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Wei Y, Wang J, Xia X. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species. Mol Biol Evol 2016; 33:2357-67. [PMID: 27297468 PMCID: PMC4989110 DOI: 10.1093/molbev/msw107] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3. This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range.
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Affiliation(s)
- Yulong Wei
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Juan Wang
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada Ottawa Institute of Systems Biology, Ottawa, ON, Canada
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52
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Lin YZ, Sun LK, Zhu DT, Hu Z, Wang XF, Du C, Wang YH, Wang XJ, Zhou JH. Equine schlafen 11 restricts the production of equine infectious anemia virus via a codon usage-dependent mechanism. Virology 2016; 495:112-21. [PMID: 27200480 DOI: 10.1016/j.virol.2016.04.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 12/21/2022]
Abstract
Human schlafen11 is a novel restriction factor for HIV-1 based on bias regarding relative synonymous codon usage (RSCU). Here, we report the cloning of equine schlafen11 (eSLFN11) and the characteristics of its role in restricting the production of equine infectious anemia virus (EIAV), a retrovirus similar to HIV-1. Overexpression of eSLFN11 inhibited EIAV replication, whereas knockdown of endogenous eSLFN11 by siRNA enhanced the release of EIAV from its principal target cell. Notably, although eSLFN11 significantly suppressed expression of viral Gag protein and EIAV release into the culture medium, the levels of intracellular viral early gene proteins Tat and Rev and viral genomic RNA were unaffected. Coincidently, similar altered patterns of codon usage bias were observed for both the early and late genes of EIAV. Therefore, our data suggest that eSLFN11 restricts EIAV production by impairing viral mRNA translation via a mechanism that is similar to that employed by hSLFN11 for HIV-1.
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Affiliation(s)
- Yue-Zhi Lin
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
| | - Liu-Ke Sun
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
| | - Dan-Tong Zhu
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China; College of Wildlife Resources, Northeast Forestry University, Harbin, China.
| | - Zhe Hu
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
| | - Xue-Feng Wang
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
| | - Cheng Du
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
| | - Yu-Hong Wang
- Department of Geriatrics And Gerontology, First Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Xiao-Jun Wang
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
| | - Jian-Hua Zhou
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
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53
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Kumar N, Bera BC, Greenbaum BD, Bhatia S, Sood R, Selvaraj P, Anand T, Tripathi BN, Virmani N. Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. PLoS One 2016; 11:e0154376. [PMID: 27119730 PMCID: PMC4847779 DOI: 10.1371/journal.pone.0154376] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.
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MESH Headings
- Adaptation, Physiological/genetics
- Animals
- Biological Evolution
- Codon
- Gene Expression Regulation, Viral
- Genetic Code
- Genome, Viral
- Horse Diseases/virology
- Horses
- Host-Pathogen Interactions
- Influenza A Virus, H3N8 Subtype/genetics
- Influenza A Virus, H3N8 Subtype/metabolism
- Influenza A Virus, H7N7 Subtype/genetics
- Influenza A Virus, H7N7 Subtype/metabolism
- Models, Statistical
- Mutation Rate
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/virology
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Species Specificity
- Virus Replication
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Affiliation(s)
- Naveen Kumar
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Bidhan Chandra Bera
- Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | - Benjamin D. Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Pathology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sandeep Bhatia
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Richa Sood
- Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India
| | - Pavulraj Selvaraj
- Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | - Taruna Anand
- Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India
| | | | - Nitin Virmani
- Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India
- * E-mail:
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54
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Exploiting tRNAs to Boost Virulence. Life (Basel) 2016; 6:life6010004. [PMID: 26797637 PMCID: PMC4810235 DOI: 10.3390/life6010004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 01/22/2023] Open
Abstract
Transfer RNAs (tRNAs) are powerful small RNA entities that are used to translate nucleotide language of genes into the amino acid language of proteins. Their near-uniform length and tertiary structure as well as their high nucleotide similarity and post-transcriptional modifications have made it difficult to characterize individual species quantitatively. However, due to the central role of the tRNA pool in protein biosynthesis as well as newly emerging roles played by tRNAs, their quantitative assessment yields important information, particularly relevant for virus research. Viruses which depend on the host protein expression machinery have evolved various strategies to optimize tRNA usage—either by adapting to the host codon usage or encoding their own tRNAs. Additionally, several viruses bear tRNA-like elements (TLE) in the 5′- and 3′-UTR of their mRNAs. There are different hypotheses concerning the manner in which such structures boost viral protein expression. Furthermore, retroviruses use special tRNAs for packaging and initiating reverse transcription of their genetic material. Since there is a strong specificity of different viruses towards certain tRNAs, different strategies for recruitment are employed. Interestingly, modifications on tRNAs strongly impact their functionality in viruses. Here, we review those intersection points between virus and tRNA research and describe methods for assessing the tRNA pool in terms of concentration, aminoacylation and modification.
