Login Register Cart 0
Generic placeholder image

Current Pharmaceutical Design

Editor-in-Chief

ISSN (Print): 1381-6128
ISSN (Online): 1873-4286

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

An Insight into Codon Pattern Analysis of Autophagy Genes Associated with Virus Infection

Author(s): Shailja Singhal, Utsang Kumar, Taha Alqahtani, Igor Vladimirovich Rzhepakovsky, Rekha Khandia*, Megha Pandey, Saud Alqahtani, Hanan Alharbi and Mohammad Amjad Kamal

Volume 29, Issue 14, 2023

Published on: 03 May, 2023

Page: [1105 - 1120] Pages: 16

DOI: 10.2174/1381612829666230418093308

Price: $65

Abstract

Introduction: Apoptosis and autophagy are the two fundamental processes involved in maintaining homeostasis, and a common stimulus may initiate the processes. Autophagy has been implicated in various diseases, including viral infections. Genetic manipulations leading to altered gene expression might be a strategy to check virus infection.

Aim: Determination of molecular patterns, relative synonymous codon usage, codon preference, codon bias, codon pair bias, and rare codons so that genetic manipulation of autophagy genes may be done to curb viral infection.

Methods: Using various software, algorithms, and statistical analysis, insights into codon patterns were obtained. A total of 41 autophagy genes were envisaged as they are involved in virus infection.

Results: The A/T and G/C ending codons are preferred by different genes. AAA-GAA and CAG-CTG codon pairs are the most abundant codon pairs. CGA, TCG, CCG, and GCG are rarely used codons.

Conclusion: The information generated in the present study helps manipulate the gene expression level of virus infection-associated autophagy genes through gene modification tools like CRISPR. Codon deoptimization for reducing while codon pair optimization for enhancing is efficacious for HO-1 gene expression.

