Mapping of the influenza A hemagglutinin serotypes evolution by the ISSCOR method

• Authors: Jan Radomski , Piotr Słonimski , Włodzimierz Zagórski-Ostoja , Piotr Borowicz
• Languages of publication: EN

Abstracts

EN

Analyses and visualizations by the ISSCOR method of influenza virus hemagglutinin genes of different A-subtypes revealed some rather striking temporal relationships between groups of individual gene subsets. Based on these findings we consider application of the ISSCOR-PCA method for analyses of large sets of homologous genes to be a worthwhile addition to a toolbox of genomics - allowing for a rapid diagnostics of trends, and ultimately even aiding an early warning of newly emerging epidemiological threats.

Keywords

EN

ISSCOR descriptors; phylogenetic analysis; influenza virus; hemagglutinin; phylogenetic maps

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2014
• Volume: 61
• Issue: 3
• Pages: 441-451

Dates

published

2014

received

2014-05-28

revised

2014-08-26

accepted

2014-09-11

(unknown)

2014-09-12

Contributors

author

Jan Radomski

• Interdisciplinary Center for Mathematical and Computational Modeling, Warsaw University, Warsaw, Poland

author

Piotr Słonimski

• Centre de Génétique Moléculaire du CNRS & Université Pierre-et-Marie Curie, Paris, Gif sur Yvette, France

