Biology subjects

Zunar, B.

Publications and source records attributed to Zunar, B..

7 recordsLinked to original sources

bioRxiv2026

Salt-enhanced surface display in the halotolerant yeast Debaryomyces hansenii

The halo-, xero-, and osmotolerant oleaginous yeast Debaryomyces hansenii can grow in extreme environments, with some isolates tolerating up to 4 M NaCl. As such, it could serve as a robust microbial chassis for non-sterile biotechnological processes based on seawater or saline side streams. However, its biotechnological toolbox lacks key genetic tools, particularly for inducible expression, secretion, and covalent anchoring of proteins to the outer cell surface. To address this gap, we characterised how growth in a medium supplemented with 1 M NaCl remodels the D. hansenii cell wall. We also developed strong constitutive, stationary-phase, and NaCl-inducible expression vectors, and designed protein tags for C- and N-terminal cell wall anchoring. These tools enabled functional surface display of {beta}-lactamase, acetylxylan esterase, and lipase A via native GPI-dependent and heterologous Pir-based anchors, while immunoblotting detected the reporters in both covalently and non-covalently bound cell wall fractions. Activities of surface-displayed enzymes increased by more than 80 % under hypersaline conditions, while DhCcw12-based C-terminal anchoring outperformed Pir-based N-terminal anchoring. Thus, we retooled the D. hansenii cell wall into a catalytically active biointerface and established this yeast as an osmotolerant chassis for hypersaline surface display.

molecular biology↗

bioRxiv2026

Mapping non-coding functional elements in allotetraploid Cyprinus carpio embryo development reveals subgenome variation of transcription regulation

Common carp (Cyprinus carpio) is an important freshwater species for ornamental and aquaculture purposes, and a key cyprinid model for studying allotetraploidy. Its two chromosomally-separated subgenomes show distinct gene expression profiles, but how their regulatory landscapes control gene expression dynamics during development remains unknown. We generated a regulatory atlas by combining transcriptomes across 12 developmental stages with chromatin accessibility maps, transcription start sites and gene regulation-associated histone post-translational modifications. Subgenome-specific annotation and comparison of 254,276 developmental regulatory elements (PADREs) revealed that regulatory subgenome divergence is most prominent during early development, converging toward the phylotypic period, mirroring expression convergence between subgenomes at the same stages. This dynamic was driven by enhancers, while promoters maintained a more stable subgenome bias, extending the hourglass model of developmental constraint to allotetraploid subgenome regulation. Subgenome-specific enhancers were preferentially retained in subgenome B, whereas subgenome A shifted toward homeologous enhancer activity near the phylotypic stage, indicating directional regulatory divergence between subgenomes. Comparison with zebrafish revealed high concordance with sequence conservation and that subgenome B retained more ancestral cyprinid regulatory elements than subgenome A. This developmental regulatory atlas provides a foundational resource for investigating cis-regulatory evolution following the fourth round of vertebrate genome duplication.

genomics↗

bioRxiv2026

A new mechanism of regulation of LIM kinases, LIMK1 and LIMK2, modulates their activity on cofilin and actin filament remodelling

LIM kinases, LIMK1 and LIMK2, play a crucial role in cytoskeleton dynamics. They are involved in many physiological processes but also in several pathologies such as cancer, neuronal diseases and neurofibromatosis. Although LIM kinases appear as promising therapeutic targets, they remain undruggable. A better understanding of their activity and regulation is thus required to better design efficient targeted therapies. Here, we have shown the impact of a single amino acid on LIMK activity on cofilin, their main substrate in actin filament remodelling. We demonstrated that Y632 and Y630, for LIMK1 and LIMK2 respectively, mediate LIMK dimerization, resulting in their transphosphorylation. This process seems to be a prerequisite for their canonical phosphorylation on their respective T508 and T505 residues within the activation loop. These Tyrosine are not phosphorylated, their aromatic nature is rather critical to ensure proper LIMK activity on cofilin. These results bring new insights into LIMK molecular features.

