Biology subjects

Wojciechowski, M.

Publications and source records attributed to Wojciechowski, M..

6 recordsLinked to original sources

bioRxiv2026

Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection

Across eukaryotes, mitochondrial (mt) and nuclear genomes coordinate the expression and interaction of gene products to maintain cellular functions. While mitonuclear coevolution has been widely explored in animals, it remains understudied in plants, despite their utility as model systems due to relatively slow mitochondrial evolutionary rates and the presence of plastids. Plants rely on oxidative phosphorylation (OXPHOS) for ATP conversion, which requires cofunctionality and likely coevolution of mitochondrial and nuclear gene products. Here, we investigated evolutionary rate covariation (ERC) between mitochondrial- and nuclear-encoded OXPHOS genes in papilionoid legumes, where plastid-nuclear coevolution and an inversion in plastid DNA have been documented previously. Using 50 legume species spanning 15 papilionoid clades, we estimated evolutionary rates for five gene sets: mt-encoded OXPHOS genes, nuclear-encoded mitochondrial-targeted (N-mt) OXPHOS genes, and three control nuclear gene sets that lack mitochondrial interactions (glycolysis, cell cycle, and cytosolic ribosomal genes). Both mt and N-mt OXPHOS genes exhibited significantly elevated nonsynonymous (dN) and synonymous substitution rates (dS) in the 50-kb inversion clade relative to other legumes, suggesting accelerated mitochondrial substitution rates. Moreover, elevated dN/dS ratios in mt and N-mt OXPHOS genes in this clade were driven by relaxed purifying, not intensified positive selection. ERCs were highest for OXPHOS complexes and genes with physical mitonuclear interactions, as predicted under mitonuclear coevolution. We discuss how these results compare to other cases of cytonuclear coevolution in plants, including plastid-nuclear coevolution in papilionoids, and why dual-targeted, nuclear-encoded genes that repair mt and plastid DNA may underly patterns of molecular evolution in both organelles. Significance StatementMitonuclear interactions are essential for cellular energy production, yet the evolutionary dynamics of these interactions remain poorly understood in plants. This study highlights papilionoid legumes as an important system for understanding how coordinated evolution between mitochondrial and nuclear genes shapes plant genomes. By identifying signatures of mitonuclear coevolution in the 50-kb inversion clade, this work demonstrates how shifts in selective pressures on mitochondrial processes can influence nuclear gene evolution. These findings advance our understanding of cytonuclear coordination in plants and provide a foundation for future studies exploring how interactions among genomic compartments contribute to plant evolution, adaptation, and resilience in agriculturally important lineages.

evolutionary biology↗

bioRxiv2025

Electrostatic Collapse of Intrinsically Disordered Acid-Rich Protein Is Sensitive to Counterion Valency

Intrinsically disordered proteins (IDPs) respond sensitively to their ionic environment, yet the mechanisms driving ion-induced conformational changes remain incompletely understood. Here, we investigate how counterion valency modulates the dimensions of an extremely charged model IDP, the aspartic and glutamic acid-rich protein AGARP. Fluorescence correlation spectroscopy and size exclusion chromatography reveal a pronounced, valency-dependent reduction in its hydrodynamic radius, with divalent cations (Ca2+, Mg2+) inducing collapse at much lower activities than monovalent cations (Na+, K+). Molecular dynamics simulations, direct sampling, and polyampholyte theory quantitatively capture the Debye-Huckel screening by monovalent ions but not the enhanced compaction driven by divalent ion binding. Circular dichroism spectroscopy shows that compaction occurs without secondary structure formation. Our results demonstrate a structure-free electrostatic collapse and suggest that specific chelation of divalent ions by disordered polyanionic protein chains is a key mechanism regulating IDP compaction, with implications for understanding their behavior in biologically relevant ionic environments. TOC GRAPHIC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/663830v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@84fba8org.highwire.dtl.DTLVardef@a5f3aforg.highwire.dtl.DTLVardef@12194a7org.highwire.dtl.DTLVardef@1a68366_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

A potential anti-amyloidogenic therapy for type 2 diabetes based on the QBP1 peptide

