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Current Genomics


ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

Research Article

New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome

Author(s): Miguel Angel Fuertes* and Carlos Alonso

Volume 23, Issue 6, 2022

Published on: 07 February, 2023

Page: [424 - 440] Pages: 17

DOI: 10.2174/1389202924666230202152351

Price: $65


Background: The coronavirus disease has led to an exhaustive exploration of the SARSCoV- 2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention.

Objective: The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome.

Methods: A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other.

Results: We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs; in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsidencoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions.

Conclusion: Some of the trinucleotide family distributions in different CoV genera are not random; they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.

Keywords: COVID-19, SARS-CoV-2, evolution, CoV genera, RNA motifs, trinucleotide family distributions.

Graphical Abstract
de Groot, R.J.; Baker, S.C.; Baric, R.; Enjuanes, L.; Gorbalenya, A.E.; Holmes, K.V. Virus Taxonomy. In: 9th report of the International Committee on Taxonomy of Viruses; Elsevier CA: San Diego,, 2011, pp. 806-828.
Woo, P.C.Y.; Lau, S.K.P.; Lam, C.S.F.; Lai, K.K.Y.; Huang, Y.; Lee, P.; Luk, G.S.M.; Dyrting, K.C.; Chan, K.H.; Yuen, K.Y. Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J. Virol., 2009, 83(2), 908-917.
[] [PMID: 18971277]
Woo, P.C. Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J. Virol., 2012, 86, 3995-4008.
Dong, B.Q.; Liu, W.; Fan, X.H.; Vijaykrishna, D.; Tang, X.C.; Gao, F.; Li, L.F.; Li, G.J.; Zhang, J.X.; Yang, L.Q.; Poon, L.L.M.; Zhang, S.Y.; Peiris, J.S.M.; Smith, G.J.D.; Chen, H.; Guan, Y. Detection of a novel and highly divergent coronavirus from asian leopard cats and Chinese ferret badgers in Southern China. J. Virol., 2007, 81(13), 6920-6926.
[] [PMID: 17459938]
Mihindukulasuriya, K.A.; Wu, G.; St Leger, J.; Nordhausen, R.W.; Wang, D. Identification of a novel coronavirus from a beluga whale by using a panviral microarray. J. Virol., 2008, 82(10), 5084-5088.
[] [PMID: 18353961]
Huang, C.; Wang, Y.; Li, X.; Ren, L.; Zhao, J. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet, 2020, 395(10223), 497-506.
Bastola, A.; Sah, R.; Rodriguez-Morales, A.J.; Lal, B.K.; Jha, R.; Ojha, H.C.; Shrestha, B.; Chu, D.K.W.; Poon, L.L.M.; Costello, A.; Morita, K.; Pandey, B.D. The first 2019 novel coronavirus case in Nepal. Lancet Infect. Dis., 2020, 20(3), 279-280.
[] [PMID: 32057299]
Rodríguez-Morales, A.J.; MacGregor, K.; Kanagarajah, S.; Patel, D.; Schlagenhauf, P. Going global – Travel and the 2019 novel coronavirus. Travel Med. Infect. Dis., 2020, 33, 101578.
[] [PMID: 32044389]
Sah, R.; Rodriguez-Morales, A.J.; Jha, R.; Chu, D.K.W.; Gu, H.; Peiris, M.; Bastola, A.; Lal, B.K.; Ojha, H.C.; Rabaan, A.A.; Zambrano, L.I.; Costello, A.; Morita, K.; Pandey, B.D.; Poon, L.L.M. Complete genome sequence of a 2019 novel coronavirus (SARS-CoV-2) strain isolated in nepal. Microbiol. Resour. Announc., 2020, 9(11), e00169-e20.
