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PROVIDER: PRJNA1144439 | ENA |
REPOSITORIES: ENA
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Project description:During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways. During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways.
2022-02-11 | PXD030626 | Pride
Project description:During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways. During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways.
2022-02-11 | PXD028413 | Pride
Project description:Proteome-wide determinants of co-translational chaperone binding in bacteria
| PRJNA1238275 | ENA
Project description:In the model green alga Chlamydomonas (Chlamydomonas reinhardtii), the synthesis of several chloroplast-encoded photosynthetic subunits is feedback-regulated by the assembly state of the respective protein complex. This regulation is known as control by epistasy of synthesis (CES) and matches protein synthesis with the requirements of protein complex assembly in photosystem II (PSII), the cytochrome b6f complex (Cyt b6f), photosystem I (PSI), ATP synthase and Rubisco . In embryophytes, however, CES was only described to coordinate synthesis of the large and small subunits of Rubisco, raising the question if additional CES mechanisms exist in land plants or if stoichiometric photosynthetic protein accumulation is only achieved by the wasteful degradation of excess subunits. We systematically examined suitable tobacco and Arabidopsis mutants with assembly defects in PSII, PSI, Cyt b6f complex, ATP synthase, NDH (NAD(P)H dehydrogenase-like) complex and Rubisco for feedback regulation. Thereby, we validated the CES in Rubisco and uncovered translational feedback regulation in PSII, involving psbA, psbB, psbD and psbH and in Cyt b6f, connecting PetA and PetB protein synthesis. Remarkably, some of these feedback regulation mechanisms are not conserved between the green alga and embryophytes. Our data do not provide any evidence for CES in PSI, ATP synthase or NDH complex assembly in embryophytes. In addition, our data disclose translational feedback regulation adjusting PSI levels with PSII accumulation. Overall, we discovered commonalities and differences in assembly-dependent feedback regulation of photosynthetic complexes between embryophytes and green algae.
2025-07-01 | GSE286011 | GEO
Project description:Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions of Arabidopsis thaliana. COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.
2019-08-25 | E-MTAB-8165 | biostudies-arrayexpress
Project description:RNA immunoprecipitation using mouse monoclonal antibody against human TAF10 protein from HeLa polysome extracts Cells dedicate significant energy to building proteins1, which are often organized in multiprotein assemblies with tightly regulated stoichiometries2. Cotranslational assembly, a process of synchronous translation and protein heterodimerization, is a potential mechanism for efficient matching of partner subunits and avoiding the negative effects of protein aggregation3. Recent studies in bacteria demonstrate that cotranslational assembly of the LuxA-LuxB dimer follows the order established by operon structure and is more efficient than post-translational assembly4. As genes encoding protein complex subunits are dispersed among chromosomes in eukaryotes, it is unclear how cotranslational assembly is accomplished mechanistically, but studies in yeast have nevertheless suggested it as a potential assembly pathway5,6,7. Here we show that mammalian transcription complexes, such as the RNA polymerase II general transcription factor TFIID and the TRanscription and EXport complex-2 (TREX-2) assemble co-translationally. Moreover, we show that the position of heterodimerization domains determines the order of cotranslational assembly in mammalian TFIID. In polysomes, the TATA binding protein associated factor 10 (TAF10), which contains a C-terminal histone-fold dimerization domain (HFD) is recruited cotranslationally to its HFD-containing binding partner TAF8. This interaction is established unidirectionally and determined by the position rather than the sequence of the dimerization domain. We further show that similar mechanisms guide the assembly of other TFIID subunits. Our results thus predict that cotranslational assembly of eukaryotic multisubunit complexes is a general principle in building multiprotein machines. We used microarrays to assess globally the mRNAs associated with TAF10 and TBP immunoprecipitations from HeLa polysomes.
2017-10-28 | GSE106299 | GEO
Project description:Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunits basal transcription factor TFIID nucleates RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation experiments, single-molecule imaging, proteomics and structure-function analyses, we show that TFIID is built using co-translational assembly. We discovered that all early steps of TFIID assembly, involving protein heterodimerization, happen during protein synthesis. Strikingly, we identify TAF1 – the largest protein in the complex – as a flexible scaffold subunit that co-translationally recruits preassembled TFIID submodules found populating the cytoplasm of cells. Consequently, TAF1 depletion leads to a cytoplasmic accumulation of TFIID building blocks. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly on nascent TAF1 polypeptide, that works as a ‘driver’ subunit. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
2023-07-04 | PXD036358 | Pride
Project description:To obtain a molecular-level understanding of biological processes, it is critical to perform structural characterization of protein complexes and their subunits directly from human tissues. Native top-down mass spectrometry (MS) has emerged as a complementary technique to traditional structural biology methods. Nonetheless, native top-down MS has primarily characterized recombinant or high-abundance protein complexes, as strategies to enrich and preserve low-abundance protein complexes from human tissues is lacking. Here we have developed a native nanoproteomics platform integrating peptide-functionalized nanoparticles to characterize low-abundance protein complexes with high-resolution native top-down MS. We then apply our native nanoproteomics strategy to enrich and structurally elucidate endogenous troponin (cTn) complexes directly from human heart tissue. Our results not only reveal the native complex assembly, post-translational modification landscape, and Ca2+ binding dynamics of the cTn complex but also enable us to propose a paradigm for structural and dynamical characterization of endogenous native protein complexes from human tissues.
2023-06-08 | MSV000092130 | MassIVE