author

Włodzimierz Zagórski-Ostoja

• Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland

author

Piotr Borowicz

• Institute of Biotechnology and Antibiotics, Warsaw, Poland

References

• Adzhubei AA, Adzhubei IA, Krasheninnikov IA, Neidle S (1996) Non-random usage of 'degenerate' codons related to protein three-dimensional structure. FEBS Lett 399: 78-82.
• Ahn I, Son HS (2012) Evolutionary analysis of human-origin influenza A virus (H3N2) genes associated with the codon usage patterns since 1993. Virus Genes 44: 198-206, doi:10.1007/s11262-011-0687-4.
• Antezana MA, Kreitman M (1999) The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences. J Mol Evol 49: 36-43.
• Berg OG, Kurland GC (1997) Growth rate-optimised tRNA abundance and codon usage. J Mol Biol 270: 544-550.
• Berhane Y, Ojkic D, Neufeld J, Leith M, Hisanaga T, Kehler H, Pasick J (2010) Molecular characterization of pandemic H1N1 influenza viruses isolated from turkeys and pathogenicity of a human pH1N1 isolate in turkeys. Avian Dis 54: 1275-1285.
• Buchan JR, Aucott LS, Stansfield I (2006) tRNA properties help shape codon pair preferences in open reading frames. Nucl Acids Res 34: 1015-1027.
• Carbone A, Kepes AF, Zinovyev A (2005) Codon bias signatures, organization of microorganisms in codon space and lifestyle. Mol Biol Evol 22: 547-561.
• Cockburn WC, Delon PJ, Ferreira W (1969) Origin and progress of the 1968-69 Hong Kong influenza epidemic. Bull World Health Org 41: 345-348.
• Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S (2008) Virus attenuation by genome-scale changes in codon pair bias. Science 320: 1784-1787.
• Collins DW (1993) Relationship between G + C in silent sites of codons and amino acids composition of proteins. J Mol Evol 36: 201-213.
• Damashek M (1995) Gauging similarity with n-grams: language-independent categorization of text. Science 267: 843-348.
• Dries M, Savva R, Wernish L (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucl Acids Res 32: 5036-5044.
• Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113; doi:10.1186/1471-2105-5-113.
• Edwards SV M (2009) Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
• Eyre-Walker A, Bulmer M (1993) Reduced synonymous substitution rate at the start of enterobacterial genes; Nucleic Acids Res 21: 4599-4603.
• Firnberg E, Ostermeier M (2013) The genetic code constrains yet facilitates Darwinian evolution. Nucl Acids Res 41: 7420-7428; doi:10.1093/nar/gkt536.
• Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C et al. (2014) Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genet 10: e1004185; doi:10.1371/journal.pgen.1004185.
• Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Donis R (2009) Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325: 197-201; doi: 10.1126/science.1176225.
• Greenbaum BD, Levine AJ, Bhanot G, Rabadan R (2008) Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PloS Pathogens 4: e1000079.
• Herfst S, Schrauwen EJ, Linster M, Chutinimitkul S, de Wit E, Munster VJ, Fouchier RA (2012) Airborne transmission of influenza A/H5N1 virus between ferrets. Science 336: 1534-1541.
• Ho SY, Jermiin LS (2004) Tracing the decay of the historical signal in biological sequence data. Syst Biol 53: 623-637.
• Huson D, Richter DC, Rausch Ch, Dezulian T, Franz TM, Rupp R (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8: 460; doi:10.1186/1471-2105-8-460.
• Ikemura T (1985) Codon usage and tRNA content of unicellular and multicellular organisms. Mol Biol Evol 2: 13-34.
• Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Kawaoka Y (2012) Experimental adaptation of an influenza H5HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 486: 420-430; doi:10.1038/nature10831.
• Kimura M (1962) On the probability of fixation of mutant genes in populations. Genetics 47: 713-719.
• Knight RD, Freeland SJ, Landweber LF (2001) A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol 2(4): research0010.1-0010.13, doi:10.1186/gb-2001-2-4-research0010.
• Leache AD, Rannala B (2011) The accuracy of species tree estimation under simulation - a comparison of methods. Syst Biol 60: 126-137.
• Lee RT, Santos CL, de Paiva TM, Cui L, Sirota FL, Eisenhaber F, Maurer-Stroh S (2010) All that glitters is not gold - founder effects complicate associations of flu mutations to disease severity. Virol J 7: 297; doi:10.1186/1743-422X-7-297.
• McHardy CA, Adams B (2009) The role of genomics in tracking the evolution of influenza A virus. PLoS Pathog 5: e1000566; doi:10.1371/journal.ppat. 1000566.
• Nelson M, Spiro D, Wentworth D, Fan J, Beck E, George KS, Henrickson K, et al. (2009) The early diversification of influenza A/H1N1pdm. PLoS Currents Influenza Nov 5 doi: 10.1371/currents.RRN1126.
• Novozhilov AS, Wolf YI, Koonin EV (2007) Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. Biol Direct http://www.biology-direct.com/content/2/1/24.
• Płoński P, Radomski JP (2010) Quick Path Finding - quick algorithmic solution for unambiguous labeling of phylogenetic tree nodes. Comput Biol Chem 34: 300.
• Radomski JP, Slonimski PP (2001) Genomic style of proteins: concepts, methods and analyses of ribosomal proteins from 16 microbial species. FEMS Microbiol Rev 25: 425-435.
• Radomski JP, Slonimski PP (2007) Primary sequences of proteins from complete genomes display a singular periodicity: Alignment-free N-gram analysis. C R Biol 330: 33-48.
• Radomski JP, Slonimski PP (2009) ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement - a new method for an alignment-free genome sequence analysis, CR Biologies 332: 336-350.
• Radomski JP, Slonimski PP (2012) Alignment free characterization of the influenza a hemagglutinin genes by the ISSCOR method. CR Biologies 335: 180-193.
• Radomski JP, Płoński P, Zagórski-Ostoja W (2014) The hemagglutinin mutation E391K of pandemic 2009 influenza revisited. Mol Phylogenet Evol 70: 29-36.
• Rannala B, Huelsenbeck JP, Yang Z, Nielsen R (1998) Taxon sampling and the accuracy of large phylogenies. Syst Biol 47: 702-710.
• Renzette N, Liu P, Caffrey D, Zeldovich K, Palmiotti C, Spain J, Camolli J, Borenstein J, Schiffer C, Wang J, Finberg R, Kowalik T (2012) In vitro culture of influenza A virus alters the evolutionary trajectories of viral populations. 15th International Conference on Infectious Diseases, Bangkok, June 13-16, 2012.
• Rodnina MV, Wintermeyer W (2001) Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Ann Rev Biochem 70: 415-435.
• Russell CA, Fonville JM, Brown AE, Burke DF, Smith DL, James SL, Herfst S, Fouchier R, Smith DJ (2012) The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. Science 336: 1541-1547.
• Schafer JR, Kawaoka Y, Bean WJ, Suss J, Senne D, Webster RG (1993) Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir. Virology 194: 781-788.
• Scholtissek C, Rohde W, Von Hoyningen V, Rott R (1978) On the origin of the human influenza virus subtypes H2N2 and H3N2. Virology 87: 13-20.
• Sharp PM, Matassi G (1994) Codon usage and genome evolution. Curr Opin Genet Dev 4: 851-860.
• Shih AC, Hsiao TC, Ho MS, Li WH (2007) Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci 104: 6283-6288.
• Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Nature 459: 1122-1126; doi:10.1038/nature08182.
• Sueoka N (1992) Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol 34: 95-114.
• Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci 101: 11030-11035.
• Than C, Nakhleh L (2009) Species tree inference by minimizing deep coalescences. PLoS Comput Biol 5(9): e1000501. doi:10.1371/journal.pcbi.1000501.
• Vijaykrishna D, Smith GJ, Pybus OG, Zhu H, Bhatt S, Poon LL, Peiris JM (2011) Long-term evolution and transmission dynamics of swine influenza A virus. Nature 473: 519-523; doi:10.1038/nature10004.
• Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191; doi:10.1093/bioinformatics/btp033.
• Whitehead TA, Fleishman SJ, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Baker D (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332: 816-821.
• Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D (2012) Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 30: 543-548.
• Wong HM, Smith DK, Rabadan R, Peiris M, Poon LL (2010) Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evolutionary Biology 10: 253; http://www.biomedcentral.com/1471-2148/10/253.
• Zama M (1990) Codon usage and secondary structure of mRNA. Nucleic Acids Symp Ser 22: 93-94.