Login Register Cart 0
Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

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

Bioinformatics Study of the DNA and RNA Viruses Infecting Plants and Bacteria that Could Potentially Affect Animals and Humans

Author(s): Carlos Polanco*, Vladimir N. Uversky, Alberto Huberman, Gilberto Vargas-Alarcon, Thomas Buhse, Manlio F. Marquez and Enrique Hernández-Lemus

Volume 18, Issue 2, 2023

Published on: 13 January, 2023

Page: [170 - 191] Pages: 22

DOI: 10.2174/1574893618666221214091824

Price: $65

Abstract

Background: From the existing knowledge of viruses, those infecting plants and bacteria and affecting animals are particularly interesting. This is because such viruses have an ability to vertically transmit to other species, including humans, and therefore could represent a public health issue of significant proportions.

Objective: This study aims to bioinformatically characterize the proteins from the DNA and RNA viruses capable of infecting plants and bacteria, and affecting animals, of which there is some evidence of contact with human beings. It follows up on our previous study “Characterization of Proteins from Putative Human DNA and RNA Viruses”.

Methods: The Polarity Index Method profile (PIM), Intrinsic Disorder Predisposition (IDPD) profiles, and a Markov chains analysis of three DNA-viruses protein sequences and four RNA-viruses protein sequences that infect plants and bacteria and affect animals, extracted from the UniProt database, were calculated using a set of in-house computational programs.

Results: Computational runs carried out in this work reveal relevant regularities at the level of the viral proteins' charge/polarity and IDPD profiles. These results enable the re-creation of the taxonomy known for the DNA- and RNA-virus protein sequences. In addition, an analysis of the entire set of proteins qualified as "reviewed" in the UniProt database was carried out for each protein viral group to discover proteins with similar PIM profiles. A significant number of proteins with such charge/polarity profiles were found.

Conclusion: The bioinformatics results obtained at the level of the amino acid sequences, generated important information that contributes to the understanding of these protein groups.

