were also stable from pH 5 to 10. No genes coding for known virulence factors or integrases were found, suggesting that the five isolated phages could be good candidates for therapeutic applications to prevent or treat C. freundii infections. In addition, this study increases our knowledge about the evolutionary relationships within the T7virus genus.
Collapse
Affiliation(s)
- Sana Hamdi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| | - Geneviève M Rousseau
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Simon J Labrie
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Rim S Kourda
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| | - Denise M Tremblay
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Karim B Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| |
Collapse
|
24
|
|
25
|
Pohane AA, Jain V. Insights into the regulation of bacteriophage endolysin: multiple means to the same end. Microbiology (Reading) 2015; 161:2269-76. [DOI: 10.1099/mic.0.000190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
26
|
Zhang J, Russu IM. Site-Resolved Structural Energetics of the T7 Concatemer Junction. Biochemistry 2014; 53:4806-13. [DOI: 10.1021/bi500393q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie Zhang
- Department of Chemistry and
Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Irina M. Russu
- Department of Chemistry and
Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
| |
Collapse
|
27
|
Denyes JM, Krell PJ, Manderville RA, Ackermann HW, She YM, Kropinski AM. The genome and proteome of Serratia bacteriophage η which forms unstable lysogens. Virol J 2014; 11:6. [PMID: 24433577 PMCID: PMC3918226 DOI: 10.1186/1743-422x-11-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/10/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Serratia marcescens phage η is a temperate unclassified member of the Siphoviridae which had been reported as containing hypermodified guanine residues. METHODS The DNA was characterized by enzymatic digestion followed by HPLC analysis of the nucleoside composition, and by DNA sequencing and proteomic analysis. Its ability to form stable lysogens and integrate was also investigated. RESULTS Enzymatic digestion and HPLC analysis revealed phage η DNA did not contain modified bases. The genome sequence of this virus, determined using pyrosequencing, is 42,724 nucleotides in length with a mol% GC of 49.9 and is circularly permuted. Sixty-nine putative CDSs were identified of which 19 encode novel proteins. While seven close genetic relatives were identified, they shared sequence similarity with only genes 40 to 69 of the phage η genome, while gp1 to gp39 shared no conserved relationship. The structural proteome, determined by SDS-PAGE and mass spectrometry, revealed seven unique proteins. This phage forms very unstable lysogens with its host S. marcescens.
Collapse
Affiliation(s)
- Jenna M Denyes
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Current address: ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Peter J Krell
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Hans-Wolfgang Ackermann
- Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Laval University, Quebec, QC G1X 4C6, Canada
| | - Yi-Min She
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, China
| | - Andrew M Kropinski
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, Ontario N1G 3W4, Canada
| |
Collapse
|
28
|
New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium. ACTA ACUST UNITED AC 2013; 14:1-10. [PMID: 23572252 DOI: 10.1007/s10969-013-9151-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 03/28/2013] [Indexed: 01/24/2023]
Abstract
Phage viruses that infect prokaryotes integrate their genome into the host chromosome; thus, microbial genomes typically contain genetic remnants of both recent and ancient phage infections. Often phage genes occur in clusters of atypical G+C content that reflect integration of the foreign DNA. However, some phage genes occur in isolation without other phage gene neighbors, probably resulting from horizontal gene transfer. In these cases, the phage gene product is unlikely to function as a component of a mature phage particle, and instead may have been co-opted by the host for its own benefit. The product of one such gene from Salmonella enterica serovar Typhimurium, STM3605, encodes a protein with modest sequence similarity to phage-like lysozyme (N-acetylmuramidase) but appears to lack essential catalytic residues that are strictly conserved in all lysozymes. Close homologs in other bacteria share this characteristic. The structure of the STM3605 protein was characterized by X-ray crystallography, and functional assays showed that it is a stable, folded protein whose structure closely resembles lysozyme. However, this protein is unlikely to hydrolyze peptidoglycan. Instead, STM3605 is presumed to have evolved an alternative function because it shows some lytic activity and partitions to micelles.