Zhang, T.; Wu, Q.; Zhang, Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr. Biol., 2020, 30(7), 1346-1351.e2.
[] [PMID: 32197085]
Jiang, C.; Gu, X.; Peterson, T. Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biol., 2004, 5(7), R46.
[] [PMID: 15239831]
Xie, X.; Lu, J.; Kulbokas, E.J.; Golub, T.R.; Mootha, V.; Lindblad-Toh, K.; Lander, E.S.; Kellis, M. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature, 2005, 434(7031), 338-345.
Fuertes, M.A.; Rodrigo, J.R.; Alonso, C. Do Intron and Coding Sequences of Some Human–Mouse Orthologs Evolve as a Single Unit? J. Mol. Evol., 2016, 82(6), 247-250.
[] [PMID: 27220874]
Fuertes, M.A.; Rodrigo, J.R.; Alonso, C. A Method for the annotation of functional similarities of coding DNA sequences: the case of a populated cluster of transmembrane proteins. J. Mol. Evol., 2017, 84(1), 29-38.
[] [PMID: 27812751]
Fuertes, M.A.; López-Arguello, S.; Alonso, C. Evolutionary conserved compositional structures hidden in genomes of the foot-and-mouth disease virus and of the human rhinovirus. Sci. Rep., 2019, 9(1), 16553.
[] [PMID: 31719605]
Yang, C-W.; Shi, Z-L. Uncovering potential host proteins and pathways that may interact with eukaryotic short linear motifs in viral proteins of MERS, SARS and SARS2 coronaviruses that infect humans. PLoS One, 2021, 16(2), e0246150.
Diella, F.; Haslam, N.; Chica, C.; Budd, A.; Michael, S.; Brown, N.P.; Trave, G.; Gibson, T.J. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci., 2008, 13, 6580-6603.
[] [PMID: 18508681]
Benson, D.A.; Cavanaugh, M.; Clark, K.; Karsch-Mizrachi, I.; Ostell, J.; Pruitt, K.D.; Sayers, E.W. GenBank. Nucleic Acids Res., 2018, 46(D1), D41-D47.
[] [PMID: 29140468]
Thiel, V.; Herold, J.; Schelle, B.; Siddell, S.G. Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus. J. Gen. Virol., 2001, 82(6), 1273-1281.
[] [PMID: 11369870]
Bridgen, A.; Duarte, M.; Tobler, K.; Laude, H.; Ackermann, M. Sequence determination of the nucleocapsid protein gene of the porcine epidemic diarrhoea virus confirms that this virus is a coronavirus related to human coronavirus 229E and porcine transmissible gastroenteritis virus. J. Gen. Virol., 1993, 74(9), 1795-1804.
[] [PMID: 8397280]
Chen, L.; Liu, W.; Zhang, Q.; Xu, K.; Ye, G.; Wu, W.; Sun, Z.; Liu, F.; Wu, K.; Zhong, B.; Mei, Y.; Zhang, W.; Chen, Y.; Li, Y.; Shi, M.; Lan, K.; Liu, Y. RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak. Emerg. Microbes Infect., 2020, 9(1), 313-319.
[] [PMID: 32020836]
Rota, P.A.; Oberste, M.S.; Monroe, S.S.; Nix, W.A.; Campagnoli, R.; Icenogle, J.P.; Peñaranda, S.; Bankamp, B.; Maher, K.; Chen, M.H.; Tong, S.; Tamin, A.; Lowe, L.; Frace, M.; DeRisi, J.L.; Chen, Q.; Wang, D.; Erdman, D.D.; Peret, T.C.; Burns, C.; Ksiazek, T.G.; Rollin, P.E.; Sanchez, A.; Liffick, S.; Holloway, B.; Limor, J.; McCaustland, K.; Olsen-Rasmussen, M.; Fouchier, R.; Günther, S.; Osterhaus, A.D.; Drosten, C.; Pallansch, M.A.; Anderson, L.J.; Bellini, W.J. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science, 2003, 300(5624), 1394-1399.