« Previous Next »
[1]
Zhao YG, Zhang H. Core autophagy genes and human diseases. Curr Opin Cell Biol 2019; 61: 117-25.
[http://dx.doi.org/10.1016/j.ceb.2019.08.003] [PMID: 31480011]
[2]
Moore MN. Lysosomes, autophagy, and hormesis in cell physiology, pathology, and age-related disease. Dose Response 2020; 18(3): 1559325820934227.
[http://dx.doi.org/10.1177/1559325820934227] [PMID: 32684871]
[3]
Che Y, Wang ZP, Yuan Y, et al. Role of autophagy in a model of obesity: A long-term high fat diet induces cardiac dysfunction. Mol Med Rep 2018; 18(3): 3251-61.
[http://dx.doi.org/10.3892/mmr.2018.9301] [PMID: 30066870]
[4]
Maron BJ, Roberts WC, Arad M, et al. Clinical outcome and phenotypic expression in LAMP2 cardiomyopathy. JAMA 2009; 301(12): 1253-9.
[http://dx.doi.org/10.1001/jama.2009.371] [PMID: 19318653]
[5]
Guo F, Liu X, Cai H, Le W. Autophagy in neurodegenerative diseases: Pathogenesis and therapy. Brain Pathol 2018; 28(1): 3-13.
[http://dx.doi.org/10.1111/bpa.12545] [PMID: 28703923]
[6]
Mancias JD, Wang X, Gygi SP, Harper JW, Kimmelman AC. Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature 2014; 509(7498): 105-9.
[http://dx.doi.org/10.1038/nature13148] [PMID: 24695223]
[7]
Su Z, Yang Z, Xu Y, Chen Y, Yu Q. Apoptosis, autophagy, necroptosis, and cancer metastasis. Mol Cancer 2015; 14(1): 48.
[http://dx.doi.org/10.1186/s12943-015-0321-5] [PMID: 25743109]
[8]
Bhattacharya D, Mukhopadhyay M, Bhattacharyya M, Karmakar P. Is autophagy associated with diabetes mellitus and its complications? A review. EXCLI J 2018; 17: 709-20.
[http://dx.doi.org/10.17179/excli2018-1353] [PMID: 30190661]
[9]
Yang Z, Goronzy JJ, Weyand CM. Autophagy in autoimmune disease. J Mol Med 2015; 93(7): 707-17.
[http://dx.doi.org/10.1007/s00109-015-1297-8] [PMID: 26054920]
[10]
Mahil SK, Twelves S, Farkas K, et al. AP1S3 mutations cause skin autoinflammation by disrupting keratinocyte autophagy and up-regulating IL-36 production. J Invest Dermatol 2016; 136(11): 2251-9.
[http://dx.doi.org/10.1016/j.jid.2016.06.618] [PMID: 27388993]
[11]
Khandia R, Dadar M, Munjal A, et al. A comprehensive review of autophagy and its various roles in infectious, non-infectious, and lifestyle diseases: Current knowledge and prospects for disease prevention, novel drug design, and therapy. Cells 2019; 8(7): 674.
[http://dx.doi.org/10.3390/cells8070674] [PMID: 31277291]
[12]
Ylä-Anttila P. Autophagy receptors as viral targets. Cell Mol Biol Lett 2021; 26(1): 29.
[http://dx.doi.org/10.1186/s11658-021-00272-x] [PMID: 34167456]
[13]
Waisner H, Kalamvoki M. The ICP0 Protein of Herpes Simplex Virus 1 (HSV-1) downregulates major autophagy adaptor proteins sequestosome 1 and optineurin during the early stages of HSV-1 infection. J Virol 2019; 93(21): e01258-19.
[http://dx.doi.org/10.1128/JVI.01258-19] [PMID: 31375597]
[14]
Dong S, Kong N, Qin W, et al. ATG4B hinders porcine epidemic diarrhea virus replication through interacting with TRAF3 and activating type-I IFN signaling. Vet Microbiol 2022; 273: 109544.
[http://dx.doi.org/10.1016/j.vetmic.2022.109544] [PMID: 36049346]
[15]
Chu P, Zhu Y, Xu L, Yao X, Liang Y, Zhang X. ATG4C positively facilitates autophagy activation and restricts GCRV replication in grass carp (Ctenopharyngodon idella). Aquaculture 2022; 549: 737797.
[http://dx.doi.org/10.1016/j.aquaculture.2021.737797]
[16]
Mohamud Y, Qu J, Xue YC, Liu H, Deng H, Luo H. CALCOCO2/NDP52 and SQSTM1/p62 differentially regulate coxsackievirus B3 propagation. Cell Death Differ 2019; 26(6): 1062-76.
[http://dx.doi.org/10.1038/s41418-018-0185-5] [PMID: 30154446]
[17]
Petkova D, Verlhac P, Rozières A, et al. Distinct Contributions of autophagy receptors in measles virus replication. Viruses 2017; 9(5): 123.
[http://dx.doi.org/10.3390/v9050123] [PMID: 28531150]