Collapse
|
29
|
Schmelcher M, Donovan DM, Loessner MJ. Bacteriophage endolysins as novel antimicrobials. Future Microbiol 2013; 7:1147-71. [PMID: 23030422 DOI: 10.2217/fmb.12.97] [Citation(s) in RCA: 474] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endolysins are enzymes used by bacteriophages at the end of their replication cycle to degrade the peptidoglycan of the bacterial host from within, resulting in cell lysis and release of progeny virions. Due to the absence of an outer membrane in the Gram-positive bacterial cell wall, endolysins can access the peptidoglycan and destroy these organisms when applied externally, making them interesting antimicrobial candidates, particularly in light of increasing bacterial drug resistance. This article reviews the modular structure of these enzymes, in which cell wall binding and catalytic functions are separated, as well as their mechanism of action, lytic activity and potential as antimicrobials. It particularly focuses on molecular engineering as a means of optimizing endolysins for specific applications, highlights new developments that may render these proteins active against Gram-negative and intracellular pathogens and summarizes the most recent applications of endolysins in the fields of medicine, food safety, agriculture and biotechnology.
Collapse
Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | | | | |
Collapse
|
30
|
Lin TY, Lo YH, Tseng PW, Chang SF, Lin YT, Chen TS. A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. PLoS One 2012; 7:e30954. [PMID: 22347414 PMCID: PMC3276506 DOI: 10.1371/journal.pone.0030954] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/27/2011] [Indexed: 11/19/2022] Open
Abstract
It is usually thought that bacteriophage T7 is female specific, while phage T3 can propagate on male and female Escherichia coli. We found that the growth patterns of phages T7M and T3 do not match the above characteristics, instead showing strain dependent male exclusion. Furthermore, a T3/7 hybrid phage exhibits a broader host range relative to that of T3, T7, as well as T7M, and is able to overcome the male exclusion. The T7M sequence closely resembles that of T3. T3/7 is essentially T3 based, but a DNA fragment containing part of the tail fiber gene 17 is replaced by the T7 sequence. T3 displays inferior adsorption to strains tested herein compared to T7. The T3 and T7 recombinant phage carries altered tail fibers and acquires better adsorption efficiency than T3. How phages T3 and T7 recombine was previously unclear. This study is the first to show that recombination can occur accurately within only 8 base-pair homology, where four-way junction structures are identified. Genomic recombination models based on endonuclease I cleavages at equivalent and nonequivalent sites followed by strand annealing are proposed. Retention of pseudo-palindromes can increase recombination frequency for reviving under stress.
Collapse
Affiliation(s)
- Tiao-Yin Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, People's Republic of China.
| | | | | | | | | | | |
Collapse
|
31
|
Häuser R, Blasche S, Dokland T, Haggård-Ljungquist E, von Brunn A, Salas M, Casjens S, Molineux I, Uetz P. Bacteriophage protein-protein interactions. Adv Virus Res 2012; 83:219-98. [PMID: 22748812 PMCID: PMC3461333 DOI: 10.1016/b978-0-12-394438-2.00006-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacteriophages T7, λ, P22, and P2/P4 (from Escherichia coli), as well as ϕ29 (from Bacillus subtilis), are among the best-studied bacterial viruses. This chapter summarizes published protein interaction data of intraviral protein interactions, as well as known phage-host protein interactions of these phages retrieved from the literature. We also review the published results of comprehensive protein interaction analyses of Pneumococcus phages Dp-1 and Cp-1, as well as coliphages λ and T7. For example, the ≈55 proteins encoded by the T7 genome are connected by ≈43 interactions with another ≈15 between the phage and its host. The chapter compiles published interactions for the well-studied phages λ (33 intra-phage/22 phage-host), P22 (38/9), P2/P4 (14/3), and ϕ29 (20/2). We discuss whether different interaction patterns reflect different phage lifestyles or whether they may be artifacts of sampling. Phages that infect the same host can interact with different host target proteins, as exemplified by E. coli phage λ and T7. Despite decades of intensive investigation, only a fraction of these phage interactomes are known. Technical limitations and a lack of depth in many studies explain the gaps in our knowledge. Strategies to complete current interactome maps are described. Although limited space precludes detailed overviews of phage molecular biology, this compilation will allow future studies to put interaction data into the context of phage biology.
Collapse
Affiliation(s)
- Roman Häuser
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Sonja Blasche
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Albrecht von Brunn
- Max-von-Pettenkofer-Institut, Lehrstuhl Virologie, Ludwig-Maximilians-Universität, München, Germany
| | - Margarita Salas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Sherwood Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ian Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, University of Texas–Austin, Austin, Texas, USA
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
| |
Collapse
|
32
|
Abstract
Tailed bacteriophages use nanomotors, or molecular machines that convert chemical energy into physical movement of molecules, to insert their double-stranded DNA genomes into virus particles. These viral nanomotors are powered by ATP hydrolysis and pump the DNA into a preformed protein container called a procapsid. As a result, the virions contain very highly compacted chromosomes. Here, I review recent progress in obtaining structural information for virions, procapsids and the individual motor protein components, and discuss single-molecule in vitro packaging reactions, which have yielded important new information about the mechanism by which these powerful molecular machines translocate DNA.
