Characterization of maltase clusters in the genus drosophila

Journal of Molecular Evolution

Volumn 72, Issue 1, 2011, Pages 104-118

  Gabriško, Marek ^a   Janeček, Štefan ^a  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

Author keywords

Alpha amylase family; Drosophila; Gene cluster; Intron exon composition; Maltase; Molecular evolution

Indexed keywords

ALPHA GLUCOSIDASE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; DROSOPHILA; ENZYMOLOGY; EXON; GENE; GENETICS; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALPHA-GLUCOSIDASES; AMINO ACID SEQUENCE; ANIMALS; BASE COMPOSITION; BASE SEQUENCE; DROSOPHILA; EVOLUTION, MOLECULAR; EXONS; GENES, INSECT; INTRONS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 79951676654     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9406-3     Document Type: Article

References (77)

1. MD Adams SE Celniker RA Holt CA Evans JC Venter, et al. 2000 The genome sequence of Drosophila melanogaster Science 287 2185 2195 10.1126/science.287. 5461.2185 10731132 (Pubitemid 30177013)
2. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D 2231712
3. DA Benson I Karsch-Mizrachi DJ Lipman J Ostell EW Sayers 2009 GenBank Nucleic Acids Res 37 Database issue D26 D31 1:CAS:528:DC%2BD1cXhsFejtLzF 10.1093/nar/gkn723 18940867
4. SM Beverley AC Wilson 1984 Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution J Mol Evol 21 1 13 1:CAS:528:DyaL2MXlvFKltA%3D%3D 10.1007/BF02100622 6442354 (Pubitemid 15172239)
5. E Birney M Clamp R Durbin 2004 GeneWise and Genomewise Genome Res 14 988 995 1:CAS:528:DC%2BD2cXjvFyku7c%3D 10.1101/gr.1865504 15123596 (Pubitemid 38660520)
6. CJ Brown CF Aquadro WW Anderson 1990 DNA sequence evolution of the amylase multigene family in Drosophila pseudoobscura Genetics 126 131 138 1:CAS:528:DyaK3MXhsFyjtL4%3D 1699840 (Pubitemid 20336279)
7. BL Cantarel PM Coutinho C Rancurel T Bernard V Lombard B Henrissat 2009 The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics Nucleic Acids Res 37 Database issue D233 D238 1:CAS:528: DC%2BD1cXhsFejtL7K 10.1093/nar/gkn663 18838391
8. S Chiba 1997 Molecular mechanism in α-glucosidase and glucoamylase Biosci Biotechnol Biochem 61 1233 1239 1:CAS:528:DyaK2sXlvFeqt7c%3D 10.1271/bbb.61.1233 9301101
9. JL Da Lage M Wegnez ML Cariou 1996 Distribution and evolution of introns in Drosophila amylase genes J Mol Evol 43 334 347 1:CAS:528:DyaK28XmtFais78%3D 10.1007/BF02339008 8798339 (Pubitemid 26337543)
10. JL Da Lage E Renard F Chartois F Lemeunier ML Cariou 1998 Amyrel, a paralogous gene of the amylase gene family in Drosophila melanogaster and the Sophophora subgenus Proc Natl Acad Sci USA 95 6848 6853 1:CAS:528: DyaK1cXjslynu78%3D 10.1073/pnas.95.12.6848 9618501 (Pubitemid 28278069)
11. JL Da Lage F Maczkowiak ML Cariou 2000 Molecular characterization and evolution of the amylase multigene family of Drosophila ananassae J Mol Evol 51 391 403 1:CAS:528:DC%2BD3cXotlWnsbY%3D 11040291
12. Drosophila 12 Genomes Consortium 2007 Evolution of genes and genomes on the Drosophila phylogeny Nature 450 184 185 10.1038/450184a (Pubitemid 350100528)
13. Eck RV, Dayhoff MO (1966) Atlas of protein sequence and structure. National Biomedical Research Foundation, Silver Springs, MD
