摘要
本文详尽报道了五步蛇毒腺细胞功能基因表达序列标签和毒素基因进化研究、家猪脑组织基因表达分析以及海洋弧菌噬菌体EH3-23P1全基因组测序及序列分析结果。
ESTs是对cDNA克隆5’端或3’端测序得到的长度在500bp左右的序列，是研究基因表达和差异表达以及功能的重要手段。作为非常特化的器官，蛇毒腺合成和分泌大量复杂的毒素蛋白。由于蛇毒素独特的药用价值，毒腺基因表达已经被广泛的研究，但毒素分泌的分子机制、毒腺的细胞结构和代谢还知之甚少，由此引发一个基本问题就是毒腺除了表达大量的毒素蛋白以外还有哪些基因表达?为了阐明这些问题，我们选取五步蛇毒腺作为基因表达研究模型，构建毒腺非标准化cDNA文库，5’末端测序得到8，696条高质量的表达序列标签序列，聚类处理后产生3，416个类，其中40.16％的ESTs编码毒素相关蛋白，39.85％的ESTs属于细胞功能基因，另外20.00％的ESTs在现有的数据库中找不到同源序列。分析细胞功能转录本，我们发现一些毒素分泌相关基因和腺体特异基因的高表达，如钙离子结合的EF-hand蛋白、蛋白质二硫键异构酶等；与能量代谢相关的基因如肌酸激酶和NADH脱氢酶也以高水平的表达；另外，毒腺细胞结构蛋白与哺乳动物肌肉组织相似。同时，和其它蛇毒腺基因表达比较分析，发现五步蛇毒液成分没有神经生长因子类毒素基因的表达。分析两个毒素蛋白家族groupⅢmetalloproteinase和serine protease在Colubroidea亚目的进化关系表明了早期的单次基因获得事件。五步蛇毒腺ESTs数据为蛇类功能基因组和毒腺的基因表达研究提供了重要的资源，也为进一步阐明蛇毒分泌机制和毒素进化提供了重要的序列信息。
为理解家猪脑组织发育过程中基因表达的变化，构建了丹麦长白猪7个脑组织不同发育时期和不同部位的非标准化cDNA文库，随机测序处理后得到43，122条高质量的5’末端ESTs序列，聚类后产生16，101个类，其中30.6％代表已知功能的基因，75.1％与已知核酸序列有显著相似性，73.3％和已有的家猪ESTs序列有显著相似性，另外21.5％找不到任何同源序列，代表新基因。通过出生前后脑组织基因表达谱的比较，发现多个基因在这两个发育阶段表达有显著差异，预示着家猪脑组织的发育和功能的分化。
基因组学的发展能够将全基因组序列应用到噬菌体鉴定以及进化研究和生物学特性的理解中。我们从中国珠江入海口海水中分离出一株弧菌EH3-23和它的裂解性噬菌体EH3-23P1，电镜图片显示EH3-23P1属于有尾噬菌体目，通过鸟枪法全基因组测序，得到一个113，861bp闭合环状的双链DNA序列，平均GC含量为40.4％。基因组注释后发现，EH3-23P1编码195个蛋白质基因，3个tRNA基因，12个不依赖于rho因子的转录终止子。在195个推定的蛋白编码基因中，30个和已知功能基因有显著相似性，30个比对上已有的未知功能基因，135个是EH3-23P1特异基因。在EH3-23P1基因组中识别出一个重要的磷酸代谢补偿基因phoH；另外，EH3-23P1基因组并没有末端冗余的重复序列，表明非序列变换的基因组复制模式。
In this report, we analyzed the expressed sequence tags involved in cellular function from the venomous gland of Deinagkistrodon acutus and the evolution of toxin related genes and gene expression of porcine brain and a complete genome sequence of vibriophage EH3-23P1.