Guan, Y.; Zheng, B.J.; He, Y.Q.; Liu, X.L.; Zhuang, Z.X.; Cheung, C.L.; Luo, S.W.; Li, P.H.; Zhang, L.J.; Guan, Y.J.; Butt, K.M.; Wong, K.L.; Chan, K.W.; Lim, W.; Shortridge, K.F.; Yuen, K.Y.; Peiris, J.S.; Poon, L.L. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science, 2003, 302(5643), 276-278.
Coley, S.E.; Lavi, E.; Sawicki, S.G.; Fu, L.; Schelle, B.; Karl, N.; Siddell, S.G.; Thiel, V. Recombinant mouse hepatitis virus strain A59 from cloned, full-length cDNA replicates to high titers in vitro and is fully pathogenic in vivo. J. Virol., 2005, 79(5), 3097-3106.
[] [PMID: 15709029]
Tang, X.C.; Zhang, J.X.; Zhang, S.Y.; Wang, P.; Fan, X.H.; Li, L.F.; Li, G.; Dong, B.Q.; Liu, W.; Cheung, C.L.; Xu, K.M.; Song, W.J.; Vijaykrishna, D.; Poon, L.L.M.; Peiris, J.S.M.; Smith, G.J.D.; Chen, H.; Guan, Y. Prevalence and genetic diversity of coronaviruses in bats from China. J. Virol., 2006, 80(15), 7481-7490.
[] [PMID: 16840328]
Callison, S.A.; Hilt, D.A.; Boynton, T.O.; Sample, B.F.; Robison, R.; Swayne, D.E.; Jackwood, M.W. Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens. J. Virol. Methods, 2006, 138(1-2), 60-65.
[] [PMID: 16934878]
Du, H.; Hu, H.; Meng, Y.; Zheng, W.; Ling, F.; Wang, J.; Zhang, X.; Nie, Q.; Wang, X. The correlation coefficient of GC content of the genome-wide genes is positively correlated with animal evolutionary relationships. FEBS Lett., 2010, 584(18), 3990-3994.
Pearson, W.R. An introduction to sequence similarity ("homology") searching. Curr. Protoc. Bioinform. 2013, 3, 3.1.1-3.1.8.
Needleman, S.B.; Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 1970, 48(3), 443-453.
[] [PMID: 5420325]
Khailany, R.A.; Safdar, M.; Ozaslan, M. Genomic characterization of a novel SARS-CoV-2. Gene Rep., 2020, 19, 100682.
[] [PMID: 32300673]
Anand, P.; Puranik, A.; Aravamudan, M.; Venkatakrishnan, A.J.; Soundararajan, V. SARS-CoV-2 strategically mimics proteolytic activation of human ENaC. eLife, 2020, 9, e58603.
Millet, J.K.; Whittaker, G.R. Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein. Proc. Natl. Acad. Sci. USA, 2014, 111(42), 15214-15219.
[] [PMID: 25288733]
Adhikari, N.; Baysia, S.K.; Saha, A.; Jha, T. Structurl Insight Into the Viral 3C-like Protease inhibitors: Comparative SAR/QSAR Approaches.In: Viral Proteases and Their Inhibitors; Gupta, S.P., Ed.; Academic Press, Elsevier: India, 2017, pp. 317-409.
Kao, R.Y.; To, A.P.; Ng, L.W.; Tsui, W.H.; Lee, T.S.; Tsoi, H.W.; Yuen, K.Y. Characterization of SARS-CoV main protease and identification of biologically active small molecule inhibitors using a continuous fluorescence-based assay. FEBS Lett., 2004, 576(3), 325-330.
Chen, C.N.; Lin, C.P.C.; Huang, K.K.; Chen, W.C.; Hsieh, H.P.; Liang, P.H.; Hsu, J.T.A. Inhibition of SARS-CoV 3C-like protease activity by theaflavin-3,3′-digallate (TF3). Evid. Based Complement. Alternat. Med., 2005, 2(2), 209-215.
[] [PMID: 15937562]
Chou, C.Y.; Chang, H.C.; Hsu, W.C.; Lin, T.Z.; Lin, C.H.; Chang, G.G. Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease. Biochemistry, 2004, 43(47), 14958-14970.
