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Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. RNA Phage Biology in a Metagenomic Era. Viruses 2018; 10:E386. [PMID: 30037084 PMCID: PMC6071253 DOI: 10.3390/v10070386] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.
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Affiliation(s)
- Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
| | - Stephen R Stockdale
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Andrey Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland.
- School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
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Abstract
Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here.
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Affiliation(s)
- Jing Yun A Zhu
- a Centre for High-Throughput Biology and Department of Computer Science and Department of Medical Genetics; University of British Columbia ; Vancouver , BC , Canada
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Reed CA, Langlais C, Wang IN, Young R. A(2) expression and assembly regulates lysis in Qβ infections. MICROBIOLOGY (READING, ENGLAND) 2013; 159:507-514. [PMID: 23329676 PMCID: PMC3709820 DOI: 10.1099/mic.0.064790-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/29/2012] [Accepted: 01/05/2013] [Indexed: 01/19/2023]
Abstract
The capsids of ssRNA phages comprise a single copy of an ~45 kDa maturation protein that serves to recognize the conjugative pilus as receptor, to protect the ends of the viral RNA and also to escort the genomic RNA into the host cytoplasm. In the Alloleviviridae, represented by the canonical phage Qβ, the maturation protein A(2) also causes lysis. This is achieved by inhibiting the activity of MurA, which catalyses the first committed step of murein biosynthesis. Previously, it was shown that Qβ virions, with a single copy of A(2), inhibit MurA activity. This led to a model for lysis timing in which, during phage infection, A(2) is not active as a MurA inhibitor until assembled into virion particles, thus preventing premature lysis before a sufficient yield of viable progeny has accumulated. Here we report that MurA inactivates purified Qβ particles, casting doubt on the notion that A(2) must assemble into particles prior to MurA inhibition. Furthermore, quantification of A(2) protein induced from a plasmid indicated that lysis is entrained when the amount of the lysis protein is approximately equimolar to that of cellular MurA. Qβ por mutants, isolated as suppressors that overcome a murA(rat) mutation that reduces the affinity of MurA for A(2), were shown to be missense mutations in A(2) that increase the translation of the maturation protein. Because of the increased production of A(2), the por mutants have an attenuated infection cycle and reduced burst size, indicating that a delicate balance between assembled and unassembled A(2) levels regulates lysis timing.
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Affiliation(s)
- Catrina A Reed
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Carrie Langlais
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Ing-Nang Wang
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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Abstract
For the past fifty-five years, much of my research has focused on the function and biogenesis of red blood cells, including the cloning and study of many membrane proteins such as glucose and anion transporters and the erythropoietin receptor. We have also elucidated the mechanisms of membrane insertion, folding, and maturation of many plasma membrane and secreted proteins. Despite all of this work and more, I remain extremely proud of our very early work on the regulation of mRNA translation: work on bacteriophage f2 RNA in the 1960s and on translation of α- and β-globin mRNAs in the early 1970s. Using techniques hopelessly antiquated by today's standards, we correctly elucidated many important aspects of translational control, and I thought readers would be interested in learning how we did these experiments.
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Affiliation(s)
- Harvey F Lodish
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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Priano C, Arora R, Jayant L, Mills DR. Translational activation in coliphage Qbeta: on a polycistronic messenger RNA, repression of one gene can activate translation of another. J Mol Biol 1997; 271:299-310. [PMID: 9268660 DOI: 10.1006/jmbi.1997.1194] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We present evidence for translational activation of the Qbeta coliphage maturation cistron, mediated by the presence of Qbeta replicase. This activation does not require RNA replication, translation of a second gene, or any direct protein-RNA binding at the maturation gene initiation site. Our data support a model in which the Qbeta maturation gene remains translationally "off" by two means: (1) the thermodynamic stability of an RNA structure that greatly discourages, but does not eliminate, ribosome access at the maturation start site; and (2) the presence of the stronger, proximal coat gene ribosome binding site. Moreover, maturation gene expression is switched "on" when ribosome entry at the coat initiation site, present on the same polycistronic RNA molecule, is repressed by Qbeta replicase, thereby allowing ribosomes to compete for the weaker, upstream maturation start site.
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Affiliation(s)
- C Priano
- Health Science Center at Brooklyn, State University of New York, , 450 Clarkson Ave., Brooklyn, NY 11203, USA
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Witherell GW, Gott JM, Uhlenbeck OC. Specific interaction between RNA phage coat proteins and RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1991; 40:185-220. [PMID: 2031083 DOI: 10.1016/s0079-6603(08)60842-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- G W Witherell
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309
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Wikström PM, Björk GR. A regulatory element within a gene of a ribosomal protein operon of Escherichia coli negatively controls expression by decreasing the translational efficiency. MOLECULAR & GENERAL GENETICS : MGG 1989; 219:381-9. [PMID: 2516239 DOI: 10.1007/bf00259610] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The trmD operon of Escherichia coli consists of the genes for the ribosomal protein (r-protein) S16, a 21 kDa protein (21K) of unknown function, the tRNA(m1G37)methyltransferase (TrmD), and r-protein L19, in this order. Previously we have shown that the steady-state amount of the two r-proteins exceeds that of the 21K and TrmD proteins 12- and 40-fold, respectively, and that this differential expression is solely explained by translational regulation. Here we have constructed translational gene fusions of the trmD operon and lacZ. The expression of a lacZ fusion containing the first 18 codons of the 21K protein gene is 15-fold higher than the expression of fusions containing 49 or 72 codons of the gene. This suggests that sequences between the 18th and the 49th codon may act as a negative element controlling the expression of the 21K protein gene. Evidence is presented which demonstrates that this regulation is achieved by reducing the efficiency of translation.