EST represents a segmental DNA sequence from cDNA 5'/3' end sequencing and has been an important tool for studying the gene expression, difference expression and function. The snake venomous gland is a specialized organ, which synthesizes and secretes the complex and abundant toxin proteins. Though gene expression in the snake venomous glands has been extensively studied, the focus has been on the components of the venom. As far as the molecular mechanism of toxin secretion and metabolism is concerned, we still knew a little. Therefore, a fundamental question being arisen is what genes are expressed in the snake venom glands besides many toxin components? To examine extensively the transcripts expressed in the venom gland of Deinagkistrodon acutus and unveil the potential of its products on cellular structure and functional aspects, we generated 8,696 expressed sequence tags (ESTs) from a non-normalized cDNA library. All ESTs were clustered into 3,416 clusters, of which 40.16% of total ESTs belong to recognized toxin-coding sequences; 39.85% are similar to cellular transcripts; and 20.00% have no significant similarity to any known sequences. By analyzing cellular functional transcripts, we found high expression of some venom related genes and gland-specific genes, such as calglandulin EF-hand protein gene and protein disulfide Isomerase gene. The transcripts of creatine kinase and NADH dehydrogenase were also identified at high level. Moreover, abundant cellular structural proteins similar to mammalian muscle tissues were also identified. The comparative analysis with gene expression of other snake venomous glands, the toxin protein of never growth factor is absent of the venom of Deinagkistrodon acutus. The phylogenetic analysis of two snake venom toxin families of group III metalloproteinase and serine protease in suborder Colubroidea showed an early single recruitment event in the viperids evolutionary process. Gene cataloguing and profiling of the venom gland of Deinagkistrodon acutus is an essential requisite to provide molecular reagents for functional genomic studies needed for elucidating mechanisms of action of toxins and surveying physiological events taking place in the very specialized secretory tissue. So this study provides a first global view of the genetic programs for the venom gland of Deinagkistrodon acutus described so far and an insight into molecular mechanism of toxin secreting.
To understand gene expression variation of porcine brain among several developmental stages, seven cDNA libraries from Landrace brain were constructed. We obtained 43,122 high quality expressed sequence tags from 5' end cDNA clone sequencing. After clustering, 16,101 clusters were produced. Of these clusters, 30.6% showed similarity with known functional sequences; 75.1% had homology with nucleic acid database; 73.3% matched porcine ESTs from database; 21.5% represented novel genes. Comparison of gene expression indicated that the level of many genes expression showed significant difference between prenatal and postnatal porcine brain, which implied the development of porcine and functional differentiation.
Based on complete genome sequences, we can identify bacteriophages and understand their evolution and biological character. We isolated a vibrio strain named EH3-23 in estuarine seawater of Southern China Pearl River and a lytic EH3-23P1. The electron micrograph showed that EH3-23P1 belong to Caudovirales. The 113,861 bp closed circular genome of EH3-23P1 was determined by whole genome shotgun sequencing, which has 40.4% of an average G+C content. EH3-23P1 encodes 195 putative protein-encoding open reading frames (CDSs), 3 tRNAs, 12 rho-independent transcription terminators. Of putative 195 CDSs, 30 match known function genes, 30 match known hypothetic genes, 135 are unique to phage EH3-23P1. We identified a phosphate starvation gene phoH in EH3-23P1. No terminal redundant repeat sequences were identified in EH3-23P1 genome, implying non-permute DNA replication mode.
引文
Aekermann H-W, Krisch HM (1997) A catalogue of T4-type bacteriophages. Archives of Virology 142:2329-2345
Ackermann HW (1998) Tailed bacteriophages: the order caudovirales. Adv Virus Res 51:135-201
Adams MD, Dubnick M, Kerlavage AR, Moreno R, Kelley JM, Utterback TR, Nagle JW, Fields C, Venter JC (1992) Sequence identification of 2,375 human brain genes. Nature 355: 632-634
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651-1656
Adams MH (1959) Bacteriophage. New York: Interscience Publishers.
