title: Characteristics and evolution of the PUF gene family in Bombyx mori and 27 other species.
abstract: The Pumilio protein is the founding member of the PUF family of RNA-binding proteins, which contains 8 repeat Puf domains and plays important roles during embryogenesis and post-embryogenesis by binding the Nanos response element (NRE) of specific target genes in eukaryotes. In addition, many other proteins containing the Puf domain were identified but with different functions from the Pumilio protein in various species. Taking advantage of the newly assembled genome sequences, in this study we performed a genome-wide analysis of PUF genes in silkworm and other 27 species. In the silkworm, three PUF genes were identified, named Bmpumilio, Bmpenguin and Bmnop by homology analysis. In fungi and animals, four evolutionarily conservational PUF gene families were identified, Group-A, -B, -C and -D. While Group-A, -C, and -D are present in all fungi and animals, Group-B was only identified in fungi. Interestingly, the number and features of the Puf domains are distinct in each group, suggesting different roles for these proteins in every group. The EST and microarray data showed that the mRNA of the three PUF genes can be widely detected in all tissues of the silkworm. Our results provide some new insights into the functions and evolutionary characteristics of PUF proteins.
authors: The Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China.
authors: Chun-Dong
authors: CD
authors: Zhang
authors: Min-Hui
authors: MH
authors: Pan
authors: Juan
authors: J
authors: Tan
authors: Fang-Fang
authors: FF
authors: Li
authors: Jun
authors: J
authors: Zhang
authors: Ting-Ting
authors: TT
authors: Wang
authors: Cheng
authors: C
authors: Lu
references: Genetics. 1997 May;146(1):275-85
references: 9136017
references: EMBO J. 2000 Dec 1;19(23):6602-11
references: 11101532
references: Dev Biol. 2007 May 15;305(2):551-63
references: 17412319
references: PLoS One. 2009;4(3):e4980
references: 19319195
references: Nature. 2005 Mar 24;434(7032):462-9
references: 15791247
references: Mol Cell Biol. 2004 Jun;24(12):5534-47
references: 15169913
references: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10893-7
references: 16037210
references: Eukaryot Cell. 2007 Feb;6(2):262-70
references: 17172436
references: Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17675-80
references: 16317069
references: Nature. 1997 Dec 4;390(6659):477-84
references: 9393998
references: Evol Dev. 2008 Sep-Oct;10(5):546-54
references: 18803773
references: Mol Biol Evol. 2007 Aug;24(8):1596-9
references: 17488738
references: Genes Dev. 2004 Jun 15;18(12):1452-65
references: 15198983
references: Dev Cell. 2004 Nov;7(5):697-707
references: 15525531
references: PLoS Biol. 2004 Mar;2(3):E79
references: 15024427
references: Curr Biol. 2003 Jan 21;13(2):134-9
references: 12546787
references: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references: 15034147
references: Nucleic Acids Res. 1993 Dec 25;21(25):5803-16
references: 8290338
references: Nature. 2002 Jun 6;417(6889):660-3
references: 12050669
references: Cell. 1995 Mar 10;80(5):747-56
references: 7889568
references: Proc Natl Acad Sci U S A. 2000 May 9;97(10):5273-8
references: 10792032
references: J Biol Chem. 2007 May 25;282(21):15430-8
references: 17389596
references: RNA. 2008 Feb;14(2):246-62
references: 18094119
references: Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):447-51
references: 8552658
references: RNA. 2007 Dec;13(12):2165-74
references: 17956976
references: Sci STKE. 2006 Sep 26;2006(354):pe37
references: 17003467
references: RNA. 2009 Jun;15(6):1090-9
references: 19369425
references: Genome Biol. 2007;8(8):R162
references: 17683582
references: Trends Genet. 2002 Mar;18(3):150-7
references: 11858839
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
references: 16381856
references: Nat Struct Mol Biol. 2005 Nov;12(11):945-51
references: 16244662
references: Dev Biol. 2007 Mar 15;303(2):635-49
references: 17234175
references: Gene Expr Patterns. 2008 Apr;8(4):254-60
references: 18267373
references: Development. 1998 Feb;125(4):679-90
references: 9435288
references: Nat Struct Mol Biol. 2006 Jun;13(6):533-9
references: 16715093
references: Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4487-92
references: 16537387
references: Mol Cell Biol. 2008 Jun;28(12):4093-103
references: 18411299
references: Bioinformatics. 1998;14(9):755-63
references: 9918945
references: RNA. 2008 Aug;14(8):1550-7
references: 18579869
references: RNA. 2005 Nov;11(11):1655-66
references: 16244132
references: RNA. 2005 Apr;11(4):447-58
references: 15769874