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55
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Seif E, Niu M, Kleiman L. In virio SHAPE analysis of tRNA(Lys3) annealing to HIV-1 genomic RNA in wild type and protease-deficient virus. Retrovirology 2015; 12:40. [PMID: 25981241 PMCID: PMC4445796 DOI: 10.1186/s12977-015-0171-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/06/2015] [Indexed: 11/29/2022] Open
Abstract
Background tRNALys3 annealing to the viral RNA of human immunodeficiency virus type-1 (HIV-1) is an essential step in the virus life cycle, because this tRNA serves as the primer for initiating reverse transcription. tRNALys3 annealing to viral RNA occurs in two steps. First, Gag promotes annealing of tRNALys3 to the viral RNA during cytoplasmic HIV-1 assembly. Second, mature nucleocapsid (NCp7), produced from the processing of Gag by viral protease during viral budding from the cell, remodels the annealed complex to form a more stable interaction between the viral RNA and tRNALys3, resulting in a more tightly bound and efficient primer for reverse transcription. Results In this report, we have used in virio SHAPE analysis of both the 5´-untranslated region in HIV-1 RNA and the annealed tRNALys3 to determine structural differences of the annealed complex that occur between protease-negative (Pr-) and wild type viruses. Our results indicate that the weaker binding of tRNALys3 annealed by Gag in Pr- virions reflects both missing interactions of tRNALys3 with viral RNA regions in the upper PBS stem, and a weaker interaction with the internal stem-loop found within the unannealed primer binding site in viral RNA. Conclusions We propose secondary structure models for the tRNALys3/viral RNA annealed complexes in PR- and wild type viruses that support the two-step annealing model by showing that Gag promotes a partial annealing of tRNALys3 to HIV-1 viral RNA, followed by a more complete annealing by NCp7. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0171-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elias Seif
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada.
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada. .,Department of Medicine, McGill University, Montreal, QC, H3A 1A1, Canada.
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56
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Li MMH, MacDonald MR, Rice CM. To translate, or not to translate: viral and host mRNA regulation by interferon-stimulated genes. Trends Cell Biol 2015; 25:320-9. [PMID: 25748385 PMCID: PMC4441850 DOI: 10.1016/j.tcb.2015.02.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/28/2015] [Accepted: 02/05/2015] [Indexed: 01/08/2023]
Abstract
Translational regulation of viral and host mRNA is an important function of a subset of interferon-stimulated genes (ISGs). These ISGs repress translation through binding to viral RNA, direct interaction with, or perturbation of the translation machinery components. Several ISGs localize to cytoplasmic granules such as stress granules (SGs) and processing bodies (PBs), and interfere with the processing or function of microRNAs (miRNAs).
Type I interferon (IFN) is one of the first lines of cellular defense against viral pathogens. As a result of IFN signaling, a wide array of IFN-stimulated gene (ISG) products is upregulated to target different stages of the viral life cycle. We review recent findings implicating a subset of ISGs in translational regulation of viral and host mRNAs. Translation inhibition is mediated either by binding to viral RNA or by disrupting physiological interactions or levels of the translation complex components. In addition, many of these ISGs localize to translationally silent cytoplasmic granules, such as stress granules and processing bodies, and intersect with the microRNA (miRNA)-mediated silencing pathway to regulate translation of cellular mRNAs.