Adelman K, Brody EN, Buckle M (1998) Stimulation of bacteriophage T4 middle transcription by the T4 proteins MotA and AsiA occurs at two distinct steps in the transcription cycle. Proc Natl Acad Sci U S A 95:15247-15252
Adelman K, Orsini G, Kolb A, Graziani L, Brody EN (1997) The interaction between the Asia protein of bacteriophage T4 and the sigma70 subunit of Escherichia coli RNA polymerase. J Biol Chem 272:27435-27443
Aird SD (2002) Ophidian envenomation strategies and the role of purines. Toxicon 40:335-393
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29
Audio S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme D J, Yeats C, Eddy SR (2004) The Pfam protein families database. Nucleic Acids Res 32:D138-141
Berry R, Stevens T J, Walter NA, Wilcox AS, Rubano T, Hopkins JA, Weber J, Goold R, Soares MB, Sikela JM (1995) Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. Nat Genet 10:415-423
Blomberg LA, Zuelke KA (2004) Serial analysis of gene expression (SAGE) during porcine embryo development. Reprod Fertil Dev 16:87-92
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13:278-284
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99:14250-14255
Brussow H (2001) Phages of dairy bacteria. Annu Rev Microbiol 55:283-303
Brussow H (2005) Phage therapy: the Escherichia coli experience. Microbiology 151:2133-2140
Brussow H, Desiere F (2001) Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol 39:213-222
Campbell A (1994) Comparative molecular biology of lambdoid phages. Annu Rev Microbiol 48: 193-222
Campbell A (2003) The future of bacteriophage biology. Nat Rev Genet 4:471-477
Canchaya C, Fournous G, Brussow H (2004) The impact of prophages on bacterial chromosomes. Mol Microbiol 53:9-18
Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brussow H (2003) Phage as agents of lateral gene transfer. Curr Opin Microbiol 6:417-424
Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H (2003) Prophage genomics. Microbiol Mol Biol Rev 67: 238-276, table of contents
Carulli JP, Artinger M, Swain PM, Root CD, Chee L, Tulig C, Guerin J, Osborne M, Stein G, Lian J, Lomedico PT (1998) High throughput analysis of differential gene expression. J Cell Biochem Suppl 30-31:286-296
Casjens S (2003) Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 49: 277-300
Chen F, Lu J (2002) Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl Environ Microbiol 68:2589-2594
Chen M, Presting G, Barbazuk WB, Goieoechea JL, Blaekmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545
Chibani-Chennoufi S, Canehaya C, Bruttin A, Brussow H (2004) Comparative Genomics of the T4-Like Escherichia coli Phage JS98: Implications for the Evolution of T4 Phages. J. Bacteriol. 186:8276-8286
Cicero MP, Alexander KA, Kreuzer KN (1998) The MotA transcriptional activator of bacteriophage T4 binds to its specific DNA site as a monomer. Biochemistry 37:4977-4984
Cirera S, Wintero AK, Fredholm M (2000) Why do we still find anonymous ESTs? Mamm Genome 11:689-693
Clark MS, Edwards Y J, Peterson D, Clifton SW, Thompson AJ, Sasaki M, Suzuki Y, Kikuehi K, Watabe S, Kawakami K, Sugano S, Elgar G, Johnson SL (2003) Fugu ESTs: new resources for transcription analysis and genome annotation. Genome Res 13:2747-2753
Culley AI, Lang AS, Suttle CA (2003) High diversity of unknown picorna-like viruses in the sea. Nature 424:1054-1057
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636-4641
Desplats C, Krisch HM (2003) The diversity and evolution of the T4-type bacteriophages. Res Microbiol 154:259-267
Diemer V, Hoyle M, Baglioni C, Millis AJ (1992) Expression of porcine complement cytolysis inhibitor mRNA in cultured aortic smooth muscle cells. Changes during differentiation in vitro. J Biol Chem 267:5257-5264
