Abstract
SUMMARYThe genetic code allows six reading frames at a double-stranded DNA locus, and many open reading frames (ORFs) overlap extensively with ORFs of annotated genes (e.g., at least 30 bp or having an embedded ORF). Currently, bacterial genome annotation systematically discards embedded overlapping ORFs of genes (OLGs) due to an assumed information-content constraint, and, consequently, very few OLGs are known. Here we use strand-specific RNAseq and ribosome profiling, detecting about 200 embedded or partially overlapping ORFs of gene candidates in the pathogenE. coliO157:H7 EDL933. These are typically short, many of them show clear promoter motifs as determined by Cappable-seq, indistinguishable from those of annotated genes, and are expressed at a low level. We could express most of them as stable proteins, and 49 displayed a potential phenotype. Ribosome profiling analyses in three otherE. colistrains predicted between 84 and 190 embedded antisense OLGs per strain except inE. coliK-12, which is an atypical lab strain. We also found evidence of homology to annotated genes for 100 to 300 OLGs perE. colistrain investigated. Based on this evidence we suggest that bacterial OLGs deserve attention with respect to genome annotation and coding complexity of bacterial genomes. Such sequences may constitute an important coding reserve, opening up new research in genetics and evolutionary biology.
Publisher
Cold Spring Harbor Laboratory
Reference104 articles.
1. Ardern, Z. , Neuhaus, K. , and Scherer, S. (2020). Are Antisense Proteins in Prokaryotes Functional? Frontiers in Molecular Biosciences accepted, 10.3389/fmolb.2020.00187.
2. Identification of unannotated small genes in Salmonella;G3: Genes, Genomes, Genetics,2017
3. A novel gene,ardD, determines antirestriction activity of the non-conjugative transposon Tn5053and is located antisense within thetniAgene
Cited by
11 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献