Biology subjects

Kuznetsova, K. G.

Publications and source records attributed to Kuznetsova, K. G..

6 recordsLinked to original sources

bioRxiv2025

MODY mutations in transcription factors HNF1A and HNF1B affect the production of interferon signaling proteins: evidence at the proteome level

We investigated the proteomic consequences of MODY-associated mutations in the transcription factors HNF1A and HNF1B using two cell line models. Quantitative label-free mass spectrometry, employing both data-dependent and data-independent acquisition methods, revealed consistent suppression of energy metabolism and interferon signaling pathways. Pathway and protein interaction analyses confirmed these findings. In cells with the HNF1A frameshift mutation, several predicted transcriptional targets, including A1CF, were significantly downregulated. These results reinforce the link between HNF1A/HNF1B function and mitochondrial activity as well as innate immune signaling, providing a foundation for further mechanistic studies and causal inference research.

systems biology↗

bioRxiv2023

ProHap enables proteomic database generation accounting for population diversity

Amid the advances in genomics, the availability of large reference panels of human haplotypes is key to account for human diversity within and across populations. However, mass spectrometry-based proteomics does not benefit from this information. To address this gap, we introduce ProHap, a Python-based tool that constructs protein sequence databases from phased genotypes of reference panels. ProHap empowers researchers to account for haplotypic diversity in proteomic searches.

bioinformatics↗

bioRxiv2022

Identifying Protein Haplotypes by Mass Spectrometry

The non-random distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples, and detectable by mass spectrometry, but are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches, and the discoverability of peptides specific to haplotypes remain unknown. Here, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 9.96 % of the discoverable amino acid substitutions encoded by common haplotypes, two or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 342 spectra that matched to such multi-variant peptides, and out of the 4,251 amino acid substitutions identified, 6.63 % were covered by multi-variant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches. As these become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.

bioinformatics↗

bioRxiv2022

Vexitoxins: a novel class of conotoxin-like venom peptides from predatory gastropods of the genus Vexillum

Venoms of predatory marine cone snails (the family Conidae, order Neogastropoda) are intensely studied because of the broad range of biomedical applications of the neuropeptides that they contain, conotoxins. Meanwhile anatomy in some other neogastropod lineages strongly suggests that they have evolved similar venoms independently of cone snails, nevertheless their venom composition remains unstudied. Here we focus on the most diversified of these lineages, the genus Vexillum (the family Costellariidae). We have generated comprehensive multi-specimen, multi-tissue RNA-Seq data sets for three Vexillum species, and supported our findings in two species by proteomic profiling. We show that venoms of Vexillum are dominated by highly diversified short cysteine-rich peptides that in many aspects are very similar to conotoxins. Vexitoxins possess the same precursor organization, display overlapping cysteine frameworks and share several common post-translational modifications with conotoxins. Some vexitoxins show detectable sequence similarity to conotoxins, and are predicted to adopt similar domain conformations, including a pharmacologically relevant inhibitory cysteine-know motif (ICK). The tubular gL of Vexillum is a notably more recent evolutionary novelty than the conoidean venom gland. Thus, we hypothesize lower divergence between the toxin genes, and their somatic counterparts compared to that in conotoxins, and we find support for this hypothesis in the molecular evolution of the vexitoxin cluster V027. We use this example to discuss how future studies on vexitoxins can inform origin and evolution of conotoxins, and how they may help addressing standing questions in venom evolution.

biochemistry↗

bioRxiv2020

Proteome-Wide Analysis of ADAR-mediated Messenger RNA Editing During Fruit Fly Ontogeny