Duvernell DD, Turner BJ (1998) Swimmer 1, a new low-copy-number LINE family in teleost genomes with sequence similarity to mammalian L1. Mol Biol Evol 15:1791-1793
Ermolaeva MD, Khalak HG, Owen W, Smith HO, Salzberg SL (2000) Prediction of Transcription Terminators in Bacterial Genomes. J Mol Biol 301:27-33
Esposito D, Fitzmaurice WP, Benjamin RC, Goodman SD, Waldman AS, Seoeea JJ (1996) The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids Res 24:2360-2368
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175-185
Fahrenkrug SC, Smith TP, Freking BA, Cho J, White J, Vallet J, Wise T, Rohrer G, Pertea G, Sultana R, Quackenbush J, Keele JW (2002) Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly. Mamm Genome 13:475-478
Filee J, Tetart F, Suttle CA, Krisch HM (2005) Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. PNAS 102:12471-12476
Francisehetti IM, My-Pham V, Harrison J, Garfield MK, Ribeiro JM (2004) Bitis gabonica (Gaboon viper) snake venom gland: toward a catalog for the full-length transcripts (cDNA) and proteins. Gene 337:55-69
Fry BG (2005) From genome to "venome": molecular origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences and related body proteins. Genome Res 15:403-420
Fry BG, Vidal N, Norman JA, Vonk F J, Scheib H, Ramjan SFR, Kuruppu S, Fung K, Hedges SB, Richardson MK, Hodgson WC, Ignjatovie V, Summerhayes R, Kochva E (2006) Early evolution of the venom system in lizards and snakes. Nature 439:584-588
Fry BG, Wuster W (2004) Assembling an arsenal: origin and evolution of the snake venom proteome inferred from phylogenetic analysis of toxin sequences. Mol Biol Evol 21:870-883
Fry BG, Wuster W, Kini RM, Brusie V, Khan A, Venkataraman D, Rooney AP (2003) Molecular evolution and phylogeny of elapid snake venom three-finger toxins. J Mol Evol 57:110-129
Giaeobini P, Kopin AS, Beart PM, Mercer LD, Fasolo A, Wray S (2004) Cholecystokinin modulates migration of gonadotropin-releasing hormone- 1 neurons. J Neurosci 24:4737-4748
Gold L(1988) Posttranscriptional regulatory mechanisms in Escherichia coli. Annu Rev Biochem 57: 199-233
Gomez SM, Eigimeier K, Segurens B, Dehoux P, Couloux A, Scarpelli C, Wincker P, Weissenbaeh J, Brey PT, Roth CW (2005) Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones. Genome Biol 6:R39
Grundling A, Manson MD, Young R (2001) Holins kill without warning. Proc Natl Acad Sci U S A 98:9348-9352
Gubler U, Chua AO, Hoffman B J, Collier K J, Eng J (1984) Cloned cDNA to cholecystokinin mRNA predicts an identical preprocholecystokinin in pig brain and gut. Proc Natl Acad Sci U S A 81:4307-4310
Guo LY, Pang S, Ruan QQ, Zhou YC (1999) Isolation and Characterization of a Neurotrophic Factor-like Substance from Venom of Agkistrodon acutus. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 31:211-214
Hardies SC, Comeau AM, Serwer P, Suttle CA (2003) The complete sequence of marine bacteriophage VpV262 infecting vibrio parahaemolyticus indicates that an ancestral component of a T7 viral supergroup is widespread in the marine environment. Virology 310: 359-371
Hendrix RW (2002) Bacteriophages: evolution of the majority. Theor Popul Biol 61:471-480
Hendrix RW (2003) Bacteriophage genomics. Curr Opin Microbiol 6:506-511
Hendrix RW, Hatfull GF, Smith MC (2003) Bacteriophages with tails: chasing their origins and evolution. Res Microbiol 154: 253-257
Hendrix RW,Lawrenee JG, Hatfull GF, Casjens S (2000) The origins and ongoing evolution of viruses. Trends Microbiol 8:504-508
Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci U S A 96:2192-2197
Hertwig S, Klein I, Schmidt V, Beck S, Hammerl JA, Appel B (2003) Sequence analysis of the genome of the temperate Yersinia enterocolitica phage PY54. J Mol Bio1331:605-622
Hishiki T, Kawamoto S, Morishita S, Okubo K (2000) BodyMap: a human and mouse gene expression database. Nucleic Acids Res 28:136-138
