Document Type: Research Paper
Department of Mathematics, Raidighi College, South 24 parganas, India
3Department of Mathematics, Uluberia College, Uluberia, Howrah,W.B, India
Department of Physics Jadavpur University, 188 Raja S.C.Mullick Road Kolkata-700032, India
Department of Physics, Dhruba Chand Halder College, Dakshin Barasat, South 24 Parganas,W.B.,INDIA
Background: 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.
Objective: 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.
Method: 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.
Results: By a comprehensive search for all kinds of missing tRNA genes, we have constructed hybrid tRNA genes containing one essential region from tDNAXYZ and the other from tDNAABC, 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.
Conclusion: Analysis of the complete genome sequences of Metallosphaera sedula 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.