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Affiliation(s)
- Melody M H Li
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
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57
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Prabhakaran R, Chithambaram S, Xia X. Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles. J Gen Virol 2015; 96:1169-1179. [PMID: 25614589 PMCID: PMC4631060 DOI: 10.1099/vir.0.000050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/11/2015] [Indexed: 12/19/2022] Open
Abstract
Rapid biosynthesis is key to the success of bacteria and viruses. Highly expressed genes in bacteria exhibit a strong codon bias corresponding to the differential availability of tRNAs. However, a large clade of lambdoid coliphages exhibits relatively poor codon adaptation to the host translation machinery, in contrast to other coliphages that exhibit strong codon adaptation to the host. Three possible explanations were previously proposed but dismissed: (1) the phage-borne tRNA genes that reduce the dependence of phage translation on host tRNAs, (2) lack of time needed for evolving codon adaptation due to recent host switching, and (3) strong strand asymmetry with biased mutation disrupting codon adaptation. Here, we examined the possibility that phages with relatively poor codon adaptation have poor translation initiation which would weaken the selection on codon adaptation. We measured translation initiation by: (1) the strength and position of the Shine-Dalgarno (SD) sequence, and (2) the stability of the secondary structure of sequences flanking the SD and start codon known to affect accessibility of the SD sequence and start codon. Phage genes with strong codon adaptation had significantly stronger SD sequences than those with poor codon adaptation. The former also had significantly weaker secondary structure in sequences flanking the SD sequence and start codon than the latter. Thus, lambdoid phages do not exhibit strong codon adaptation because they have relatively inefficient translation initiation and would benefit little from increased elongation efficiency. We also provided evidence suggesting that phage lifestyle (virulent versus temperate) affected selection intensity on the efficiency of translation initiation and elongation.
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Affiliation(s)
- Ramanandan Prabhakaran
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada
| | - Shivapriya Chithambaram
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada
| | - Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada
- Correspondence Xuhua Xia
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58
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Margaliot M, Sontag ED, Tuller T. Entrainment to periodic initiation and transition rates in a computational model for gene translation. PLoS One 2014; 9:e96039. [PMID: 24800863 PMCID: PMC4011696 DOI: 10.1371/journal.pone.0096039] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/02/2014] [Indexed: 01/09/2023] Open
Abstract
Periodic oscillations play an important role in many biomedical systems. Proper functioning of biological systems that respond to periodic signals requires the ability to synchronize with the periodic excitation. For example, the sleep/wake cycle is a manifestation of an internal timing system that synchronizes to the solar day. In the terminology of systems theory, the biological system must entrain or phase-lock to the periodic excitation. Entrainment is also important in synthetic biology. For example, connecting several artificial biological systems that entrain to a common clock may lead to a well-functioning modular system. The cell-cycle is a periodic program that regulates DNA synthesis and cell division. Recent biological studies suggest that cell-cycle related genes entrain to this periodic program at the gene translation level, leading to periodically-varying protein levels of these genes. The ribosome flow model (RFM) is a deterministic model obtained via a mean-field approximation of a stochastic model from statistical physics that has been used to model numerous processes including ribosome flow along the mRNA. Here we analyze the RFM under the assumption that the initiation and/or transition rates vary periodically with a common period . We show that the ribosome distribution profile in the RFM entrains to this periodic excitation. In particular, the protein synthesis pattern converges to a unique periodic solution with period . To the best of our knowledge, this is the first proof of entrainment in a mathematical model for translation that encapsulates aspects such as initiation and termination rates, ribosomal movement and interactions, and non-homogeneous elongation speeds along the mRNA. Our results support the conjecture that periodic oscillations in tRNA levels and other factors related to the translation process can induce periodic oscillations in protein levels, and may suggest a new approach for re-engineering genetic systems to obtain a desired, periodic, protein synthesis rate.
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Affiliation(s)
- Michael Margaliot
- School of Electrical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Eduardo D. Sontag
- Dept. of Mathematics and Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
| | - Tamir Tuller
- Dept. of Biomedical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
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59
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Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses. Proc Natl Acad Sci U S A 2014; 111:5054-9. [PMID: 24639520 DOI: 10.1073/pnas.1402285111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We outline a theory to quantify the interplay of entropic and selective forces on nucleotide organization and apply it to the genomes of single-stranded RNA viruses. We quantify these forces as intensive variables that can easily be compared between sequences, outline a computationally efficient transfer-matrix method for their calculation, and apply this method to influenza and HIV viruses. We find viruses altering their dinucleotide motif use under selective forces, with these forces on CpG dinucleotides growing stronger in influenza the longer it replicates in humans. For a subset of genes in the human genome, many involved in antiviral innate immunity, the forces acting on CpG dinucleotides are even greater than the forces observed in viruses, suggesting that both effects are in response to similar selective forces involving the innate immune system. We further find that the dynamics of entropic forces balancing selective forces can be used to predict how long it will take a virus to adapt to a new host, and that it would take H1N1 several centuries to adapt to humans from birds, typically contributing many of its synonymous substitutions to the forcible removal of CpG dinucleotides. By examining the probability landscape of dinucleotide motifs, we predict where motifs are likely to appear using only a single-force parameter and uncover the localization of UpU motifs in HIV. Essentially, we extend the natural language and concepts of statistical physics, such as entropy and conjugated forces, to understanding viral sequences and, more generally, constrained genome evolution.