Collapse
|
33
|
Zhu J, Rao X, Tan Y, Xiong K, Hu Z, Chen Z, Jin X, Li S, Chen Y, Hu F. Identification of lytic bacteriophage MmP1, assigned to a new member of T7-like phages infecting Morganella morganii. Genomics 2010; 96:167-72. [DOI: 10.1016/j.ygeno.2010.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 06/05/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022]
|
34
|
Medema MH, Zhou M, van Hijum SAFT, Gloerich J, Wessels HJCT, Siezen RJ, Strous M. A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. BMC Genomics 2010; 11:299. [PMID: 20459862 PMCID: PMC2881027 DOI: 10.1186/1471-2164-11-299] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/12/2010] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Anaerobic ammonium-oxidizing (anammox) bacteria perform a key step in global nitrogen cycling. These bacteria make use of an organelle to oxidize ammonia anaerobically to nitrogen (N2) and so contribute approximately 50% of the nitrogen in the atmosphere. It is currently unknown which proteins constitute the organellar proteome and how anammox bacteria are able to specifically target organellar and cell-envelope proteins to their correct final destinations. Experimental approaches are complicated by the absence of pure cultures and genetic accessibility. However, the genome of the anammox bacterium Candidatus "Kuenenia stuttgartiensis" has recently been sequenced. Here, we make use of these genome data to predict the organellar sub-proteome and address the molecular basis of protein sorting in anammox bacteria. RESULTS Two training sets representing organellar (30 proteins) and cell envelope (59 proteins) proteins were constructed based on previous experimental evidence and comparative genomics. Random forest (RF) classifiers trained on these two sets could differentiate between organellar and cell envelope proteins with ~89% accuracy using 400 features consisting of frequencies of two adjacent amino acid combinations. A physicochemically distinct organellar sub-proteome containing 562 proteins was predicted with the best RF classifier. This set included almost all catabolic and respiratory factors encoded in the genome. Apparently, the cytoplasmic membrane performs no catabolic functions. We predict that the Tat-translocation system is located exclusively in the organellar membrane, whereas the Sec-translocation system is located on both the organellar and cytoplasmic membranes. Canonical signal peptides were predicted and validated experimentally, but a specific (N- or C-terminal) signal that could be used for protein targeting to the organelle remained elusive. CONCLUSIONS A physicochemically distinct organellar sub-proteome was predicted from the genome of the anammox bacterium K. stuttgartiensis. This result provides strong in silico support for the existing experimental evidence for the existence of an organelle in this bacterium, and is an important step forward in unravelling a geochemically relevant case of cytoplasmic differentiation in bacteria. The predicted dual location of the Sec-translocation system and the apparent absence of a specific N- or C-terminal signal in the organellar proteins suggests that additional chaperones may be necessary that act on an as-yet unknown property of the targeted proteins.
Collapse
Affiliation(s)
- Marnix H Medema
- Department of Microbiology, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, the Netherlands
| | | | | | | | | | | | | |
Collapse
|
35
|
Compensatory evolution for a gene deletion is not limited to its immediate functional network. BMC Evol Biol 2009; 9:106. [PMID: 19445716 PMCID: PMC2696425 DOI: 10.1186/1471-2148-9-106] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 05/16/2009] [Indexed: 12/25/2022] Open
Abstract
Background Genetic disruption of an important phenotype should favor compensatory mutations that restore the phenotype. If the genetic basis of the phenotype is modular, with a network of interacting genes whose functions are specific to that phenotype, compensatory mutations are expected among the genes of the affected network. This perspective was tested in the bacteriophage T3 using a genome deleted of its DNA ligase gene, disrupting DNA metabolism. Results In two replicate, long-term adaptations, phage compensatory evolution accommodated the low ligase level provided by the host without reinventing its own ligase. In both lines, fitness increased substantially but remained well below that of the intact genome. Each line accumulated over a dozen compensating mutations during long-term adaptation, and as expected, many of the compensatory changes were within the DNA metabolism network. However, several compensatory changes were outside the network and defy any role in DNA metabolism or biochemical connection to the disruption. In one line, these extra-network changes were essential to the recovery. The genes experiencing compensatory changes were moderately conserved between T3 and its relative T7 (25% diverged), but the involvement of extra-network changes was greater in T3. Conclusion Compensatory evolution was only partly limited to the known functionally interacting partners of the deleted gene. Thus gene interactions contributing to fitness were more extensive than suggested by the functional properties currently ascribed to the genes. Compensatory evolution offers an easy method of discovering genome interactions among specific elements that does not rest on an a priori knowledge of those elements or their interactions.
