Insights into the molecular evolution of the PDZ/LIM family and identification of a novel conserved protein motif

PLoS ONE

Volumn 2, Issue 2, 2007, Pages

  te Velthuis, Aartjan J W ^a   Isogai, Tadamoto ^a   Gerrits, Lieke ^a   Bagowski, Christoph P ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENE PRODUCT; LIM KINASE 1; LIM KINASE 2; LIM PROTEIN; PDZ PROTEIN; PROTEIN ALP; PROTEIN LMO 7; PROTEIN ZASP; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; CONVERGENT EVOLUTION; DROSOPHILA MELANOGASTER; EXPRESSED SEQUENCE TAG; GENE DUPLICATION; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC IDENTIFICATION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN MOTIF; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ANIMAL; CHROMOSOME MAP; COMPARATIVE STUDY; CONSENSUS SEQUENCE; EXON; FUNGUS; GENETICS; HUMAN; INTRON; INVERTEBRATE; PDZ DOMAIN; PLANT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; VERTEBRATE;

EUKARYOTA; MAMMALIA; PROTOZOA; VERTEBRATA;

AMINO ACID MOTIFS; ANIMALS; CHROMOSOME MAPPING; CONSENSUS SEQUENCE; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; EXONS; FUNGI; HUMANS; INTRONS; INVERTEBRATES; MULTIGENE FAMILY; PDZ DOMAINS; PHYLOGENY; PLANTS; PROTEIN INTERACTION DOMAINS AND MOTIFS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; VERTEBRATES; ZINC FINGERS;

EID: 34548737494     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000189     Document Type: Article

References (62)

