title: The distribution of GYR- and YLP-like motifs in Drosophila suggests a general role in cuticle assembly and other protein-protein interactions.
abstract: BACKGROUND
  Arthropod cuticle is composed predominantly of a self-assembling matrix of chitin and protein. Genes encoding structural cuticular proteins are remarkably abundant in arthropod genomes, yet there has been no systematic survey of conserved motifs across cuticular protein families.
  
  
  RESULTS
  Two short sequence motifs with conserved tyrosines were identified in Drosophila cuticular proteins that were similar to the GYR and YLP Interpro domains. These motifs were found in members of the CPR, Tweedle, CPF/CPFL, and (in Anopheles gambiae) CPLCG cuticular protein families, and the Dusky/Miniature family of cuticle-associated proteins. Tweedle proteins have a characteristic motif architecture that is shared with the Drosophila protein GCR1 and its orthologs in other species, suggesting that GCR1 is also cuticular. A resilin repeat, which has been shown to confer elasticity, matched one of the motifs; a number of other Drosophila proteins of unknown function exhibit a motif architecture similar to that of resilin. The motifs were also present in some proteins of the peritrophic matrix and the eggshell, suggesting molecular convergence among distinct extracellular matrices. More surprisingly, gene regulation, development, and proteolysis were statistically over-represented ontology terms for all non-cuticular matches in Drosophila. Searches against other arthropod genomes indicate that the motifs are taxonomically widespread.
  
  
  CONCLUSIONS
  This survey suggests a more general definition for GYR and YLP motifs and reveals their contribution to several types of extracellular matrix. They may define sites of protein interaction with DNA or other proteins, based on ontology analysis. These results can help guide experimental studies on the biochemistry of cuticle assembly.
authors.affiliation: Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America. scott.cornman@gmail.com
authors.forename: R Scott
authors.initials: RS
authors.lastname: Cornman
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D004330:Drosophila / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D029721:Drosophila Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D019476:Insect Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D007313:Insecta / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D016415:Sequence Alignment
chemical_list: D029721:Drosophila Proteins; D019476:Insect Proteins; C047663:cuticle proteins, insects
references.citation: J Comput Biol. 1998 Summer;5(2):211-21
references.pmid: 9672829
references.citation: Insect Biochem Mol Biol. 2007 Aug;37(8):754-60
references.pmid: 17628275
references.citation: Insect Biochem Mol Biol. 2002 Nov;32(11):1577-83
references.pmid: 12530225
references.citation: Insect Biochem Mol Biol. 2004 Oct;34(10):1059-67
references.pmid: 15475300
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16794-9
references.pmid: 17075064
references.citation: Tissue Cell. 1971;3(3):477-97
references.pmid: 18631567
references.citation: Insect Biochem Mol Biol. 1995 Feb;25(2):153-76
references.pmid: 7711748
references.citation: Insect Biochem Mol Biol. 2001 Oct;31(11):1083-93
references.pmid: 11520687
references.citation: Genetics. 2005 Sep;171(1):109-17
references.pmid: 15965255
references.citation: EMBO J. 1988 Sep;7(9):2681-6
references.pmid: 3181138
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W585-7
references.pmid: 17517783
references.citation: Nature. 2005 Oct 13;437(7061):999-1002
references.pmid: 16222249
references.citation: Insect Biochem Mol Biol. 2008 Jun;38(6):661-76
references.pmid: 18510978
references.citation: PLoS One. 2008 Aug 22;3(8):e3041
references.pmid: 18725942
references.citation: Biomacromolecules. 2009 Dec 14;10(12):3227-34
references.pmid: 19928816
references.citation: DNA Res. 2004 Feb 29;11(1):27-35
references.pmid: 15141943
references.citation: Science. 2000 Feb 25;287(5457):1477-9
references.pmid: 10688794
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: BMC Genomics. 2008 Jan 18;9:22
references.pmid: 18205929
references.citation: Insect Mol Biol. 2009 Oct;18(5):607-22
references.pmid: 19754739
references.citation: Biochim Biophys Acta. 1964 Oct 9;93:213-5
references.pmid: 14249161
references.citation: Science. 2004 Dec 10;306(5703):1937-40
references.pmid: 15591204
references.citation: Curr Biol. 2009 Jul 28;19(14):1200-5
references.pmid: 19540119
references.citation: Insect Biochem Mol Biol. 2010 Jul;40(7):541-51
references.pmid: 20457254
references.citation: J Mol Biol. 2004 Jul 16;340(4):783-95
references.pmid: 15223320
references.citation: PLoS One. 2009 Dec 17;4(12):e8345
references.pmid: 20019874
references.citation: Bioinformatics. 2004 Mar 1;20(4):578-80
references.pmid: 14990455
references.citation: Nature. 2008 Apr 24;452(7190):949-55
references.pmid: 18362917
references.citation: Insect Biochem Mol Biol. 2007 Feb;37(2):135-46
references.pmid: 17244542
references.citation: Science. 2002 Oct 4;298(5591):129-49
references.pmid: 12364791
references.citation: Nature. 2006 Oct 26;443(7114):931-49
references.pmid: 17073008
references.citation: J Cell Sci. 2003 Apr 1;116(Pt 7):1199-207
references.pmid: 12615963
references.citation: Curr Protoc Bioinformatics. 2002 Nov;Chapter 7:Unit 7.2
references.pmid: 18792943
references.citation: Plant J. 1994 Feb;5(2):157-72
references.pmid: 8148875
references.citation: Biochim Biophys Acta. 1982 May 3;703(2):216-22
references.pmid: 7082682
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Insect Biochem Mol Biol. 2010 Mar;40(3):189-204
references.pmid: 20171281
references.citation: Gene. 1995 Oct 3;163(2):GC17-26
references.pmid: 7590261
references.citation: J Struct Biol. 2004 Mar;145(3):226-35
references.pmid: 14960373
references.citation: Glycobiology. 2005 Feb;15(2):153-64
references.pmid: 15385431
references.citation: Bioinformatics. 2000 Mar;16(3):233-44
references.pmid: 10869016
references.citation: Nucleic Acids Res. 1987 May 26;15(10):4035-48
references.pmid: 2884623