Collapse
|
36
|
Heineman RH, Bull JJ, Molineux IJ. Layers of evolvability in a bacteriophage life history trait. Mol Biol Evol 2009; 26:1289-98. [PMID: 19264970 PMCID: PMC2680503 DOI: 10.1093/molbev/msp037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Exploring the extent to which this recovery alters gene networks can illuminate how functional gene interactions change through time. Here, the evolvability of lysis was studied in bacteriophage T7, revealing hidden functional interactions. Lysis is the destruction of host cell wall and membranes that releases progeny and is therefore essential for phage propagation. In most phages, lysis is mediated by a two-component genetic module: a muralytic enzyme that degrades the bacterial cell wall (endolysin) and a holin that permeabilizes the inner membrane to allow the endolysin access to the cell wall. T7 carries one known holin, one endolysin, and a second muralytic enzyme that plays little role in lysis by wild-type phage. If the primary endolysin is deleted, the second muralytic enzyme evolves to restore normal lysis after selection for faster growth. Here, a second level of evolutionary redundancy was revealed. When the second muralytic enzyme was prevented from adapting in a genome lacking the primary endolysin, the phage reevolved lysis de novo in the absence of any known muralytic enzymes by changes in multiple genes outside the original lysis module. This second level of redundancy proved to be evolutionarily inferior to the first, and both result in a lower fitness and slower lysis than wild-type T7. Deletion of the holin gene delayed lysis time modestly; fitness was restored by compensatory substitutions in genes that lack known roles in lysis of the wild type.
Collapse
|
37
|
Casjens SR, Gilcrease EB. Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol 2009; 502:91-111. [PMID: 19082553 DOI: 10.1007/978-1-60327-565-1_7] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Tailed-bacteriophage virions contain a single linear dsDNA chromosome which can range in size from about 18 to 500 kbp across the known tailed-phage types. These linear chromosomes can have one of several known types of termini as follows: cohesive ends (5'- or 3'-single-strand extensions), circularly permuted direct terminal repeats, short or long exact direct terminal repeats, terminal host DNA sequences, or covalently bound terminal proteins. These different types of ends reflect differing DNA replication strategies and especially differing terminase actions during DNA packaging. In general, complete genome sequence determination does not by itself elucidate the nature of these ends, so directed experimental analysis is usually required to understand the nature of the virion chromosome ends. This chapter discusses these methods.
Collapse
Affiliation(s)
- Sherwood R Casjens
- Division of Cell Biology and Immunology, Department of Pathology, University of Utah Medical School, Salt Lake City, UT, USA
| | | |
Collapse
|
38
|
Predicting evolution from genomics: experimental evolution of bacteriophage T7. Heredity (Edinb) 2008; 100:453-63. [PMID: 18212807 DOI: 10.1038/sj.hdy.6801087] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
A wealth of molecular biology has been exploited in designing and interpreting experimental evolution studies with bacteriophage T7. The modest size of its genome (40 kb dsDNA) and the ease of making genetic constructs, combined with the many genetic resources for its host (Escherichia coli), have enabled comprehensive and detailed studies of experimental adaptations. In several studies, the genome was specifically altered (gene knockouts, gene replacements, reordering of genetic elements) such that a priori knowledge of genetics and biochemistry of the phage could be used to predict the pathways of compensatory evolution when the modified phage is adapted to recover fitness. In other work, the phage has been adapted to specific environmental conditions chosen to select phenotypic outcomes with a quantitative basis, and the molecular bases of that evolution have been explored. Predicting the outcomes of these adaptations has been challenging. In hindsight, one-third to one-half of the compensatory nucleotide changes observed during the adaptation can be rationalized based on T7 biology. This rationalization usually only applies at the genetic level-a gene product may be known to be involved in the affected pathway, but it usually remains unknown how the observed change affects activity. The progress is encouraging, but the prediction of experimental evolution pathways remains far from complete, and is still sometimes confounded by observation when an adaptation yields a completely unexpected outcome.
