Li Ling, Ilarslan Hilal, James Martha G, Myers Alan M, Wurtele Eve Syrkin
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
J Exp Bot. 2007;58(12):3323-42. doi: 10.1093/jxb/erm180. Epub 2007 Sep 20.
Each of four starch debranching enzymes (DBE) is distinct and highly conserved across the plant kingdom; however, the specific functions of these proteins in carbohydrate metabolism are not well understood. DBEs function in both biosynthesis and degradation of starch, and two have been shown to function as multimers in various quarternary structures that can contain one or more DBE proteins, i.e. ISA1 homomultimers and ISA1/ISA2 heteromultimers. This study characterizes potential functional relationships between the three isoamylase-type DBE proteins (ISA) of Arabidopsis using a comprehensive bioinformatics analysis and promoter fusion approach to determine tissue-, subcellular-, and temporal specificity of gene expression. The results reveal complementary sets of expression patterns, in particular that AtISA1 (known to be involved in starch biosynthesis) and AtISA2 (a non-catalytic polypeptide) are co-expressed in some conditions in the absence of AtISA3 (known to be involved in starch degradation), whereas in other conditions AtISA2 is co-expressed with AtISA3 in the absence of AtISA1 (AtISA2 and AtISA3, but not AtISA1, are co-expressed specially in root columella cells and leaf hydathodes). Thus, AtISA2 may function in starch degradation, in addition to its role in starch biosynthesis. AtISA3 and several other potential regulatory genes, starch metabolic genes, and transcription factors, are specifically induced during cold acclimation; these transcription factors are candidates for involvement of cold-induced changes in starch metabolism. Finally, bioinformatics analysis using MetaOmGraph (http://www.metnetdb.org/MetNet_MetaOmGraph.htm) identifies Arabidopsis genes of unknown function that might be involved in starch metabolism in the cold.
四种淀粉去分支酶（DBE）中的每一种都各不相同，且在植物界高度保守；然而，这些蛋白质在碳水化合物代谢中的具体功能尚未完全了解。DBE在淀粉的生物合成和降解中均发挥作用，并且已经证明其中两种酶在各种四级结构中作为多聚体发挥作用，这些四级结构可以包含一种或多种DBE蛋白，即ISA1同型多聚体和ISA1/ISA2异型多聚体。本研究使用全面的生物信息学分析和启动子融合方法来确定基因表达的组织、亚细胞和时间特异性，从而对拟南芥的三种异淀粉酶型DBE蛋白（ISA）之间的潜在功能关系进行了表征。结果揭示了互补的表达模式集，特别是AtISA1（已知参与淀粉生物合成）和AtISA2（一种非催化多肽）在某些条件下在没有AtISA3（已知参与淀粉降解）的情况下共同表达，而在其他条件下，AtISA2在没有AtISA1的情况下与AtISA3共同表达（AtISA2和AtISA3，但不是AtISA1，特别在根冠细胞和叶水孔中共同表达）。因此，AtISA2除了在淀粉生物合成中的作用外，可能还在淀粉降解中发挥作用。AtISA3和其他几个潜在的调控基因、淀粉代谢基因和转录因子在冷驯化过程中被特异性诱导；这些转录因子是参与冷诱导淀粉代谢变化的候选因子。最后，使用MetaOmGraph（http://www.metnetdb.org/MetNet_MetaOmGraph.htm）进行的生物信息学分析确定了拟南芥中可能参与低温下淀粉代谢的功能未知基因。