Liu, Y.C.; Huang, V.; Chao, T.C.; Hsiao, C.D.; Lin, A.; Chang, M.F.; Chow, L.P. Screening of drugs by FRET analysis identifies inhibitors of SARS-CoV 3CL protease. Biochem. Biophys. Res. Commun., 2005, 333(1), 194-199.
Chen, Y.W.; Yiu, C.B.; Wong, K.Y. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease Characterization of SARS-CoV main protease and identification of biologically active small molecule (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000 Res., 2020, 9, 129.
Guillén, J.; Kinnunen, P.K.J.; Villalaín, J. Membrane insertion of the three main membranotropic sequences from SARS-CoV S2 glycoprotein. Biochim. Biophys. Acta Biomembr., 2008, 1778(12), 2765-2774.
[] [PMID: 18721794]
Guillén, J.; Pérez-Berná, A.J.; Moreno, M.R.; Villalaín, J. Identification of the membrane-active regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: Implications for the viral fusion mechanism. J. Virol., 2005, 79(3), 1743-1752.
[] [PMID: 15650199]
Guillén, J.; Almeida, R.F.M.; Prieto, M.; Villalaín, J. Structural and dynamic characterization of the interaction of the putative fusion peptide of the S2 SARS-CoV virus protein with lipid membranes. J. Phys. Chem. B, 2008, 112(23), 6997-7007.
[] [PMID: 18489147]
Guillén, J.; Pérez-Berná, A.J.; Moreno, M.R.; Villalaín, J. A second SARS-CoV S2 glycoprotein internal membrane-active peptide. Biophysical characterization and membrane interaction. Biochemistry, 2008, 47(31), 8214-8224.
[] [PMID: 18616295]
Sainz, B., Jr; Rausch, J.M.; Gallaher, W.R.; Garry, R.F.; Wimley, W.C. The aromatic domain of the coronavirus class I viral fusion protein induces membrane permeabilization: putative role during viral entry. Biochemistry, 2005, 44(3), 947-958.
[] [PMID: 15654751]
Sainz, B., Jr; Rausch, J.M.; Gallaher, W.R.; Garry, R.F.; Wimley, W.C. Identification and characterization of the putative fusion peptide of the severe acute respiratory syndrome-associated coronavirus spike protein. J. Virol., 2005, 79(11), 7195-7206.
[] [PMID: 15890958]
Lu, Y.; Neo, T.L.; Liu, D.X.; Tam, J.P. Importance of SARS-CoV spike protein Trp-rich region in viral infectivity. Biochem. Biophys. Res. Commun., 2008, 371(3), 356-360.
[] [PMID: 18424264]
Liao, Y.; Zhang, S.M.; Neo, T.L.; Tam, J.P. Tryptophan-dependent membrane interaction and heteromerization with the internal fusion peptide by the membrane proximal external region of SARS-CoV spike protein. Biochemistry, 2015, 54(9), 1819-1830.
[] [PMID: 25668103]
Mulpuru, V.; Mishra, N. Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2. Sci. Rep., 2021, 11(1), 4516.
[] [PMID: 33633155]
Chou, K.C.; Kézdy, F.J.; Reusser, F. Kinetics of processive nucleic acid polymerases and nucleases. Anal. Biochem., 1994, 221(2), 217-230.
[] [PMID: 7529005]
Gan, Y.R.; Huang, H.; Huang, Y.D.; Rao, C.M.; Zhao, Y.; Liu, J.S.; Wu, L.; Wei, D.Q. Synthesis and activity of an octapeptide inhibitor designed for SARS coronavirus main proteinase. Peptides, 2006, 27(4), 622-625.
[] [PMID: 16242214]
Bonaldi, T.; Talamo, F.; Scaffidi, P.; Ferrera, D.; Porto, A.; Bachi, A.; Rubartelli, A.; Agresti, A.; Bianchi, M.E. Monocytic cells hyperacetylate chromatin protein HMGB1 to redirect it towards secretion. EMBO J., 2003, 22(20), 5551-5560.