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60
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Abstract
Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C→T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C→T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.
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61
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Chithambaram S, Prabhakaran R, Xia X. Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. Mol Biol Evol 2014; 31:1606-17. [PMID: 24586046 PMCID: PMC4032129 DOI: 10.1093/molbev/msu087] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Because phages use their host translation machinery, their codon usage should evolve toward that of highly expressed host genes. We used two indices to measure codon adaptation of phages to their host, rRSCU (the correlation in relative synonymous codon usage [RSCU] between phages and their host) and Codon Adaptation Index (CAI) computed with highly expressed host genes as the reference set (because phage translation depends on host translation machinery). These indices used for this purpose are appropriate only when hosts exhibit little mutation bias, so only phages parasitizing Escherichia coli were included in the analysis. For double-stranded DNA (dsDNA) phages, both rRSCU and CAI decrease with increasing number of transfer RNA genes encoded by the phage genome. rRSCU is greater for dsDNA phages than for single-stranded DNA (ssDNA) phages, and the low rRSCU values are mainly due to poor concordance in RSCU values for Y-ending codons between ssDNA phages and the E. coli host, consistent with the predicted effect of C→T mutation bias in the ssDNA phages. Strong C→T mutation bias would improve codon adaptation in codon families (e.g., Gly) where U-ending codons are favored over C-ending codons (“U-friendly” codon families) by highly expressed host genes but decrease codon adaptation in other codon families where highly expressed host genes favor C-ending codons against U-ending codons (“U-hostile” codon families). It is remarkable that ssDNA phages with increasing C→T mutation bias also increased the usage of codons in the “U-friendly” codon families, thereby achieving CAI values almost as large as those of dsDNA phages. This represents a new type of codon adaptation.
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Affiliation(s)
- Shivapriya Chithambaram
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
| | - Ramanandan Prabhakaran
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
| | - Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
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62
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Frias D, Monteiro-Cunha JP, Mota-Miranda AC, Fonseca VS, de Oliveira T, Galvao-Castro B, Alcantara LCJ. Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights. Bioinform Biol Insights 2013; 7:335-45. [PMID: 24151425 PMCID: PMC3798314 DOI: 10.4137/bbi.s12093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study was to investigate the balance between transfer ribonucleic acid (tRNA) supply and demand in retrovirus-infected cells, seeking the best targets for antiretroviral therapy based on the hypothetical tRNA Inhibition Therapy (TRIT). Codon usage and tRNA gene data were retrieved from public databases. Based on logistic principles, a therapeutic score (T-score) was calculated for all sense codons, in each retrovirus-host system. Codons that are critical for viral protein translation, but not as critical for the host, have the highest T-score values. Theoretically, inactivating the cognate tRNA species should imply a severe reduction of the elongation rate during viral mRNA translation. We developed a method to predict tRNA species critical for retroviral protein synthesis. Four of the best TRIT targets in HIV-1 and HIV-2 encode Large Hydrophobic Residues (LHR), which have a central role in protein folding. One of them, codon CUA, is also a TRIT target in both HTLV-1 and HTLV-2. Therefore, a drug designed for inactivating or reducing the cytoplasmatic concentration of tRNA species with anticodon TAG could attenuate significantly both HIV and HTLV protein synthesis rates. Inversely, replacing codons ending in UA by synonymous codons should increase the expression, which is relevant for DNA vaccine design.
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Affiliation(s)
- Diego Frias
- Bahia State University, Salvador, Bahia, Brazil
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63
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Xia X. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 2013; 30:1720-8. [PMID: 23564938 PMCID: PMC3684854 DOI: 10.1093/molbev/mst064] [Citation(s) in RCA: 739] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).