[18]
Sun D, Wen X, Wang M, et al. Apoptosis and autophagy in picornavirus infection. Front Microbiol 2019; 10: 2032.
[http://dx.doi.org/10.3389/fmicb.2019.02032] [PMID: 31551969]
[19]
Maiuri MC, Zalckvar E, Kimchi A, Kroemer G. Self-eating and self-killing: Crosstalk between autophagy and apoptosis. Nat Rev Mol Cell Biol 2007; 8(9): 741-52.
[http://dx.doi.org/10.1038/nrm2239] [PMID: 17717517]
[20]
Eisenberg-Lerner A, Bialik S, Simon H-U, Kimchi A. Life and death partners: Apoptosis, autophagy and the cross-talk between them. Cell Death Differ 2009; 16(7): 966-75.
[http://dx.doi.org/10.1038/cdd.2009.33] [PMID: 19325568]
[21]
Behura SK, Severson DW. Codon usage bias: Causative factors, quantification methods and genome-wide patterns: With emphasis on insect genomes. Biol Rev Camb Philos Soc 2013; 88(1): 49-61.
[http://dx.doi.org/10.1111/j.1469-185X.2012.00242.x] [PMID: 22889422]
[22]
Rahman SU, Abdullah M, Khan AW, et al. A detailed comparative analysis of codon usage bias in Alongshan virus. Virus Res 2022; 308: 198646.
[http://dx.doi.org/10.1016/j.virusres.2021.198646] [PMID: 34822954]
[23]
Marin M. Folding at the rhythm of the rare codon beat. Biotechnol J 2008; 3(8): 1047-57.
[http://dx.doi.org/10.1002/biot.200800089] [PMID: 18624343]
[24]
Mehrbod P, Ande SR, Alizadeh J, et al. The roles of apoptosis, autophagy and unfolded protein response in arbovirus, influenza virus, and HIV infections. Virulence 2019; 10(1): 376-413.
[http://dx.doi.org/10.1080/21505594.2019.1605803] [PMID: 30966844]
[25]
Lin Y, Huang C, Gao H, et al. AMBRA1 promotes dsRNA- and virus-induced apoptosis through interacting with and stabilizing MAVS. J Cell Sci 2022; 135(1): jcs258910.
[http://dx.doi.org/10.1242/jcs.258910] [PMID: 34859815]
[26]
Döring T, Zeyen L, Bartusch C, Prange R. Hepatitis B virus subverts the autophagy elongation complex Atg5-12/16L1 and does not require Atg8/LC3 lipidation for viral maturation. J Virol 2018; 92(7): e01513-7.
[http://dx.doi.org/10.1128/JVI.01513-17] [PMID: 29367244]
[27]
Moloughney JG, Monken CE, Tao H, et al. Vaccinia virus leads to ATG12–ATG3 conjugation and deficiency in autophagosome formation. Autophagy 2011; 7(12): 1434-47.
[http://dx.doi.org/10.4161/auto.7.12.17793] [PMID: 22024753]
[28]
Hait AS, Olagnier D, Sancho-Shimizu V, et al. Defects in LC3B2 and ATG4A underlie HSV2 meningitis and reveal a critical role for autophagy in antiviral defense in humans. Sci Immunol 2020; 5(54): eabc2691.
[http://dx.doi.org/10.1126/sciimmunol.abc2691] [PMID: 33310865]
[29]
Chu P, He L, Huang R, et al. Autophagy Inhibits Grass Carp Reovirus (GCRV) replication and protects Ctenopharyngodon idella Kidney (CIK) cells from excessive inflammatory responses after GCRV infection. Biomolecules 2020; 10(9): 1296.
[http://dx.doi.org/10.3390/biom10091296] [PMID: 32911775]
[30]
Li C, Liu J, Zhang X, et al. Fish Autophagy Protein 5 exerts negative regulation on antiviral immune response against iridovirus and nodavirus. Front Immunol 2019; 10: 517.
[http://dx.doi.org/10.3389/fimmu.2019.00517] [PMID: 30941145]
[31]
Yang M, Zhang Y, Xie X, et al. Barley stripe mosaic virus γb Protein subverts autophagy to promote viral infection by disrupting the ATG7-ATG8 interaction. Plant Cell 2018; 30(7): 1582-95.
[http://dx.doi.org/10.1105/tpc.18.00122] [PMID: 29848767]
[32]
Sharma M, Bhattacharyya S, Nain M, et al. Japanese encephalitis virus replication is negatively regulated by autophagy and occurs on LC3-I- and EDEM1-containing membranes. Autophagy 2014; 10(9): 1637-51.
[http://dx.doi.org/10.4161/auto.29455] [PMID: 25046112]
[33]
Mailler E, Waheed AA, Park SY, Gershlick DC, Freed EO, Bonifacino JS. The autophagy protein ATG9A promotes HIV-1 infectivity. Retrovirology 2019; 16(1): 18.
