Analyses of the structural organization of unidentified open reading frames from metagenome.
Although there is no sequence information, activity-based screening methods can select positive clones from a metagenomic library. However, the low frequency of positive hits that is caused by improper expression of proteins in the cloning host Escherichia coli might be improved. In order to investigate whether the metagenome can be expressed in E. coli, the structural organization of URFs from metagenome was analyzed in terms of transcription and translation factors, and compared to those of 4300 ORFs of E. coli K12. Considerable differences in amino acid composition and codon usage occurred between the metagenome URFs and E. coli ORFs, reflecting a barrier for protein expression within the host E. coli. From the analyses of the promoter and RBS regions, sequences or patterns in the corresponding region of metagenome URFs were found to be dissimilar to E. coli consensus. These results suggested that these factors are considerable to screen the clones from metagenomic library with the activity-based approach.
Park
Seung-Hye
SH
Institute of Biotechnological Industry, Inha University, Incheon 402-751, Republic of Korea.
Cheong
Dae-Eun
DE
Lee
Jin-Young
JY
Han
Sang-Soo
SS
Lee
Jin-Ho
JH
Kim
Geun-Joong
GJ
D001483:Base Sequence; D016384:Consensus Sequence; D048168:Escherichia coli K12 / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D020543:Proteome