14. HA Ernst L Lo Leggio M Willemoes G Leonard P Blum S Larsen 2006 Structure of the Sulfolobus solfataricus α-glucosidase: implicationsfor domain conservation and substrate recognition in GH31 J Mol Biol 358 1106 1124 1:CAS:528:DC%2BD28XjvVamurk%3D 10.1016/j.jmb.2006.02.056 16580018 (Pubitemid 44403821)
15. J Felsenstein 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach J Mol Evol 17 368 376 1:CAS:528:DyaL3MXls1Cisr8%3D 10.1007/BF01734359 7288891 (Pubitemid 11016207)
16. J Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791 10.2307/2408678
17. M Gabrisko S Janecek 2009 Looking for the ancestry of the heavy-chain subunits of heteromeric amino acid transporters rBAT and 4F2hc within the GH13 α-amylase family FEBS J 276 7265 7278 1:CAS:528:DC%2BD1MXhsFGqtr3F 10.1111/j.1742-4658.2009.07434.x 19878315
18. MW Gaunt MA Miles 2002 An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks Mol Biol Evol 19 748 761 1:CAS:528:DC%2BD38XjsFaku7g%3D 11961108 (Pubitemid 34521306)
19. DG Gilbert 2007 DroSpeGe: rapid access database for new Drosophila species genomes Nucleic Acids Res 35 Database issue D480 D485 1:CAS:528:DC%2BD2sXivFKksA%3D%3D 10.1093/nar/gkl997 17202166 (Pubitemid 46056255)
20. TM Gloster JP Turkenburg JR Potts B Henrissat GJ Davies 2008 Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora Chem Biol 15 1058 1067 1:CAS:528:DC%2BD1cXht1KmsrfE 10.1016/j.chembiol.2008.09.005 18848471
21. A Godany K Majzlova V Horvathova B Vidova S Janecek 2010 Tyrosine 39 of GH13 α-amylase from Thermococcus hydrothermalis contributes to its thermostability Biologia 65 408 415 1:CAS:528:DC%2BC3cXlt1agurs%3D 10.2478/s11756-010-0030-x
22. S Guindon O Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
23. Hartl DL, Lozovskaya ER (1994) Genome evolution: between the nucleosome and the chromosome. In: Schierwater B, Streit B, Wagner GP, DeSalle R (eds) Molecular ecology and evolution: approaches and applications. Birkhäuser Verlag, Basel, pp 579-592
24. S Henikoff JC Wallace 1988 Detection of protein similarities using nucleotide sequence databases Nucleic Acids Res 16 6191 6204 1:CAS:528:DyaL1cXlt1Cls7Y%3D 10.1093/nar/16.13.6191 3135536
25. RE Huber DJ Thompson 1973 Studies on a honey bee sucrase exhibiting unusual kinetics and transglucolytic activity Biochemistry 12 4011 4020 1:CAS:528:DyaE2cXisVamsA%3D%3D 10.1021/bi00744a035 4745659
26. N Inomata T Yamazaki 2000 Evolution of nucleotide substitutions and gene regulation in the amylase multigenes in Drosophila kikkawai and its sibling species Mol Biol Evol 17 601 615 1:CAS:528:DC%2BD3cXisVSgtL8%3D 10742051 (Pubitemid 30210705)
27. AA James K Blackmer JV Racioppi 1989 A salivary gland-specific, maltase-like gene of the vector mosquito, Aedes aegypti Gene 75 73 83 1:CAS:528:DyaK3cXhs1eg 10.1016/0378-1119(89)90384-3 2470653
28. 8-barrel domains Biochem J 288 1069 1070 1:CAS:528:DyaK38XmsVOksb8%3D 1471979 (Pubitemid 23031796)
29. S Janecek 1994 Sequence similarities and evolutionary relationships of microbial, plant and animal α-amylases Eur J Biochem 224 519 524 1:CAS:528:DyaK2cXlslWqurs%3D 10.1111/j.1432-1033.1994.00519.x 7925367 (Pubitemid 24282835)
30. S Janecek 1994 Parallel β/α-barrels of α-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of β-amylase: evolutionary distance is a reflection of unrelated sequences FEBS Lett 353 119 123 1:CAS:528:DyaK2MXhsVajtLg%3D 10.1016/0014-5793(94)01019-6 7926034
