title: Revising the taxonomic distribution, origin and evolution of ribosome inactivating protein genes.
abstract: Ribosome inactivating proteins are enzymes that depurinate a specific adenine residue in the alpha-sarcin-ricin loop of the large ribosomal RNA, being ricin and Shiga toxins the most renowned examples. They are widely distributed in plants and their presence has also been confirmed in a few bacterial species. According to this taxonomic distribution, the current model about the origin and evolution of RIP genes postulates that an ancestral RIP domain was originated in flowering plants, and later acquired by some bacteria via horizontal gene transfer. Here, we unequivocally detected the presence of RIP genes in fungi and metazoa. These findings, along with sequence and phylogenetic analyses, led us to propose an alternative, more parsimonious, hypothesis about the origin and evolutionary history of the RIP domain, where several paralogous RIP genes were already present before the three domains of life evolved. This model is in agreement with the current idea of the Last Universal Common Ancestor (LUCA) as a complex, genetically redundant organism. Differential loss of paralogous genes in descendants of LUCA, rather than multiple horizontal gene transfer events, could account for the complex pattern of RIP genes across extant species, as it has been observed for other genes.
authors.affiliation: Área de Biología Molecular, Departamento de Bioquímica y Ciencias Biológicas, UNSL and Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL-CONICET), San Luis, Argentina.
authors.forename: Walter J
authors.initials: WJ
authors.lastname: Lapadula
authors.forename: María Virginia
authors.initials: MV
authors.lastname: Sánchez Puerta
authors.forename: Maximiliano
authors.initials: M
authors.lastname: Juri Ayub
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics; D030541:Databases, Genetic; D056890:Eukaryota / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D005658:Fungi / Q000145:classification / Q000235:genetics; D023061:Gene Order; D016678:Genome; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D054788:Ribosome Inactivating Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D054788:Ribosome Inactivating Proteins
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3503-6
references.pmid: 12824354
references.citation: Biol Direct. 2008 Jul 09;3:29
references.pmid: 18613974
references.citation: Plant Physiol. 2001 Feb;125(2):866-76
references.pmid: 11161044
references.citation: Bioinformatics. 2005 May 1;21(9):2104-5
references.pmid: 15647292
references.citation: Mol Biol Evol. 1998 Mar;15(3):277-83
references.pmid: 9501494
references.citation: Biochem Biophys Res Commun. 2001 Jul 27;285(4):1071-5
references.pmid: 11467862
references.citation: Nat Rev Genet. 2002 Nov;3(11):838-49
references.pmid: 12415314
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Eur J Biochem. 1986 Nov 17;161(1):111-7
references.pmid: 3780730
references.citation: Toxicon. 2001 Nov;39(11):1629-35
references.pmid: 11595626
references.citation: Biochim Biophys Acta. 1993 Dec 21;1154(3-4):237-82
references.pmid: 8280743
references.citation: J Biol Chem. 1987 Jun 15;262(17):8128-30
references.pmid: 3036799
references.citation: J Mol Biol. 1998 Dec 11;284(4):1201-10
references.pmid: 9837738
references.citation: FEBS Lett. 2001 Sep 7;505(1):196-7
references.pmid: 11557068
references.citation: Toxicon. 2012 Mar 1;59(3):427-32
references.pmid: 22245625
references.citation: Life Sci. 2001 Mar 23;68(18):2151-8
references.pmid: 11324720
references.citation: J Agric Food Chem. 1998 Feb 16;46(2):788-792
references.pmid: 10554316
references.citation: Cell Mol Life Sci. 2006 Aug;63(16):1850-66
references.pmid: 16799768
references.citation: Mini Rev Med Chem. 2004 Jun;4(5):461-76
references.pmid: 15180503
references.citation: FASEB J. 2001 Jul;15(9):1493-506
references.pmid: 11427481
references.citation: Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
references.pmid: 12136088
references.citation: Biochemistry. 2001 Aug 7;40(31):9104-14
references.pmid: 11478877
references.citation: J Mol Biol. 2000 Sep 8;302(1):205-17
references.pmid: 10964570
references.citation: Arch Biochem Biophys. 2001 Sep 15;393(2):271-80
references.pmid: 11556814
references.citation: Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):13028-33
references.pmid: 9371794
references.citation: Toxicon. 2004 Sep 15;44(4):371-83
references.pmid: 15302521
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
references.pmid: 21593126
references.citation: J Mol Evol. 2009 Nov;69(5):470-80
references.pmid: 19784557
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: J Biol Chem. 1991 Dec 5;266(34):23422-7
references.pmid: 1744135
references.citation: BMC Evol Biol. 2004 Nov 09;4:44
references.pmid: 15535883
references.citation: Microbiology (Reading). 2010 Oct;156(Pt 10):3021-3030
references.pmid: 20595260
references.citation: J Biol Chem. 1987 Apr 25;262(12):5908-12
references.pmid: 3571242
references.citation: Biochem J. 1973 Nov;136(3):813-5
references.pmid: 4360718
references.citation: Peptides. 2004 Jun;25(6):929-33
references.pmid: 15203238
references.citation: Int J Biochem Cell Biol. 2003 Jan;35(1):61-78
references.pmid: 12467648
references.citation: J Biol Chem. 1999 Feb 5;274(6):3859-64
references.pmid: 9920941
references.citation: Mol Biol Evol. 2005 May;22(5):1273-84
references.pmid: 15703240
references.citation: Mol Biol Evol. 2004 Feb;21(2):364-73
references.pmid: 14660694