Journal of Molecular Evolution

, Volume 72, Issue 1, pp 104–118

Characterization of Maltase Clusters in the Genus Drosophila



To reveal evolutionary history of maltase gene family in the genus Drosophila, we undertook a bioinformatics study of maltase genes from available genomes of 12 Drosophila species. Molecular evolution of a closely related glycoside hydrolase, the α-amylase, in Drosophila has been extensively studied for a long time. The α-amylases were even used as a model of evolution of multigene families. On the other hand, maltase, i.e., the α-glucosidase, got only scarce attention. In this study, we, therefore, investigated spatial organization of the maltase genes in Drosophila genomes, compared the amino acid sequences of the encoded enzymes and analyzed the intron/exon composition of orthologous genes. We found that the Drosophila maltases are more numerous than previously thought (ten instead of three genes) and are localized in two clusters on two chromosomes (2L and 2R). To elucidate the approximate time line of evolution of the clusters, we estimated the order and dated duplication of all the 10 genes. Both clusters are the result of ancient series of subsequent duplication events, which took place from 352 to 61 million years ago, i.e., well before speciation to extant Drosophila species. Also observed was a remarkable intron/exon composition diversity of particular maltase genes of these clusters, probably a result of independent intron loss after duplication of intron-rich gene ancestor, which emerged well before speciation in a common ancestor of all extant Drosophila species.


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



Carbohydrate-Active enZymes


Conserved sequence region


Expressed sequence tags


Glycoside hydrolase


Kilo base


Likelihood-ratio test


Maximum likelihood


Maximum parsimony


Million years ago




Standard error

Supplementary material

239_2010_9406_MOESM1_ESM.xls (38 kb)
Supplementary material 1 (XLS 38 kb)


  1. Adams MD, Celniker SE, Holt RA, Evans CA, Venter JC et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195CrossRefPubMedGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37(Database issue):D26–D31CrossRefPubMedGoogle Scholar
  4. Beverley SM, Wilson AC (1984) Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution. J Mol Evol 21:1–13CrossRefPubMedGoogle Scholar
  5. Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14:988–995CrossRefPubMedGoogle Scholar
  6. Brown CJ, Aquadro CF, Anderson WW (1990) DNA sequence evolution of the amylase multigene family in Drosophila pseudoobscura. Genetics 126:131–138PubMedGoogle Scholar
  7. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37(Database issue):D233–D238CrossRefPubMedGoogle Scholar
  8. Chiba S (1997) Molecular mechanism in α-glucosidase and glucoamylase. Biosci Biotechnol Biochem 61:1233–1239CrossRefPubMedGoogle Scholar
  9. Da Lage JL, Wegnez M, Cariou ML (1996) Distribution and evolution of introns in Drosophila amylase genes. J Mol Evol 43:334–347CrossRefPubMedGoogle Scholar
  10. Da Lage JL, Renard E, Chartois F, Lemeunier F, Cariou ML (1998) Amyrel, a paralogous gene of the amylase gene family in Drosophila melanogaster and the Sophophora subgenus. Proc Natl Acad Sci USA 95:6848–6853CrossRefPubMedGoogle Scholar
  11. Da Lage JL, Maczkowiak F, Cariou ML (2000) Molecular characterization and evolution of the amylase multigene family of Drosophila ananassae. J Mol Evol 51:391–403PubMedGoogle Scholar
  12. Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:184–185CrossRefGoogle Scholar
  13. Eck RV, Dayhoff MO (1966) Atlas of protein sequence and structure. National Biomedical Research Foundation, Silver Springs, MDGoogle Scholar
  14. Ernst HA, Lo Leggio L, Willemoes M, Leonard G, Blum P, Larsen S (2006) Structure of the Sulfolobus solfataricus α-glucosidase: implicationsfor domain conservation and substrate recognition in GH31. J Mol Biol 358:1106–1124CrossRefPubMedGoogle Scholar
  15. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  16. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  17. Gabrisko M, Janecek S (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 276:7265–7278CrossRefPubMedGoogle Scholar
  18. Gaunt MW, Miles MA (2002) An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol Biol Evol 19:748–761PubMedGoogle Scholar
  19. Gilbert DG (2007) DroSpeGe: rapid access database for new Drosophila species genomes. Nucleic Acids Res 35(Database issue):D480–D485CrossRefPubMedGoogle Scholar
  20. Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ (2008) Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Chem Biol 15:1058–1067CrossRefPubMedGoogle Scholar
  21. Godany A, Majzlova K, Horvathova V, Vidova B, Janecek S (2010) Tyrosine 39 of GH13 α-amylase from Thermococcus hydrothermalis contributes to its thermostability. Biologia 65:408–415CrossRefGoogle Scholar
  22. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704CrossRefPubMedGoogle Scholar
  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 579–592Google Scholar
  24. Henikoff S, Wallace JC (1988) Detection of protein similarities using nucleotide sequence databases. Nucleic Acids Res 16:6191–6204CrossRefPubMedGoogle Scholar
  25. Huber RE, Thompson DJ (1973) Studies on a honey bee sucrase exhibiting unusual kinetics and transglucolytic activity. Biochemistry 12:4011–4020CrossRefPubMedGoogle Scholar
  26. Inomata N, Yamazaki T (2000) Evolution of nucleotide substitutions and gene regulation in the amylase multigenes in Drosophila kikkawai and its sibling species. Mol Biol Evol 17:601–615PubMedGoogle Scholar
  27. James AA, Blackmer K, Racioppi JV (1989) A salivary gland-specific, maltase-like gene of the vector mosquito, Aedes aegypti. Gene 75:73–83CrossRefPubMedGoogle Scholar
  28. Janecek S (1992) New conserved amino acid region of α-amylases in the third loop of their (β/α)8-barrel domains. Biochem J 288:1069–1070PubMedGoogle Scholar
  29. Janecek S (1994a) Sequence similarities and evolutionary relationships of microbial, plant and animal α-amylases. Eur J Biochem 224:519–524CrossRefPubMedGoogle Scholar
  30. Janecek S (1994b) 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 353:119–123CrossRefPubMedGoogle Scholar
  31. Janecek S (1995) Close evolutionary relatedness among functionally distantly related members of the (α/β)8-barrel glycosyl hydrolases suggested by the similarity of their fifth conserved sequence region. FEBS Lett 377:6–8CrossRefPubMedGoogle Scholar
  32. Janecek S (2002) How many conserved sequence regions are there in the α-amylase family? Biologia 57(Suppl. 11):29–41Google Scholar
  33. Janecek S, Svensson B, Henrissat B (1997) Domain evolution in the α-amylase family. J Mol Evol 45:322–331CrossRefPubMedGoogle Scholar
  34. Janecek S, Svensson B, MacGregor EA (2003) Relation between domain evolution, specificity, and taxonomy of the α-amylase family members containing a C-terminal starch-binding domain. Eur J Biochem 270:635–645CrossRefPubMedGoogle Scholar
  35. Janecek S, Svensson B, MacGregor EA (2007) A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31. FEBS Lett 581:1261–1268CrossRefPubMedGoogle Scholar
  36. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403–405CrossRefPubMedGoogle Scholar
  37. Jeffs PS, Holmes EC, Ashburner M (1994) The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup. Mol Biol Evol 11:287–304PubMedGoogle Scholar
  38. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4:18CrossRefPubMedGoogle Scholar
  39. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Applic Biosci 8:275–282Google Scholar
  40. Kimura A, Takewaki S, Matsui H, Kubota M, Chiba S (1990) Allosteric properties, substrate specificity, and subsite affinities of honeybee α-glucosidase I. J Biochem 107:762–768PubMedGoogle Scholar
  41. Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M (2008) Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J Biol Chem 283:36328–36337CrossRefPubMedGoogle Scholar
  42. Kubota M, Tsuji M, Nishimoto M, Wongchawalit J, Okuyama M, Mori H, Matsui H, Surarit R, Svasti J, Kimura A, Chiba S (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 68:2346–2352CrossRefPubMedGoogle Scholar
  43. Kuriki T, Imanaka T (1999) The concept of the α-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng 87:557–565CrossRefPubMedGoogle Scholar
  44. Lajoie M, Bertrand D, El-Mabrouk N (2010) Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Mol Biol Evol 27:761–772CrossRefPubMedGoogle Scholar
  45. Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25:132–1307CrossRefGoogle Scholar
  46. Lehmann J, Eisenhardt C, Stadler PF, Krauss V (2010) Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. BMC Evol Biol 10:156CrossRefPubMedGoogle Scholar
  47. Lin K, Zhang DY (2005) The excess of 5′ introns in eukaryotic genomes. Nucleic Acids Res 33:6522–6527CrossRefPubMedGoogle Scholar
  48. Lodge JA, Maier T, Liebl W, Hoffmann V, Sträter N (2003) Crystal structure of Thermotoga maritima α-glucosidase AglA defines a new clan of NAD+-dependent glycosidases. J Biol Chem 278:19151–19158CrossRefPubMedGoogle Scholar
  49. MacGregor EA, Janecek S, Svensson B (2001) Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim Biophys Acta 1546:1–20CrossRefPubMedGoogle Scholar
  50. Machovic M, Janecek S (2006a) The evolution of putative starch-binding domains. FEBS Lett 580:6349–6356CrossRefPubMedGoogle Scholar
  51. Machovic M, Janecek S (2006b) Starch-binding domains in the post-genome era. Cell Mol Life Sci 63:2710–2724CrossRefPubMedGoogle Scholar
  52. Machovic M, Janecek S (2008) Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48. Biologia 63:1053–1064CrossRefGoogle Scholar
  53. Maczkowiak F, Da Lage JL (2006) Origin and evolution of the Amyrel gene in the α-amylase multigene family of Diptera. Genetica 128:145–158CrossRefPubMedGoogle Scholar
  54. Matsuura Y, Kusunoki M, Harada W, Kakudo M (1984) Structure and possible catalytic residues of Taka-amylase A. J Biochem 95:697–702PubMedGoogle Scholar
  55. Mitri C, Parmentier ML, Pin JP, Bockaert J, Grau Y (2004) Divergent evolution in metabotropic glutamate receptors. A new receptor activated by an endogenous ligand different from glutamate in insects. J Biol Chem 279:9313–9320CrossRefPubMedGoogle Scholar
  56. Mitri C, Soustelle L, Framery B, Bockaert J, Parmentier ML, Grau Y (2009) Plant insecticide L-canavanine repels Drosophila via the insect orphan GPCR DmX. PLoS Biol 7:e1000147CrossRefPubMedGoogle Scholar
  57. Nakajima R, Imanaka T, Aiba S (1986) Comparison of amino acid sequences of eleven different α-amylases. Appl Microbiol Biotechnol 23:355–360CrossRefGoogle Scholar
  58. Nishimoto M, Kubota M, Tsuji M, Mori H, Kimura A, Matsui H, Chiba S (2001) Purification and substrate specificity of honeybee. Apis mellifera L., α-glucosidase III. Biosci Biotechnol Biochem 65:1610–1616CrossRefPubMedGoogle Scholar
  59. Oslancova A, Janecek S (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 59:1945–1959CrossRefPubMedGoogle Scholar
  60. Popadic A, Anderson WW (1995) Evidence for gene conversion in the amylase multigene family of Drosophila pseudoobscura. Mol Biol Evol 12:564–572PubMedGoogle Scholar
  61. Rigden DJ (2002) Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13. FEBS Lett 523:17–22CrossRefPubMedGoogle Scholar
  62. Russo CA, Takezaki N, Nei M (1995) Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 12:391–404PubMedGoogle Scholar
  63. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  64. Shirai T, Hung VS, Morinaka K, Kobayashi T, Ito S (2008) Crystal structure of GH13 α-glucosidase GSJ from one of the deepest sea bacteria. Proteins 73:126–133CrossRefPubMedGoogle Scholar
  65. Snyder M, Davidson N (1983) Two gene families clustered in a small region of the Drosophila genome. J Mol Biol 166:101–118CrossRefPubMedGoogle Scholar
  66. Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B (2006) Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng Des Sel 19:555–562CrossRefPubMedGoogle Scholar
  67. Stoltzfus A, Logsdon JM Jr, Palmer JD, Doolittle WF (1997) Intron “sliding” and the diversity of intron positions. Proc Natl Acad Sci USA 94:10739–10744CrossRefPubMedGoogle Scholar
  68. Takewaki S, Chiba S, Kimura A, Matsui H, Koike Y (1980) Purification and properties of α-glucosidases of the honey bee Apis mellifera L. Agric Biol Chem 44:731–740Google Scholar
  69. Takewaki S, Kimura A, Kubota M, Chiba S (1993) Substrate specificity and subsite affinities of honeybee α-glucosidase II. Biosci Biotechnol Biochem 57:1508–1513CrossRefGoogle Scholar
  70. Tamura K, Subramanian S, Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21:36–44CrossRefPubMedGoogle Scholar
  71. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  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 421–470Google Scholar
  73. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, The FlyBase Consortium (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 37(Database issue):D555–D559CrossRefPubMedGoogle Scholar
  74. Vieira CP, Vieira J, Hartl DL (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 14:985–993PubMedGoogle Scholar
  75. Zhang Z, Inomata N, Cariou ML, Da Lage JL, Yamazaki T (2003a) Phylogeny and the evolution of the amylase multigenes in the Drosophila montium species subgroup. J Mol Evol 56:121–130CrossRefPubMedGoogle Scholar
  76. Zhang Z, Inomata N, Yamazaki T, Kishino H (2003b) Evolutionary history and mode of the amylase multigene family in Drosophila. J Mol Evol 57:702–709CrossRefPubMedGoogle Scholar
  77. Zheng L, Whang LH, Kumar V, Kafatos FC (1995) Two genes encoding midgut-specific maltase-like polypeptides from Anopheles gambiae. Exp Parasitol 81:272–283CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Institute of Molecular BiologySlovak Academy of SciencesBratislavaSlovakia

Personalised recommendations