31. 8-barrel glycosyl hydrolases suggested by the similarity of their fifth conserved sequence region FEBS Lett 377 6 8 1:CAS:528:DyaK2MXhtVSgtr7P 10.1016/0014-5793(95)01309-1 8543020 (Pubitemid 26008975)
32. S Janecek 2002 How many conserved sequence regions are there in the α-amylase family? Biologia 57 Suppl. 11 29 41 1:CAS:528: DC%2BD3sXhtVClurc%3D (Pubitemid 135713689)
33. S Janecek B Svensson B Henrissat 1997 Domain evolution in the α-amylase family J Mol Evol 45 322 331 1:CAS:528:DyaK2sXms1Gis7Y%3D 10.1007/PL00006236 9302327 (Pubitemid 27418360)
34. S Janecek B Svensson EA MacGregor 2003 Relation between domain evolution, specificity, and taxonomy of the α-amylase family members containing a C-terminal starch-binding domain Eur J Biochem 270 635 645 1:CAS:528: DC%2BD3sXhslCru7k%3D 10.1046/j.1432-1033.2003.03404.x 12581203 (Pubitemid 36286576)
35. S Janecek B Svensson EA MacGregor 2007 A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31 FEBS Lett 581 1261 1268 1:CAS:528:DC%2BD2sXjsVWnsr4%3D 10.1016/j.febslet.2007.02.036 17349635 (Pubitemid 46463954)
36. F Jeanmougin JD Thompson M Gouy DG Higgins TJ Gibson 1998 Multiple sequence alignment with Clustal X Trends Biochem Sci 23 403 405 1:CAS:528:DyaK1cXntlansLg%3D 10.1016/S0968-0004(98)01285-7 9810230 (Pubitemid 28511382)
37. PS Jeffs EC Holmes M Ashburner 1994 The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup Mol Biol Evol 11 287 304 1:CAS:528: DyaK2cXjtFKqtb4%3D 8170369 (Pubitemid 24075753)
38. G Jobb A von Haeseler K Strimmer 2004 TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics BMC Evol Biol 4 18 10.1186/1471-2148-4-18 15222900 (Pubitemid 40205271)
39. DT Jones WR Taylor JM Thornton 1992 The rapid generation of mutation data matrices from protein sequences Comput Applic Biosci 8 275 282 1:CAS:528:DyaK38Xlt1Okt7w%3D
40. A Kimura S Takewaki H Matsui M Kubota S Chiba 1990 Allosteric properties, substrate specificity, and subsite affinities of honeybee α-glucosidase I J Biochem 107 762 768 1:CAS:528:DyaK3cXkt1Sjs7Y%3D 2204617 (Pubitemid 20173324)
41. M Kitamura M Okuyama F Tanzawa H Mori Y Kitago N Watanabe A Kimura I Tanaka M Yao 2008 Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron J Biol Chem 283 36328 36337 1:CAS:528:DC%2BD1cXhsFWnsrjF 10.1074/jbc.M806115200 18981178
42. M Kubota M Tsuji M Nishimoto J Wongchawalit M Okuyama H Mori H Matsui R Surarit J Svasti A Kimura S Chiba 2004 Localization of α-glucosidases I, II and III in organs of European honeybee. Apis mellifera L., and origin of α-glucosidase in honey Biosci Biotechnol Biochem 68 2346 2352 1:CAS:528:DC%2BD2cXhtVKltr%2FN 10.1271/bbb.68.2346 15564675 (Pubitemid 40033511)
43. T Kuriki T Imanaka 1999 The concept of the α-amylase family: structural similarity and common catalytic mechanism J Biosci Bioeng 87 557 565 1:CAS:528:DyaK1MXltFCmu74%3D 10.1016/S1389-1723(99)80114-5 16232518 (Pubitemid 29315284)
44. M Lajoie D Bertrand N El-Mabrouk 2010 Inferring the evolutionary history of gene clusters from phylogenetic and gene order data Mol Biol Evol 27 761 772 1:CAS:528:DC%2BC3cXjslaltLw%3D 10.1093/molbev/msp271 19903657
45. SQ Le O Gascuel 2008 An improved general amino acid replacement matrix Mol Biol Evol 25 132 1307 10.1093/molbev/msn067 (Pubitemid 351882003)
