Mandal Uttam Roy, Das Shib Sankar, Chattopadhyay Brajadulal, Sahoo Satyabrata
Department of Mathematics, Raidighi College, Raidighi, W.B., India.
Department of Mathematics, Uluberia College, Uluberia, Howrah, W.B, India.
Iran J Biotechnol. 2019 Sep 1;17(3):e2254. doi: 10.29252/ijb.2254. eCollection 2019 Sep.
In Archaea, previous studies have revealed the presence of multiple intron-containing tRNAs and split tRNAs. The full unexpurgated analysis of archaeal tRNA genes remains a challenging task in the field of bioinformatics, because of the presence of various types of hidden tRNA genes in archaea. Here, we suggested a computational method that searched for widely separated genes encoding tRNA halves to generate suppressive variants of missing tRNAs.
The exploration of tRNA genes from a genome with varying hypotheses, among all three domain of life (eukaryotes, bacteria and archaea), has been rapidly identified in different ways in the field of bioinformatics. Like eukaryotic tRNA genes, it has been established that two separated regions of the coding sequence of a tRNA gene are essential and sufficient for promotion of transcription. Our objective is to find out the two essential regions in the genome sequence which comprises two halves of the hidden tRNAs.
Considering the existence of split tRNA genes widely separated throughout the genome, we developed our tRNA search algorithm to predict such separated tRNA genes by searching both a conserved terminal 5'- and 3'-motif of tRNA in agreement with the split hypothesis on the basis of cloverleaf prediction and precise insilico determination of bulge-helix-bulge secondary structure at the splice sites.
By a comprehensive search for all kinds of missing tRNA genes, we have constructed hybrid tRNA genes containing one essential region from tDNA (XYZ) and the other from tDNA (ABC), both from same species in the archaea. We have also found, this type of hybrid tRNA genes are identified in the different species of the archaea (XYZ ASN, ARG and MET; ABC ASP,SER, ARG and PRO).These hybrid split tRNA share a common structural motif called bulge-helix-bulge (BHB) a more relaxed bulge-helix loop (BHL), at the leader exon boundary and suggested to be evolutionary interrelated.
Analysis of the complete genome sequences of DSM 5348, Desulfurococcus kamchatkensis 1221n and Ignicoccus hospitalis KIN4/I in archaea by our algorithm revealed that a number of hybrid tRNAs are constructed from different tDNAs . Asymmetric combination of 5' and 3' tRNA halves may have generated the diversity of tRNA molecules. Our study of hybrid tRNA genes will provide a new molecular basis for upcoming tRNA studies.
在古菌中，先前的研究已经揭示了存在多个含内含子的tRNA和分裂tRNA。由于古菌中存在各种类型的隐藏tRNA基因，对古菌tRNA基因进行全面的未删减分析在生物信息学领域仍然是一项具有挑战性的任务。在此，我们提出了一种计算方法，该方法搜索编码tRNA半体的广泛分离的基因，以生成缺失tRNA的抑制变体。
在生物信息学领域，已经以不同方式迅速确定了在生命的所有三个域（真核生物、细菌和古菌）中，从具有不同假设的基因组中探索tRNA基因。与真核生物tRNA基因一样，已经确定tRNA基因编码序列的两个分离区域对于促进转录是必不可少且足够的。我们的目标是在基因组序列中找出构成隐藏tRNA两半的两个必需区域。
考虑到分裂tRNA基因在整个基因组中广泛分离的存在，我们开发了tRNA搜索算法，通过在三叶草叶型预测的基础上搜索与分裂假设一致的tRNA保守末端5'-和3'-基序，并精确地在计算机上确定剪接位点处的凸起-螺旋-凸起二级结构，来预测这种分离的tRNA基因。
通过全面搜索各种缺失的tRNA基因，我们构建了杂种tRNA基因，其一个必需区域来自tDNA（XYZ），另一个来自tDNA（ABC），二者均来自古菌中的同一物种。我们还发现，这种类型的杂种tRNA基因在古菌的不同物种中被鉴定出来（XYZ为天冬酰胺、精氨酸和甲硫氨酸；ABC为天冬氨酸、丝氨酸、精氨酸和脯氨酸）。这些杂种分裂tRNA在前导外显子边界共享一个称为凸起-螺旋-凸起（BHB）的共同结构基序，一个更宽松的凸起-螺旋环（BHL），并被认为在进化上相互关联。
通过我们的算法对古菌中DSM 5348、堪察加脱硫球菌1221n和医院火球菌KIN4/I的完整基因组序列进行分析，结果显示许多杂种tRNA是由不同的tDNA构建而成的。5'和3'tRNA半体的不对称组合可能产生了tRNA分子的多样性。我们对杂种tRNA基因的研究将为未来的tRNA研究提供新的分子基础。