The self-assembly and aggregation of human islet amyloid polypeptide (hIAPP, or amylin) into {beta}-sheet-rich structures, such as oligomers and fibrils, are implicated in pancreatic {beta}-cell dysfunction and failure, contributing to the pathogenesis of Type 2 Diabetes (T2D). Consequently, extensive research has focused on identifying inhibitors, particularly short peptides, capable of targeting hIAPP and disrupting its amyloidogenic process, offering potential therapeutic strategies to prevent or slow T2D progression. In this study, we demonstrate the effectiveness of the anti-amyloidogenic peptide QBP1 in blocking the critical conformational transition to {beta}-structure experienced by the hIAPP monomer, thereby in preventing amyloidogenesis and in reducing the cytotoxicity associated with its amyloid forms. First, we evaluated the anti-amyloidogenic effects of QBP1 through an in vitro aggregation methods, including a Thioflavin-T binding assay, dot blotting using the oligomer-specific A11 and fibril-specific OC antibodies, and negative staining electron microscopy. To assess its cytoprotective potential of QBP1 on hIAPP-induced toxicity, we examined its effects when fused to a protein transduction domain (penetratin) in INS-1E pancreatic {beta}-cells, using viability assays and transcriptome analysis. Our results demonstrate that QBP1 effectively halts the formation of early toxic hIAPP intermediates, preventing amyloid progression and preserving {beta}-cell viability and function. Additionally, molecular dynamics simulations revealed that QBP1 stabilizes amylin through strong van der Waals interactions and {pi}-H bonds at hydrophobic and aromatic residues (i.e., W, F), forming a stable binding network that prevents aggregation. Binding free energy analysis confirmed its high affinity, driven by favourable non-polar solvation energy and optimized structural complementarity. Collectively, these findings position QBP1 as a promising therapeutic candidate for preventing islet amyloid formation and mitigating {beta}-cell dysfunction in T2D. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/652241v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1e7ed7borg.highwire.dtl.DTLVardef@1985667org.highwire.dtl.DTLVardef@509779org.highwire.dtl.DTLVardef@108a3c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2021

Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function

TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic cores of mammalian TET enzymes favor CpGs embedded within bHLH and bZIP transcription factor binding sites, with 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intra-substrate interactions and CpG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germline. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and OCT4, respectively, illuminating TET function in transcriptional responses and pluripotency support. One-Sentence SummaryThe catalytic domains of the enzymes that facilitate passive and drive active DNA demethylation have intrinsic sequence preferences that target DNA demethylation to bHLH and bZIP transcription factor binding sites.

molecular biology↗

bioRxiv2020

A new (old) approach to genotype-based phylogenomic inference within species, with an example from the saguaro cactus (Carnegiea gigantea)

AO_SCPLOWBSTRACTC_SCPLOWGenome sequence data are routinely being used to infer phylogenetic history within and between closely related diploid species, but few tree inference methods are specifically tailored to diploid genotype data. Here we re-examine the method of "polymorphism parsimony" (Inger 1967; Farris 1978; Felsenstein 1979), originally introduced to study morphological characters and chromosome inversion polymorphisms, to evaluate its utility for unphased diploid genotype data in large scale phylogenomic data sets. We show that it is equivalent to inferring species trees by minimizing deep coalescences--assuming an infinite sites model. Two potential advantages of this approach are scalability and estimation of a rooted tree. As with some other single nucleotide polymorphism (SNP) based methods, it requires thinning of data sets to statistically independent sites, and we describe a genotype-based test for phylogenetic independence. To evaluate this approach in genome scale data, we construct intraspecific phylogenies for 10 populations of the saguaro cactus using 200 Gbp of resequencing data, and then use these methods to test whether the population with highest genetic diversity corresponds to the root of the genotype trees. Results were highly congruent with the (unrooted) trees obtained using SVDquartets, a scalable alternative method of phylogenomic inference.

evolutionary biology↗

bioRxiv2019

smFRET Detects Dual Binding Modes Modulated by Proline Isomerization in a Mega-Dalton Multi-Enzyme Complex

Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule Fluorescence Resonance Energy Transfer, molecular dynamics simulations and NMR measurements on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