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Affiliation(s)
- P M Wikström
- Department of Microbiology, University of Umeå, Sweden
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Berkhout B, van Duin J. Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2. Nucleic Acids Res 1985; 13:6955-67. [PMID: 3840590 PMCID: PMC322015 DOI: 10.1093/nar/13.19.6955] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have analyzed the molecular mechanism that makes translation of the MS2 replicase cistron dependent on the translation of the upstream coat cistron. Deletion mapping on cloned cDNA of the phage shows that the ribosomal binding site of the replicase cistron is masked by a long distance basepairing to an internal coat cistron region. Removal of the internal coat cistron region leads to uncoupled replicase synthesis. Our results confirm the model as originally proposed by Min Jou et al. (1). Activation of the replicase start is sensitive to the frequency of upstream translation, but never reaches the level of uncoupled replicase synthesis.
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Fiers W, Contreras R, Duerinck F, Haegmean G, Merregaert J, Jou WM, Raeymakers A, Volckaert G, Ysebaert M, Van de Kerckhove J, Nolf F, Van Montagu M. A-protein gene of bacteriophage MS2. Nature 1975; 256:273-8. [PMID: 806810 DOI: 10.1038/256273a0] [Citation(s) in RCA: 141] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Hunter T, Hunt T, Jackson RJ, Robertson HD. The characteristics of inhibition of protein synthesis by double-stranded ribonucleic acid in reticulocyte lysates. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41914-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Steitz JA. Discriminatory ribosome rebinding of isolated regions of protein synthesis initiation from the ribonucleic acid of bacteriophage R17. Proc Natl Acad Sci U S A 1973; 70:2605-9. [PMID: 4582190 PMCID: PMC427065 DOI: 10.1073/pnas.70.9.2605] [Citation(s) in RCA: 48] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
To determine whether bacterial ribosomes recognize a distinguishing feature in the immediate vicinity of actual initiator codons or are directed to these sites through involvement of other portion(s) of the mRNA molecule, the interaction between ribosomes and defined (32)P-labeled initiator fragments from R17 RNA was studied. When incubated with mixtures of the three sites, ribosomes from Bacillus stearothermophilus (which initiate only the A protein on intact phage RNA) are able to select out the A fragment and discriminate against the coat and replicase initiator regions. By contrast, Escherichia coli ribosomes do not rebind that coat-protein region of R17 most efficiently, as they in the native RNA, but likewise prefer the A-protein initiator fragment. In both cases, ribosome binding of the isolated A site is comparable by several criteria to normal polypeptide-chain initiation on an intact R17 messenger RNA in vitro. E. coli ribosomal preference for the A site is confirmed in experiments with randomly fragmented R17 RNA, by both the initiation dipeptide and ribosome protection assay. Thus the A-protein ribosome-binding site of R17 RNA appears intrinsically to be a good initiator, while efficient recognition of the coat and replicase regions requires the participation of some portion of the remainder of the phage RNA molecule.
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Weissmann C, Billeter MA, Weber H, Goodman HM, Hindley J. Structure and function of phage RNA: a summary of current knowledge. BASIC LIFE SCIENCES 1973; 1:13-28. [PMID: 4589675 DOI: 10.1007/978-1-4684-0877-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Weber H, Billeter MA, Kahane S, Weissmann C, Hindley J, Porter A. Molecular basis for repressor activity of Q replicase. NATURE: NEW BIOLOGY 1972; 237:166-70. [PMID: 4556377 DOI: 10.1038/newbio237166a0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Kozak M, Nathans D. Translation of the genome of a ribonucleic acid bacteriophage. BACTERIOLOGICAL REVIEWS 1972; 36:109-34. [PMID: 4555183 PMCID: PMC378432 DOI: 10.1128/br.36.1.109-134.1972] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Berissi H, Groner Y, Revel M. Effect of a purified initiation factor F3 (B) on the selection of ribosomal binding sites on phage MS2 RNA. NATURE: NEW BIOLOGY 1971; 234:44-7. [PMID: 5288730 DOI: 10.1038/newbio234044a0] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Staples DH, Hindley J, Billeter MA, Weissmann C. Localization of Q-beta maturation cistron ribosome binding site. NATURE: NEW BIOLOGY 1971; 234:202-4. [PMID: 5288805 DOI: 10.1038/newbio234202a0] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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