杨树基因组AMT转运蛋白的生物信息学特性

本研究中，通过隐马尔科夫模型（HMM）和杨树蛋白质库搜索，共找到17个杨树铵转运体蛋白（PtAMTs）。利用生物信息学方法，我们对杨树家族17条AMT蛋白序列的系统发生和AMT基因组定位进行分析，然后对其氨基酸组成成分、理化性质以及二级结构进行预测和分析，同时还分析了杨树与拟南芥、水稻、番茄、百脉根和欧洲油菜的AMT基因家族之间的联系。二级结构预测结果发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异；仪一螺旋和无规则卷曲为主要二级结构组成部分。同源性比对分析表明，PtAMT基因家族主要分为2个亚家族，AMT1（11个成员）和AMT2（6个成员），基因结果分析表明AMT2亚家族成员不含内含子。杨树AMT蛋白的亚细胞定位分析表明PtAMT主要定位于膜结构上。电子表达图谱分析结果表明：只有XP002309151和XP002334025基因有对应的EST序列，并有相应的电子表达谱，并主要在花蕾表达。

Bioinformatical Characterization of Putative Ammonium Transporters in Pop ulus tric hoc arp a Genome

Using Hidden Markov Model （HMM） scan strategy and searching the protein database, 17 ammonium transport proteins （PtAMTs） were identified from the genome of Populus trichocarpa （hereafter P. trichocarpa）. Utilizing bioinformatic methods, we carried out phylogeny analyses and genome localization of the 17 AMT pro- teins, and analyzed their amino acid composition, physical and chemical characteristics as well as secondary struc- ture prediction. Moreover, we assayed the evolutionary relationship of AMT gene families among P. trichocarpa and Arabidopsis thaliana （A. thaliana）, Oryza sativa （0. sativa）, Lycopersicon esculentum （L. esculentum）, Lotus japonicus （L. japonicus）, and Brassica napus （B. napus）. Secondary structure assay revealed that hydrophobic amino acid sequences varied during the different PtAMTs and alpha helix and random coil were the two mainly predicted patterns. Homology alignment showed that PtAMTs were classified into 2 sub-families, 11 members in AMT 1 and 6 in AMT2. Structural analyses of extrons and introns showed that all A MT2 members had no introns. Subcellular localization of protein analysis showed that： All 17 VvAMTs had delicate distribution, and were main- ly located in the plasma membrane. EST analyses showed that only XP_002309151 and XP_002334025 had corre- sponding EST sequences and electronic expression profiles, which presumably expressed in bud.