Hoog C (1991) Isolation of a large number of novel mammalian genes by a differential cDNA library screening strategy. Nucleic Acids Res 19:6123-6127
Ha W, Yan Q, Shen DK, Liu F, Zhu ZD, Song HD, Xu XR, Wang ZJ, Rong YP, Zeng LC, Wu J, Zhang X, Wang JJ, Xu XN, Wang SY, Fu G, Zhang XL, Wang ZQ, Brindley PJ, McManus DP, Xue CL, Feng Z, Chen Z, Han ZG (2003) Evolutionary and biomedical implications of a Schistosoma japonicum complementary DNA resource. Nat Genet 35: 139-147
Igarashi K, Fujita N, Ishihama A (1991) Identification of a subunit assembly domain in the alpha subunit, of Escherichia coli RNA polymerase. J Mol Biol 218:1-6
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuehi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes A J, Bruford E, Carninci P, Chelala C, Couillault C, de Souza S J, Debily MA, Devignes MD, Dubehak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson A J, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2: e 162
Jiang Z, Zhang M, Wasem VD, Michal JJ, Zhang H, Wright RW, Jr. (2003) Census of genes expressed in porcine embryos and reproductive tissues by mining an expressed sequence tag database based on human genes. Biol Reprod 69: 1177-1182
Joseph R, Dou D, Tsang W (1995) Neuronatin mRNA: alternatively spliced forms of a novel brain-specific mammalian developmental gene. Brain Res 690:92-98
Junqueira-de-Azevedo Ide L, Ho PL (2002) A survey of gene expression and diversity in the venom glands of the pitviper snake Bothrops insularis through the generation of expressed sequence tags (ESTs). Gene 299:279-291
Junqueira-de-Azevedo Ide L, Pertinhez T, Spisni A, Carreno FR, Farah CS, Ho PL (2003) Cloning and expression of calglandulin, a new EF-hand protein from the venom glands of Bothrops insularis snake in E. coli. Biochim Biophys Acta 1648:90-98
Kajikawa M, Ohshima K, Okada N (1997) Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. Mol Biol Evol 14:1206-1217
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277-280
Kao SH, McClain WH (1980) Roles of bacteriophage T4 gene 5 and gene s products in cell lysis. J Virol 34:104-107
Kapfhammer D, Blass J, Evers S, Reidl J (2002) Vibrio cholerae phage K139: complete genome sequence and comparative genomics of related phages. J Bacteriol 184:6592-6601
Kashima S, Roberto PG, Soares AM, Astolfi-Filho S, Pereira JO, Giuliati S, Faria M, Jr., Xavier MA, Fontes MR, Giglio JR, Franca SC (2004) Analysis of Bothrops jararacussu venomous gland transcriptome focusing on structural and functional aspects: I--gene expression profile of highly expressed phospholipases A2. Biochimie 86:211-219
Khan AS, Wilcox AS, Polymeropoulos MH, Hopkins JA, Stevens TJ, Robinson M, Orpana AK, Sikela JM (1992) Single pass sequencing and physical and genetic mapping of human brain cDNAs. Nat Genet 2:180-185
Kikuehi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376-379
Kinkead B, Nemeroff CB (2002) Neurotensin: an endogenous antipsychotic? Curr Opin Pharmacol 2: 99-103
Krogh A, Brown M, Mian IS, Sjolander K, Haussler D (1994) Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235:1501-1531
Kudva IT, Jelacic S, Tarr PI, Youderian P, Hovde CJ (1999) Biocontrol of Escherichia coli O157 with O157-specific bacteriophages. Appl Environ Microbiol 65:3767-3773
Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5: 150-163
Kunin V, Goidovsky L, Darzentas N, Ouzounis CA (2005) The net of life: Reconstructing the microbial phylogenetic network. Genome Res.: gr.3666505
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoezky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T., Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouek JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wineker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstoek K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Sehultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Horniseher K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chert HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent W J, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara V J, Ponting CP,Sehuler G, Sehultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