Collapse
|
39
|
Qimron U, Kulczyk AW, Hamdan SM, Tabor S, Richardson CC. Inadequate inhibition of host RNA polymerase restricts T7 bacteriophage growth on hosts overexpressing udk. Mol Microbiol 2007; 67:448-57. [PMID: 18067538 DOI: 10.1111/j.1365-2958.2007.06058.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Overexpression of udk, an Escherichia coli gene encoding a uridine/cytidine kinase, interferes with T7 bacteriophage growth. We show here that inhibition of T7 phage growth by udk overexpression can be overcome by inhibition of host RNA polymerase. Overexpression of gene 2, whose product inhibits host RNA polymerase, restores T7 phage growth on hosts overexpressing udk. In addition, rifampicin, an inhibitor of host RNA polymerase, restores the burst size of T7 phage on udk-overexpressing hosts to normal. In agreement with these findings, suppressor mutants that overcome the inhibition arising from udk overexpression gain the ability to grow on hosts that are resistant to inhibition of RNA polymerase by gene 2 protein, and suppressor mutants that overcome a lack of gene 2 protein gain the ability to grow on hosts that overexpress udk. Mutations that eliminate or weaken strong promoters for host RNA polymerase in T7 DNA, and mutations in T7 gene 3.5 that affect its interaction with T7 RNA polymerase, also reduce the interference with T7 growth by host RNA polymerase. We propose a general model for the requirement of host RNA polymerase inhibition.
Collapse
Affiliation(s)
- Udi Qimron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | |
Collapse
|
40
|
Alcantara EH, Kim DH, Do SI, Lee SS. Bi-functional activities of chimeric lysozymes constructed by domain swapping between bacteriophage T7 and K11 lysozymes. BMB Rep 2007; 40:539-46. [PMID: 17669270 DOI: 10.5483/bmbrep.2007.40.4.539] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lysozymes encoded by bacteriophage T7 and K11 are both bifunctional enzymes sharing an extensive sequence homology (75%). The constructions of chimeric lysozymes were carried out by swapping the N-terminal and C-terminal domains between phage T7 and K11 lysozymes. This technique generated two chimeras, T7K11-lysozyme (N-terminal T7 domain and C-terminal K11 domain) and K11T7-lysozyme (N-terminal K11 domain and C-terminal T7 domain), which are both enzymatically active. The amidase activity of T7K11-lysozyme is comparable with the parental enzymes while K11T7-lysozyme exhibits an activity that is approximately 45% greater than the wild-type lysozymes. Moreover, these chimeric constructs have optimum pH of 7.2-7.4 similar to the parental lysozymes but exhibit greater thermal stabilities. On the other hand, the chimeras inhibit transcription comparable with the parental lysozymes depending on the source of their N-terminals. Taken together, our results indicated that domain swapping technique localizes the N-terminal region as the domain responsible for the transcription inhibition specificity of the wild type T7 and K11 lysozymes. Furthermore, we were able to develop a simple and rapid purification scheme in purifying both the wild-type and chimeric lysozymes.
Collapse
Affiliation(s)
- Ethel H Alcantara
- Research Center for Bio-Medicinal Resources and Department of Life Science and Technology, Pai Chai University, 439-6 Doma-dong, Seo-gu, Daejeon 302-735, Korea
| | | | | | | |
Collapse
|
41
|
Abstract
BACKGROUND The genomes of both long-genome (> 200 Kb) bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions. HYPOTHESIS Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1) Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2) Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection). (3) The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection). (4) The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems. TESTING THE HYPOTHESIS I propose testing this hypothesis by controlled evolution in microbial communities to (1) determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2) find the environmental conditions that select for the presence of cellular gene homologs, (3) determine which, if any, bacteriophage genes were selected for maintaining the homologs and (4) determine the dynamics of homolog evolution. IMPLICATIONS OF THE HYPOTHESIS This hypothesis is an explanation of evolutionary leaps in general. If accurate, it will assist both understanding and influencing the evolution of microbes and their communities. Analysis of evolutionary complexity increase for at least prokaryotes should include analysis of genomes of long-genome bacteriophages.
