A5026031535- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Enzyme Structure and Function
- Peptidase Inhibition and Analysis
- RNA modifications and cancer
- RNA Research and Splicing
- Amyotrophic Lateral Sclerosis Research
- Parkinson's Disease Mechanisms and Treatments
- Fungal and yeast genetics research
- Mass Spectrometry Techniques and Applications
- Bioinformatics and Genomic Networks
- Bacterial Genetics and Biotechnology
- Ubiquitin and proteasome pathways
- Pancreatic and Hepatic Oncology Research
- Signaling Pathways in Disease
- Microbial bioremediation and biosurfactants
- Infectious Diseases and Tuberculosis
- Iron Metabolism and Disorders
- Gene expression and cancer classification
- Nuclear Receptors and Signaling
- Redox biology and oxidative stress
- DNA Repair Mechanisms
- Trace Elements in Health
Université de Sherbrooke
2014-2024
Genomics (United Kingdom)
2024
PROTEO
2017-2023
Université Laval
2020
Université de Lille
2018
Queen's University Belfast
1970
The Royal Free Hospital
1969
University College London
1969
St. Stephen’s Hospital
1969
Plymouth Hospital
1969
Summary RyhB is a small RNA (sRNA) that downregulates about 20 genes involved in iron metabolism. It expressed under low conditions and pairs with specific mRNAs to trigger their rapid degradation by the degradosome. In contrast this, another study has suggested also activates several increasing mRNA level. Among these activated shiA , which encodes permease of shikimate, an aromatic compound participating biosynthesis siderophores. Here, we demonstrate vivo vitro directly at 5′‐untranslated...
Small RNA (sRNA)-induced mRNA degradation occurs through binding of an sRNA to a target with the concomitant action degradosome, which induces endoribonuclease E (RNase E)-dependent cleavage and targeted mRNA. Because many sRNAs bind at ribosome-binding site (RBS), it is possible that resulting translation block sufficient promote rapid Contrary this mechanism, we report here pairing RyhB sodB initiates even in absence on target. Remarkably, though pairs RBS, vivo distal located >350...
Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion one coding sequence (CDS) per transcript, leading to a substantial underestimation the potential eukaryotes. Here, we present OpenProt, first database fully endorsing polycistronic model genomes...
Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently demonstrated the translation of alternative open-reading frames (altORFs) addition to annotated protein coding sequences (CDSs). We show that a large number small proteins could fact be coded by these altORFs. The putative translated from altORFs orthologs many species contain functional domains. Evolutionary analyses indicate often more extreme conservation patterns than their CDSs. Thousands are...
OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides deeper of open reading frames (ORFs) while mining experimental data evidence using cutting-edge algorithms. This update presents major improvements since initial release OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported Using 131 ribosome profiling datasets re-analysed by to date,...
Abstract The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome various species, as well functional annotations corresponding protein sequences not found in standard databases. Enhancements this update are largely result user feedback include prediction structure, subcellular localization, intrinsic disorder, using cutting-edge algorithms...
Summary The small RNA RyhB has recently been shown to negatively regulate a number of mRNAs encoding dispensable iron‐using proteins in Escherichia coli . resulting decrease the synthesis is thought spare iron order ensure its availability for iron‐requiring that are indispensable. Indeed, expression from heterologous promoter activates iron‐sensing repressor Fur, which suggests an increase pool free intracellular (iron‐sparing). In accordance with these observations, we report here...
Abstract Background Mitochondria have a central role in cellular functions, aging, and certain diseases. They possess their own genome, vestige of bacterial ancestor. Over the course evolution, most genes ancestor been lost or transferred to nucleus. In humans, mtDNA is very small circular molecule with functional repertoire limited only 37 genes. Its extremely compact nature arranged one after other separated by short non-coding regions suggests that there little room for evolutionary...
Over the past 20 years there has been a striking change in clinical pattern of miliary tuberculosis, which is now more common adults than children. This shown by comparative study necropsy records such cases seen same group hospitals 1946-9 and 1966-9. In early period tuberculosis occurred 1·7% necropsies, 54% patients being under age suffering from classical form tuberculosis. By 1966-9 incidence had fallen to 0·47% but all were over 30 age, majority having `cryptic9 presentation. The...
