Comparative analysis of contextual bias around the translation initiation sites in plant genomes.
Nucleotide distribution around translation initiation site (TIS) is thought to play an important role in determining translation efficiency. Kozak in vertebrates and later Joshi et al. in plants identified context sequence having a key role in translation efficiency, but a great variation regarding this context sequence has been observed among different taxa. The present study aims to refine the context sequence around initiation codon in plants and addresses the sampling error problem by using complete genomes of 7 monocots and 7 dicots separately. Besides positions -3 and +4, significant conservation at -2 and +5 positions was also found and nucleotide bias at the latter two positions was shown to directly influence translation efficiency in the taxon studied. About 1.8% (monocots) and 2.4% (dicots) of the total sequences fit the context sequence from positions -3 to +5, which might be indicative of lower number of housekeeping genes in the transcriptome. A three base periodicity was observed in 5' UTR and CDS of monocots and only in CDS of dicots as confirmed against random occurrence and annotation errors. Deterministic enrichment of GCNAUGGC in monocots, AANAUGGC in dicots and GCNAUGGC in plants around TIS was also established (where AUG denotes the start codon), which can serve as an arbiter of putative TIS with efficient translation in plants.
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
Paras
P
Gupta
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India. Electronic address: latha_rangan@yahoo.com.
Latha
L
Rangan
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
T Venkata
TV
Ramesh
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
Mudit
M
Gupta
D020121:5' Untranslated Regions / Q000235:genetics; D001483:Base Sequence; D015982:Bias; D016000:Cluster Analysis; D018745:Genome, Plant; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010442:Peptide Chain Initiation, Translational; D010507:Periodicity; D010944:Plants / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
D020121:5' Untranslated Regions; D009711:Nucleotides; D012333:RNA, Messenger
Consensus sequence; Dicots; Kozak sequence; Monocots; Translation initiation site