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Affiliation(s)
- Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada
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64
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Katibah GE, Lee HJ, Huizar JP, Vogan JM, Alber T, Collins K. tRNA binding, structure, and localization of the human interferon-induced protein IFIT5. Mol Cell 2013; 49:743-50. [PMID: 23317505 PMCID: PMC3615435 DOI: 10.1016/j.molcel.2012.12.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
Abstract
Interferon-induced proteins, including the largely uncharacterized interferon-induced tetratricopeptide repeat (IFIT) protein family, provide defenses against pathogens. Differing from expectations for tetratricopeptide repeat (TPR) proteins and from human IFIT1, IFIT2, and IFIT3, we show that human IFIT5 recognizes cellular RNA instead of protein partners. In vivo and in vitro, IFIT5 bound to endogenous 5'-phosphate-capped RNAs, including transfer RNAs. The crystal structure of IFIT5 revealed a convoluted intramolecular packing of eight TPRs as a fold that we name the TPR eddy. Additional, non-TPR structural elements contribute to an RNA binding cleft. Instead of general cytoplasmic distribution, IFIT5 concentrated in actin-rich protrusions from the apical cell surface colocalized with the RNA-binding retinoic acid-inducible gene-I (RIG-I). These findings establish compartmentalized cellular RNA binding activity as a mechanism for IFIT5 function and reveal the TPR eddy as a scaffold for RNA recognition.
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MESH Headings
- Actins/metabolism
- Amino Acid Substitution
- Animals
- Crystallography, X-Ray
- DEAD Box Protein 58
- DEAD-box RNA Helicases/chemistry
- DEAD-box RNA Helicases/isolation & purification
- DEAD-box RNA Helicases/metabolism
- HEK293 Cells
- Humans
- Mice
- Models, Molecular
- Mutagenesis, Site-Directed
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/isolation & purification
- Neoplasm Proteins/metabolism
- Protein Binding
- Protein Interaction Mapping
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Transport
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- Receptors, Immunologic
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Affiliation(s)
- George E. Katibah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Ho Jun Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - John P. Huizar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Jacob M. Vogan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Tom Alber
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
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65
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Jones CP, Saadatmand J, Kleiman L, Musier-Forsyth K. Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing. RNA (NEW YORK, N.Y.) 2013; 19:219-29. [PMID: 23264568 PMCID: PMC3543088 DOI: 10.1261/rna.036681.112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/14/2012] [Indexed: 05/18/2023]
Abstract
The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNA(Lys3). Host cell tRNA(Lys) is selectively packaged into HIV-1 through a specific interaction between the major tRNA(Lys)-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNA(Lys3) is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNA(Lys) and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNA(Lys3) in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNA(Lys) to increase the efficiency of tRNA(Lys3) annealing to viral RNA.
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MESH Headings
- Base Pairing
- Electrophoretic Mobility Shift Assay
- Genome, Viral/genetics
- HIV Enhancer/genetics
- HIV-1/genetics
- HIV-1/physiology
- Humans
- Lysine-tRNA Ligase/genetics
- Lysine-tRNA Ligase/metabolism
- Molecular Mimicry
- Mutation
- Protein Structure, Tertiary
- RNA
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Virus Assembly/genetics
- Virus Replication/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Christopher P. Jones
- Department of Chemistry and Biochemistry, Center for Retroviral Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jenan Saadatmand
- Lady Davis Institute for Medical Research, McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada, H3T1E2
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research, McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada, H3T1E2
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retroviral Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Corresponding authorE-mail
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66
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Pavon-Eternod M, David A, Dittmar K, Berglund P, Pan T, Bennink JR, Yewdell JW. Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation. Nucleic Acids Res 2012; 41:1914-21. [PMID: 23254333 PMCID: PMC3561966 DOI: 10.1093/nar/gks986] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are central to protein synthesis and impact translational speed and
fidelity by their abundance. Here we examine the extent to which viruses manipulate tRNA
populations to favor translation of their own genes. We study two very different viruses:
influenza A virus (IAV), a medium-sized (13 kB genome) RNA virus; and vaccinia virus (VV),
a large (200 kB genome) DNA virus. We show that the total cellular tRNA population remains
unchanged following viral infection, whereas the polysome-associated tRNA population
changes dramatically in a virus-specific manner. The changes in polysome-associated tRNA
levels reflect the codon usage of viral genes, suggesting the existence of local tRNA
pools optimized for viral translation.