Lane D J, Pace B, Olsen G J, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82: 6955-6959
Lawrenee JG, Hatfull GF, Hendrix RW (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 184:4891-4905
Leiman PG, Chipman PR, Kostyuchenko VA, Mesyanzhinov VV, Rossmann MG (2004) Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host. Cell 118:419-429
Liberopouios E, Siamopoulos K, Elisaf M (2004) Apolipoprotein E and renal disease. Am J Kidney Dis 43:223-233
Liu Q, Zhang X, Yin W, Li C, Han Y, Qiu P, Su X, Hu S, Yan G (2006) A catalog for transcripts in the venom gland of the Agkistrodon acutus: identification of the toxins potentially involved in coagulopathy. Biochem Biophys Res Commun 341:522-531
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:95.5-964
Lueehini S, Desiere F, Brussow H (1999) Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. J Virol 73:8647-8656
Luke K, Radek A, Liu X, Campbell J, Uzan M, Haselkorn R, Kogan Y (2002) Microarray analysis of gene expression during bacteriophage T4 infection. Virology 299:182-191
Mann NH, Clokie MRJ, Millard A, Cook A, Wilson WH, Wheatley PJ, Letarov A, Krisch HM (2005) The Genome of S-PM2, a "Photosynthetic" T4-Type Bacteriophage That Infects Marine Synechococcus Strains. J. Bacteriol. 187:3188-3200
Mannisto RH, Kivela HM, Paulin L, Bamford DH, Bamford JK (1999) The complete genome sequence of PM2, the first lipid-containing bacterial virus To Be isolated. Virology 262: 355-363
Marshall P, Sharma M, Hinton DM (1999) The bacteriophage T4 transcriptional activator MotA accepts various base-pair changes within its binding sequence. J Mol Biol 285:931-944
Matsuzaki S, Rashel M, Uehiyama J, Sakurai S, Ujihara T, Kuroda M, Ikeuehi M, Tani T, Fujieda M, Wakiguchi H, Imai S (2005) Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. J Infect Chemother 11: 211-219
McGrath S, Fitzgerald GF, van Sinderen D (2004) The impact of bacteriophage genomics. Curr Opin Bioteclmol 15:94-99
Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Cieeko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szezypinski B, Fraser CM (2003) Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol 185:5220-5233
Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W (2003) Bacteriophage T4 genome. Microbiol Mol Biol Rev 67:86-156
Mironov AA, Fiekett JW, Gelfand MS (1999) Frequent alternative splicing of human genes. Genome Res 9:1288-1293
Mody M, Cao Y, Cui Z, Tay KY, Shyong A, Shimizu E, Pham K, Sehultz P, Welsh D, Tsien JZ (2001) Genome-wide gene expression profiles of the developing mouse hippocampus. Proc Natl Acad Sci U S A 98:8862-8867
Moore R J, Chamberlain RM, Khuri FR (2004) Apolipoprotein E and the risk of breast cancer in African-American and non-Hispanic white women. A review. Oncology 66:79-93
Mosig G, Gewin J, Luder A, Colowick N, Vo D (2001) Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer. Proc Natl Acad Sci U S A 98:8306-8311
Mou CY, Zhang SC, Lin JH, Yang WL, Wu WY, Wei JW, Wu XK, Du JC, Fu ZY, Ye LT, Lu Y, Xie XJ, Wang YL, Xu AL (2002) EST analysis of mRNAs expressed in neurula of Chinese amphioxus. Biochem Biophys Res Commun 299:74-84
Nagase T, Kikuno R, Ohara O (2001) Prediction of the coding sequences of unidentified human genes. ⅩⅪ. The complete sequences of 60 new. cDNA clones from brain which code for large proteins. DNA Res 8:179-187
Nobis W, Ren X, Suehyta SP, Suehyta TR, Zanella AJ, Coussens PM (2003) Development of a porcine brain cDNA library, EST database, and microarray resource. Physiol Genomics 16: 153-159