Collapse
Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA.
| |
Collapse
|
42
|
Zlatanova J, McAllister WT, Borukhov S, Leuba SH. Single-molecule approaches reveal the idiosyncrasies of RNA polymerases. Structure 2006; 14:953-66. [PMID: 16765888 DOI: 10.1016/j.str.2006.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 02/05/2006] [Accepted: 03/23/2006] [Indexed: 11/16/2022]
Abstract
Recently developed single-molecule techniques have provided new insights into the function of one of the most complex and highly regulated processes in the cell--the transcription of the DNA template into RNA. This review discusses methods and results from this emerging field, and it puts them in perspective of existing biochemical and structural data.
Collapse
Affiliation(s)
- Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA.
| | | | | | | |
Collapse
|
43
|
Black LW, Peng G. Mechanistic coupling of bacteriophage T4 DNA packaging to components of the replication-dependent late transcription machinery. J Biol Chem 2006; 281:25635-43. [PMID: 16807240 DOI: 10.1074/jbc.m602093200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Regulation of the terminal stage of viral DNA development, DNA packaging, is poorly understood. A new phage T4 in vitro DNA packaging assay employed purified proheads, terminase (gp17 + gp16), and ATP to encapsidate DNA resistant to nuclease. Mature phage T4 DNA and linearized plasmid DNAs containing or lacking a cloned T4 gene were packaged with high (approximately 10%) efficiency. Supercoiled, relaxed covalently closed, and nicked circular plasmid DNAs were packaged inefficiently, if at all, by these components. However, efficient packaging is achieved for nicked circular plasmid DNA, but not covalently closed plasmid DNA, upon addition to packaging mixtures of the purified T4 late transcription-replication machinery proteins: gp45 (sliding clamp), gp44/gp62 (clamp loader complex), gp55 (late sigma-factor), and gp33 (transcriptional co-activator). The small terminase subunit (gp16) is inhibitory for packaging linear DNAs, but enhances the transcription-replication protein packaging of nicked plasmid DNA. Taken together with genetic and biochemical evidence of a requirement for gp55 for concatemer packaging to assemble active wild-type phage particles (1), the plasmid packaging results show that initiation of phage T4 packaging on "endless" concatemeric DNA in vivo by terminase depends upon interaction with the DNA loaded gp45 coupled late transcription-replication machinery. The results suggest a close mechanistic connection in vivo between DNA packaging and developmentally concurrent replication-dependent late transcription.
Collapse
Affiliation(s)
- Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, Maryland 21201-1503, USA.
| | | |
Collapse
|
44
|
Scholl D, Merril C. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J Bacteriol 2006; 187:8499-503. [PMID: 16321955 PMCID: PMC1317022 DOI: 10.1128/jb.187.24.8499-8503.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage K1F specifically infects Escherichia coli strains that produce the K1 polysaccharide capsule. Like several other K1 capsule-specific phages, K1F encodes an endo-neuraminidase (endosialidase) that is part of the tail structure which allows the phage to recognize and degrade the polysaccharide capsule. The complete nucleotide sequence of the K1F genome reveals that it is closely related to bacteriophage T7 in both genome organization and sequence similarity. The most striking difference between the two phages is that K1F encodes the endosialidase in the analogous position to the T7 tail fiber gene. This is in contrast with bacteriophage K1-5, another K1-specific phage, which encodes a very similar endosialidase which is part of a tail gene "module" at the end of the phage genome. It appears that diverse phages have acquired endosialidase genes by horizontal gene transfer and that these genes or gene products have adapted to different genome and virion architectures.
Collapse
Affiliation(s)
- Dean Scholl
- National Institutes of Mental Health, National Institutes of Health, Building 49, Room B1B20, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | | |
Collapse
|
45
|
Ma K, Temiakov D, Anikin M, McAllister WT. Probing conformational changes in T7 RNA polymerase during initiation and termination by using engineered disulfide linkages. Proc Natl Acad Sci U S A 2005; 102:17612-7. [PMID: 16301518 PMCID: PMC1308916 DOI: 10.1073/pnas.0508865102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During the transition from an initiation complex to an elongation complex (EC), the single-subunit bacteriophage T7 RNA polymerase (RNAP) undergoes dramatic conformational changes. To explore the significance of these changes, we constructed mutant RNAPs that are able to form disulfide bonds that limit the mobility of elements that are involved in the transition (or its reversal) and examined the effects of the crosslinks on initiation and termination. A crosslink that is specific to the initiation complex conformation blocks transcription at 5-6 nt, presumably by preventing isomerization to an EC. A crosslink that is specific to the EC conformation has relatively little effect on elongation or on termination at a class I terminator (T), which involves the formation of a stable stem-loop structure in the RNA. Crosslinked ECs also pause and resume transcription normally at a class II pause site (concatamer junction) but are deficient in termination at a class II terminator (PTH, which is found in human preparathyroid hormone gene), both of which involve a specific recognition sequence. The crosslinked amino acids in the EC lie close to the upstream end of the RNA-DNA hybrid and may prevent a movement of the polymerase that would assist in displacing or releasing RNA from a relatively unstable DNA-RNA hybrid in the paused PTH complex.
