Biology subjects

Provaznik, J.

Publications and source records attributed to Provaznik, J..

6 recordsLinked to original sources

bioRxiv2026

Ubiquitin selective ribosome profiling reveals systematic principles of co-translational quality control

Protein biogenesis is a stress- and error-sensitive process that can lead to nascent protein misfolding and aggregation, challenging cellular proteostasis.1 Co-translational ubiquitination (CTU) is a critical surveillance mechanism,2,3 yet its regulatory principles remain unclear due to limited known substrates and the lack of translatome-wide methods to query CTU. Here, we introduce UbSeRP, an approach that enables ubiquitin linkage-specific, and translatome-wide mapping of CTU. Focusing on ribosome-associated quality control (RQC), we expand the known endogenous RQC substrates in S. cerevisiae from few4-7 to thousands, reveal that only a subset of all identified disomes undergoes RQC, and uncover biophysical features of nascent chains that predict RQC engagement. We also identify widespread RQC-independent ubiquitination of nascent proteins, implicating broader roles of CTU in protein complex assembly. In a chronological aging model, we show that aging remodels translation and diminishes RQC engagement, favoring RQC-independent proteasomal pathways. Our findings provide systematic insight into the determinants and adaptability of CTU in maintaining proteostasis under changing physiological conditions.

biochemistry↗

bioRxiv2024

A genome resource for the marine annelid Platynereis dumerilii

The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of [~]1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation ([~]3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.

genomics↗

bioRxiv2023

Multiple sex chromosomes of Yponomeuta ermine moths suggest a role of sexual antagonism in sex chromosome turnover in Lepidoptera

Sex chromosome-autosome fusions give rise to neo-sex chromosomes, which provide an insight into early evolution of sex chromosomes and drivers of chromosomal fusions. While sex chromosome-autosome fusions are scarce in vertebrates with female heterogamety ([female]ZW/[male]ZZ), they are common in moths and butterflies (Lepidoptera), the most species rich group with heterogametic females. This contradicts theoretical model that assumes chromosome fusions to be random and predicts them to be rare in taxa with high chromosome number such as Lepidoptera. In the present study we analyzed sex chromosomes in nine ermine moths of the genus Yponomeuta (Yponomeutidae) and their two outgroups, Teinoptila gutella (Yponomeutidae) and Plutella xylostella (Plutellidae). We employed genomic in situ hybridization to identify sex chromosomes and used a custom designed microarray to identify Z-linked genes. Our results confirmed a multiple sex chromosome system Z1Z2W to be present in T. gutella and all Yponomeuta spp. except for Y. tokyonella. The multiple sex chromosome system resulted from a fusion between the W chromosome and autosome homeologous to the Bombyx mori chromosome 2 (BmChr2). The BmChr2 bears a cluster of genes with ovary-specific expression which suggests that sexually antagonistic selection could have driven fixation of the fusion in a common ancestor of Yponomeuta and Teinoptila genera. We hypothesize that sex chromosome turnover in Lepidoptera could be driven by sexual antagonism.

evolutionary biology↗

bioRxiv2022

Co-translational binding of importins to nascent proteins

Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesized that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measured the nascent chain association of all importins in Saccharomyces cerevisiae by selective ribosome profiling. We identified a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This included ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning. One-Sentence SummaryWe describe an unanticipated connection between co-translational protein chaperoning and the nuclear import system.

molecular biology↗

bioRxiv2022

The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera

Genes for major ribosomal RNAs (rDNA) are present in multiple copies organized in tandem arrays. Number and position of rDNA loci can change dynamically and their re-patterning is presumably driven by repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second and third generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses between the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on proximity of homologous sequences to telomeres.

genomics↗

bioRxiv2019

Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods

Long read sequencing is increasingly being used to determine eukaryotic genomes. We used nanopore technology to generate chromosome-level assemblies for 3 different strains of Drechmeria coniospora, a nematophagous fungus used extensively in the study of innate immunity in Caenorhabditis elegans. One natural geographical isolate demonstrated high stability over decades, whereas a second isolate, not only had a profoundly altered genome structure, but exhibited extensive instability. We conducted an in-depth analysis of sequence errors within the 3 genomes and established that even with state-of-the-art tools, nanopore methods alone are insufficient to generate eukaryotic genome sequences of sufficient accuracy to merit inclusion in public databases.

genomics↗