Phylogenetic analysis of kindlins suggests subfunctionalization of an ancestral unduplicated kindlin into three paralogs in vertebrates

Evolutionary Bioinformatics

Volumn 2011, Issue 7, 2011, Pages 7-19

  Khan, Ammad Aslam ^a   Janke, Axel ^b   Shimokawa, Takashi ^a   Zhang, Hongquan ^a,c  

^a KAROLINSKA INSTITUTE   (Sweden)

^b BIODIVERSITY AND CLIMATE RESEARCH CENTRE BIK F   (Germany)

^c BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

Cell adhesion molecules; Integrin interacting proteins; Kindlins; Molecular evolution; Natural selection; Phylogenetics

Indexed keywords

CELL ADHESION MOLECULE; INTEGRIN; KINDLIN 1; KINDLIN 2; KINDLIN 3; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; FOCAL ADHESION; GENE DUPLICATION; HUMAN; METAZOON; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; VERTEBRATE;

HEXAPODA; HYDRA; METAZOA; VERTEBRATA;

EID: 79959277102     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S6179     Document Type: Article

References (31)

1. Siegel DH, Ashton GH, Penagos HG, et al. Loss of kindlin-1, a human homolog of the Caenorhabditis elegans actin-extracellular-matrix linker protein UNC-112, causes Kindler syndrome. Am J Hum Genet. 2003;73:174-187.
2. Lai-Cheong JE, Parsons M, McGrath JA. The role of kindlins in cell biology and relevance to human disease. The International Journal of Biochemistry and Cell Biology. 2010;42:595-603.
3. Kloeker S, Major MB, Calderwood DA, Ginsberg MH, Jones DA, Beckerle MC. The Kindler syndrome protein is regulated by transforming growth factor-beta and involved in integrin-mediated adhesion. J Biol Chem. 2004;279:6824-6833.
4. Shi X, Ma YQ, Tu Y, et al. The MIG-2/integrin interaction strengthens cell-matrix adhesion and modulates cell motility. J Biol Chem. 2007;282: 20455-20466.
5. Rogalski TM, Mullen GP, Gilbert MM, Williams BD, Moerman DG. The UNC-112 gene in Caenorhabditis elegans encodes a novel component of cell-matrix adhesion structures required for integrin localization in the muscle cell membrane. 2000;150(1):253-264.
6. Larjava H, Plow EF, Wu C. Kindlins: essential regulators of integrin signaling and cell-matrix adhesion. EMBO Rep. 2008;9(12):1203-1208.
7. Svensson L, Howarth K, McDowall A, Patzak I, Evans R, Ussar S, Moser M, Metin A, Fried M, Tomlinson I, Hogg N. Leukocyte adhesion deficiency-III is caused by mutations in KINDLIN3 affecting integrin activation. Nat Med. 2009;15(3):306-312.
8. Kindler T. Congenital poikiloderma with traumatic bulla formation and progressive cutaneous atrophy. The British Journal of Dermatology. 1954:66, 104-111.
9. Sharma RC, Mahajan V, Sharma NL, Sharma AK. Kindler syndrome. International Journal of Dermatology. 2003;42:727-732.
10. Ussar S, Wang HV, Linder S, Fassler R, Moser M. The Kindlins: subcellular localization and expression during murine development. Experimental Cell Research. 2006;312:3142-3151.
11. Dowling JJ, Gibbs E, Russell M, et al. Kindlin-2 is an essential component of intercalated discs and is required for vertebrate cardiac structure and function. Circ Res. 2008a;102:423-431.
12. Dowling JJ, Vreede AP, Kim S, Golden J, Feldman EL. Kindlin- 2 is required for myocyte elongation and is essential for myogenesis. BMC Cell Biol. 2008b;9:36.
13. Kruger M, Moser M, Ussar S, et al. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell. 2008;134:353-364.
14. Moser M, Nieswandt B, Ussar S, Pozgajova M, Fassler R. Kindlin-3 is essential for integrin activation and platelet aggregation. Nature Medicine. 2008;14:325-430.
15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 1994;22:4673-4680.
16. Jobb G, von Haeseler A, Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology. 2004;4:18.
17. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution. 2001;18:691-699.
18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 1987;4:406-425.
19. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 2007;24:1596-1599.
20. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution. 1986;3:418-426.
21. Pond SL, Frost SD. A genetic algorithm approach to detecting lineagespecific variation in selection pressure. Molecular Biology and Evolution. 2005;22:478-485.
22. Tajima F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics. 1993;135:599-607.
23. Hallstrom BM, Janke A. Gnathostome phylogenomics utilizing lungfish EST sequences. Molecular Biology and Evolution. 2009;26:463-471.
24. Aburomia R, Khaner O, Sidow A. Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail. Journal of Structural and Functional Genomics. 2003; 3:45-52.
25. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Development (Cambridge, England), 1994:125-133.
26. Ruddle FH, Bentley KL, Murtha MT, Risch N. Gene loss and gain in the evolution of the vertebrates. Development (Cambridge, England). 1994; 155-161.
27. Wagner GP, Amemiya C, Ruddle F. Hox cluster duplications and the opportunity for evolutionary novelties. Proceedings of the National Academy of Sciences of the United States of America. 2003;100:14603-14606.
28. Zhu J, He F, Hu S, Yu J. On the nature of human housekeeping genes. Trends Genet. 2008;24:481-484.
29. Montanez E, Ussar S, Schifferer M, et al. Kindlin-2 controls bidirectional signaling of integrins. Genes and Development. 2008;22:1325-1330.
30. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Selection in the evolution of gene duplications. Genome Biology. 2002;3: RESEARCH0008.
31. Lynch M, Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics. 2000;154:459-473.