46. J Lehmann C Eisenhardt PF Stadler V Krauss 2010 Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication BMC Evol Biol 10 156 10.1186/1471-2148-10-156 20500887
47. K Lin DY Zhang 2005 The excess of 5 introns in eukaryotic genomes Nucleic Acids Res 33 6522 6527 1:CAS:528:DC%2BD2MXhtlSjurfI 10.1093/nar/gki970 16314314 (Pubitemid 41806416)
48. +-dependent glycosidases J Biol Chem 278 19151 19158 1:CAS:528:DC%2BD3sXjvVSksLo%3D 10.1074/jbc.M211626200 12588867 (Pubitemid 36799304)
49. EA MacGregor S Janecek B Svensson 2001 Relationship of sequence and structure to specificity in the α-amylase family of enzymes Biochim Biophys Acta 1546 1 20 1:CAS:528:DC%2BD3MXhvVagtLk%3D 10.1016/S0167-4838(00) 00302-2 11257505 (Pubitemid 32217799)
50. M Machovic S Janecek 2006 The evolution of putative starch-binding domains FEBS Lett 580 6349 6356 1:CAS:528:DC%2BD28Xht1els77E 10.1016/j.febslet.2006.10.041 17084392 (Pubitemid 44750919)
51. M Machovic S Janecek 2006 Starch-binding domains in the post-genome era Cell Mol Life Sci 63 2710 2724 1:CAS:528:DC%2BD2sXhtFSrt78%3D 10.1007/s00018-006-6246-9 17013558 (Pubitemid 44913313)
52. M Machovic S Janecek 2008 Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48 Biologia 63 1053 1064 10.2478/s11756-008-0162-4
53. F Maczkowiak JL Da Lage 2006 Origin and evolution of the Amyrel gene in the α-amylase multigene family of Diptera Genetica 128 145 158 1:CAS:528:DC%2BD28XhtVCntbnM 10.1007/s10709-005-5578-y 17028947 (Pubitemid 44544110)
54. Y Matsuura M Kusunoki W Harada M Kakudo 1984 Structure and possible catalytic residues of Taka-amylase A J Biochem 95 697 702 1:CAS:528: DyaL2cXhsFejtbo%3D 6609921
55. C Mitri ML Parmentier JP Pin J Bockaert Y Grau 2004 Divergent evolution in metabotropic glutamate receptors. A new receptor activated by an endogenous ligand different from glutamate in insects J Biol Chem 279 9313 9320 1:CAS:528:DC%2BD2cXhs1OmsLc%3D 10.1074/jbc.M310878200 14660580 (Pubitemid 38295995)
56. C Mitri L Soustelle B Framery J Bockaert ML Parmentier Y Grau 2009 Plant insecticide L-canavanine repels Drosophila via the insect orphan GPCR DmX PLoS Biol 7 e1000147 10.1371/journal.pbio.1000147 19564899
57. R Nakajima T Imanaka S Aiba 1986 Comparison of amino acid sequences of eleven different α-amylases Appl Microbiol Biotechnol 23 355 360 1:CAS:528:DyaL28Xhs1Chu7g%3D 10.1007/BF00257032 (Pubitemid 16131888)
58. M Nishimoto M Kubota M Tsuji H Mori A Kimura H Matsui S Chiba 2001 Purification and substrate specificity of honeybee. Apis mellifera L., α-glucosidase III Biosci Biotechnol Biochem 65 1610 1616 1:CAS:528:DC%2BD3MXlvVSmtr0%3D 10.1271/bbb.65.1610 11515546 (Pubitemid 33617628)
59. A Oslancova S Janecek 2002 Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the α-amylase family defined by the fifth conserved sequence region Cell Mol Life Sci 59 1945 1959 1:CAS:528: DC%2BD38Xps1enur8%3D 10.1007/PL00012517 12530525 (Pubitemid 36015867)
60. A Popadic WW Anderson 1995 Evidence for gene conversion in the amylase multigene family of Drosophila pseudoobscura Mol Biol Evol 12 564 572 1:CAS:528:DyaK2MXmsVOqs78%3D 7659012
61. DJ Rigden 2002 Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13 FEBS Lett 523 17 22 1:CAS:528:DC%2BD38Xlt12mu7s%3D 10.1016/S0014-5793(02)02879-X 12123797 (Pubitemid 34786051)
