Biology subjects

Pietras, Z.

Publications and source records attributed to Pietras, Z..

4 recordsLinked to original sources

bioRxiv2024

No evidence that proteome composition is associated with realised thermal limit and dietary niche breadth in butterflies

Amino acids are the building blocks of proteins that perform essential physiological functions. Theory suggests that the proteome composition, the amino acid frequencies across all proteins in a genome, is associated with an organisms optimal growth temperature, offering insights into species temperature limits. However, this hypothesis, based on prokaryotes, has not been tested in complex multicellular eukaryotes where many amino acids are strictly acquired through diet. Here, we analysed amino acid frequencies in the proteomes of orthologous and non-orthologous genes from 35 butterfly species to test for correlations with maximum observed temperatures and diet breadth. Using a comparative approach, we found no evidence that proteome composition correlates with temperature or diet breadth. Our findings suggest that animal proteome composition is likely shaped more strongly by energetic and biophysical constraints rather than by ecological factors.

zoology↗

bioRxiv2024

Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities

BackgroundAmino acids are the building blocks of proteins and enzymes, which are pivotal for life on Earth. Amino acid usage provides critical insights into the functional constraints acting on proteins and illuminates molecular mechanisms underpinning traits. Despite this, we have limited knowledge of the genome-wide signatures of amino acid usage across domains of life, precluding new genome and proteome patterns to being discovered. ResultsHere, we analysed the proteomes of 5,590 species across four domains of life and found that only a small subset of amino acids is most and least frequently used across proteomes. This creates a ubiquitous edge effect on amino acid usage diversity by rank that arises from protein secondary structural constrains. This edge effect was not driven by the evolutionary chronology of amino acids, showing that functional rather than evolutionary constrains shape amino acid usage in the proteome. We also tested contemporary hypotheses about similarities in amino acid usage profiles and the relationship between amino acid usage and growth temperature, and found that, contrary to previous beliefs, amino acid usage varies across domains of life and temperature only weakly contributes to variance in amino acid usage. ConclusionWe have described a novel and ubiquitous pattern of amino acid usage signature across genomes, which reveals how structural constrains shape amino acid usage at the proteome level. This can ultimately influence the way in which we probe deep evolutionary relationships of protein families across the tree of life and engineer biology in synthetic biology.

molecular biology↗

bioRxiv2024

Structural plasticity of 2A proteins in the Parechovirus family

Parechoviruses, including Parechovirus A that infects humans as well as Parechovirus B (formerly Ljungan virus) and Parechovirus C (formerly Sebokele virus) that infect rodents, belong to a group of picornaviruses whose 2A proteins, instead of being proteases, contain a conserved H-box and NC-motif and are homologous to a small cellular lipid-modifying enzyme (PLAAT3) that acts as a host factor, enabling the picornavirus life cycle. Despite the common evolutionary origin, 2AH/NC proteins and PLAAT3 have no conserved function, as the active site of the viral proteins cannot support catalysis. Here, we set out to find if all Parechovirus species share the structural rearrangement that destroys the active site configuration of the cellular enzyme. This has revealed a remarkable structural plasticity of these 2AH/NC proteins that arises not only from sequence differences between species, but also from differences in the length of the recombinantly expressed proteins, resulting in large structural rearrangements. These include rerouting of a large internal loop and repositioning of the C-terminal helix with respect to the central {beta}-sheet, and these in turn influence the oligomeric state of the protein. We discuss how this structural plasticity could correlate with the function of these proteins in the viral life cycle and how this could recapitulate the possible evolution of this protein from host factor to viral 2AH/NC protein, with new independent functions in RNA replication.

biochemistry↗

bioRxiv2024

Structural characterization of the Pseudomonas Aeruginosa MexR-mexR repressor-operator complex: a small-angle X-ray and neutron scattering perspective

The rapid spread of acquired multidrug resistance (MDR) in bacteria is a world-wide health threat. The MexR protein regulates the expression of the MexAB-OprM efflux pump, which actively extrudes chemical compounds with high toxicity to the host organism Pseudomonas Aeruginosa. In repression mode, two MexR dimers bind to an operator with two homologous pseudo-palindromic boxes located in proximity (named PI and PII). Here we report a first structural characterization of the complex in solution using small angle X-ray scattering (SAXS), small-angle neutron scattering (SANS) and rigid body modelling. The spacing between the PI and PII boxes is rich in AT base pairs indicate possible flexibility between the two MexR dimer binding sites. In agreement, our best modelling fits show a requirement for DNA bending between the two MexR binding sites to optimally fit SAS data as well as known biological properties of the MexR operons. Taken together, this study contributes to better understanding of the structural properties of bacterial operators and their repressor proteins.

biophysics↗