O'Flynn G, Ross RP, Fitzgerald GF, Coffey A (2004) Evaluation of a cocktail of three bacteriophages for biocontrol of Escherichia coli O157:H7. Appl Environ Microbiol 70: 3417-3424
Oakey HJ, Cullen BR, Owens L (2002) The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML. J Appl Microbiol 93:1089-1098
Ohara O, Nagase T, Ishikawa K, Nakajima D, Ohira M, Seki N, Nomura N (1997) Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins. DNA Res 4:53-59
Ohno M, Chijiwa T, Oda-Ueda N, Ogawa T, Hattori S (2003) Molecular evolution of myotoxic phospholipases A2 from snake venom. Toxicon 42:841-854
Onishi A, Iwamoto M, Akita T, Mikawa S, Takeda K, Awata T, Hanada H, Perry AC (2000) Pig cloning by microinjection of fetal fibroblast nuclei. Science 289:1188-1190
Papke RT, Doolittle WF (2003) Phage evolution: new worlds of genomic diversity. Curt Biol 13: R606-607
Paul JH, Sullivan MB (2005) Marine phage genomics: what have we learned? Curr Opin Biotechnol 16:299-307
Paul JH, Sullivan MB, Segall AM, Rohwer F (2002) Marine phage genomics. Comp Biochem Physiol B Biochem Mol Biol 133:463-476
Paul JH, Williamson S J, Long A, Authement RaN, John D, Segall AM, Rohwer FL, Androlewicz M, Patterson S (2005) Complete genome sequence of phiHSIC, a pseudotemperate marine phage of Listonella pelagia. Appl Environ Microbiol 71:3311-3320
Pednlla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, Brueker W, Kumar V, Kandasamy J, Keenan L, Bardarov S, Kriakov J, Lawrence JG, Jacobs WR, Jr., Hendrix RW, Hatfull GF (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113:171 - 182
Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Niekerson DA, Boyce-Jacino M (1999) Mining SNPs from EST databases. Genome Res 9:167-174
Pierre LS, Woods R, Earl S, Masci PP, Lavin MF (2005) Identification and analysis of venom gland-specific genes from the coastal taipan (Oxyuranus scutellatus) and related species. Cell Mol Life Sci 62:2679-2693
Poirier J (2003) Apolipoprotein E and cholesterol metabolism in the pathogenesis and treatment of Alzheimer's disease. Trends Mol Med 9:94-101
Ramanculov E, Young R (2001) Functional analysis of the phage T4 holin in a lambda context. Mol Genet Genomics 265:345-353
Rice P, Longden I, Bleasby A (2000) EMBOSS; The European Molecular Biology Open Software Suite. Trends Genet 16: 276-277
Rogic S, Mackworth AK, Ouellette FB (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res 11: 817-832
Rohwer F, Edwards R (2002) The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184: 4529-4535
Romualdi C, Bortoluzzi S, D'Alessi F, Danieli GA (2003) IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics 12:159-162
Sandegren L, Nord D, Sjoberg BM (2005) SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages. Nucleic Acids Res 33: 6203-6213
Sandegren L, Sjoberg B-M (2004) Distribution, Sequence Homology, and Homing of Group Ⅰ Introns among T-even-like Bacteriophages. J. Biol. Chem 279: 22218-22227
Seguritan V, Feng I-W, Rohwer F, Swift M, Segall AM (2003) Genome Sequences of Two Closely Related Vibrio parahaemolyticus Phages, VP16T and VP16C. J. Bacteriol. 185: 6434-6447
Sharma M, Marshall P, Hinton DM (1999) Binding of the bacteriophage T4 transcriptional activator, MotA, to T4 middle promoter DNA: evidence for both major and minor groove contacts. J Mol Biol 290: 905-915
Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1-10
Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW (2005) Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations. PLoS Biology 3: e144
Sutcliffe JG (1988) mRNA in the mammalian central nervous system. Annu Rev Neurosci 11: 157-198
Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL (2001) A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17: 1123-1130
