Biology subjects

Balparda, M.

Publications and source records attributed to Balparda, M..

4 recordsLinked to original sources

bioRxiv2023

Natural variation in Arabidopsis thaliana identifies GlyoxalaseI;2 as key for the detoxification of glucose-derived reactive carbonyl species

Reactive carbonyl species (RCS) are toxic byproducts of normal metabolism that become more prevalent under oxidative stress. Here, we show that Arabidopsis thaliana ecotypes exhibit natural variation in their ability to detoxify glucose-derived RCS. We identified the IP-Pal-0 ecotype showing enhanced tolerance to glucose-derived RCS via upregulation of the glyoxalase system. In particular, the Viridiplantae-specific isoforms GLXI;2, GLXII;4, and GLXII;5 are highly expressed in IP-Pal-0 when plants are grown in the presence of 2-keto-D-glucose (KDG; glucosone) or methylglyoxal, and protein extracts from these plants display enhanced GLXI activity on KDG than other ecotypes. We identified specific motif/cis-regulatory elements in the GLXI;2 promoter regions of Col-0 and IP-Pal-0 that may underlie the differential expression of GLXI;2 associated with KDG detoxification. IP-Pal-0 GLXI;2 contains two different amino acids compared to Col-0, but these do not affect the basic kinetics of the protein. Interestingly, we found that the simultaneous change of these amino acids also occurs together in the GLXI proteins of some other organisms, suggesting a convergence in the simultaneous change of both amino acid residues. Our findings underscore the importance of Viridiplantae-specific glyoxalase isoforms in detoxifying glucose-derived RCS, particularly KDG, and highlight the promise of harnessing natural genetic diversity in the glyoxalase pathway to enhance plant stress tolerance.

plant biology↗

bioRxiv2022

Viridiplantae-specific GLXI and GLXII isoforms co-evolved and detoxify glucosone in planta

Reactive carbonyl species (RCS) such as methylglyoxal (MGO) and glyoxal (GO) are highly reactive, unwanted side-products of cellular metabolism maintained at harmless intracellular levels by specific scavenging mechanisms. MGO and GO are metabolized through the glyoxalase (GLX) system, which consists of two enzymes acting in sequence, GLXI and GLXII. While plant genomes encode a large number of different GLX isoforms, it is unclear what their specific functions are and how these arose in evolution. Here, we show that plants possess two GLX systems of different evolutionary origins and with distinct structural and functional properties. The first system is shared by all eukaryotes, scavenges MGO and GO especially during seedling establishment, and features Zn2+-type GLXI, a metal co-factor preference that arose already in the last eukaryotic common ancestor. The GLXI and GLXII of the second system can together metabolize KDG, a glucose-derived RCS, and were acquired by the last common ancestor of viridiplantae through horizontal gene transfer from proteobacteria. In contrast to bacterial GLXI homologs, which are active as dimers, plant Ni2+-type GLXI contain a domain duplication, are active as monomers, and have modified their second active site. The acquisition and neofunctionalization of a structurally, biochemically, and functionally distinct GLX systems indicate that viridiplantae are under strong selection to detoxify a diversity of RCS.

plant biology↗

bioRxiv2020

An evolutionary conserved lysine acetylation hotspot regulates plant mitochondrial malate dehydrogenase activity

Plants need to rapidly and flexibly adjust their metabolism to changes of their immediate environment. Since this necessity results from the sessile lifestyle of land plants, key mechanisms for orchestrating central metabolic acclimation are likely to have evolved early. Here, we explore the role of lysine acetylation as a posttranslational modification to directly modulate metabolic function. We generated a lysine acetylome of the moss Physcomitrium patens and identified 638 lysine acetylation sites, mostly found in mitochondrial and plastidial proteins. A comparison with available angiosperm data pinpointed lysine acetylation as a conserved regulatory strategy in land plants. Focusing on mitochondrial central metabolism, we functionally analyzed acetylation of malate dehydrogenase (mMDH), which acts as a hub of plant metabolic flexibility. In P. patens mMDH1, we detected a single acetylated lysine located next to one of the four acetylation sites detected in Arabidopsis thaliana mMDH1. We assessed the kinetic behavior of recombinant A. thaliana and P. patens mMDH1 with site-specifically incorporated acetyl-lysines. Acetylation of A. thaliana mMDH1 at K169, K170, and K334 decreases its oxaloacetate reduction activity, while acetylation of P. patens mMDH1 at K172 increases this activity. We found modulation of the malate oxidation activity only in A. thaliana mMDH1, where acetylation of K334 highly activated it. Comparative homology modelling of MDH proteins revealed that evolutionarily conserved lysines serve as hotspots of acetylation. Our combined analyses indicate lysine acetylation as a common strategy to fine-tune the activity of central metabolic enzymes with likely impact on plant acclimation capacity. Significance statementWe explore the role of lysine acetylation as a mechanism to directly modulate mitochondrial metabolism in land plants by generating the lysine acetylome of the moss Physcomitrium patens and comparing with available angiosperm data. We found acetylation of evolutionarily conserved lysines as a strategy to fine-tune the activity of mitochondrial malate dehydrogenase in a species-dependent molecular context.

plant biology↗

bioRxiv2020

GENis, an open-source multi-tier forensic DNA information system

GENis is an open source multi-tier information system developed to run a forensic DNA database at local, regional and national levels.1 It was conceived as a highly customizable system, enforcing several security policies including: data encryption, double factor identification, structure of users roles and permissions, system-wide secure log auditing, non-repudiation protocols and a blockchain-based option to reinforce genetic profiles integrity. GENis is able to perform genetic profile queries of autosomal STRs and its design follows ENFSI2 and ISFG3 standards and recommendations. In this work, we present a summary of GENis architecture, the implemented matching rule definitions, and the Bayesian framework used to provide statistical significance of cold hits, that includes a new strategy to identify common contributors in mixture pairs.

bioinformatics↗