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Affiliation(s)
- Mariana Pavon-Eternod
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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67
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van Hemert FJ, van der Kuyl AC, Berkhout B. The A-nucleotide preference of HIV-1 in the context of its structured RNA genome. RNA Biol 2012; 10:211-5. [PMID: 23235488 PMCID: PMC3594280 DOI: 10.4161/rna.22896] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A bipartition of HIV-1 RNA genome sequences into single- and double-stranded nucleotides is possible based on the secondary structure model of a complete 9 kb genome. Subsequent analysis revealed that the well-known lentiviral property of A-accumulation is profoundly present in single-stranded domains, yet absent in double-stranded domains. Mutational rate analysis by means of an unrestricted model of nucleotide substitution suggests the presence of an evolutionary equilibrium to preserve this biased nucleotide distribution.
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Affiliation(s)
- Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam CINIMA, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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68
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Goñi N, Iriarte A, Comas V, Soñora M, Moreno P, Moratorio G, Musto H, Cristina J. Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development. Virol J 2012; 9:263. [PMID: 23134595 PMCID: PMC3543350 DOI: 10.1186/1743-422x-9-263] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 11/02/2012] [Indexed: 11/20/2022] Open
Abstract
Background Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed. Results We performed a comprehensive codon usage analysis of 310 IAV strains from the pandemic of 2009. Highly biased codon usage for Ala, Arg, Pro, Thr and Ser were found. Codon usage is strongly influenced by underlying biases in base composition. When correspondence analysis (COA) on relative synonymous codon usage (RSCU) is applied, the distribution of IAV ORFs in the plane defined by the first two major dimensional factors showed that different strains are located at different places, suggesting that IAV codon usage also reflects an evolutionary process. Conclusions A general association between codon usage bias, base composition and poor adaptation of the virus to the respective host tRNA pool, suggests that mutational pressure is the main force shaping H1N1 pdm IAV codon usage. A dynamic process is observed in the variation of codon usage of the strains enrolled in these studies. These results suggest a balance of mutational bias and natural selection, which allow the virus to explore and re-adapt its codon usage to different environments. Recoding of IAV taking into account codon bias, base composition and adaptation to host tRNA may provide important clues to develop new and appropriate vaccines.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay
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69
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van der Kuyl AC, Berkhout B. The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology 2012; 9:92. [PMID: 23131071 PMCID: PMC3511177 DOI: 10.1186/1742-4690-9-92] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/14/2012] [Indexed: 01/09/2023] Open
Abstract
Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, AZ 1105, The Netherlands.
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70
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Margaliot M, Tuller T. On the steady-state distribution in the homogeneous ribosome flow model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:1724-1736. [PMID: 23221086 DOI: 10.1109/tcbb.2012.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A central biological process in all living organisms is gene translation. Developing a deeper understanding of this complex process may have ramifications to almost every biomedical discipline. Reuveni et al. recently proposed a new computational model of gene translation called the Ribosome Flow Model (RFM). In this paper, we consider a particular case of this model, called the Homogeneous Ribosome Flow Model (HRFM). From a biological viewpoint, this corresponds to the case where the transition rates of all the coding sequence codons are identical. This regime has been suggested recently based on experiments in mouse embryonic cells. We consider the steady-state distribution of the HRFM. We provide formulas that relate the different parameters of the model in steady state. We prove the following properties: 1) the ribosomal density profile is monotonically decreasing along the coding sequence; 2) the ribosomal density at each codon monotonically increases with the initiation rate; and 3) for a constant initiation rate, the translation rate monotonically decreases with the length of the coding sequence. In addition, we analyze the translation rate of the HRFM at the limit of very high and very low initiation rate, and provide explicit formulas for the translation rate in these two cases. We discuss the relationship between these theoretical results and biological findings on the translation process.
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Affiliation(s)
- Michael Margaliot
- School of Electrical Engineering-Systems, Tel-Aviv University, Tel-Aviv.
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71
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Li M, Kao E, Gao X, Sandig H, Limmer K, Pavon-Eternod M, Jones TE, Landry S, Pan T, Weitzman MD, David M. Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11. Nature 2012; 491:125-8. [PMID: 23000900 DOI: 10.1038/nature11433] [Citation(s) in RCA: 249] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 07/23/2012] [Indexed: 01/26/2023]
Abstract
In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination.
