Identified Hybrid tRNA Structure Genes in Archaeal Genome.
Helix (Snails)
Open Reading Frames
RNA, Transfer
Journal
Iranian journal of biotechnology
ISSN: 1728-3043
Titre abrégé: Iran J Biotechnol
Pays: Iran
ID NLM: 101276796
Informations de publication
Date de publication:
Sep 2019
Sep 2019
Historique:
entrez:
21
3
2020
pubmed:
21
3
2020
medline:
21
3
2020
Statut:
epublish
Résumé
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
Sections du résumé
BACKGROUND
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.
OBJECTIVES
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.
MATERIAL AND METHODS
METHODS
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
RESULTS
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.
CONCLUSIONS
CONCLUSIONS
Analysis of the complete genome sequences of
Identifiants
pubmed: 32195286
doi: 10.29252/ijb.2254
pii: IJB-17-3
pmc: PMC7080975
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e2254Informations de copyright
Copyright: © 2019 The Author(s); Published by National Institute of Genetic Engineering and Biotechnology.
Références
Cell Mol Life Sci. 2007 Sep;64(18):2404-12
pubmed: 17599240
RNA. 2007 May;13(5):671-81
pubmed: 17369313
Biol Bull. 1999 Jun;196(3):327-8; discussion 329-30
pubmed: 10390830
J Mol Evol. 2009 Nov;69(5):497-504
pubmed: 19826747
In Silico Biol. 2006;6(5):411-8
pubmed: 17274770
Cell. 1981 May;24(2):573-85
pubmed: 7237560
Nucleic Acids Res. 1984;12 Suppl:r1-57
pubmed: 6728685
Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):17934-9
pubmed: 16330750
J Mol Evol. 2005 Oct;61(4):524-30
pubmed: 16155749
J Theor Biol. 1999 Apr 7;197(3):403-14
pubmed: 10089150
Proc Natl Acad Sci U S A. 1982 Feb;79(4):1195-9
pubmed: 6951168
Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27;366(1580):2936-41
pubmed: 21930585
Nucleic Acids Res. 2011 Dec;39(22):9695-704
pubmed: 21880595
Cell. 1980 Nov;22(2 Pt 2):405-13
pubmed: 7448868
J Theor Biol. 2006 Jun 7;240(3):343-52
pubmed: 16289209
J Mol Biol. 1996 Nov 22;264(1):46-55
pubmed: 8950266
RNA. 2002 Oct;8(10):1189-232
pubmed: 12403461
Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6729-34
pubmed: 8041690
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Nature. 2005 Feb 3;433(7025):537-41
pubmed: 15690044
J Mol Evol. 2008 Jan;66(1):21-35
pubmed: 18058157
Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7
pubmed: 18984615
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2683-7
pubmed: 19190180
Nucleic Acids Res. 2006 May 08;34(8):e63
pubmed: 16682442
Cell. 1980 Jan;19(1):27-35
pubmed: 7357604
J Mol Biol. 2008 Aug 29;381(2):289-99
pubmed: 18602113
Orig Life Evol Biosph. 2004 Dec;34(6):549-70
pubmed: 15570708
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15418-22
pubmed: 16221764
Nucleic Acids Res. 2004 Jan 02;32(1):11-6
pubmed: 14704338
J Biomol Struct Dyn. 2011 Apr;28(5):827-31
pubmed: 21294593
Nat Rev Microbiol. 2005 Jun;3(6):479-88
pubmed: 15931166
Proc Natl Acad Sci U S A. 1981 Jun;78(6):3378-82
pubmed: 6943546
Cell. 1980 Jan;19(1):13-25
pubmed: 7357599