« Previous Next »
[1]
Polanco C, Uversky VN, Vargas-Alarcón G, et al. Characterization of proteins from putative human DNA and RNA viruses. Curr Proteomics 2022; 19(1): 65-82.
[http://dx.doi.org/10.2174/1570164618666210212123850]
[2]
Mandal B, Jain RK. Can plant virus infect human beings? Indian J Virol 2010; 21(1): 92-3.
[http://dx.doi.org/10.1007/s13337-010-0014-z] [PMID: 23637486]
[3]
Colson P, Richet H, Desnues C, et al. Pepper mild mottle virus, a plant virus associated with specific immune responses, Fever, abdominal pains, and pruritus in humans. PLoS One 2010; 5(4): e10041.
[http://dx.doi.org/10.1371/journal.pone.0010041] [PMID: 20386604]
[4]
Zhang T, Breitbart M, Lee WH, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 2005; 4(1): e3.
[http://dx.doi.org/10.1371/journal.pbio.0040003] [PMID: 16336043]
[5]
Kikkert M, Verschoor A, Kormelink R, Rottier P, Goldbach R. Tomato spotted wilt virus glycoproteins exhibit trafficking and localization signals that are functional in mammalian cells. J Virol 2001; 75(2): 1004-12.
[http://dx.doi.org/10.1128/JVI.75.2.1004-1012.2001] [PMID: 11134314]
[6]
Liu R, Vaishnav RA, Roberts AM, Friedland RP. Humans have antibodies against a plant virus: evidence from tobacco mosaic virus. PLoS One 2013; 8(4): e60621.
[http://dx.doi.org/10.1371/journal.pone.0060621] [PMID: 23573274]
[7]
de Medeiros RB, Figueiredo J, Resende RO, De Avila AC. Expression of a viral polymerase-bound host factor turns human cell lines permissive to a plant- and insect-infecting virus. Proc Natl Acad Sci USA 2005; 102(4): 1175-80.
[http://dx.doi.org/10.1073/pnas.0406668102] [PMID: 15657123]
[8]
Balique F, Lecoq H, Raoult D, Colson P. Can plant viruses cross the kingdom border and be pathogenic to humans? Viruses 2015; 7(4): 2074-98.
[http://dx.doi.org/10.3390/v7042074] [PMID: 25903834]
[9]
Bachofen C. Selected viruses detected on and in our food. Curr Clin Microbiol Rep 2018; 5(2): 143-53.
[http://dx.doi.org/10.1007/s40588-018-0087-9] [PMID: 32226717]
[10]
Nieuwenhuijse DF, Koopmans MPG. Metagenomic sequencing for surveillance of food- and waterborne viral diseases. Front Microbiol 2017; 8: 230.
[http://dx.doi.org/10.3389/fmicb.2017.00230] [PMID: 28261185]
[11]
Barr JJ. A bacteriophages journey through the human body. Immunol Rev 2017; 279(1): 106-22.
[http://dx.doi.org/10.1111/imr.12565] [PMID: 28856733]
[12]
Chalberg TW, Portlock JL, Olivares EC, et al. Integration specificity of phage phiC31 integrase in the human genome. J Mol Biol 2006; 357(1): 28-48.
[http://dx.doi.org/10.1016/j.jmb.2005.11.098] [PMID: 16414067]
[13]
Vassart G, Georges M, Monsieur R, Brocas H, Lequarre AS, Christophe D. A sequence in M13 phage detects hypervariable minisatellites in human and animal DNA. Science 1987; 235(4789): 683-4.
[http://dx.doi.org/10.1126/science.2880398] [PMID: 2880398]
[14]
Goerke C, Wirtz C, Flückiger U, Wolz C. Extensive phage dynamics in Staphylococcus aureus contributes to adaptation to the human host during infection. Mol Microbiol 2006; 61(6): 1673-85.
[15]
Van Belleghem JD, Clement F, Merabishvili M, Lavigne R, Vaneechoutte M. Pro- and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages. Sci Rep 2017; 7(1): 8004.
[http://dx.doi.org/10.1038/s41598-017-08336-9] [PMID: 28808331]
[16]
Dąbrowska K, Abedon ST. Pharmacologically aware phage therapy: pharmacodynamic and pharmacokinetic obstacles to phage antibacterial action in animal and human bodies. Microbiol Mol Biol Rev 2019; 83(4): e00012-9.
[http://dx.doi.org/10.1128/MMBR.00012-19] [PMID: 31666296]
[17]
Santiago-Rodriguez TM, Hollister EB. Human virome and disease: high-throughput sequencing for virus discovery, identification of phage-bacteria dysbiosis and development of therapeutic approaches with emphasis on the human gut. Viruses 2019; 11(7): 656.
[http://dx.doi.org/10.3390/v11070656] [PMID: 31323792]
[18]
Housby JN, Mann NH. Phage therapy. Drug Discov Today 2009; 14(11-12): 536-40.
[http://dx.doi.org/10.1016/j.drudis.2009.03.006] [PMID: 19508915]
[19]
Zhang Z, Yu F, Zou Y, et al. Phage protein receptors have multiple interaction partners and high expressions. Bioinformatics 2020; 36(10): 2975-9.
[http://dx.doi.org/10.1093/bioinformatics/btaa123] [PMID: 32096819]
[20]
Rohwer F, Edwards R. The Phage Proteomic Tree: A genome-based taxonomy for phage. J Bacteriol 2002; 184(16): 4529-35.
[http://dx.doi.org/10.1128/JB.184.16.4529-4535.2002] [PMID: 12142423]
[21]
Jahn MT, Arkhipova K, Markert SM, et al. A phage protein aids bacterial symbionts in eukaryote immune evasion. Cell Host Microbe 2019; 26(4): 542-550.e5.
