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During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life's most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.
Pubmed ID: 28575669 RIS Download
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Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
View all literature mentionsThis genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature. Transfer RNAs (tRNAs) represent the single largest, best-understood class of non-protein coding RNA genes found in all living organisms. By far, the major source of new tRNAs is computational identification of genes within newly sequenced genomes. To organize the rapidly growing collection and enable systematic analyses, we created the Genomic tRNA Database (GtRNAdb). The web resource provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions (esp. due to variable post-transcriptional anticodon modification), and questionable tRNA identifications (due to pseudogenes, SINES, or other tRNA-derived elements). We attempt to document all cases we come across, and welcome feedback on new or unrecognized discrepancies.
View all literature mentionsA generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsUltrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.
View all literature mentionsSoftware performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsSoftware performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsCore mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.
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View all literature mentionsThis monoclonal targets Mitochondrial ribosomal protein L11
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View all literature mentionsThis monoclonal targets Puromycin from Streptomyces alboniger
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View all literature mentionsThis polyclonal secondary targets IgG
View all literature mentionsThis monoclonal targets Rabbit TrueBlot: Anti-Rabbit IgG HRP
View all literature mentionsThis polyclonal targets IgG
View all literature mentionsThis monoclonal targets Mouse TrueBlot ULTRA: Anti-Mouse Ig HRP
View all literature mentionsThis unknown targets Human EIF3H
View all literature mentionsThis polyclonal targets RPS3
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View all literature mentionsThis polyclonal targets ACOT1 antibody
View all literature mentionsThis polyclonal targets NSUN2
View all literature mentionsThis monoclonal targets HSPA8 (D12F2) Rabbit mAb
View all literature mentionsThis polyclonal targets OGT / O-Linked N-Acetylglucosamine Transferase antibody
View all literature mentionsThis polyclonal targets YTHDF1
View all literature mentionsThis monoclonal targets Argonaute 2
View all literature mentionsThis monoclonal targets UFM1 antibody [EPR4264(2)]
View all literature mentionsThis polyclonal targets UFL1
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View all literature mentionsThis polyclonal targets SFRS3 antibody
View all literature mentionsThis monoclonal targets Human PABPC1
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View all literature mentionsThis polyclonal targets PKM2 (isoform M1) antibody produced in rabbit
View all literature mentionsThis monoclonal targets PKM2
View all literature mentionsThis polyclonal targets Pkm2
View all literature mentionsThis polyclonal targets Pyruvate Kinase antibody
View all literature mentionsThis monoclonal targets Pkm2
View all literature mentionsThis polyclonal targets PKM2 (isoform M1) antibody produced in rabbit
View all literature mentionsThis monoclonal targets alpha Adaptin
View all literature mentionsThis monoclonal targets FLAG
View all literature mentionsThis unknown targets FXR1
View all literature mentionsThis polyclonal targets CNOT1
View all literature mentionsThis monoclonal targets Tubulin
View all literature mentionsThis polyclonal targets Pyruvate Kinase antibody
View all literature mentionsThis polyclonal targets SFRS3 antibody
View all literature mentionsThis polyclonal targets Lin28B antibody
View all literature mentionsThis polyclonal targets UFL1
View all literature mentionsThis polyclonal targets Clathrin heavy chain
View all literature mentionsThis polyclonal targets ACOT1 antibody
View all literature mentionsThis polyclonal targets OGT / O-Linked N-Acetylglucosamine Transferase antibody
View all literature mentionsThis monoclonal targets UFM1 antibody [EPR4264(2)]
View all literature mentionsThis monoclonal targets Argonaute 2
View all literature mentionsThis monoclonal targets HSPA8 (D12F2) Rabbit mAb
View all literature mentionsThis polyclonal targets IgG
View all literature mentionsThis polyclonal targets MDH2 antibody
View all literature mentionsThis polyclonal secondary targets IgG
View all literature mentionsThis polyclonal targets NSUN2
View all literature mentionsThis monoclonal targets Pkm2
View all literature mentionsThis polyclonal targets Pkm2
View all literature mentionsThis monoclonal targets PKM2
View all literature mentionsThis monoclonal targets Rabbit TrueBlot: Anti-Rabbit IgG HRP
View all literature mentionsThis monoclonal targets Mouse TrueBlot ULTRA: Anti-Mouse Ig HRP
View all literature mentionsThis unknown targets Human EIF3H
View all literature mentionsThis polyclonal targets RPS3
View all literature mentionsThis monoclonal targets Puromycin from Streptomyces alboniger
View all literature mentionsThis polyclonal targets YTHDF1
View all literature mentionsThis monoclonal targets Human PABPC1
View all literature mentionsThis polyclonal targets MVP/LRP
View all literature mentionsThis unknown targets NEMF
View all literature mentionsThis unknown targets RPL14/Ribosomal Protein L14
View all literature mentionsThis polyclonal targets DDX1
View all literature mentionsThis unknown targets
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