Small proteins in bacteria–big challenges in prediction and identification
S Fuchs, S Engelmann - Proteomics, 2023 - Wiley Online Library
Proteins with up to 100 amino acids have been largely overlooked due to the challenges
associated with predicting and identifying them using traditional methods. Recent advances …
associated with predicting and identifying them using traditional methods. Recent advances …
Understanding small ORF diversity through a comprehensive transcription feature classification
D Guerra-Almeida, DA Tschoeke… - DNA …, 2021 - academic.oup.com
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences
smaller than 100 codons that have historically been considered junk DNA by gene …
smaller than 100 codons that have historically been considered junk DNA by gene …
Identifying small proteins by ribosome profiling with stalled initiation complexes
Small proteins consisting of 50 or fewer amino acids have been identified as regulators of
larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the …
larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the …
Unraveling the hidden universe of small proteins in bacterial genomes
S Miravet‐Verde, T Ferrar… - Molecular systems …, 2019 - embopress.org
Identification of small open reading frames (sm ORF s) encoding small proteins (≤ 100
amino acids; SEP s) is a challenge in the fields of genome annotation and protein discovery …
amino acids; SEP s) is a challenge in the fields of genome annotation and protein discovery …
A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq
Ribosome profiling (Ribo-seq) has catalyzed a paradigm shift in our understanding of the
translational 'vocabulary'of the human genome, discovering thousands of translated open …
translational 'vocabulary'of the human genome, discovering thousands of translated open …
Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides
I Fijalkowski, P Willems, V Jonckheere, L Simoens… - …, 2022 - academic.oup.com
Genomic studies of bacteria have long pointed toward widespread prevalence of small open
reading frames (sORFs) encoding for short proteins,< 100 amino acids in length. Despite the …
reading frames (sORFs) encoding for short proteins,< 100 amino acids in length. Despite the …
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 …
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 …
Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells
NE Shirokikh - Critical reviews in biochemistry and molecular …, 2022 - Taylor & Francis
During protein biosynthesis, ribosomes bind to messenger (m) RNA, locate its protein-
coding information, and translate the nucleotide triplets sequentially as codons into the …
coding information, and translate the nucleotide triplets sequentially as codons into the …
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 …