62. CA Russo N Takezaki M Nei 1995 Molecular phylogeny and divergence times of drosophilid species Mol Biol Evol 12 391 404 1:CAS:528:DyaK2MXltF2ntb8%3D 7739381
63. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425 1:STN:280: DyaL1c7ovFSjsA%3D%3D 3447015
64. T Shirai VS Hung K Morinaka T Kobayashi S Ito 2008 Crystal structure of GH13 α-glucosidase GSJ from one of the deepest sea bacteria Proteins 73 126 133 1:CAS:528:DC%2BD1cXhtVyksLnE 10.1002/prot.22044 18398906
65. M Snyder N Davidson 1983 Two gene families clustered in a small region of the Drosophila genome J Mol Biol 166 101 118 1:STN:280:DyaL3s3hs1WhtA%3D%3D 10.1016/S0022-2836(83)80001-1 6854639 (Pubitemid 13079456)
66. MR Stam EG Danchin C Rancurel PM Coutinho B Henrissat 2006 Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins Protein Eng Des Sel 19 555 562 1:CAS:528:DC%2BD28Xht1Ohu7rJ 10.1093/protein/gzl044 17085431 (Pubitemid 44950461)
67. A Stoltzfus JM Logsdon Jr JD Palmer WF Doolittle 1997 Intron "sliding" and the diversity of intron positions Proc Natl Acad Sci USA 94 10739 10744 1:CAS:528:DyaK2sXmtlekt7g%3D 10.1073/pnas.94.20.10739 9380704 (Pubitemid 27430804)
68. S Takewaki S Chiba A Kimura H Matsui Y Koike 1980 Purification and properties of α-glucosidases of the honey bee Apis mellifera L Agric Biol Chem 44 731 740 1:CAS:528:DyaL3cXktVarsL0%3D
69. S Takewaki A Kimura M Kubota S Chiba 1993 Substrate specificity and subsite affinities of honeybee α-glucosidase II Biosci Biotechnol Biochem 57 1508 1513 1:CAS:528:DyaK2cXhtVSiu7s%3D 10.1271/bbb.57.1508
70. K Tamura S Subramanian S Kumar 2004 Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks Mol Biol Evol 21 36 44 1:CAS:528:DC%2BD2cXhvVKqsrg%3D 10.1093/molbev/msg236 12949132 (Pubitemid 38233516)
71. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
72. Throckmorton LH (1975) The phylogeny, ecology and geography of Drosophila. In: King RC (ed) Handbook of genetics, volume 3, invertebrates of genetic interest. Plenum Publishing, New York, pp 421-470
73. S Tweedie M Ashburner K Falls P Leyland P McQuilton S Marygold G Millburn D Osumi-Sutherland A Schroeder R Seal H Zhang The FlyBase Consortium 2009 FlyBase: enhancing Drosophila Gene Ontology annotations Nucleic Acids Res 37 Database issue D555 D559 1:CAS:528:DC%2BD1cXhsFejtLnN 10.1093/nar/gkn788 18948289
74. CP Vieira J Vieira DL Hartl 1997 The evolution of small gene clusters: evidence for an independent origin of the maltase gene cluster in Drosophila virilis and Drosophila melanogaster Mol Biol Evol 14 985 993 1:CAS:528:DyaK2sXms1entro%3D 9335139 (Pubitemid 27419235)
75. Z Zhang N Inomata ML Cariou JL Da Lage T Yamazaki 2003 Phylogeny and the evolution of the amylase multigenes in the Drosophila montium species subgroup J Mol Evol 56 121 130 1:CAS:528:DC%2BD3sXhtFKltr4%3D 10.1007/s00239-002-2384-3 12574858 (Pubitemid 36169680)
76. Z Zhang N Inomata T Yamazaki H Kishino 2003 Evolutionary history and mode of the amylase multigene family in Drosophila J Mol Evol 57 702 709 1:CAS:528:DC%2BD2cXjsVemtA%3D%3D 10.1007/s00239-003-2521-7 14745539 (Pubitemid 37543984)
77. L Zheng LH Whang V Kumar FC Kafatos 1995 Two genes encoding midgut-specific maltase-like polypeptides from Anopheles gambiae Exp Parasitol 81 272 283 1:CAS:528:DyaK28XhtVSltrk%3D 10.1006/expr.1995.1118 7498424 (Pubitemid 26024428)