[http://dx.doi.org/10.1016/j.chom.2019.08.019] [PMID: 31561965]
[22]
Ranawaka B, Hayashi S, Waterhouse PM, de Felippes FF. Homo sapiens: The Superspreader of Plant Viral Diseases. Viruses 2020; 12(12): 1462.
[http://dx.doi.org/10.3390/v12121462] [PMID: 33348905]
[23]
Syller J. Facilitative and antagonistic interactions between plant viruses in mixed infections. Mol Plant Pathol 2012; 13(2): 204-16.
[http://dx.doi.org/10.1111/j.1364-3703.2011.00734.x] [PMID: 21726401]
[24]
Jones RAC. Global plant virus disease pandemics and epidemics. Plants 2021; 10(2): 233.
[http://dx.doi.org/10.3390/plants10020233] [PMID: 33504044]
[25]
Trebicki P. Climate change and plant virus epidemiology. Virus Res 2020; 286: 198059.
[http://dx.doi.org/10.1016/j.virusres.2020.198059] [PMID: 32561376]
[26]
Polanco C. Polarity index in Polarity Index in Proteins-A Bioinformatics Tool. U.A.E: Bentham Science Publishers Sharjah 2016.
[http://dx.doi.org/10.2174/97816810826911160101]
[27]
Seymour L, Lipson L. Marc Schaum’s Outline of Probability. U.S.A.: McGraw-Hill 1965.
[28]
Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK. Sequence complexity of disordered protein. Proteins 2001; 42(1): 38-48.
[http://dx.doi.org/10.1002/1097-0134(20010101)42:1<38::AIDPROT50>3.0.CO;2-3] [PMID: 11093259]
[29]
Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z. Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol 2005; 3(1): 35-60.
[http://dx.doi.org/10.1142/S0219720005000886] [PMID: 15751111]
[30]
Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 2005; 61(S7) (Suppl. 7): 176-82.
[http://dx.doi.org/10.1002/prot.20735] [PMID: 16187360]
[31]
Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: A meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta Proteins Proteomics 2010; 1804(4): 996-1010.
[http://dx.doi.org/10.1016/j.bbapap.2010.01.011] [PMID: 20100603]
[32]
Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005; 21(16): 3433-4.
[http://dx.doi.org/10.1093/bioinformatics/bti541] [PMID: 15955779]
[33]
Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK. Comparing and combining predictors of mostly disordered proteins. Biochemistry 2005; 44(6): 1989-2000.
[http://dx.doi.org/10.1021/bi047993o] [PMID: 15697224]
[34]
Gautam A, Singh H, Tyagi A, et al. CPPsite: A curated database of cell penetrating peptides. Database (Oxford) 2012; 2012: bas015.
[http://dx.doi.org/10.1093/database/bas015] [PMID: 22403286]
[35]
Beaty BJ, Calisher CH. Bunyaviridae--natural history. Curr Top Microbiol Immunol 1991; 169: 27-78.
[http://dx.doi.org/10.1007/978-3-642-76018-1_2] [PMID: 1935229]
[36]
Wilson WH, Van Etten JL, Allen MJ. The Phycodnaviridae: the story of how tiny giants rule the world. Curr Top Microbiol Immunol 2009; 328: 1-42.
[http://dx.doi.org/10.1007/978-3-540-68618-7_1] [PMID: 19216434]
[37]
Morozova V, Babkin I, Kozlova Y, et al. Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8. Viruses 2019; 11(12): 1115.
[http://dx.doi.org/10.3390/v11121115] [PMID: 31810319]
[38]
Gray SM, Banerjee N. Mechanisms of arthropod transmission of plant and animal viruses. Microbiol Mol Biol Rev 1999; 63(1): 128-48.
[http://dx.doi.org/10.1128/MMBR.63.1.128-148.1999] [PMID: 10066833]
[39]
Bouziat R, Hinterleitner R, Brown JJ, et al. Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Science 2017; 356(6333): 44-50.
[http://dx.doi.org/10.1126/science.aah5298] [PMID: 28386004]
[40]
Dietzgen RG, Kondo H, Goodin MM, Kurath G, Vasilakis N. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins. Virus Res 2017; 227: 158-70.
[http://dx.doi.org/10.1016/j.virusres.2016.10.010] [PMID: 27773769]
[41]
Apweiler R, Bairoch A, Wu CH, et al. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 2004; 32(90001): 115D-9.
[http://dx.doi.org/10.1093/nar/gkh131] [PMID: 14681372]
[42]
Dunker AK, Lawson JD, Brown CJ, et al. Intrinsically disordered protein. J Mol Graph Model 2001; 19(1): 26-59.
[http://dx.doi.org/10.1016/S1093-3263(00)00138-8] [PMID: 11381529]
[43]
He B, Wang K, Liu Y, Xue B, Uversky VN, Dunker AK. Predicting intrinsic disorder in proteins: an overview. Cell Res 2009; 19(8): 929-49.
[http://dx.doi.org/10.1038/cr.2009.87] [PMID: 19597536]
[44]
Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Intrinsic disorder and functional proteomics. Biophys J 2007; 92(5): 1439-56.
[http://dx.doi.org/10.1529/biophysj.106.094045] [PMID: 17158572]
[45]
Uversky VN, Gillespie JR, Fink AL. Why are? natively unfolded? proteins unstructured under physiologic conditions? Proteins 2000; 41(3): 415-27.