Molecular Biology↗

bioRxiv2025

Salmonids reveal principles of regulatory evolution following autotetraploidization

Early vertebrate autotetraploidization events may have enabled major innovations by expanding the genetic material for functional diversification, yet their ancient timing obscures how genome doubling reshaped gene regulatory evolution. Salmonids provide a unique window to these mechanisms, because they experienced a comparatively recent autotetraploidization and are earlier in the rediploidization process - which creates new genes and regulatory elements during evolution. Here, using large-scale multiomics spanning embryonic and adult tissues in two salmonids, we investigate gene regulatory evolution following genome doubling and rediploidization, which we show is governed by developmental and tissue-specific context, with a period of maximal constraint at advanced stages of embryogenesis. This work advances understanding of vertebrate genome evolution, while providing an open resource supporting salmonid aquaculture and conservation.

evolutionary biology↗

bioRxiv2024

DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localizes to cleavage bodies, which are enriched for 3-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.

molecular biology↗

bioRxiv2023

Boosting N-terminally anchored yeast surface display via structural insights into S. cerevisiae Pir proteins

Surface display co-opts yeasts innate ability to embellish its cell wall with mannoproteins, thus converting the yeasts outer surface into a growing and self-sustaining catalyst. However, the efficient toolbox for converting the enzyme of interest into its surface-displayed isoform is currently lacking, especially if the isoform needs to be anchored to the cell wall near the isoforms N-terminus. Aiming to advance such N-terminally anchored surface display, we employed in silico and machine-learning strategies to study the 3D structure, function, genomic organisation, and evolution of the Pir protein family, whose members evolved to covalently attach themselves near their N-terminus to the {beta}-1,3-glucan of the cell wall. Through the newly-gained insights, we rationally engineered 14 S. cerevisiae Hsp150 (Pir2)-based fusion proteins. We quantified their performance, uncovering guidelines for efficient yeast surface display while developing a construct that promoted a 2.5-fold more efficient display than the full-length Hsp150 and a Pir-tag, i.e., a peptide spanning only 4.5 kDa but promoting as efficient surface display as the full-length Hsp150. These constructs fortify the existing surface display toolbox, allowing for a prompt and routine refitting of any protein into its N-terminally anchored isoform. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/538238v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@909e7aorg.highwire.dtl.DTLVardef@9480ceorg.highwire.dtl.DTLVardef@1945bdcorg.highwire.dtl.DTLVardef@11ae505_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Re-engineering of CUP1 promoter and Cup2/Ace1 transactivator to convert Saccharomyces cerevisiae into a whole-cell eukaryotic biosensor capable of detecting 10 nM of bioavailable copper

While copper is an essential micronutrient and a technologically indispensable heavy metal, it is toxic at high concentrations, harming the environment and human health. Currently, copper is monitored with costly and low-throughput analytical techniques that do not evaluate bioavailability, a crucial parameter which can be measured only with living cells. We overcame these limitations by building upon yeast S. cerevisiaes native copper response and constructed a promising next-generation eukaryotic whole-cell copper biosensor. We combined a dual-reporter fluorescent system with an engineered CUP1 promoter and overexpressed Cup2 transactivator, constructing through four iterations a total of 16 variants of the biosensor, with the best one exhibiting a linear range of 10-8 to 10-3 M of bioavailable copper. Moreover, this variant distinguishes itself by superior specificity, detection limit, and linear range, compared to other currently reported eukaryotic and prokaryotic whole-cell copper biosensors. By re-engineering the transactivator, we altered the systems sensitivity and growth rate, while assessing the performance of Cup2 with heterologous activation domains. Thus, in addition to presenting the next-generation whole-cell copper biosensor, this work urges for an iterative design of eukaryotic biosensors and paves the way toward higher sensitivity through transactivator engineering. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

molecular biology↗