[http://dx.doi.org/10.1186/s12977-019-0480-3] [PMID: 31269971]
[34]
Long D, Ma P, Wang C, Zeng Y, Xue Y, Yang X. ATG13 restricts viral replication by induction of type I interferon. J Cell Mol Med 2019; 23(9): 6508-11.
[http://dx.doi.org/10.1111/jcmm.14483]
[35]
Ma P, Li L, Jin L, et al. Antiviral responses of ATG13 to the infection of peste des petits ruminants virus through activation of interferon response. Gene 2020; 754: 144858.
[http://dx.doi.org/10.1016/j.gene.2020.144858] [PMID: 32531455]
[36]
Jefferson M, Bone B, Buck JL, Powell PP. The autophagy protein ATG16L1 is required for sindbis virus-induced eIF2α phosphorylation and stress granule formation. Viruses 2019; 12(1): 39.
[http://dx.doi.org/10.3390/v12010039] [PMID: 31905741]
[37]
Corona Velazquez A, Corona AK, Klein KA, Jackson WT. Poliovirus induces autophagic signaling independent of the ULK1 complex. Autophagy 2018; 14(7): 1201-13.
[http://dx.doi.org/10.1080/15548627.2018.1458805] [PMID: 29929428]
[38]
Gallo A, Lampe M, Günther T, Brune W. The viral Bcl-2 homologs of kaposi’s sarcoma-associated herpesvirus and rhesus rhadinovirus share an essential role for viral replication. J Virol 2017; 91(6): e01875-16.
[http://dx.doi.org/10.1128/JVI.01875-16] [PMID: 28053098]
[39]
Haldar A, Yadav KK, Singh S, Yadav PK, Singh AK. In silico analysis highlighting the prevalence of BCL2L1 gene and its correlation to miRNA in human coronavirus (HCoV) genetic makeup. Infect Genet Evol 2022; 99: 105260.
[http://dx.doi.org/10.1016/j.meegid.2022.105260] [PMID: 35240314]
[40]
Lee AJ, Liao HJ, Hong JR. Overexpression of Bcl2 and Bcl2L1 can suppress betanodavirus-induced Type III cell death and autophagy induction in GF-1 cells. Symmetry 2022; 14(2): 360.
[http://dx.doi.org/10.3390/sym14020360]
[41]
Lee JH, Oh SJ, Yun J, Shin OS. Nonstructural Protein NS1 of influenza virus disrupts mitochondrial dynamics and enhances mitophagy via ULK1 and BNIP3. Viruses 2021; 13(9): 1845.
[http://dx.doi.org/10.3390/v13091845] [PMID: 34578425]
[42]
O’Sullivan TE, Johnson LR, Kang HH, Sun JC. BNIP3- and BNIP3L-mediated mitophagy promotes the generation of natural killer cell memory. Immunity 2015; 43(2): 331-42.
[http://dx.doi.org/10.1016/j.immuni.2015.07.012] [PMID: 26253785]
[43]
Maul GG, Jensen DE, Ishov AM, Herlyn M, Rauscher FJ III. Nuclear redistribution of BRCA1 during viral infection. Cell Growth Differ 1998; 9(9): 743-55.
[PMID: 9751118]
[44]
Chappell WH, Gautam D, Ok ST, Johnson BA, Anacker DC, Moody CA. Homologous recombination repair factors Rad51 and BRCA1 are necessary for productive replication of human papillomavirus 31. J Virol 2016; 90(5): 2639-52.
[http://dx.doi.org/10.1128/JVI.02495-15] [PMID: 26699641]
[45]
Hou P, Yang K, Jia P, et al. A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection. Cell Res 2021; 31(1): 62-79.
[http://dx.doi.org/10.1038/s41422-020-0362-1] [PMID: 32612200]
[46]
Hou P, Lin Y, Li Z, et al. Autophagy receptor CCDC50 tunes the STING-mediated interferon response in viral infections and autoimmune diseases. Cell Mol Immunol 2021; 18(10): 2358-71.
[http://dx.doi.org/10.1038/s41423-021-00758-w] [PMID: 34453126]
[47]
Killian M. Dual role of autophagy in HIV-1 replication and pathogenesis. AIDS Res Ther 2012; 9(1): 16.
[http://dx.doi.org/10.1186/1742-6405-9-16] [PMID: 22606989]
[48]
Sawaged S, Mota T, Piplani H, et al. TBK1 and GABARAP family members suppress Coxsackievirus B infection by limiting viral production and promoting autophagic degradation of viral extracellular vesicles. PLoS Pathog 2022; 18(8): e1010350.
[http://dx.doi.org/10.1371/journal.ppat.1010350] [PMID: 36044516]
[49]
Soh TK, Davies CTR, Muenzner J, et al. Temporal proteomic analysis of herpes simplex virus 1 infection reveals cell-surface remodeling via pUL56-mediated GOPC degradation. Cell Rep 2020; 33(1): 108235.