1. Hergyi H, Gerstein M (1999) The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. Journal of Molecular Evolution 288: 147-164.
2. Apic G, Gough J, Teichmann SA (2001) An insight into domain combinations. Bioinformatics 17: S83-89.
3. Copley RR, Doerks T, Letunic I, Bork P (2002) Protein domain analysis in the era of complete genomes. FEBS Letters 513: 129-134.
4. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402.
5. Eddy SR (1996) Hidden Markov models. Current Opinion in Structural Biology 6: 361-365.
6. Chothia C (1992) One thousand families for the molecular biologist. Nature 357: 543-544.
7. Yuri I, Wolf GKEVK (2002) Scale-free networks in biology: new insights into the fundamentals of evolution? BioEssays 24: 105-109.
8. Hegyi H, Gerstein M (1999) The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. Journal of Molecular Biology 288: 147-164.
9. Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, et al. (1997) Gene Families: The Taxonomy of Protein Paralogs and Chimeras. Science 278: 609-614.
10. Gough J (2005) Convergent evolution of domain architectures (is rare). Bioinformatics 21: 1464-1471.
11. Cho K-O, Hunt CA, Kennedy MB (1992) The rat brain postsynaptic density fraction contains a homolog of the drosophila discs-large tumor suppressor protein. Neuron 9: 929-942.
12. Woods DF, Bryant PJ (1991) The discs-large tumor suppressor gene of Drosophila encodes a guanylate kinase homolog localized at septate junctions. Cell 66: 451-464.
13. Itoh M, Nagafuchi A, Yonemura S, Kitani-Yasuda T, Tsukita S, et al. (1993) The 220-kD protein colocalizing with cadherins in non-epithelial cells is identical to ZO-1, a tight junction-associated protein in epithelial cells: cDNA cloning and immunoelectron microscopy. J Cell Biol 121: 491-502.
14. Harris BZ, Lim WA (2001) Mechanism and role of PDZ domains in signaling complex assembly. J Cell Sci 114: 3219-3231.
15. Ponting CP (1997) Evidence for PDZ domains in bacteria, yeast, and plants. Protein Sci 6: 464-468.
16. Ponting CP, Phillips C, Davies KE, Blake DJ (1997) PDZ domains: targeting signalling molecules to sub-membranous sites. Bioessays 19: 469-479.
17. Jelen F, Oleksy A, Smietana K, Otlewski J (2003) PDZ domains - common players in the cell signaling. Acta Biochim Pol 50: 985-1017.
18. Pallen MJ, Ponting CP (1997) PDZ domains in bacterial proteins. Molecular Microbiology 26: 411-413.
19. Bach I (2000) The LIM domain: regulation by association. Mech Dev 91: 5-17.
20. Dawid IB, Breen JJ, Toyama R (1998) LIM domains: multiple roles as adapters and functional modifiers in protein interactions. Trends in Genetics 14: 156-162.
21. Kadrmas JL, Beckerle MC (2004) THE LIM DOMAIN: FROM THE CYTOSKELETON TO THE NUCLEUS. Nature Reviews Molecular Cell Biology 5: 920-931.
22. Briere C, Bordel A-C, Barthou H, Jauneau A, Steinmetz A, et al. (2003) Is the LIM-domain Protein HaWLIM1 Associated with Cortical Microtubules in Sunflower Protoplasts? Plant Cell Physiol 44: 1055-1063.
23. Thornton JW, DeSalle R (2000) Gene family evolution and homology: Genomics Meets Phylogenetics. Annual Review of Genomics and Human Genetics 1: 41-73.
24. Koonin EV, Aravind L, Kondrashov AS (2000) The Impact of Comparative Genomics on Our Understanding of Evolution. Cell 101: 573-576.
25. Ponting CP, Russell RR (2002) The natural history of protein domains. Annual Review of Biophysics and Biomolecular Structure 31: 45-71.
26. Santoni M-J, Pontarotti P, Birnbaum D, Borg J-P (2002) The LAP family: a phylogenetic point of view. Trends in Genetics 18: 494-497.
27. Yang N, Higuchi O, Ohashi K, Nagata K, Wada A, et al. (1998) Cofilin phosphorylation by LIM-kinase 1 and its role in Rac-mediated actin reorganization. Nature 393: 809-812.
28. Klaavuniemi T, Ylanne J (2006) Zasp/Cypher internal ZM-motif containing fragments are sufficient to co-localize with α-actinin - Analysis of patient mutations. Experimental Cell Research 312: 1299-1311.
29. Vallenius T, Luukko K, Makela TP (2000) CLP-36 PDZ-LIM Protein Associates with Nonmuscle alpha -Actinin-1 and alpha -Actinin-4. J Biol Chem 275: 11100-11105.
30. Nakagawa N, Hoshijima M, Oyasu M, Saito N, Tanizawa K, et al. (2000) ENH, Containing PDZ and LIM Domains, Heart/Skeletal Muscle-Specific Protein, Associates with Cytoskeletal Proteins through the PDZ Domain. Biochemical and Biophysical Research Communications 272: 505.
31. Ooshio T, Irie K, Morimoto K, Fukuhara A, Imai T, et al. (2004) Involvement of LMO7 in the association of two cell-cell adhesion molecules, nectin and E-cadherin, through afadin and alpha-actinin in epithelial cells. Journal of Biological Chemistry 279: 31365-31373.
32. Andersen O, Ostbye TK, Gabestad I, Nielsen C, Bardal T, et al. (2004) Molecular characterization of a PDZ-LIM protein in Atlantic salmon (Salmo salar): a fish ortholog of the alpha-actinin-associated LIM-protein (ALP). Journal of Muscle Research and Cell Motility 25: 61.