Collapse
Affiliation(s)
- Kaiyu Ma
- Department of Microbiology and Immunology, Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203-2098, USA
| | | | | | | |
Collapse
|
46
|
Duplessis M, Russell WM, Romero DA, Moineau S. Global gene expression analysis of two Streptococcus thermophilus bacteriophages using DNA microarray. Virology 2005; 340:192-208. [PMID: 16043205 DOI: 10.1016/j.virol.2005.05.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 04/26/2005] [Accepted: 05/27/2005] [Indexed: 11/23/2022]
Abstract
A custom microarray was developed to study the temporal gene expression of the two groups of phages infecting the Gram-positive lactic acid bacterium Streptococcus thermophilus. The complete genomic sequence of the virulent cos-type phage DT1 (34,815 bp) and the pac-type phage 2972 (34,704 bp) were used for the construction of the microarray. Gene expression was measured at nine time intervals (0, 2, 7, 12, 17, 22, 27, 32 and 37 min) during phage infection and an expression curve was determined for each gene. Each phage gene was then classified into one of the three traditional transcription classes and these data were used to generate the complete transcriptional map of DT1 and 2972. Phage DT1 possesses 18 early genes, 12 middle genes and 12 late-expressed genes whereas 2972 has 16 early, 11 middle and 14 late genes. The trends of the phage gene expression profiles were also confirmed by slot blot hybridizations. Significant differences were observed when comparing the transcriptional maps of DT1 and 2972 with those already available for the S. thermophilus phages Sfi19 and Sfi21. To our knowledge, this report presents the first complete transcription analysis of bacteriophages infecting Gram-positive bacteria using the DNA microarray technology.
Collapse
Affiliation(s)
- Martin Duplessis
- Département de biochimie et de microbiologie, Faculté des sciences et de génie, Université Laval, Québec City, Canada
| | | | | | | |
Collapse
|
47
|
Loessner MJ. Bacteriophage endolysins--current state of research and applications. Curr Opin Microbiol 2005; 8:480-7. [PMID: 15979390 DOI: 10.1016/j.mib.2005.06.002] [Citation(s) in RCA: 362] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 06/09/2005] [Indexed: 11/27/2022]
Abstract
Endolysins are phage-encoded enzymes that break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. Their action is tightly regulated by holins, by membrane arrest, and by conversion from their inactive to active state. Recent research has not only revealed the unexpected diversity of these highly specific hydrolases but has also yielded insights into their modular organization and their three-dimensional structures. Their N-terminal catalytic domains are able to target almost every possible bond in the peptidoglycan network, and their corresponding C-terminal cell wall binding domains target the enzymes to their substrate. Owing to their specificity and high activity, endolysins have been employed for various in vitro and in vivo aims, in food science, in microbial diagnostics, and for treatment of experimental infections. Clearly, phage endolysins represent great tools for use in molecular biology, biotechnology and in medicine, and we are just beginning to tap this potential.
Collapse
Affiliation(s)
- Martin J Loessner
- Institute of Food Science and Nutrition, Swiss Federal Institute of Technology (ETH), Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland.
