Human leucine-rich repeat proteins: A genome-wide bioinformatic categorization and functional analysis in innate immunity

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue SUPPL. 1, 2011, Pages 4631-4638

  Ng, Aylwin C Y ^a,b   Eisenberg, Jason M ^a,b   Heath, Robert J W ^a   Huett, Alan ^a   Robinson, Cory M ^c   Nau, Gerard J ^c   Xavier, Ramnik J ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Anti bacterial; Autophagy; Inflammation; Pathogen sensors; Pathogen response

Indexed keywords

CYSTEINE; LEUCINE; LEUCINE RICH REPEAT PROTEIN; PATTERN RECOGNITION RECEPTOR; PROTEIN; SMALL INTERFERING RNA; TOLL LIKE RECEPTOR; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

AUTOPHAGY; BIOINFORMATICS; CONFERENCE PAPER; GENE EXPRESSION; GENOME; HELA CELL; HOST PATHOGEN INTERACTION; HUMAN; HUMAN CELL; INNATE IMMUNITY; MACROPHAGE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SALMONELLA; SIGNAL TRANSDUCTION;

BACTERIA (MICROORGANISMS); FUNGI;

EID: 79952742148     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1000093107     Document Type: Article

References (42)

1. Medzhitov R (2007) Recognition of microorganisms and activation of the immune response. Nature 449:819-826.
2. Pålsson-McDermott EM, O'Neill LA (2007) Building an immune system from nine domains. Biochem Soc Trans 35:1437-1444.
3. Huang S, et al. (2008) Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity. Genome Res 18:1112-1126. (Pubitemid 351931162)
4. Nagawa F, et al. (2007) Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice. Nat Immunol 8:206-213. (Pubitemid 46152652)
5. Alder MN, et al. (2005) Diversity and function of adaptive immune receptors in a jawless vertebrate. Science 310:1970-1973. (Pubitemid 43005993)
6. Akira S, Uematsu S, Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124:783-801. (Pubitemid 43261452)
7. Peter ME, Kubarenko AV, Weber AN, Dalpke AH (2009) Identification of an N-terminal recognition site in TLR9 that contributes to CpG-DNA-mediated receptor activation. J Immunol 182:7690-7697.
8. Hugot JP, et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411:599-603.
9. Ogura Y, et al. (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411:603-606. (Pubitemid 32531409)
10. Swanberg M, et al. (2005) MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction. Nat Genet 37:486-494. (Pubitemid 40617276)
11. Hawn TR, et al. (2003) A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to Legionnaires' disease. J Exp Med 198:1563-1572. (Pubitemid 37467170)
12. Enkhbayar P, Kamiya M, Osaki M, Matsumoto T, Matsushima N (2004) Structural principles of leucine-rich repeat (LRR) proteins. Proteins 54:394-403. (Pubitemid 38197354)
13. Kobe B, Kajava AV (2001) The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 11:725-732. (Pubitemid 34076634)
14. Kajava AV (1998) Structural diversity of leucine-rich repeat proteins. J Mol Biol 277:519-527.
15. Matsushima N, et al. (2007) Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC Genomics 8:124.
16. Brodsky I, Medzhitov R (2007) Two modes of ligand recognition by TLRs. Cell 130:979-981. (Pubitemid 47410282)
17. Wei T, et al. (2008) LRRML: A conformational database and an XML description of leucine-rich repeats (LRRs). BMC Struct Biol 8:47.
18. Hunter S, et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37 (database issue):D211-D215.
19. The UniProt Consortium (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38 (database issue):D142-D148.
20. Schuster-Böckler B, Schultz J, Rahmann S (2004) HMM Logos for visualization of protein families. BMC Bioinformatics 5:7.
21. Dolan J, et al. (2007) The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns. BMC Genomics 8:320.
22. Matsushima N, Ohyanagi T, Tanaka T, Kretsinger RH (2000) Super-motifs and evolution of tandem leucine-rich repeats within the small proteoglycans - biglycan, decorin, lumican, fibromodulin, PRELP, keratocan, osteoadherin, epiphycan, and osteoglycin. Proteins 38:210-225. (Pubitemid 30051420)
23. Käll L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338:1027-1036. (Pubitemid 38542831)
24. Mi H, et al. (2010) PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38 (database issue):D204-D210.
25. Su AI, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062-6067. (Pubitemid 38520528)
26. Marín I, van Egmond WN, van Haastert PJ (2008) The Roco protein family: A functional perspective. FASEB J 22:3103-3110.
27. Huett A, et al. (2009) A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy. J Immunol 182:4917-4930.
28. Simonsen A, et al. (2004) Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. J Cell Sci 117:4239-4251. (Pubitemid 39328311)
29. McGovern DP, et al.; NIDDK IBD Genetics Consortium (2010) Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 42:332-337.
30. Brass AL, et al. (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139:1243-1254.
31. Hao L, et al. (2008) Drosophila RNAi screen identifies host genes important for influenza virus replication. Nature 454:890-893.
32. Amit I, et al. (2004) Tal, a Tsg101-specific E3 ubiquitin ligase, regulates receptor endocytosis and retrovirus budding. Genes Dev 18:1737-1752. (Pubitemid 38938189)
33. Zheng YT, et al. (2009) The adaptor protein p62/SQSTM1 targets invading bacteria to the autophagy pathway. J Immunol 183:5909-5916.
34. Shevchenko DV, et al. (1997) Molecular characterization and cellular localization of TpLRR, a processed leucine-rich repeat protein of Treponema pallidum, the syphilis spirochete. J Bacteriol 179:3188-3195. (Pubitemid 27202992)
35. Zhang XS, Choi JH, Heinz J, Chetty CS (2006) Domain-specific positive selection contributes to the evolution of Arabidopsis leucine-rich repeat receptor-like kinase (LRR RLK) genes. J Mol Evol 63:612-621. (Pubitemid 44833226)
36. Larkin MA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. (Pubitemid 350162903)
37. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755-763.
38. McQuitty LL (1966) Similarity analysis by reciprocal pairs for discrete and continuous data. Educ Psychol Meas 26:825-831.
39. Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128. (Pubitemid 46017867)
40. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 57:289-300.
41. Chen F, Mackey AJ, Stoeckert CJ, Jr, Roos DS (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34 (database issue): D363-D368.
42. de Hoon MJ, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20:1453-1454. (Pubitemid 38931415)