[http://dx.doi.org/10.1016/j.celrep.2020.108235] [PMID: 33027661]
[50]
Chen H, Qian Y, Chen X, et al. HDAC6 restricts influenza a virus by deacetylation of the RNA Polymerase PA subunit. J Virol 2019; 93(4): e01896-18.
[http://dx.doi.org/10.1128/JVI.01896-18] [PMID: 30518648]
[51]
Nath P, Chauhan NR, Jena KK, et al. Inhibition of IRGM establishes a robust antiviral immune state to restrict pathogenic viruses. EMBO Rep 2021; 22(11): e52948.
[http://dx.doi.org/10.15252/embr.202152948] [PMID: 34467632]
[52]
Morris S, Swanson MS, Lieberman A, et al. Autophagy-mediated dendritic cell activation is essential for innate cytokine production and APC function with respiratory syncytial virus responses. J Immunol 2011; 187(8): 3953-61.
[http://dx.doi.org/10.4049/jimmunol.1100524] [PMID: 21911604]
[53]
Hafrén A, Macia JL, Love AJ, Milner JJ, Drucker M, Hofius D. Selective autophagy limits cauliflower mosaic virus infection by NBR1-mediated targeting of viral capsid protein and particles. Proc Natl Acad Sci USA 2017; 114(10): E2026-35.
[http://dx.doi.org/10.1073/pnas.1610687114] [PMID: 28223514]
[54]
Ames J, Yadavalli T, Suryawanshi R, et al. OPTN is a host intrinsic restriction factor against neuroinvasive HSV-1 infection. Nat Commun 2021; 12(1): 5401.
[http://dx.doi.org/10.1038/s41467-021-25642-z] [PMID: 34518549]
[55]
Wen W, Li X, Yin M, et al. Selective autophagy receptor SQSTM1/p62 inhibits Seneca Valley virus replication by targeting viral VP1 and VP3. Autophagy 2021; 17(11): 3763-75.
[http://dx.doi.org/10.1080/15548627.2021.1897223] [PMID: 33719859]
[56]
Zhang Y, Hu B, Li Y, et al. Binding of Avibirnavirus VP3 to the PIK3C3-PDPK1 complex inhibits autophagy by activating the AKT-MTOR pathway. Autophagy 2020; 16(9): 1697-710.
[http://dx.doi.org/10.1080/15548627.2019.1704118] [PMID: 31885313]
[57]
Eekels JJM, Sagnier S, Geerts D, Jeeninga RE, Biard-Piechaczyk M, Berkhout B. Inhibition of HIV-1 replication with stable RNAi-mediated knockdown of autophagy factors. Virol J 2012; 9(1): 69.
[http://dx.doi.org/10.1186/1743-422X-9-69] [PMID: 22424437]
[58]
Caillet M, Janvier K, Pelchen-Matthews A, et al. Rab7A is required for efficient production of infectious HIV-1. PLoS Pathog 2011; 7(11): e1002347.
[http://dx.doi.org/10.1371/journal.ppat.1002347] [PMID: 22072966]
[59]
Mauthe M, Reggiori F. ATG proteins: Are we always looking at autophagy? Autophagy 2016; 12(12): 2502-3.
[http://dx.doi.org/10.1080/15548627.2016.1236878] [PMID: 27662039]
[60]
Wan Y, Cao W, Han T, et al. Inducible Rubicon facilitates viral replication by antagonizing interferon production. Cell Mol Immunol 2017; 14(7): 607-20.
[http://dx.doi.org/10.1038/cmi.2017.1] [PMID: 28392573]
[61]
Wang L, Tian Y, Ou JJ. HCV induces the expression of Rubicon and UVRAG to temporally regulate the maturation of autophagosomes and viral replication. PLoS Pathog 2015; 11(3): e1004764.
[http://dx.doi.org/10.1371/journal.ppat.1004764] [PMID: 25807108]
[62]
Campbell GR, Spector SA. Inhibition of human immunodeficiency virus type-1 through autophagy. Curr Opin Microbiol 2013; 16(3): 349-54.
[http://dx.doi.org/10.1016/j.mib.2013.05.006] [PMID: 23747172]
[63]
Qian G, Hu X, Li G, et al. Smurf1 restricts the antiviral function mediated by USP25 through promoting its ubiquitination and degradation. Biochem Biophys Res Commun 2018; 498(3): 537-43.
[http://dx.doi.org/10.1016/j.bbrc.2018.03.015] [PMID: 29518389]
[64]
Choi YB, Shembade N, Parvatiyar K, Balachandran S, Harhaj EW. TAX1BP1 restrains virus-induced apoptosis by facilitating itch-mediated degradation of the mitochondrial adaptor MAVS. Mol Cell Biol 2017; 37(1): e00422-16.
[http://dx.doi.org/10.1128/MCB.00422-16] [PMID: 27736772]