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Affiliation(s)
- Manqing Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
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72
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Margaliot M, Tuller T. Stability analysis of the ribosome flow model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:1545-52. [PMID: 22732691 DOI: 10.1109/tcbb.2012.88] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Gene translation is a central process in all living organisms. Developing a better understanding of this complex process may have ramifications to almost every biomedical discipline. Recently, Reuveni et al. proposed a new computational model of this process called the ribosome flow model (RFM). In this study, we show that the dynamical behavior of the RFM is relatively simple. There exists a unique equilibrium point e and every trajectory converges to e. Furthermore, convergence is monotone in the sense that the distance to e can never increase. This qualitative behavior is maintained for any feasible set of parameter values, suggesting that the RFM is highly robust. Our analysis is based on a contraction principle and the theory of monotone dynamical systems. These analysis tools may prove useful in studying other properties of the RFM as well as additional intracellular biological processes.
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Affiliation(s)
- Michael Margaliot
- School of Electrical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel.
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73
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Sun X, Yang Q, Xia X. An improved implementation of effective number of codons (nc). Mol Biol Evol 2012; 30:191-6. [PMID: 22915832 DOI: 10.1093/molbev/mss201] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The effective number of codons (N(c)) is a widely used index for characterizing codon usage bias because it does not require a set of reference genes as does codon adaptation index (CAI) and because of the freely available computational tools such as CodonW. However, N(c), as originally formulated has many problems. For example, it can have values far greater than the number of sense codons; it treats a 6-fold compound codon family as a single-codon family although it is made of a 2-fold and a 4-fold codon family that can be under dramatically different selection for codon usage bias; the existing implementations do not handle all different genetic codes; it is often biased by codon families with a small number of codons. We developed a new N(c) that has a number of advantages over the original N(c). Its maximum value equals the number of sense codons when all synonymous codons are used equally, and its minimum value equals the number of codon families when exactly one codon is used in each synonymous codon family. It handles all known genetic codes. It breaks the compound codon families (e.g., those involving amino acids coded by six synonymous codons) into 2-fold and 4-fold codon families. It reduces the effect of codon families with few codons by introducing pseudocount and weighted averages. The new N(c) has significantly improved correlation with CAI than the original N(c) from CodonW based on protein-coding genes from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Bacillus subtilis, Micrococcus luteus, and Mycoplasma genitalium. It also correlates better with protein abundance data from the yeast than the original N(c).
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Affiliation(s)
- Xiaoyan Sun
- State Key Laboratory of Paleobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Science, Nanjing, China
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74
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Pintó RM, D'Andrea L, Pérez-Rodriguez FJ, Costafreda MI, Ribes E, Guix S, Bosch A. Hepatitis A virus evolution and the potential emergence of new variants escaping the presently available vaccines. Future Microbiol 2012; 7:331-46. [PMID: 22393888 DOI: 10.2217/fmb.12.5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hepatitis A is the most common infection of the liver worldwide and is fecal-orally transmitted. Its incidence tends to decrease with improvements in hygiene conditions but at the same time its severity increases. Hepatitis A virus is the causative agent of acute hepatitis in humans and belongs to the Hepatovirus genus in the Picornaviridae family, and it has very unique characteristics. This article reviews some molecular and biological properties that allow the virus to live in a very quiescent way and to build an extremely stable capsid that is able to persist in and out of the body. Additionally, the relationship between the genomic composition and the structural and antigenic properties of the capsid is discussed, and the potential emergence of antigenic variants is evaluated from an evolutionary perspective.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, School of Biology, University of Barcelona, Barcelona, Spain.
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75
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Pandit A, Sinha S. Differential trends in the codon usage patterns in HIV-1 genes. PLoS One 2011; 6:e28889. [PMID: 22216135 PMCID: PMC3245234 DOI: 10.1371/journal.pone.0028889] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 11/16/2011] [Indexed: 12/27/2022] Open
Abstract
Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level.
