Protein Repeats Show Clade-Specific Volatility in Aves

Marcotte E.M., Pellegrini M., Yeates T.O., Eisenberg D. 1999. A census of protein repeats. J. Mol. Biol. 293, 151–160.

Article  CAS  PubMed  Google Scholar 

Andrade M.A., Perez-Iratxeta C., Ponting C.P. 2001. Protein repeats: Structures, functions, and evolution. J. Struct. Biol. 134, 117–131.

Article  CAS  PubMed  Google Scholar 

Albà M.M., Tompa P., Veitia R.A. 2007. Amino acid repeats and the structure and evolution of proteins. In Gene and Protein Evolution. vol. 3. Basel: Karger, pp. 119–130.

Google Scholar 

Persi E., Wolf Y.I., Koonin E.V. 2016. Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins. Nat. Commun. 7, 13570.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karlin S., Brocchieri L., Bergman A., Mrázek J., Gentles A.J. 2002. Amino acid runs in eukaryotic proteomes and disease associations. Proc. Natl. Acad. Sci. U. S. A. 99, 333–338.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Toll-Riera M., Radó-Trilla N., Martys F., Albá M.M. 2012. Role of low-complexity sequences in the formation of novel protein coding sequences. Mol. Biol. Evol. 29, 883–886.

Article  CAS  PubMed  Google Scholar 

Schmitz-Linneweber C., Small I. 2008. Pentatricopeptide repeat proteins: A socket set for organelle gene expression. Trends Plant Sci. 13, 663–670.

Article  CAS  PubMed  Google Scholar 

Renault L., Nassar N., Vetter I., Becker J., Klebe C., Roth M., Wittinghofer A. 1998. The 1.7  Å crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller. Nature. 392 (6671), 97–101.

Article  CAS  PubMed  Google Scholar 

Jacobsen S.E., Binkowski K.A., Olszewski N.E. 1996. SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 93, 9292–9296.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Varela M., Diaz-Rosales P., Pereiro P., Forn-Cuní G., Costa M.M., Dios S., Romero A., Figueras A., Novoa B. 2014. Interferon-induced genes of the expanded IFIT family show conserved antiviral activities in non-mammalian species. PLoS One. 9, e100015.

Article  PubMed  PubMed Central  Google Scholar 

Cerveny L., Straskova A., Dankova V., Hartlova A., Ceckova M., Staud F., Stulik J. 2013. Tetratricopeptide repeat motifs in the world of bacterial pathogens: Role in virulence mechanisms. Infect. Immun. 81, 629–635.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lynch V.J., Wagner G.P. 2008. Resurrecting the role of transcription factor change in developmental evolution. Evolution. 62, 2131–2154.

Article  CAS  PubMed  Google Scholar 

Emili A., Greenblatt J., Ingles C.J. 1994. Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein. Mol. Cell. Biol. 14, 1582–1593.

CAS  PubMed  PubMed Central  Google Scholar 

Pelassa I., Corà D., Cesano F., Monje F.J., Montarolo P.G., Fiumara F. 2014. Association of polyalanine and polyglutamine coiled coils mediates expansion disease-related protein aggregation and dysfunction. Hum. Mol. Genet. 23, 3402–3420.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gemayel R., Chavali S., Pougach K., Legendre M., Zhu B., Boeynaems S., van der Zande E., Gevaert K., Rousseau F., Schymkowitz J., Babu M.M., Verstrepen K.J. 2015. Variable glutamine-rich repeats modulate transcription factor activity. Mol. Cell. 59, 615–627.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fiumara F., Fioriti L., Kandel E.R., Hendrickson W.A. 2010. Essential role of coiled coils for aggregation and activity of Q/N-rich prions and PolyQ proteins. Cell. 143, 1121–1135.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thirunavukkarasu K., Mahajan M., McLarren K.W., Stifani S., Karsenty G. 1998. Two domains unique to osteoblast-specific transcription factor Osf2/Cbfa1 contribute to its transactivation function and its inability to heterodimerize with Cbfβ. Mol. Cell. Biol. 18, 4197–4208.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brown L.Y., Brown S.A. 2004. Alanine tracts: The expanding story of human illness and trinucleotide repeats. Trends Genet. 20, 51–58.

Article  CAS  PubMed  Google Scholar 

Malik I., Kelley C.P., Wang E.T., Todd P.K. 2021. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat. Rev. Mol. Cell Biol. 22, 589–607.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mularoni L., Guigó R., Albà M.M. 2006. Mutation patterns of amino acid tandem repeats in the human proteome. Genome Biol. 7 (4), R33.

Article  PubMed  PubMed Central  Google Scholar 

Wren J.D., Forgacs E., Fondon J.W., 3rd, Pertsemlidis A., Cheng S.Y., Gallardo T., Williams R.S., Shohet R.V., Minna J.D., Garner H.R. 2000. Repeat polymorphisms within gene regions: Phenotypic and evolutionary implications. Am. J. Hum. Genet. 67, 345–356.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Newton A.H., Pask A.J. 2020. Evolution and expansion of the RUNX2 QA repeat corresponds with the emergence of vertebrate complexity. Commun. Biol. 3, 771.