[65]
Mohamud Y, Xue YC, Liu H, et al. The papain-like protease of coronaviruses cleaves ULK1 to disrupt host autophagy. Biochem Biophys Res Commun 2021; 540: 75-82.
[http://dx.doi.org/10.1016/j.bbrc.2020.12.091] [PMID: 33450483]
[66]
König P, Svrlanska A, Read C, Feichtinger S, Stamminger T. The Autophagy-Initiating Protein Kinase ULK1 phosphorylates human cytomegalovirus tegument protein pp28 and regulates efficient virus release. J Virol 2021; 95(6): e02346-20.
[http://dx.doi.org/10.1128/JVI.02346-20] [PMID: 33328309]
[67]
Pirooz SD, He S, Zhang T, et al. UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs. Proc Natl Acad Sci USA 2014; 111(7): 2716-21.
[http://dx.doi.org/10.1073/pnas.1320629111] [PMID: 24550300]
[68]
Puigbò P, Bravo IG, Garcia-Vallve S. CAIcal: A combined set of tools to assess codon usage adaptation. Biol Direct 2008; 3(1): 38.
[http://dx.doi.org/10.1186/1745-6150-3-38] [PMID: 18796141]
[69]
Kunec D, Osterrieder N. Codon pair bias is a direct consequence of dinucleotide bias. Cell Rep 2016; 14(1): 55-67.
[http://dx.doi.org/10.1016/j.celrep.2015.12.011] [PMID: 26725119]
[70]
Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 1986; 24(1-2): 28-38.
[http://dx.doi.org/10.1007/BF02099948] [PMID: 3104616]
[71]
Khandia R, Singhal S, Kumar U, et al. Analysis of nipah virus codon usage and adaptation to hosts. Front Microbiol 2019; 10(MAY): 886.
[http://dx.doi.org/10.3389/fmicb.2019.00886] [PMID: 31156564]
[72]
Sharp PM, Li WH. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987; 15(3): 1281-95.
[http://dx.doi.org/10.1093/nar/15.3.1281] [PMID: 3547335]
[73]
Wright F. The ‘effective number of codons’ used in a gene. Gene 1990; 87(1): 23-9.
[http://dx.doi.org/10.1016/0378-1119(90)90491-9] [PMID: 2110097]
[74]
Sueoka N. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 1999; 238(1): 53-8.
[http://dx.doi.org/10.1016/S0378-1119(99)00320-0] [PMID: 10570983]
[75]
Metsalu T, Vilo J. ClustVis: A web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res 2015; 43(W1): W566-70.
[http://dx.doi.org/10.1093/nar/gkv468] [PMID: 25969447]
[76]
Irwin B, Heck JD, Hatfield GW. Codon pair utilization biases influence translational elongation step times. J Biol Chem 1995; 270(39): 22801-6.
[http://dx.doi.org/10.1074/jbc.270.39.22801] [PMID: 7559409]
[77]
Chevance FFV, Le Guyon S, Hughes KT. The effects of codon context on in vivo translation speed. PLoS Genet 2014; 10(6): e1004392.
[http://dx.doi.org/10.1371/journal.pgen.1004392] [PMID: 24901308]
[78]
Lanza AM, Curran KA, Rey LG, Alper HS. A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae. BMC Syst Biol 2014; 8(1): 33.
[http://dx.doi.org/10.1186/1752-0509-8-33] [PMID: 24636000]
[79]
Moura G, Pinheiro M, Silva R, Miranda I, Afreixo V, Dias G. Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol 2005; 6(3): 1-14.
[http://dx.doi.org/10.1186/gb-2005-6-3-r28]
[80]
McNulty DE, Claffee BA, Huddleston MJ, Kane JF, Cavnar KM, Kane JF. Mistranslational errors associated with the rare arginine codon CGG in Escherichia coli. Protein Expr Purif 2003; 27(2): 365-74.
[http://dx.doi.org/10.1016/S1046-5928(02)00610-1] [PMID: 12597898]
[81]
Yu X, Liu J, Li H, Liu B, Zhao B, Ning Z. Comprehensive analysis of synonymous codon usage bias for complete genomes and E2 gene of atypical porcine pestivirus. Biochem Genet 2021; 59(3): 799-812.
[http://dx.doi.org/10.1007/s10528-021-10037-y] [PMID: 33538926]
[82]
Jernigan RW, Baran RH. Pervasive properties of the genomic signature. BMC Genomics 2002; 3(1): 23.
[http://dx.doi.org/10.1186/1471-2164-3-23] [PMID: 12171605]
[83]
Baha S, Behloul N, Liu Z, Wei W, Shi R, Meng J. Comprehensive analysis of genetic and evolutionary features of the hepatitis E virus. BMC Genomics 2019; 20(1): 790.