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Affiliation(s)
- Aridaman Pandit
- Mathematical Modeling and Computational Biology Group, Centre for Cellular & Molecular Biology (CSIR), Hyderabad, Andhra Pradesh, India
| | - Somdatta Sinha
- Mathematical Modeling and Computational Biology Group, Centre for Cellular & Molecular Biology (CSIR), Hyderabad, Andhra Pradesh, India
- Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
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76
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Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts. ISME JOURNAL 2011; 6:619-28. [PMID: 22011720 DOI: 10.1038/ismej.2011.146] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic prokaryotes in oceanic environments, and are key contributors to global CO(2) fixation, chlorophyll biomass and primary production. Cyanophages, viruses infecting cyanobacteria, are a major force in the ecology of their hosts. These phages contribute greatly to cyanobacterial mortality, therefore acting as a powerful selective force upon their hosts. Phage reproduction is based on utilization of the host transcription and translation mechanisms; therefore, differences in the G+C genomic content between cyanophages and their hosts could be a limiting factor for the translation of cyanophage genes. On the basis of comprehensive genomic analyses conducted in this study, we suggest that cyanophages of the Myoviridae family, which can infect both Prochlorococcus and Synechococcus, overcome this limitation by carrying additional sets of tRNAs in their genomes accommodating AT-rich codons. Whereas the tRNA genes are less needed when infecting their Prochlorococcus hosts, which possess a similar G+C content to the cyanophage, the additional tRNAs may increase the overall translational efficiency of their genes when infecting a Synechococcus host (with high G+C content), therefore potentially enabling the infection of multiple hosts.
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77
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Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 2011; 189:469-78. [PMID: 21840854 PMCID: PMC3189813 DOI: 10.1534/genetics.111.132068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The 5'-UTR serves as the loading dock for ribosomes during translation initiation and is the key site for translation regulation. Many genes in the yeast Saccharomyces cerevisiae contain poly(A) tracts in their 5'-UTRs. We studied these pre-AUG poly(A) tracts in a set of 3274 recently identified 5'-UTRs in the yeast to characterize their effect on in vivo protein abundance, ribosomal density, and protein synthesis rate in the yeast. The protein abundance and the protein synthesis rate increase with the length of the poly(A), but exhibit a dramatic decrease when the poly(A) length is ≥12. The ribosomal density also reaches the lowest level when the poly(A) length is ≥12. This supports the hypothesis that a pre-AUG poly(A) tract can bind to translation initiation factors to enhance translation initiation, but a long (≥12) pre-AUG poly(A) tract will bind to Pab1p, whose binding size is 12 consecutive A residues in yeast, resulting in repression of translation. The hypothesis explains why a long pre-AUG poly(A) leads to more efficient translation initiation than a short one when PABP is absent, and why pre-AUG poly(A) is short in the early genes but long in the late genes of vaccinia virus.
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78
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Schmid P, Flegel WA. Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations. J Transl Med 2011; 9:87. [PMID: 21651781 PMCID: PMC3123582 DOI: 10.1186/1479-5876-9-87] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 06/08/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Codon usage in genomes is biased towards specific subsets of codons. Codon usage bias affects translational speed and accuracy, and it is associated with the tRNA levels and the GC content of the genome. Spontaneous mutations drive genomes to a low GC content. Active cellular processes are needed to maintain a high GC content, which influences the codon usage of a species. Loss-of-function mutations, such as nonsense mutations, are the molecular basis of many recessive alleles, which can greatly affect the genome of an organism and are the cause of many genetic diseases in humans. METHODS We developed an event based model to calculate the risk of acquiring nonsense mutations in coding sequences. Complete coding sequences and genomes of 40 eukaryotes were analyzed for GC and CpG content, codon usage, and the associated risk of acquiring nonsense mutations. We included one species per genus for all eukaryotes with available reference sequence. RESULTS We discovered that the codon usage bias detected in genomes of high GC content decreases the risk of acquiring nonsense mutations (Pearson's r = -0.95; P < 0.0001). In the genomes of all examined vertebrates, including humans, this risk was lower than expected (0.93 ± 0.02; mean ± SD) and lower than the risk in genomes of non-vertebrates (1.02 ± 0.13; P = 0.019). CONCLUSIONS While the maintenance of a high GC content is energetically costly, it is associated with a codon usage bias harboring a low risk of acquiring nonsense mutations. The reduced exposure to this risk may contribute to the fitness of vertebrates.
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Affiliation(s)
- Pirmin Schmid
- National Institutes of Health, Clinical Center, Bethesda, MD, USA
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