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Ahmed W, Gupta S, Singh D, Singh R. Insight of genetic features prevalent in three Echinoderm species (Apostichopus japonicus, Heliocedaris erythrogramma and Asterias rubens) and their evolutionary association using comparative codon pattern analysis. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Valdez F, Salvador J, Palermo PM, Mohl JE, Hanley KA, Watts D, Llano M. Schlafen 11 Restricts Flavivirus Replication. J Virol 2019; 93:e00104-19. [PMID: 31118262 PMCID: PMC6639263 DOI: 10.1128/jvi.00104-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/14/2019] [Indexed: 02/07/2023] Open
Abstract
Schlafen 11 (Slfn11) is an interferon-stimulated gene that controls the synthesis of proteins by regulating tRNA abundance. Likely through this mechanism, Slfn11 has previously been shown to impair human immunodeficiency virus type 1 (HIV-1) infection and the expression of codon-biased open reading frames. Because replication of positive-sense single-stranded RNA [(+)ssRNA] viruses requires the immediate translation of the incoming viral genome, whereas negative-sense single-stranded RNA [(-)ssRNA] viruses carry at infection an RNA replicase that makes multiple translation-competent copies of the incoming viral genome, we reasoned that (+)ssRNA viruses will be more sensitive to the effect of Slfn11 on protein synthesis than (-)ssRNA viruses. To evaluate this hypothesis, we tested the effects of Slfn11 on the replication of a panel of ssRNA viruses in the human glioblastoma cell line A172, which naturally expresses Slfn11. Depletion of Slfn11 significantly increased the replication of (+)ssRNA viruses from the Flavivirus genus, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV), but had no significant effect on the replication of the (-)ssRNA viruses vesicular stomatitis virus (VSV) (Rhabdoviridae family) and Rift Valley fever virus (RVFV) (Phenuiviridae family). Quantification of the ratio of genome-containing viral particles to PFU indicated that Slfn11 impairs WNV infectivity. Intriguingly, Slfn11 prevented WNV-induced downregulation of a subset of tRNAs implicated in the translation of 11.8% of the viral polyprotein. Low-abundance tRNAs might promote optimal protein folding and enhance viral infectivity, as previously reported. In summary, this study demonstrates that Slfn11 restricts flavivirus replication by impairing viral infectivity.IMPORTANCE We provide evidence that the cellular protein Schlafen 11 (Slfn11) impairs replication of flaviviruses, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV). However, replication of single-stranded negative RNA viruses was not affected. Specifically, Slfn11 decreases the infectivity of WNV potentially by preventing virus-induced modifications of the host tRNA repertoire that could lead to enhanced viral protein folding. Furthermore, we demonstrate that Slfn11 is not the limiting factor of this novel broad antiviral pathway.
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Affiliation(s)
- Federico Valdez
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Julienne Salvador
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Pedro M Palermo
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Jonathon E Mohl
- Department of Bioinformatics, The University of Texas at El Paso, El Paso, Texas, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Douglas Watts
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Manuel Llano
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
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Ma XX, Ma LN, Chang QY, Ma P, Li LJ, Wang YY, Ma ZR, Cao X. Type I Interferon Induced and Antagonized by Foot-and-Mouth Disease Virus. Front Microbiol 2018; 9:1862. [PMID: 30150977 PMCID: PMC6099088 DOI: 10.3389/fmicb.2018.01862] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
Viral infections trigger the innate immune system, serving as the first line of defense, and are characterized by the production of type I interferon (IFN). Type I IFN is expressed in a broad spectrum of cells and tissues in the host and includes various subtypes (IFN-α, IFN-β, IFN-δ, IFN-ε, IFN-κ, IFN-τ, IFN-ω, IFN-ν, and IFN-ζ). Since the discovery of type I IFN, our knowledge of the biology of type I IFN has accumulated immensely, and we now have a substantial amount of information on the molecular mechanisms of the response and induction of type I IFN, as well as the strategies utilized by viruses to evade the type I IFN response. Foot-and-mouth disease virus (FMDV) can selectively alter cellular pathways to promote viral replication and evade antiviral immune activation of type I IFN. RNA molecules generated by FMDV are sensed by the cellular receptor for pathogen-associated molecular patterns (PAMPs). FMDV preferentially activates different sensor molecules and various signal transduction pathways. Based on knowledge of the virus or RNA pathogen specificity as well as the function-structure relationship of RNA sensing, it is necessary to summarize numerous signaling adaptors that are reported to participate in the regulation of IFN gene activation.
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Affiliation(s)
- Xiao-Xia Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Li-Na Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qiu-Yan Chang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Peng Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Lin-Jie Li
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Yue-Ying Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhong-Ren Ma
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Xin Cao
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus. Genes Genomics 2018; 40:905-912. [DOI: 10.1007/s13258-018-0684-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/23/2018] [Indexed: 02/02/2023]
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Ma XX, Cao X, Ma P, Chang QY, Li LJ, Zhou XK, Zhang DR, Li MS, Ma ZR. Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas. J Basic Microbiol 2018. [PMID: 29537653 DOI: 10.1002/jobm.201700490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.