[http://dx.doi.org/10.1186/s12864-019-6100-8] [PMID: 31664890]
[84]
Luehrsen K, Walbot V. The impact of AUG start codon context on maize gene expression in vivo. Plant Cell Rep 1994; 13(8): 454-8.
[http://dx.doi.org/10.1007/BF00231966] [PMID: 24194025]
[85]
Sun J, Chen M, Xu J, Luo J. Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes. J Mol Evol 2005; 61(4): 437-44.
[http://dx.doi.org/10.1007/s00239-004-0277-3] [PMID: 16170455]
[86]
Freire CC de M, Palmisano G, Braconi CT, Cugola FR, Russo FB. Beltrão-Braga PCB. NS1 codon usage adaptation to humans in pandemic Zika virus. Mem Inst Oswaldo Cruz 2018; 113(5): e170385.
[87]
Duan J, Wainwright MS, Comeron JM, et al. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 2003; 12(3): 205-16.
[http://dx.doi.org/10.1093/hmg/ddg055] [PMID: 12554675]
[88]
Friedman RC, Farh KKH, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19(1): 92-105.
[http://dx.doi.org/10.1101/gr.082701.108] [PMID: 18955434]
[89]
Bartoszewski RA, Jablonsky M, Bartoszewska S, et al. A synonymous single nucleotide polymorphism in DeltaF508 CFTR alters the secondary structure of the mRNA and the expression of the mutant protein. J Biol Chem 2010; 285(37): 28741-8.
[http://dx.doi.org/10.1074/jbc.M110.154575] [PMID: 20628052]
[90]
Sauna ZE, Kimchi-Sarfaty C. Synonymous Mutations as a Cause of Human Genetic Disease eLS. John Wiley & Sons: Hoboken, New Jersey, U.S. Ltd (Ed.) 2013.
[http://dx.doi.org/10.1002/9780470015902.a0025173]
[91]
Du MZ, Zhang C, Wang H, Liu S, Wei W, Guo FB. The GC content as a main factor shaping the amino acid usage during bacterial evolution process. Front Microbiol 2018; 9: 2948.
[http://dx.doi.org/10.3389/fmicb.2018.02948] [PMID: 30581420]
[92]
Li J, Zhou J, Wu Y, Yang S, Tian D. GC-content of synonymous codons profoundly influences amino acid usage. G3 Genes, Genomes. G3 2015; 5(10): 2027-36.
[http://dx.doi.org/10.1534/g3.115.019877] [PMID: 26248983]
[93]
Khandia R, Ali Khan A, Alexiou A, Povetkin SN, Verevkina MN. Codon usage analysis of pro-apoptotic bim gene isoforms. J Alzheimers Dis 2022; 86(4): 1711-25.
[http://dx.doi.org/10.3233/JAD-215691] [PMID: 35253767]
[94]
Wojciechowski M, Czapinska H, Bochtler M. CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Proc Natl Acad Sci USA 2013; 110(1): 105-10.
[http://dx.doi.org/10.1073/pnas.1207986110] [PMID: 23248272]
[95]
Khandia R, Alqahtani T, Alqahtani AM. Genes common in primary immunodeficiencies and cancer display overrepresentation of codon ctg and dominant role of selection pressure in shaping codon usage. Biomedicines 2021; 9(8): 1001.
[http://dx.doi.org/10.3390/biomedicines9081001] [PMID: 34440205]
[96]
Kumar U, Khandia R, Singhal S, et al. Insight into codon utilization pattern of tumor suppressor gene EPB41L3 from different mammalian species indicates dominant role of selection force. Cancers 2021; 13(11): 2739.
[http://dx.doi.org/10.3390/cancers13112739] [PMID: 34205890]
[97]
Alqahtani T, Khandia R, Puranik N, Alqahtani AM, Almikhlafi MA, Algahtany MA. Leucine encoding codon TTG shows an inverse relationship with GC content in genes involved in neurodegeneration with iron accumulation. J Integr Neurosci 2021; 20(4): 905-18.
[http://dx.doi.org/10.31083/j.jin2004092] [PMID: 34997714]
[98]
Chakraborty S, Barbhuiya PA, Paul S, et al. Codon usage trend in genes associated with obesity. Biotechnol Lett 2020; 42(10): 1865-75.
[http://dx.doi.org/10.1007/s10529-020-02931-z] [PMID: 32488444]
[99]
Uddin A. Compositional features and codon usage pattern of genes associated with anxiety in human. Mol Neurobiol 2020; 57(12): 4911-20.
[http://dx.doi.org/10.1007/s12035-020-02068-0] [PMID: 32813237]
[100]
