Biology subjects

Pawlak, J.

Publications and source records attributed to Pawlak, J..

3 recordsLinked to original sources

bioRxiv2025

Weak effects of local prey density and spatial overlap on predation intensity in a temperate marine ecosystem

Quantifying the impact of lower trophic level species abundance on higher trophic level predators (and vice versa) is critical for understanding marine ecosystem dynamics and for implementing ecosystem-based management. Trophic ecosystem models generally predict a tight coupling between prey and fish predators, such that higher abundance of lower trophic species increases abundance of higher trophic level predators. This assumes that predator feeding rates are limited by prey availability to some degree. Despite being a key component of predator-prey interactions and multi-species fisheries management, relatively few studies have assessed the impacts of prey availability on predation patterns of mobile, generalist fish predators using spatiotemporal models and local-scale stomach content, predator, and prey data. In this study, we explore the association between local density of key prey and predator stomach contents, and predator-prey spatiotemporal overlap and predation indices, using the Baltic Sea as a case study. We use three decades of spatially resolved biomass and stomach content data on Atlantic cod (Gadus morhua), and biomass data on three of its key prey: herring (Clupea harengus), the isopod Saduria entomon, and sprat (Sprattus sprattus). Using geostatistical generalized linear mixed effects models fitted to relative biomass density and prey-weight-per-predator-weight, we estimate spatiotemporal trends and annual indices of biomass weighted and area-expanded per-capita and population-level predation, predator-prey overlap, and the correlation between these indices. Range shifts have resulted in reduced predator-prey overlap over time, which is now the lowest in three decades. For Saduria, we find an association between prey availability and stomach contents, but not for herring or sprat. Similarly, only in Saduria do we find a positive correlation between population-level predation indices and the spatiotemporal overlap. Although behavioral interactions with pelagic prey are challenging to infer from stomach content and acoustic data due to high mobility leading to fine-scale spatiotemporal mismatch, the weak connection with local-scale availability, and low correlation between population-level predation and spatial overlap, could imply weaker coupling between pelagic prey and cod than previously thought. These findings provide key information on the strength of species interactions, which is crucial for the continued development of multispecies models and ecosystem-based fisheries management.

ecology↗

bioRxiv2023

Structural insights into rice KAI2 receptor provide functional implications for perception and signal transduction

KAI2 proteins, classified as plant /{beta} hydrolase receptors, are capable of perceiving smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). While the number of functional KAI2 receptors varies among land plant species, rice possesses only one KAI2 gene. Rice, a significant crop and representative of grasses, relies on KAI2-mediated Arbuscular mycorrhiza (AM) symbioses to flourish in traditionally arid and nutrient-poor environments. This study presents the first crystal structure of an active rice KAI2 hydrolase receptor. Our structural and biochemical analyses uncover grass-unique pocket residues influencing ligand sensitivity and hydrolytic activity. Through structure-guided analysis, we identify a specific residue whose mutation enables the increase or decrease of ligand perception, catalytic activity, and signal transduction. Furthermore, we investigate rice KAI2-mediated signaling by examining its ability to form a complex with its binding partner, the F-box protein DWARF3 (D3) ubiquitin ligase, demonstrating the significant role of hydrophobic interactions in the KAI2-D3 interface. This study provides new insights into the diverse and pivotal roles of the KAI2 signaling pathway in the plant kingdom, particularly in grasses.

biochemistry↗

bioRxiv2022

SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression

Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small protein {beta}2-microglobulin ({beta}2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that downregulate MHC-I expression to avoid CD8+ T cell recognition. Here we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, downregulate MHC-I expression using distinct mechanisms. One, ORF3a, a viroporin, reduces global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of {beta}2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a novel and specific mechanism that allows immune evasion by SARS-CoV-2. Significance StatementViruses may down-regulate MHC class I expression on infected cells to avoid elimination by cytotoxic T cells. We report that the accessory proteins ORF7a and ORF3a of SARS-CoV-2 mediate this function and delineate the two distinct mechanisms involved. While ORF3a inhibits global protein trafficking to the cell surface, ORF7a acts specifically on MHC-I by competing with {beta}2m for binding to the MHC-I heavy chain. This is the first account of molecular mimicry of {beta}2m as a viral mechanism of MHC-I down-regulation to facilitate immune evasion.

immunology↗