| |
Collapse
|
48
|
Springman R, Badgett MR, Molineux IJ, Bull JJ. Gene order constrains adaptation in bacteriophage T7. Virology 2005; 341:141-52. [PMID: 16081122 DOI: 10.1016/j.virol.2005.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 06/15/2005] [Accepted: 07/08/2005] [Indexed: 11/24/2022]
Abstract
The order of genes in the genome is commonly thought to have functional significance for gene regulation and fitness but has not heretofore been tested experimentally. We adapted a bacteriophage T7 variant harboring an ectopically positioned RNA polymerase gene to determine whether it could regain the fitness of the wild type. Two replicate lines maintained the starting gene order and showed only modest recovery of fitness, despite the accumulation of over a dozen mutations. In both lines, a mutation in the early terminator signal is responsible for the majority of the fitness recovery. In a third line, the phage evolved a new gene order, restoring the wild-type position of the RNA polymerase gene but also displacing several other genes to ectopic locations. Due to the recombination, the fitness of this replicate was the highest obtained but it falls short of the wild type adapted to the same growth conditions. The large benefits afforded by the terminator mutation and the recombination are explicable in terms of T7 biology, whereas several mutations with lesser benefits are not easily accounted for. These results support the premise that gene order is important to fitness and that wild-type fitness is not rapidly re-evolved in reorganized genomes.
Collapse
Affiliation(s)
- R Springman
- Section of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | | | | | | |
Collapse
|
49
|
Chan LY, Kosuri S, Endy D. Refactoring bacteriophage T7. Mol Syst Biol 2005; 1:2005.0018. [PMID: 16729053 PMCID: PMC1681472 DOI: 10.1038/msb4100025] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Accepted: 07/23/2005] [Indexed: 11/30/2022] Open
Abstract
Natural biological systems are selected by evolution to continue to exist and evolve. Evolution likely gives rise to complicated systems that are difficult to understand and manipulate. Here, we redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. Our initial design goals were to physically separate and enable unique manipulation of primary genetic elements. Implicit in our design are the hypotheses that overlapping genetic elements are, in aggregate, nonessential for T7 viability and that our models for the functions encoded by elements are sufficient. To test our initial design, we replaced the left 11 515 base pairs (bp) of the 39 937 bp wild-type genome with 12 179 bp of engineered DNA. The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.
Collapse
MESH Headings
- Algorithms
- Bacteriophage T7/genetics
- Bacteriophage T7/growth & development
- Bacteriophage T7/physiology
- Base Pairing
- DNA, Recombinant/chemical synthesis
- DNA, Recombinant/genetics
- DNA, Viral/genetics
- Escherichia coli/virology
- Genes, Overlapping
- Genes, Viral
- Genetic Engineering
- Genome, Viral
- Models, Biological
- Models, Genetic
- Molecular Sequence Data
- Organisms, Genetically Modified/genetics
- Organisms, Genetically Modified/growth & development
- Organisms, Genetically Modified/physiology
- Sequence Deletion
- Systems Biology/methods
- Transfection
- Viral Proteins/genetics
- Viral Proteins/physiology
- Virus Replication
Collapse
Affiliation(s)
- Leon Y Chan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sriram Kosuri
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Drew Endy
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Biological Engineering, Massachusetts Institute of Technology, 68-580, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Tel.: +1 617 258 5152; Fax: +1 617 253 5865; E-mail:
| |
Collapse
|
50
|
Heineman RH, Molineux IJ, Bull JJ. Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene. J Mol Evol 2005; 61:181-91. [PMID: 16096681 DOI: 10.1007/s00239-004-0304-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Accepted: 03/21/2005] [Indexed: 11/30/2022]
Abstract
Optimality models are frequently used to create expectations about phenotypic evolution based on the fittest possible phenotype. However, they often ignore genetic details, which could confound these expectations. We experimentally analyzed the ability of organisms to evolve towards an optimum in an experimentally tractable system, lysis time in bacteriophage T7. T7 lysozyme helps lyse the host cell by degrading its cell wall at the end of infection, allowing viral escape to infect new hosts. Artificial deletion of lysozyme greatly reduced fitness and delayed lysis, but after evolution both phenotypes approached wild-type values. Phage with a lysis-deficient lysozyme evolved similarly. Several mutations were involved in adaptation, but most of the change in lysis timing and fitness increase was mediated by changes in gene 16, an internal virion protein not formerly considered to play a role in lysis. Its muralytic domain, which normally aids genome entry through the cell wall, evolved to cause phage release. Theoretical models suggest there is an optimal lysis time, and lysis more rapid or delayed than this optimum decreases fitness. Artificially constructed lines with very rapid lysis had lower fitness than wild-type T7, in accordance with the model. However, while a slow-lysing line also had lower fitness than wild-type, this low fitness resulted at least partly from genetic details that violated model assumptions.
Collapse
Affiliation(s)
- Richard H Heineman
- Section of Integrative Biology, University of Texas, Austin, TX 78712, USA.
| | | | | |
Collapse
|