Biology subjects

Sokolova, I.

Publications and source records attributed to Sokolova, I..

4 recordsLinked to original sources

bioRxiv2025

Unraveling Hypoxia Tolerance: Transcriptomic and Metabolic Insights from Lucinoma capensis in an Oxygen Minimum Zone

The lucinid clam Lucinoma capensis thrives at the oxygen minimum zone margins in the Benguela Upwelling System, where oxygen levels fluctuate dramatically. Understanding its adaptation to such extreme conditions provides key insights into survival strategies under fluctuating oxygen availability. We investigated the transcriptomic and metabolomic responses of L. capensis under normoxia, hypoxia, and recovery, focusing on the gills and digestive gland. Our findings highlight distinct organ-specific responses, with the gills showing strong transcriptional changes to oxygen fluctuations, in contrast to the more stable profile observed in the digestive gland. Under hypoxic conditions, the gills exhibited coordinated downregulation of critical metabolic processes, including protein synthesis, transposable element activity, and immune function, suggesting a tightly regulated energy conservation strategy and mechanisms to preserve symbiont stability and genomic integrity. Activation of prokaryotic metabolism in the gills supports the symbionts role in host energy acquisition and sulfide detoxification during hypoxia. In contrast, the digestive gland showed minimal transcriptional shifts during anoxia, with upregulation of pathways supporting structural maintenance. Upon reoxygenation, the gills displayed an active and asymmetric recovery, characterized by rapid restoration of protein synthesis and gradual normalization of protein degradation and immune functions. Despite significant transcriptomic changes, the metabolome remained largely stable, reflecting L. capensiss resilience to oxygen fluctuations. However, an overshoot in TCA cycle intermediates and derepression of previously downregulated pathways indicate that reoxygenation involves active metabolic reprogramming, not merely a return to baseline. This study highlights the specialized tissue responses and symbiotic contributions that enable L. capensis to thrive in one of the oceans most challenging environments.

physiology↗

bioRxiv2021

VirB4- and VirD4-like ATPases, components of a putative type 4C secretion system in Clostridioides difficile

The type 4 secretion system (T4SS) represents a bacterial nanomachine capable of trans-cell wall transportation of proteins and DNA and which has attracted intense interest due to its roles in the pathogenesis of infectious diseases. During the current investigation we uncovered three distinct gene clusters in Clostridioides difficile strain 630 coding for proteins structurally related to components of the VirB4/D4 type 4C secretion system from Streptococcus suis strain 05ZYH33 and located within sequences of conjugative transposons (CTn). Phylogenic analysis shows that VirB4- and VirD4-like proteins of CTn4 locus, on one hand, and those of CTn2 and CTn5 loci, on the other hand, fit into separate clades, suggesting specific roles of identified secretion system variants in physiology of C. difficile. Our further study on VirB4- and VirD4-like products coded by CTn4 revealed that both proteins possess Mg2+-dependent ATPase activity, form oligomers (most probably, hexamers) in water solutions, and rely on potassium but not sodium ions for the highest catalytic rate. VirD4 binds nonspecifically to DNA and RNA. Its DNA binding activity strongly decreased with the W241A variant. Mutations in the nucleotide sequences coding for presumable Walker A and Walker B motifs decreased stability of the oligomers and significantly but not completely attenuated enzymatic activity of VirB4. In VirD4, substitutions of amino acid residues in the peptides reminiscent of Walker structural motifs resulted neither in attenuation of enzymatic activity of the protein nor influenced the oligomerization state of the ATPase. ImportanceC. difficile is a Gram-positive, anaerobic, spore-forming bacterium that causes life-threatening colitis in humans. Major virulence factors of the microorganism include toxins TcdA, TcdB and CDT. However, other bacterial products, including a type 4C secretion system, have been hypothesized to contribute to the pathogenesis of the infection and are considered as possible virulence factors of C. difficile. In the current paper we describe structural organization of putative T4SS machinery in C. difficile and characterize its VirB4- and VirD4-like components. Our studies, in addition to significance for basic science, can potentially aid development of anti-virulence drugs suitable for treatment of C. difficile infection.

microbiology↗

bioRxiv2020

Temperature but not ocean acidification affects energy metabolism and enzyme activities in the blue mussel, Mytilus edulis

O_LIIn mosaic marine habitats such as intertidal zones ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO2 production. The non-linear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation. C_LIO_LIWe were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of Gulf of Maine (GOM), USA for this study. GOM is a hot spot of global climate change (average SST increasing by > 0.2 {degrees}C y-1) with > 60% decline in mussel population over the past 40 years. C_LIO_LIHere, we utilize bioenergetic underpinnings to identify limits of stress tolerance in M. edulis from GOM exposed to warming and OA. We have measured whole-organism oxygen consumption rates and metabolic biomarkers in mussels exposed to control and elevated temperatures (10 vs. 15 {degrees}C) and moderate PCO2 levels (~ 400 vs. 800 atm). C_LIO_LIOur study demonstrates that adult M. edulis from GOM are metabolically resilient to the moderate OA scenario but responsive to warming as seen in changes in metabolic rate, energy reserves, metabolite profiles and enzyme activities. C_LIO_LIOur results are in agreement with recent literature that OA scenarios for the next 100-300 years do not affect this species, possibly as a consequence of maintaining its in vivo acid-base balance. C_LI

ecology↗

bioRxiv2018

Biomarker-based assessment of the muscle maintenance and energy status of anurans from an extremely seasonal semi-arid environment, the Brazillian Caatinga

Strongly seasonal environments pose challenges for performance and survival of animals, especially when resource abundance seasonally fluctuates. We investigated the seasonal variation of expression of key metabolic biomarkers in the muscles of three species of anurans from the drastically seasonal Brazilian semi-arid area, Caatinga. The three studied anuran species (Rhinella jimi, R. granulosa and Pleurodema diplolister) differ in their seasonal activity patterns. We examined the expression of proteins regulating energy turnover (AMP-activated protein kinase [AMPK] and protein kinase B [AKT]), protein synthesis and homeostasis (total and phosphorylated eukaryotic initiation factor 2 [eIF2 and p-eIF2] and chaperone proteins [HSP 60, 70, and 90]) in muscles related to reproduction and locomotion. Cytochrome c oxidase (COX) activity was also assessed as an index of the muscle aerobic capacity. Our results point to the importance of metabolic regulators mediating the muscular function during the drastic seasonal variation. The toads that remain active during the drought appear to maintain muscles through more energy extensive pathways including elevated protein synthesis, while the aestivating species employs energy conservation strategy suppressing protein synthesis, decreasing chaperone expression and increasing expression of AMPK. All three studied species activate cell survival pathways during the drought likely to prevent muscle atrophy, and maintain the muscle capacity throughout the year, despite the resource limitation. These strategies are important considering the unpredictability of the reproductive event and high demand on muscular activity during the reproductive season in these amphibians.\n\nSummary statementWe studied seasonal variation of key metabolic regulators in the muscles of anurans that experience drastic variation in environmental conditions and differ in the seasonal activity patterns.

physiology↗