Chen, G.; Li, J.; Ochani, M.; Rendon-Mitchell, B.; Qiang, X.; Susarla, S.; Ulloa, L.; Yang, H.; Fan, S.; Goyert, S.M.; Wang, P.; Tracey, K.J.; Sama, A.E.; Wang, H. Bacterial endotoxin stimulates macrophages to release HMGB1 partly through CD14- and TNF-dependent mechanisms. J. Leukoc. Biol., 2004, 76(5), 994-1001.
[] [PMID: 15331624]
Liu, K.; Mori, S.; Takahashi, H.K.; Tomono, Y.; Wake, H.; Kanke, T.; Sato, Y.; Hiraga, N.; Adachi, N.; Yoshino, T.; Nishibori, M. Anti‐high mobility group box 1 monoclonal antibody ameliorates brain infarction induced by transient ischemia in rats. FASEB J., 2007, 21(14), 3904-3916.
[] [PMID: 17628015]
Knapp, S.; Müller, S.; Digilio, G.; Bonaldi, T.; Bianchi, M.E.; Musco, G. The long acidic tail of high mobility group box 1 (HMGB1) protein forms an extended and flexible structure that interacts with specific residues within and between the HMG boxes. Biochemistry, 2004, 43(38), 11992-11997.
Wang, H.; Yang, H.; Tracey, K.J. Extracellular role of HMGB1 in inflammation and sepsis. J. Intern. Med., 2004, 255(3), 320-331.
[] [PMID: 14871456]
Harcourt, B.H.; Jukneliene, D.; Kanjanahaluethai, A.; Bechill, J.; Severson, K.M.; Smith, C.M.; Rota, P.A.; Baker, S.C. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. J. Virol., 2004, 78(24), 13600-13612.
[] [PMID: 15564471]
Yang, H.; Bartlam, M.; Rao, Z. Drug design targeting the main protease, the Achilles’ heel of coronaviruses. Curr. Pharm. Des., 2006, 12(35), 4573-4590.
[] [PMID: 17168763]
Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Zhang, Q.; Shi, X.; Wang, Q.; Zhang, L.; Wang, X. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 2020, 581(7807), 215-220.
[] [PMID: 32225176]
Gui, M.; Song, W.; Zhou, H.; Xu, J.; Chen, S.; Xiang, Y.; Wang, X. Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding. Cell Res., 2017, 27(1), 119-129.
[] [PMID: 28008928]
Pushpakumara, P.D.; Madhusanka, D.; Dhanasekara, S.; Jeewandara, C.; Ogg, G.S.; Malavige, G.N. Identification of novel candidate CD8+ T cell epitopes of the SARS-CoV2 with homology to other seasonal coronaviruses. Viruses, 2021, 13(6), 972.
Ong, E.; Wong, M.U.; Huffman, A.; He, Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. Front. Immunol., 2020, 11, 1581.
[] [PMID: 32719684]
Kushwaha, S.K.; Kesarwani, V.; Choudhury, S.; Gandhi, S.; Sharma, S. SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design. Genomics, 2020, 112(6), 5044-5054.
[] [PMID: 32920121]
Prachar, M.; Justesen, S.; Steen-Jensen, D.B.; Thorgrimsen, S.; Jurgons, E.; Winther, O.; Bagger, F.O. Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools. Sci. Rep., 2020, 10(1), 20465.
Hemmati, S.; Behzadipour, Y.; Haddad, M. Decoding the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for cell-penetrating peptides involved in pathogenesis or applicable as drug delivery vectors. Infect. Genet. Evol., 2020, 85, 104474.
[] [PMID: 32712315]
Kim, D.; Kim, S.; Park, J.; Chang, H.R.; Chang, J.; Ahn, J.; Park, H.; Park, J.; Son, N.; Kang, G.; Kim, J.; Kim, K.; Park, M.S.; Kim, Y.K.; Baek, D. A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. Nat. Commun., 2021, 12(1), 5120.

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