33. Zhou Q, Ruiz-Lozano P, Martone ME, Chen J (1999) Cypher, a striated muscle-restricted PDZ and LIM domain-containing protein, binds to alpha-actinin-2 and protein kinase C. Journal of Biological Chemistry 274: 19807-19813.
34. Zhou Q, Chu P-H, Huang C, Cheng C-F, Martone ME, et al. (2001) Ablation of Cypher, a PDZ-LIM domain Z-line protein, causes a severe form of congenital myopathy. J Cell Biol 155: 605-612.
35. van der Meer DLM, Marques IJ, Leito JTD, Besser J, Bakkers J, et al. (2006) Zebrafish cypher is important for somite formation and heart development. Developmental Biology 299: 356-372.
36. Pashmforoush M, Pomies P, Peterson KL, Kubalak S, Ross J, et al. (2001) Adult mice deficient in actinin-associated LIM-domain protein reveal a developmental pathway for right ventricular cardiomyopathy. Nat Med 7: 591.
37. Boden SD, Liu Y, Hair GA, Helms JA, Hu D, et al. (1998) LMP-1, A LIM-Domain Protein, Mediates BMP-6 Effects on Bone Formation. Endocrinology 139: 5125-5134.
38. Takahashi T, Aoki S, Nakamura T, Koshimizu U, Matsumoto K, et al. (1997) Xenopus LIM motif-containing protein kinase, Xlimk1, is expressed in the developing head structure of the embryo. Developmental Dynamics 209: 196-205.
39. Foletta VC, Moussi N, Sarmiere PD, Bamburg JR, Bernard O (2004) LIM kinase 1, a key regulator of actin dynamics, is widely expressed in embryonic and adult tissues. Experimental Cell Research 294: 392-405.
40. Takahashi H, Koshimizu U, Miyazaki J-i, Nakamura T (2002) Impaired Spermatogenic Ability of Testicular Germ Cells in Mice Deficient in the LIM-Kinase 2 Gene. Developmental Biology 241: 259-272.
41. Takahashi T, Koshimizu U, Abe H, Obinata T, Nakamura T (2001) Functional involvement of Xenopus LIM kinases in progression of oocyte maturation. Developmental Biology 229: 554-567.
42. Kang S, Xu H, Duan X, Liu J-J, He Z, et al. (2000) PCD1, a Novel Gene Containing PDZ and LIM Domains, Is Overexpressed in Several Human Cancers. Cancer Res 60: 5296-5302.
43. Loughran G, Healy NC, Kiely PA, Huigsloot M, Kedersha NL, et al. (2005) Mystique is a new insulin-like growth factor-I-regulated PDZ-LIM domain protein that promotes cell attachment and migration and suppresses Anchorage-independent growth. Mol Biol Cell 16: 1811-1822.
44. Yoshioka K, Foletta V, Bernard O, Itoh K (2003) A role for LIM kinase in cancer invasion. PNAS 100: 7247-7252.
45. Kiess M, Scharm B, Aguzzi A, Hajnal A, Klemenz R, et al. (1995) Expression of ril, a novel LIM domain gene, is down-regulated in Hras-transformed cells and restored in phenotypic revertants. Oncogene 10: 61-68.
46. Bagheri-Yarmand R, Mazumdar A, Sahin AA, Kumar R (2006) LIM kinase 1 increases tumor metastasis of human breast cancer cells via regulation of the urokinase-type plasminogen activator system. International Journal of Cancer 118: 2703-2710.
47. Suyama E, Wadhwa R, Kawasaki H, Yaguchi T, Kaul SC, et al. (2004) LIM kinase-2 targeting as a possible anti-metastasis therapy. The Journal of Gene Medicine 6: 357-363.
48. Lehman W, Craig R, Kendrick-Jones J, Sutherland-Smith A (2004) An open or closed case for the conformation of calponin homology domains on F-actin? Journal of Muscle Research and Cell Motility 25: 351-358.
49. Klaavuniemi T, Kelloniemi A, Ylanne J (2004) The ZASP-like Motif in Actinin-associated LIM Protein Is Required for Interaction with the {alpha}-Actinin Rod and for Targeting to the Muscle Z-line. J Biol Chem 279: 26402-26410.
50. McKeown CR, Hand H-F, Berckerle MC (2006) Molecular characterization of the Caenorhabditis elegans ALP/Enigma gene alp-1. Developmental Dynamics 235: 530-538.
51. te Velthuis AJW, Ott EB, Marques IJ, Bagowski CP (2007) Gene expression patterns of the ALP family during zebrafish development. Gene Expression Patterns 7: 297-305.
52. A Faiella MDE, M Rambaldi, D Acampora, S Balsofiore, A Stornaiuolo, A Mallamaci, E Migliaccio, M Gulisano, A Simeone (1991) Isolation and mapping of EVX1, a human homeobox gene homologous to even-skipped, localized at the 5′ end of HOX1 locus on chromosome 7. Nucleic Acids Research 19: 6541-6545.
53. Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, et al. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Research 34: D257-260.
54. Schultz J, Copley RR, Doerks T, Ponting CP, Bork P (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Research 28: 231-234.
55. Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proceedings of the National Academy of Sciences of the United States of America 95: 5857-5864.
56. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.
57. Castresana J (2000) Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. Mol Biol Evol 17: 540-552.
58. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
59. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
60. Guindon Sp, Gascuel O (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology 52: 696-704.
61. Perriere G, Gouy M (1996) WWW-query: An on-line retrieval system for biological sequence banks. Biochimie 78: 364-369.
62. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Briefings in Bioinformatics 5: 150-163.