Proteogenomics and ribosome profiling concurrently show that genes may code for both a large one or more small proteins translated from annotated coding sequences (CDSs) unannotated alternative open reading frames (named ORFs altORFs), respectively, but the stoichiometry between same gene is unknown. MIEF1, recently identified as dual-coding gene, harbors CDS newly actively altORF located in 5'UTR. Here, we use absolute quantification with stable isotope-labeled peptides parallel reaction...
Recently, it was demonstrated that proteins can be translated from alternative open reading frames (altORFs), increasing the size of actual proteome. Top-down mass spectrometry-based proteomics allows identification intact containing post-translational modifications (PTMs) as well truncated forms reference ORFs or altORFs.
Pseudogenes are mutated copies of protein-coding genes that cannot be translated into proteins, but a small subset pseudogenes has been detected at the protein level. Although ubiquitin represent one most abundant pseudogene families in many organisms, little is known about their expression and signaling potential. By re-analyzing public RNA-sequencing proteomics datasets, we here provide evidence for several including UBB 4 (UBBP4), which encodes UbKEKS (Q2K, K33E, Q49K, N60S). The...
Article23 November 2020Open Access Transparent process The FUS gene is dual-coding with both proteins contributing to FUS-mediated toxicity Marie A Brunet Corresponding Author [email protected] orcid.org/0000-0001-5973-3522 Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada PROTEO, Quebec Network for Research on Protein Function, Structure, Engineering, Quebec, Search more papers by this author Jean-Francois Jacques orcid.org/0000-0002-0465-0313 Sonya...
Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-based proteomics using customized protein databases generated from sets of transcripts previously detected RNA-seq. This has only been increased the recent discovery that many translated alternative open reading frames rest unannotated at unsuspected locations mRNAs and ncRNAs. These novel products, termed proteins, have left out all previous custom database generation tools. Consequently, genetic...
Iron is required for several metabolic functions involved in cellular growth. Although players iron transport have been identified, the mechanisms by which iron-responsive transcription factors are controlled still poorly understood. In Schizosaccharomyces pombe, Fep1 factor represses genes acquisition response to high levels of iron. contrast, when low, becomes inactive and loses its ability associate with chromatin. molecular basis inactivated under starvation remains unknown, this process...
The Bol2 homolog Fra2 and monothiol glutaredoxin Grx4 together play essential roles in regulating iron homeostasis Schizosaccharomyces pombe. In vivo studies indicate that act as coinhibitory partners inactivate the transcriptional repressor Fep1 response to deficiency. Saccharomyces cerevisiae, is known form a [2Fe-2S]-bridged heterodimer with Grxs Grx3 Grx4, cluster ligands provided by conserved residues Grx3/4 well GSH. this study, we characterized analogous Grx4-Fra2 complex S. pombe...
Abstract Proteogenomics has enabled the detection of novel proteins encoded in non-canonical or alternative open reading frames (altORFs) genes already coding a reference protein. Reanalysis proteomic and ribo-seq data revealed that p53-induced death domain-containing protein (or PIDD1 ) gene encodes second 171 amino acid protein, altPIDD1, addition to known 910 acid-long The two ORFs overlap almost completely, translation initiation site altPIDD1 is located upstream PIDD1. AltPIDD1 more...
Recent functional and proteomic studies in eukaryotes (www.openprot.org) predict the translation of alternative open reading frames (AltORFs) mature G-protein-coupled receptor (GPCR) mRNAs, including that bradykinin B2 (B2R). Our main objective was to determine implication a newly discovered AltORF resulting protein, termed AltB2R, known signaling properties B2R using complementary methodological approaches. When ectopically expressed HeLa cells, AltB2R presented predominant punctate...
Php4 is a nucleo-cytoplasmic shuttling protein that accumulates in the nucleus during iron deficiency. When present nucleus, associates with CCAAT-binding complex and represses genes encoding iron-using proteins. Here, we show nuclear import of independent other subunits complex. relies on two functionally localization sequences (NLSs) are located between amino acid residues 171 to 174 (KRIR) 234 240 (KSVKRVR). Specific substitutions basic alanines within these sufficient abrogate targeting...