[http://dx.doi.org/10.1002/1097-0134(20001115)41:3<415:AID-PROT130>3.0.CO;2-7] [PMID: 11025552]
[46]
Vacic V, Uversky VN, Dunker AK, Lonardi S. Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics 2007; 8(1): 211.
[http://dx.doi.org/10.1186/1471-2105-8-211] [PMID: 17578581]
[47]
Meng F, Uversky VN, Kurgan L. Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions. Cell Mol Life Sci 2017; 74(17): 3069-90.
[http://dx.doi.org/10.1007/s00018-017-2555-4] [PMID: 28589442]
[48]
Prilusky J, Felder CE, Zeev-Ben-Mordehai T, et al. FoldIndex(C): a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 2005; 21(16): 3435-8.
[http://dx.doi.org/10.1093/bioinformatics/bti537] [PMID: 15955783]
[49]
Campen A, Williams R, Brown C, Meng J, Uversky V, Dunker A. TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett 2008; 15(9): 956-63.
[http://dx.doi.org/10.2174/092986608785849164] [PMID: 18991772]
[50]
Walsh I, Giollo M, Di Domenico T, Ferrari C, Zimmermann O, Tosatto SCE. Comprehensive large-scale assessment of intrinsic protein disorder. Bioinformatics 2015; 31(2): 201-8.
[http://dx.doi.org/10.1093/bioinformatics/btu625] [PMID: 25246432]
[51]
Parkhill J, Dougan G, James KD, et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001; 413(6858): 848-52.
[http://dx.doi.org/10.1038/35101607] [PMID: 11677608]
[52]
Elegans C. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 1998; 282(5396): 2012-8.
[http://dx.doi.org/10.1126/science.282.5396.2012] [PMID: 9851916]
[53]
Welch RA, Burland V, Plunkett G III, et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 2002; 99(26): 17020-4.
[http://dx.doi.org/10.1073/pnas.252529799] [PMID: 12471157]
[54]
Touchon M, Hoede C, Tenaillon O, et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009; 5(1): e1000344.
[http://dx.doi.org/10.1371/journal.pgen.1000344] [PMID: 19165319]
[55]
Oshima K, Toh H, Ogura Y, et al. Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res 2008; 15(6): 375-86.
[http://dx.doi.org/10.1093/dnares/dsn026] [PMID: 18931093]
[56]
Rasko DA, Rosovitz MJ, Myers GSA, et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 2008; 190(20): 6881-93.
[http://dx.doi.org/10.1128/JB.00619-08] [PMID: 18676672]
[57]
Yang F, Yang J, Zhang X, et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 2005; 33(19): 6445-58.
[http://dx.doi.org/10.1093/nar/gki954] [PMID: 16275786]
[58]
Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proc Natl Acad Sci USA 2011; 108(50): 20142-7.
[http://dx.doi.org/10.1073/pnas.1107176108] [PMID: 22135463]
[59]
Jin Q, Yuan Z, Xu J, et al. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res 2002; 30(20): 4432-41.
[http://dx.doi.org/10.1093/nar/gkf566] [PMID: 12384590]
[60]
Nie H, Yang F, Zhang X, et al. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 2006; 7(1): 173.
[http://dx.doi.org/10.1186/1471-2164-7-173] [PMID: 16822325]
[61]
Makarova K, Slesarev A, Wolf Y, et al. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 2006; 103(42): 15611-6.
[http://dx.doi.org/10.1073/pnas.0607117103] [PMID: 17030793]
[62]
Wang F, Wang J, Jian H, et al. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS One 2008; 3(4): e1937.
[http://dx.doi.org/10.1371/journal.pone.0001937] [PMID: 18398463]
[63]
Ntefidou M, Häder DP. Photoactivated adenylyl cyclase (PAC) genes in the flagellate Euglena gracilis mutant strains. Photochem Photobiol Sci 2005; 4(9): 732-9.
[http://dx.doi.org/10.1039/b502002f] [PMID: 16121285]
[64]
Siegel S. Estadística no paramétrica aplicada a las ciencias. (1st ed.), México: Trillas 1985.
[65]
Finn RD, Clements J, Eddy SR. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res 2011; 39(Web Server issue): W29-37.
[http://dx.doi.org/10.1093/nar/gkr367] [PMID: 21593126]
[66]
Bailey TL, Gribskov M. Score distributions for simultaneous matching to multiple motifs. J Comput Biol 1997; 4(1): 45-59.
[http://dx.doi.org/10.1089/cmb.1997.4.45] [PMID: 9109037]
[67]
Frith MC, Hansen U, Spouge JL, Weng Z. Finding functional sequence elements by multiple local alignment. Nucleic Acids Res 2004; 32(1): 189-200.
[http://dx.doi.org/10.1093/nar/gkh169] [PMID: 14704356]
[68]
Polanco C, Samaniego JL. Detection of selective cationic amphipatic antibacterial peptides by Hidden Markov models. Acta Biochim Pol 2009; 56(1): 167-76.
[http://dx.doi.org/10.18388/abp.2009_2529] [PMID: 19294233]
[69]
Lodish H, Berk A, Zipursky SL. Molecular Cell Biology. 4th ed New York: W H Freeman. 2000. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21475/

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