Escherichia coli Small Proteome
Escherichia coli was one of the first species to have its genome sequenced and remains one
of the best-characterized model organisms. Thus, it is perhaps surprising that recent studies …
of the best-characterized model organisms. Thus, it is perhaps surprising that recent studies …
Alternative reading frames are an underappreciated source of protein sequence novelty
Z Ardern - Journal of Molecular Evolution, 2023 - Springer
Protein-coding DNA sequences can be translated into completely different amino acid
sequences if the nucleotide triplets used are shifted by a non-triplet amount on the same …
sequences if the nucleotide triplets used are shifted by a non-triplet amount on the same …
RiboReport-benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
R Gelhausen, T Müller, SL Svensson… - Briefings in …, 2022 - academic.oup.com
Small proteins encoded by short open reading frames (ORFs) with 50 codons or fewer are
emerging as an important class of cellular macromolecules in diverse organisms. However …
emerging as an important class of cellular macromolecules in diverse organisms. However …
Are antisense proteins in prokaryotes functional?
Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes.
Across bacterial species hundreds of short open reading frames antisense to annotated …
Across bacterial species hundreds of short open reading frames antisense to annotated …
[HTML][HTML] Optimality in the standard genetic code is robust with respect to comparison code sets
S Wichmann, Z Ardern - Biosystems, 2019 - Elsevier
The genetic code and its evolution have been studied by many different approaches. One
approach is to compare the properties of the standard genetic code (SGC) to theoretical …
approach is to compare the properties of the standard genetic code (SGC) to theoretical …
Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers
Abstract Analysis of genome wide transcription start sites (TSSs) revealed an unexpected
complexity since not only canonical TSS of annotated genes are recognized by RNA …
complexity since not only canonical TSS of annotated genes are recognized by RNA …
Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data
Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation,
including finding many unannotated genes. However, protocols for RIBO-Seq and …
including finding many unannotated genes. However, protocols for RIBO-Seq and …
Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome
All genomes include gene families with very limited taxonomic distributions that potentially
represent new genes and innovations in protein-coding sequence, raising questions on the …
represent new genes and innovations in protein-coding sequence, raising questions on the …
Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes
our understanding of genomic complexity. We report two exceptionally long (957 nt and …
our understanding of genomic complexity. We report two exceptionally long (957 nt and …
A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC)
B Zehentner, Z Ardern, M Kreitmeier… - Frontiers in …, 2020 - frontiersin.org
Antisense transcription is well known in bacteria. However, translation of antisense RNAs is
typically not considered, as the implied overlapping coding at a DNA locus is assumed to be …
typically not considered, as the implied overlapping coding at a DNA locus is assumed to be …