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Affiliation(s)
- Xiao-Xia Ma
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Xin Cao
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Peng Ma
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Qiu-Yan Chang
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Lin-Jie Li
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Xiao-Kai Zhou
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - De-Rong Zhang
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Ming-Sheng Li
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Zhong-Ren Ma
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
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Ma XX, Chang QY, Ma P, Li LJ, Zhou XK, Zhang DR, Li MS, Cao X, Ma ZR. Analyses of nucleotide, codon and amino acids usages between peste des petits ruminants virus and rinderpest virus. Gene 2017; 637:115-123. [PMID: 28947301 DOI: 10.1016/j.gene.2017.09.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/03/2017] [Accepted: 09/21/2017] [Indexed: 10/18/2022]
Abstract
Peste des petits ruminants virus (PPRV) and rinderpest virus (RPV) are two causative agents of an economically important disease for ruminants (i.e., sheep, cattle and goat). In this study, the nucleotide, codon and amino acid usages for PPRV and RPV have been analyzed by multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis represents that ACG for Thr and GCG for Ala are selected with under-representation in both PPRV and RPV, and AGA for Arg in PPRV and AGG for Arg in RPV are used with over-representation. The usage of nucleotide pair (CpG) tends to be removed from viral genes of the two viruses, suggesting that other evolutionary forces take part in evolutionary processes for viral genes in addition to mutation pressure from nucleotide usage at the third codon position. The overall nucleotide usage of viral gene is not major factor in shaping synonymous codon usage patterns, while the nucleotide usages at the third codon position and the nucleotide pairs play important roles in shaping synonymous codon usage patterns. Although PPRV and RPV are closely related antigenically, the codon and amino acid usage patterns for viral genes represent a significant genetic diversity between PPRV and RPV. Moreover, the overall codon usage trends for viral genes between PPRV and RPV are mainly influenced by mutation pressure from nucleotide usage at the third codon position and translation selection from hosts. Taken together, this is first comprehensive analyses for nucleotide, codon and amino acid usages of viral genes of PPRV and RPV and the findings are expected to increase our understanding of evolutionary forces influencing viral evolutionary pathway and adaptation toward hosts.
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Affiliation(s)
- Xiao-Xia Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Qiu-Yan Chang
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Peng Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Lin-Jie Li
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Xiao-Kai Zhou
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - De-Rong Zhang
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Ming-Sheng Li
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China
| | - Xin Cao
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China.
| | - Zhong-Ren Ma
- Engineering & Technology Research Center for Animal Cell, Gansu College of Life Science and Engineering, Northwest Minzu University, Gansu 730030, PR China.
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Stabell AC, Hawkins J, Li M, Gao X, David M, Press WH, Sawyer SL. Non-human Primate Schlafen11 Inhibits Production of Both Host and Viral Proteins. PLoS Pathog 2016; 12:e1006066. [PMID: 28027315 PMCID: PMC5189954 DOI: 10.1371/journal.ppat.1006066] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/15/2016] [Indexed: 11/18/2022] Open
Abstract
Schlafen11 (encoded by the SLFN11 gene) has been shown to inhibit the accumulation of HIV-1 proteins. We show that the SLFN11 gene is under positive selection in simian primates and is species-specific in its activity against HIV-1. The activity of human Schlafen11 is relatively weak compared to that of some other primate versions of this protein, with the versions encoded by chimpanzee, orangutan, gibbon, and marmoset being particularly potent inhibitors of HIV-1 protein production. Interestingly, we find that Schlafen11 is functional in the absence of infection and reduces protein production from certain non-viral (GFP) and even host (Vinculin and GAPDH) transcripts. This suggests that Schlafen11 may just generally block protein production from non-codon optimized transcripts. Because Schlafen11 is an interferon-stimulated gene with a broad ability to inhibit protein production from many host and viral transcripts, its role may be to create a general antiviral state in the cell. Interestingly, the strong inhibitors such as marmoset Schlafen11 consistently block protein production better than weak primate Schlafen11 proteins, regardless of the virus or host target being analyzed. Further, we show that the residues to which species-specific differences in Schlafen11 potency map are distinct from residues that have been targeted by positive selection. We speculate that the positive selection of SLFN11 could have been driven by a number of different factors, including interaction with one or more viral antagonists that have yet to be identified. Schlafen11 was recently identified as a human antiviral protein with activity against HIV-1. Here we show that some nonhuman primate versions of Schlafen11 are much stronger at blocking the accumulation of viral proteins than is human Schlafen11. These relatively larger phenotypes of nonhuman primate Schlafen11 allowed us to explore further into the mechanism of this protein. We present data showing that Schlafen11 may not be a classic restriction factor, but rather an interferon-stimulated gene with broad ability to inhibit protein production from many host and viral transcripts, creating a general antiviral state in the cell.
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Affiliation(s)
- Alex C. Stabell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - John Hawkins
- Institute for Computational Engineering and Sciences, University of Texas at Austin, TX, United States of America
| | - Manqing Li
- Division of Biological Sciences, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - Xia Gao
- Division of Biological Sciences, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - Michael David
- Division of Biological Sciences, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - William H. Press
- Institute for Computational Engineering and Sciences, University of Texas at Austin, TX, United States of America
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States of America
- * E-mail:
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