Alqahtani T, Khandia R, Puranik N, et al. Codon usage is influenced by compositional constraints in genes associated with dementia. Front Genet 2022; 13: 884348.
[http://dx.doi.org/10.3389/fgene.2022.884348] [PMID: 36017501]
[101]
Mazumder TH, Uddin A, Chakraborty S. Insights into the nucleotide composition and codon usage pattern of human tumor suppressor genes. Mol Carcinog 2020; 59(1): 15-23.
[http://dx.doi.org/10.1002/mc.23124] [PMID: 31583785]
[102]
Beutler E, Gelbart T, Han JH, Koziol JA, Beutler B. Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc Natl Acad Sci USA 1989; 86(1): 192-6.
[http://dx.doi.org/10.1073/pnas.86.1.192] [PMID: 2463621]
[103]
Jenkins GM, Holmes EC. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res 2003; 92(1): 1-7.
[http://dx.doi.org/10.1016/S0168-1702(02)00309-X] [PMID: 12606071]
[104]
Wei L, He J, Jia X, et al. Analysis of codon usage bias of mitochondrial genome in Bombyx moriand its relation to evolution. BMC Evol Biol 2014; 14(1): 262.
[http://dx.doi.org/10.1186/s12862-014-0262-4] [PMID: 25515024]
[105]
Hodgman MW, Miller JB, Meurs TE, Kauwe JSK. CUBAP: An interactive web portal for analyzing codon usage biases across populations. Nucleic Acids Res 2020; 48(19): 11030-9.
[http://dx.doi.org/10.1093/nar/gkaa863] [PMID: 33045750]
[106]
Miller JB, McKinnon LM, Whiting MF, Kauwe JSK, Ridge PG. Codon Pairs are phylogenetically conserved: A comprehensive analysis of codon pairing conservation across the tree of life. PLoS One 2020; 15(5): e0232260.
[http://dx.doi.org/10.1371/journal.pone.0232260] [PMID: 32401752]
[107]
Brest P, Lapaquette P, Souidi M, et al. A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn’s disease. Nat Genet 2011; 43(3): 242-5.
[http://dx.doi.org/10.1038/ng.762] [PMID: 21278745]
[108]
Groenke N, Trimpert J, Merz S, et al. Mechanism of virus attenuation by codon pair deoptimization. Cell Rep 2020; 31(4): 107586.
[http://dx.doi.org/10.1016/j.celrep.2020.107586] [PMID: 32348767]
[109]
Friberg M, von Rohr P, Gonnet G. Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression inSaccharomyces cerevisiae. Yeast 2004; 21(13): 1083-93.
[http://dx.doi.org/10.1002/yea.1150] [PMID: 15484285]
[110]
Sahoo S, Das SS, Rakshit R. Codon usage pattern and predicted gene expression in Arabidopsis thaliana. Gene 2019; 721: 100012.
[http://dx.doi.org/10.1016/j.gene.2019.100012] [PMID: 32550546]
[111]
Horn D. Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids. BMC Genomics 2008; 9(1): 2.
[http://dx.doi.org/10.1186/1471-2164-9-2] [PMID: 18173843]
[112]
Liu H, He R, Zhang H, Huang Y, Tian M, Zhang J. Analysis of synonymous codon usage in Zea mays. Mol Biol Rep 2010; 37(2): 677-84.
[http://dx.doi.org/10.1007/s11033-009-9521-7] [PMID: 19330534]
[113]
Newman ZR, Young JM, Ingolia NT, Barton GM. Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9. Proc Natl Acad Sci USA 2016; 113(10): E1362-71.
[http://dx.doi.org/10.1073/pnas.1518976113] [PMID: 26903634]
[114]
Mazumder TH, Chakraborty S, Paul P. A cross talk between codon usage bias in human oncogenes. Bioinformation 2014; 10(5): 256-62.
[http://dx.doi.org/10.6026/97320630010256] [PMID: 24966531]
[115]
Pershing NLK, Lampson BL, Belsky JA, Kaltenbrun E, MacAlpine DM, Counter CM. Rare codons capacitate Kras-driven de novo tumorigenesis. J Clin Invest 2015; 125(1): 222-33.
[http://dx.doi.org/10.1172/JCI77627] [PMID: 25437878]
[116]
Miller JB, Brase LR, Ridge PG. ExtRamp: A novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness. Nucleic Acids Res 2019; 47(3): 1123-31.
[http://dx.doi.org/10.1093/nar/gky1193] [PMID: 30649455]
[117]
Allen SR, Stewart RK, Rogers M, et al. Distinct responses to rare codons in select Drosophila tissues. eLife 2022; 11: e76893.
[http://dx.doi.org/10.7554/eLife.76893] [PMID: 35522036]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy