Beta-amylase (BAM) plays a central role in the complete degradation of starch tometabolisable or fermentable sugars during the germination or maltingof cereal grains. It was found to be involved in the abiotic stress responsesof crops. A genome-wide survey of BAM genes in 5 grass species was performed, including rice, maize, sorghum, Setaria, and Brachypodium, by describing their phylogenetic relationships, functional divergence, and adaptive evolution. The phylogeny classified the gramineous BAM genes into 10 clusters of orthologous genes (COGs), and the genes in the same COG shared the syntenic region. Functional divergence analysis provided statistical evidence that both the shift in the evolutionary rate pattern and cluster-specific alterations of amino acid physiochemical properties contributed to COG-specific functional evolution of BAM genes in grasses. In addition, 3 COGs were found to be influenced by positive selection through maximum likelihood analysis. The expression patterns of rice BAM genes were investigated, and the resultsrevealed that they were differentially expressed under the treatments of abiotic stresses. These observations may provide useful references for further functional detection of BAM genes in grasses.
[1] Zhang D, Wang Y. Beta-amylase in developing apple fruits: Activities, amounts and subcellular localization[J]. Science in China Series C: Life Sciences, 2002, 45(4): 429-440.
[2] Rejzek M, Stevenson C E, Southard A M, et al. Chemical genetics and cereal starch metabolism: Structural basis of the non- covalent and covalent inhibition of barley beta- amylase[J]. Molecular BioSystems, 2011, 7(3): 718-730.
[3] Vinje M A, Willis D K, Duke S H, et al. Differential expression of two beta-amylase genes (Bmy1 and Bmy2) in developing and mature barley grain[J]. Planta, 2011, 233(5): 1001-1010.
[4] Totsuka A, Nong V H, Kadokawa H, et al. Residues essential for catalytic activity of soybean beta-amylase[J]. European Journal of Biochemistry, 1994, 221(2): 649-654.
[5] Valerio C, Costa A, Marri L, et al. Thioredoxin-regulated beta-amylase (BAM1) triggers diurnal starch degradation in guard cells, and in mesophyll cells under osmotic stress[J]. Journal of Experimental Botany, 2011, 62(2): 545-555.
[6] Reinhold H, Soyk S, Simkova K, et al. Beta-amylase-like proteins function as transcription factors in Arabidopsis, controlling shoot growth and development[J]. Plant Cell, 2011, 23(4): 1391-1403.
[7] Mason-Gamer R J. The β-amylase genes of grasses and a phylogenetic analysis of the Triticeae (Poaceae)[J]. Ameican Jounal of Botany, 2005, 92(6): 1045-1058.
[8] Goodstein D M, Shu S, Howson R, et al. Phytozome: Acomparative platform for green plant genomics[J]. Nucleic Acids Research, 2012, 40:D1178- D1186.
[9] Robert D, Finn, John Tate, Jaina Mistry, et al. The Pfam protein families database[J]. Nucleic Acids Research, 2008, 36(1): D281-D288.
[10] Larkin M A, Blackshields G, Brown N P, et al. Clustal W and Clustal X version 2.0[J]. Bioinformatics, 2007, 23(21): 2947-2948.
[11] Tamura K, Peterson D, Peterson N, et al. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods[J]. Molecular Biology and Evolution, 2011, 28(10): 2731-2739.
[12] Guindon S, Delsuc F, Dufayard JF, et al.Estimating maximum likelihood phylogenies with PhyML[J]. Methods in Molecular Biology, 2009, 537 (1): 113-137.
[13] Gu X, Velden K V. DIVERGE: Phylogeny-based analysis for functionalstructural divergence of a protein family[J]. Bioinformatics, 2002, 18(3): 500-501.
[14] Suyama M, Torrents D, Bork P. PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments[J]. Nucleic Acids Research, 2006, 34: W609-W612.
[15] Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood[J]. Molecular Biology and Evolution, 2007, 24(8): 1586-1591.
[16] Yang Z, Bielawski J P. Statistical methods for detecting molecular adaptation[J]. Trends in Ecology & Evolution, 2000, 15(12): 496-503.
[17] Tusher V G, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response[J]. Proceedings of the National Academy of Sciences, 2001, 98(9): 5116-5121.
[18] Yang Z, Wang Y, Xu S, et al. Molecular evolution and functional divergence of soluble starch synthase genes in cassava (manihot esculenta crantz)[J]. Evolutionary Bioinformatics Online, 2013, 9: 239- 249.
[19] Gu X. Functional divergence in protein (family) sequence evolution[J]. Genetica, 2003, 118(2/3): 133-141.
[20] Liu Q, Wang H, Zhang Z, et al. Divergence in function and expression of the NOD26- like intrinsic proteins in plants[J]. BMC Genomics, 2009, 10: 313.
[21] Suárez-Castillo E C, García-Arrarás J E. Molecular evolution of the ependymin protein family: A necessary update[J]. BMC Evolutionary Biology, 2007, 7: 23.
[22] Yang Z, Nielsen R, Goldman N, et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites[J]. Genetics, 2000, 155(1): 431-449.
[23] Yang Z, Wong W, Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection[J]. Molecular Biology and Evolution, 2005, 22(4): 1107-1118.
[24] Singh A, Pandey A, Baranwal V, et al. Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development[J]. Plant Signal & Behavior, 2012, 7(7): 847-855.
[25] Vinje M A, Willis D K, Duke SH, et al. Differential expression of two β -amylase genes (Bmy1 and Bmy2) in developing and mature barley grain[J]. Planta, 2011, 233(5): 1001-1010.
[26] Song R, Llaca V, Linton E, et al. Sequence, regulation, and evolution of the maize 22- kD alpha zein gene family[J]. Genome Research, 2001, 11(11): 1817-1825.
[27] Lynch M, O'Hely M, Walsh B, et al. The probability of preservation of a newly arisen gene duplicate[J]. Genetics, 2001, 159(4): 1789-1804.
