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Woodbury BM, Motwani T, Leroux MN, Barnes LF, Lyktey NA, Banerjee S, Dedeo CL, Jarrold MF, Teschke CM. Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22. Viruses 2022; 14:1400. [PMID: 35891382 PMCID: PMC9320234 DOI: 10.3390/v14071400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
The oligomerization and incorporation of the bacteriophage P22 portal protein complex into procapsids (PCs) depends upon an interaction with scaffolding protein, but the region of the portal protein that interacts with scaffolding protein has not been defined. In herpes simplex virus 1 (HSV-1), conserved tryptophan residues located in the wing domain are required for portal-scaffolding protein interactions. In this study, tryptophan residues (W) present at positions 41, 44, 207 and 211 within the wing domain of the bacteriophage P22 portal protein were mutated to both conserved and non-conserved amino acids. Substitutions at each of these positions were shown to impair portal function in vivo, resulting in a lethal phenotype by complementation. The alanine substitutions caused the most severe defects and were thus further characterized. An analysis of infected cell lysates for the W to A mutants revealed that all the portal protein variants except W211A, which has a temperature-sensitive incorporation defect, were successfully recruited into procapsids. By charge detection mass spectrometry, all W to A mutant portal proteins were shown to form stable dodecameric rings except the variant W41A, which dissociated readily to monomers. Together, these results suggest that for P22 conserved tryptophan, residues in the wing domain of the portal protein play key roles in portal protein oligomerization and incorporation into procapsids, ultimately affecting the functionality of the portal protein at specific stages of virus assembly.
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Affiliation(s)
- Brianna M. Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Tina Motwani
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Makayla N. Leroux
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Lauren F. Barnes
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Nicholas A. Lyktey
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Sanchari Banerjee
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Corynne L. Dedeo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Carolyn M. Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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A Raman-spectroscopy-based approach for detection and discrimination of Streptococcus thermophilus and Lactobacillus bulgaricus phages at low titer in raw milk. Folia Microbiol (Praha) 2018; 63:627-636. [DOI: 10.1007/s12223-018-0604-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/02/2018] [Indexed: 12/11/2022]
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Kornfeind EM, Visalli RJ. Human herpesvirus portal proteins: Structure, function, and antiviral prospects. Rev Med Virol 2018; 28:e1972. [PMID: 29573302 DOI: 10.1002/rmv.1972] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 01/28/2023]
Abstract
Herpesviruses (Herpesvirales) and tailed bacteriophages (Caudovirales) package their dsDNA genomes through an evolutionarily conserved mechanism. Much is known about the biochemistry and structural biology of phage portal proteins and the DNA encapsidation (viral genome cleavage and packaging) process. Although not at the same level of detail, studies on HSV-1, CMV, VZV, and HHV-8 have revealed important information on the function and structure of herpesvirus portal proteins. During dsDNA phage and herpesviral genome replication, concatamers of viral dsDNA are cleaved into single length units by a virus-encoded terminase and packaged into preformed procapsids through a channel located at a single capsid vertex (portal). Oligomeric portals are formed by the interaction of identical portal protein monomers. Comparing portal protein primary aa sequences between phage and herpesviruses reveals little to no sequence similarity. In contrast, the secondary and tertiary structures of known portals are remarkable. In all cases, function is highly conserved in that portals are essential for DNA packaging and also play a role in releasing viral genomic DNA during infection. Preclinical studies have described small molecules that target the HSV-1 and VZV portals and prevent viral replication by inhibiting encapsidation. This review summarizes what is known concerning the structure and function of herpesvirus portal proteins primarily based on their conserved bacteriophage counterparts and the potential to develop novel portal-specific DNA encapsidation inhibitors.
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Affiliation(s)
- Ellyn M Kornfeind
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, GA, USA
| | - Robert J Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, GA, USA
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Nemecek D, Stepanek J, Thomas GJ. Raman Spectroscopy of Proteins and Nucleoproteins. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.8. [DOI: 10.1002/0471140864.ps1708s71] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Daniel Nemecek
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health Bethesda Maryland
- Central European Institute of Technology, Masaryk University Brno Czech Republic
| | - Josef Stepanek
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics Prague Czech Republic
| | - George J. Thomas
- School of Biological Sciences, University of Missouri‐Kansas City Kansas City Missouri
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Dyson OF, Ford PW, Chen D, Li YQ, Akula SM. Raman tweezers provide the fingerprint of cells supporting the late stages of KSHV reactivation. J Cell Mol Med 2008; 13:1920-1932. [PMID: 18752634 DOI: 10.1111/j.1582-4934.2008.00481.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) has both latent and lytic phases of replication. The molecular switch that triggers a reactivation is still unclear. Cells from the S phase of the cell cycle provide apt conditions for an active reactivation. In order to specifically delineate the Raman spectra of cells supporting KSHV reactivation, we followed a novel approach where cells were sorted based on the state of infection (latent versus lytic) by a flow cytometer and then analysed by the Raman tweezers. The Raman bands at 785, 813, 830, 1095 and 1128 cm(-1) are specifically altered in cells supporting KSHV reactivation. These five peaks make up the Raman fingerprint of cells supporting KSHV reactivation. The physiological relevance of the changes in these peaks with respect to KSHV reactivation is discussed in the following report.
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Affiliation(s)
- Ossie F Dyson
- Department of Microbiology & Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Patrick W Ford
- Department of Microbiology & Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - De Chen
- Department of Physics, East Carolina University, Greenville, NC, USA
| | - Yong-Qing Li
- Department of Physics, East Carolina University, Greenville, NC, USA
| | - Shaw M Akula
- Department of Microbiology & Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
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