Adenosine-to-inosine RNA editing is an enzymatic post-transcriptional modification which modulates immunity and neural transmission in multicellular organisms. Some of its functions are enforced through editing of mRNA codons with the resulting amino acid substitutions. We identified these sites originated from the RNA editing for developmental proteomes of Drosophila melanogaster at the protein level using available proteomic data for fifteen stages of fruit fly development from egg to imago and fourteen time points of embryogenesis. In total, 42 sites each belonging to a unique protein were found including four sites related to embryogenesis. The interactome analysis has revealed that most of the edited proteins are associated with synaptic vesicle trafficking and actomyosin organization. Quantitation data analysis suggested the existence of phase-specific RNA editing regulation by yet unknown mechanisms. These results support transcriptome analyses showing that a burst in RNA editing occurs during insect metamorphosis from pupa to imago. Further, targeted proteomics was employed to quantify edited and genomically encoded versions of five proteins in brains of larvae, pupae, and imago insects showing a clear trend towards an increase in editing rate for all of them. Our results may help to reveal the protein functions in physiological effects of RNA editing. SignificanceAdenosine-to-inosine RNA editing has multiple effects on body functions in many multicellular organisms from insects and molluscs to humans. Recent studies show that at least some of these effects are mediated by changes in protein sequences due to editing of codons in mRNA. However, it is not known how exactly the edited proteins can participate in RNA editing-mediated pathways. Moreover, most studies of edited proteins are based on the deduction of protein sequence changes from analysis of transcriptome without measurements of proteins themselves. Earlier, we explored for the first time the edited proteins of Drosophila melanogaster proteome. In this work, we continued the proteome-wide analysis of RNA editome using shotgun proteomic data of ontogeny phases of this model insect. It was found that non-synonymous RNA editing, which led to translation of changed proteins, is specific to the life cycle phase. Identification of tryptic peptides containing edited protein sites provides a basis for further direct and quantitative analysis of their editing rate by targeted proteomics. The latter was demonstrated in this study by multiple reaction monitoring experiments which were used to observe the dynamics of editing in selected brain proteins during developmental phases of fruit fly. HighlightsO_LIProteogenomic approach was applied to shotgun proteomics data of fruit fly ontogeny for identification of proteoforms originating from adenosine-to-inosine RNA editing. C_LIO_LIEdited proteins identified at all life cycle stages are enriched in annotated protein-protein interactions at statistically significant level with many of them associated with actomyosin and synaptic vesicle functions. C_LIO_LIProteome-wide RNA editing event profiles were found specific to life cycle phase and independent of the protein abundances. C_LIO_LIA majority of RNA editing events at the protein level was observed after metamorphosis in late pupae to adult insects, which was consistent with transcriptome data. C_LIO_LITargeted proteomic analysis of five selected edited sites and their genomic counterparts in brains for three phases of the fruit fly life cycle have demonstrated a clear increase in editing rate of up to 80% for the endophilin A protein in adult flies. C_LI

systems biology↗

bioRxiv2017

Proteogenomics of adenosine-to-inosine RNA editing in fruit fly

Adenosine-to-inosine RNA editing is one of the most common types of RNA editing, a posttranscriptional modification made by special enzymes. We present a proteomic study on this phenomenon for Drosophila melanogaster. Three proteome data sets were used in the study: two taken from public repository and the third one obtained here. A customized protein sequence database was generated using results of genome-wide adenosine-to-inosine RNA studies and applied for identifying the edited proteins. The total number of 68 edited peptides belonging to 59 proteins was identified in all data sets. Eight of them being shared between the whole insect, head and brain proteomes. Seven edited sites belonging to synaptic vesicle and membrane trafficking proteins were selected for validation by orthogonal analysis by Multiple Reaction Monitoring. Five editing events in cpx, Syx1A, Cadps, CG4587 and EndoA were validated in fruit fly brain tissue at the proteome level using isotopically labeled standards. Ratios of unedited-to-edited proteoforms varied from 35:1 (Syx1A) to 1:2 (EndoA). Lys-137 to Glu editing of endophilin A may have functional consequences for its interaction to membrane. The work demonstrates the feasibility to identify the RNA editing event at the proteome level using shotgun proteomics and customized edited protein database.

biochemistry↗