Takahashi Y (2003) The 14-3-3 proteins: gene, gene expression, and function. Neurochem Res 28: 1265-1273
Tetart F, Desplats C, Kutateladze M, Monod C, Ackermann H-W, Krisch HM (2001) Phylogeny of the Major Head and Tail Genes of the Wide-Ranging T4-Type Bacteriophages. J. Bacteriol. 183: 358-366
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
Tiemann B, Depping R, Ruger W (1999) Overexpression, purification, and partial characterization of ADP-ribosyltransferases modA and modB of bacteriophage T4. Gene Expr 8:187-196
Tuggle CK, Green JA, Fitzsimmons C, Woods R, Prather RS, Malchenko S, Soares BM, Kucaba T, Crouch K, Smith C, Tack D, Robinson N, O'Leary B, Scheetz T, Casavant T, Pomp D, Edeal BJ, Zhang Y, Rothschild MF, Garwood K, Beavis W (2003) EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm Genome 14: 565-579
Urbauer JL, Simeonov MF, Urbauer RJ, Adelman K, Gilmore JM, Brody EN (2002) Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions. Proc Natl Acad Sci U S A 99: 1831-1835
Verjovski-Almeida S, DeMarco R, Martins EA, Guimaraes PE, Ojopi EP, Paquola AC, Piazza JP, Nishiyama MY, Jr., Kitajima JP, Adamson RE, Ashton PD, Bonaldo MF, Coulson PS, Dillon GP, Farias LP, Gregorio SP, Ho PL, Leite RA, Malaquias LC, Marques RC, Miyasato PA, Nascimento AL, Ohlweiler FP, Reis EM, Ribeiro MA, Sa RG, Stukart GC, Soares MB, Gargioni C, Kawano T, Rodrigues V, Madeira AM, Wilson RA, Menck CF, Setubal JC, Leite LC, Dias-Neto E (2003) Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nat Genet 35: 148-157
Vidal N, Hedges SB (2002) Higher-level relationships of caenophidian snakes inferred from four nuclear and mitochondrial genes. C R Biol 325: 987-995
Waldor MK, Mekalanos JJ (1996) Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272: 1910-1914
Wang J, Li S, Zhang Y, Zheng H, Xu Z, Ye J, Yu J, Wong GK (2003) Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 4: 741-749
Whanger PD (2000) Selenoprotein W: a review. Cell Mol Life Sci 57: 1846-1852
Wilcox AS, Khan AS, Hopkins JA, Sikela JM (1991) Use of 3' untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome. Nucleic Acids Res 19: 1837-1843
Wilkens K, Ruger W (1996) Characterization of bacteriophage T4 early promoters in vivo with a new promoter probe vector. Plasmid 35: 108-120
Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T (2002) A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525-535
Yoong P, Schuch R, Nelson D, Fischetti VA (2004) Identification of a broadly active phage lytic enzyme with lethal activity against antibiotic-resistant Enterococcus faecalis and Enterococcus faecium. J Bacteriol 186: 4808-4812
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92
Zachary A (1976) Physiology and ecology of bacteriophages of the marine bacterium Beneckea natriegens: salinity. Appl Environ Microbiol 31: 415-422
Zang J, Zhu Z, Yu Y, Teng M, Niu L, Huang Q, Liu Q, Hao Q (2003) Purification, partial characterization and crystallization of acucetin, a protein containing both disintegrin-like and cysteine-rich domains released by auto-proteolysis of a P-Ⅲ-type metalloproteinase AaH-Ⅳ from Agkistrodon acutus venom. Acta Crystallogr D Biol Crystallogr 59: 2310-2312
Zdobnov EM, Apweiler R (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848
Zha XD, Liu J, Xu KS (2004) cDNA cloning, sequence analysis, and recombinant expression of akitonin beta, a C-type lectin-like protein from Agkistrodon acutus. Acta Pharmacol Sin 25: 372-377
Zhao SH, Nettleton D, Liu W, Fitzsimmons C, Ernst CW, Raney NE, Tuggle CK (2003) Complementary DNA macroarray analyses of differential gene expression in porcine fetal and postnatal muscle. J Anim Sci 81: 2179-2188
Zhu Z, Liang Z, Zhang T, Zhu Z, Xu W, Teng M, Niu L (2005) Crystal structures and amidolytic activities of two glycosylated snake venom serine proteinases. J Biol Chem 280: 10524-10529