Article  CAS  PubMed  PubMed Central  Google Scholar 

King D.G., Soller M., Kashi Y. 1997. Evolutionary tuning knobs. Endeavour. 21, 36–40.

Article  Google Scholar 

Hancock J.M., Simon M. 2005. Simple sequence repeats in proteins and their significance for network evolution. Gene. 345, 113–118.

Article  CAS  PubMed  Google Scholar 

Fondon J.W., Garner H.R. 2004. Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. U. S. A. 101, 18058–18063.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mularoni L., Ledda A., Toll-Riera M., Albà M.M. 2010. Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Res. 20, 745–754.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kashi Y., King D.G. 2006. Simple sequence repeats as advantageous mutators in evolution. Trends Genet. 22, 253–259.

Article  CAS  PubMed  Google Scholar 

Schüler A., Bornberg-Bauer E. 2016. Evolution of protein domain repeats in metazoa. Mol. Biol. Evol. 33, 3170–3182.

Article  PubMed  PubMed Central  Google Scholar 

Teekas L., Sharma S., Vijay N. 2022. Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes. Genes Immun. 23 (7), 218‒234.

Article  CAS  PubMed  Google Scholar 

Mier P., Alanis-Lobato G., Andrade-Navarro M.A. 2017. Context characterization of amino acid homorepeats using evolution, position, and order. Proteins Struct. Funct. Bioinform. 85, 709–719.

Article  CAS  Google Scholar 

Schweizer M., Liu Y. 2018. Avian Diversity and Distributions and Their Evolution Through Space and Time. Cham: Springer, pp. 129–145.

Book  Google Scholar 

de Oliveira T.D., Kretschmer R., Bertocchi N.A., Degrandi T.M., de Oliveira E.H.C., Cioffi M. de B., Garnero A.D.V., Gunski R.J. 2017. Genomic organization of repetitive DNA in woodpeckers (Aves, Piciformes): Implications for karyotype and ZW sex chromosome differentiation. Lustig A.J., Ed. PLoS One. 12, e0169987.

Zhang G., Li C., Li Q., Li B., Larkin D.M., Lee C., Storz J.F., Antunes A., Greenwold M.J., Meredith R.W., Ödeen A., Cui J., Zhou Q., Xu L., Pan H., Wang Z., Jin L., Zhang P., Hu H., Yang W., Hu J., Xiao J., Yang Z., Liu Y., Xie Q., Yu H., Lian J., Wen P., Zhang F., Li H., Zeng Y., Xiong Z., Liu S., Zhou L., Huang Z., An N., Wang J., Zheng Q., Xiong Y., Wang G., Wang B., Wang J., Fan Y., da Fonseca R.R., Alfaro-Núñez A., Schubert M., Orlando L., Mourier T., Howard J.T., Ganapathy G., Pfenning A., Whitney O., Rivas M.V., Hara E., Smith J., Farré M., Narayan J., Slavov G., Romanov M.N., Borges R., Machado J.P., Khan I., Springer M.S., Gatesy J., Hoffmann F.G., Opazo J.C., Håstad O., Sawyer R.H., Kim H., Kim K.W., Kim H.J., Cho S., Li N., Huang Y., Bruford M.W., Zhan X., Dixon A., Bertelsen M.F., Derryberry E., Warren W., Wilson R.K., Li S., Ray D.A., Green R.E., O’Brien S.J., Griffin D., Johnson W.E., Haussler D., Ryder O.A., Willerslev E., Graves G.R., Alström P., Fjeldså J., Mindell D.P., Edwards S.V., Braun E.L., Rahbek C., Burt D.W., Houde P., Zhang Y., Yang H., Wang J.; Avian Genome Consortium; Jarvis E.D., Gilbert M.T., Wang J. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 346 (6215), 1311‒1320.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andrews C.B., Mackenzie S.A., Gregory T.R. 2009. Genome size and wing parameters in passerine birds. Proc. R. Soc. B. 276, 55–61.

Article  PubMed  Google Scholar 

Schmid M., Nanda I., Guttenbach M., Steinlein C., Hoehn M., Schartl M., Haaf T., Weigend S., Fries R., Buerstedde J.M., Wimmers K., Burt D.W., Smith J., A’Hara S., Law A., Griffin D.K., Bumstead N., Kaufman J., Thomson P.A., Burke T., Groenen M.A., Crooijmans R.P., Vignal A., Fillon V., Morisson M., Pitel F., Tixier-Boichard M., Ladjali-Mohammedi K., Hillel J., Mäki-Tanila A., Cheng H.H., Delany M.E., Burnside J., Mizuno S. 2000. First report on chicken genes and chromosomes 2000. Cytogenet. Cell Genet. 90, 169–218.

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