Biology subjects

Vanholme, B.

Publications and source records attributed to Vanholme, B..

4 recordsLinked to original sources

bioRxiv2026

The Arabidopsis PAL3 is a carboxy-tyrosine ammonia lyase

Phenylalanine ammonia lyase (PAL) catalyses the deamination of L-phenylalanine, which is the first step of the plant-specific phenylpropanoid pathway. Its position at the intersection of primary and specialized metabolism, combined with its important role in plant growth and adaptive stress response, has made it a subject of extensive studies. We identified key amino acids in the catalytic pocket of several PAL enzymes, including PAL3 of Arabidopsis, that are different from the canonical PAL sites, suggesting these enzymes have a different substrate specificity and have been miscategorised for decades. By combining untargeted metabolomics with enzyme assays, we discovered that PAL3 converts 3-carboxy-tyrosine into carboxy-p-coumaric acid. Based on this specific function, we propose to denote it as a 3-carboxy-tyrosine ammonia lyase (CAL). In addition to its discovery as a novel enzyme class, paving the way for biotechnological applications, we introduce the carboxy-phenylpropanoids as a new class of specialised metabolites.

biochemistry↗

bioRxiv2025

Metabolic engineering of a tyrosine-specific phenylpropanoid pathway in plants

While all plants use L-phenylalanine for phenylpropanoid biosynthesis, grasses can also initiate the pathway from L-tyrosine. Curiously, no plant has evolved an exclusive tyrosine-derived route. We generate plants with phenylpropanoid biosynthesis initiated from phenylalanine, tyrosine, or both by expressing a Brachypodium phenylalanine/tyrosine ammonia-lyase (PTAL) in Arabidopsis WT and c4h mutants. Engineering a bifunctional phenylpropanoid pathway in WT plants did not negatively impact growth, while introducing a tyrosine-specific pathway in the c4h mutant could overcome the seedling-lethal phenotype. Interestingly, restored c4h mutants relying solely on the tyrosine route displayed developmental defects linked to the strong overaccumulation of the auxin transport inhibitor cis-cinnamic acid. Our findings suggest that the requirement of this widely overlooked plant metabolite could be the crucial factor for the evolutionary retention of the canonical phenylpropanoid biosynthesis route via L-phenylalanine in plants.

plant biology↗

bioRxiv2023

Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment

Seagrasses comprise the only submerged marine angiosperms, a feat of adaptation from three independent freshwater lineages within the Alismatales. These three parallel lineages offer the unique opportunity to study convergent versus lineage-specific adaptation to a fully marine lifestyle. Here, we present chromosome-level genome assemblies from a representative species of each of the seagrass lineages - Posidonia oceanica (Posidoniaceae), Cymodocea nodosa (Cymodoceaceae), and Thalassia testudinum (Hydrocharitaceae) - along with an improved assembly for Zostera marina (Zosteraceae). We also include a draft genome of Potamogeton acutifolius, a representative of Potamogetonaceae, the freshwater sister lineage to the Zosteraceae. Genome analysis reveals that all seagrasses share an ancient whole genome triplication (WGT) event, dating to the early evolution of the Alismatales. An additional whole genome duplication (WGD) event was uncovered for C. nodosa and P. acutifolius. Dating of ancient WGDs and more recent bursts of transposable elements correlate well with major geological and recent climatic events, supporting their role as rapid generators of genetic variation. Comparative analysis of selected gene families suggests that the transition from the submerged-freshwater to submerged-marine environment did not require revolutionary changes. Major gene losses related to, e.g., stomata, volatiles, defense, and lignification, are likely a consequence of the submerged lifestyle rather than the cause ( use it or lose it). Likewise, genes, often retained from the WGD and WGT, were co-opted for functions requiring the alignment of many small adaptations ( tweaking), e.g., osmoregulation, salinity, light capture, carbon acquisition, and temperature. Our ability to manage and conserve seagrass ecosystems depends on our understanding of the fundamental processes underpinning their resilience. These new genomes will accelerate functional studies and are expected to contribute to transformative solutions -- as continuing worldwide losses of the savannas of the sea are of major concern in times of climate change and loss of biodiversity.

evolutionary biology↗

bioRxiv2021

NON-SPECIFIC EFFECTS OF A CINNAMATE-4-HYDROXYLASE INHIBITOR ON AUXIN HOMEOSTASIS

Chemical inhibitors are often implemented for the functional characterization of genes to overcome the limitations associated with genetic approaches. Although being a powerful tool, off-target effects of these inhibitors are easily overlooked in a complex biological setting. Here we illustrate the implications of such secondary effects by focusing on piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H) that is often used to investigate the involvement of lignin during plant growth and development. When supplied to plants, we found that PA is recognized as a substrate by GRETCHEN HAGEN 3.6 (GH3.6), an amido synthetase involved in the formation of the auxin catabolite indole-3-acetic acid (IAA)-Asp. By competing for the same enzyme, PA interferes with auxin conjugation, resulting in an increase in cellular auxin concentrations. These increased auxin levels likely further contribute to an increase in adventitious rooting previously observed upon PA-treatment. Despite the focus on GH3.6 in this report, PA is conjugated by an array of enzymes and their subsequent reduced activity on native substrates could potentially affect a whole set of physiological processes in the plant. We conclude that surrogate occupation of the endogenous conjugation machinery in the plant by exogenous compounds is likely a more general phenomenon that is rarely considered in pharmacological studies. Our results hereby provide an important basis for future reference in studies using chemical inhibitors.

plant biology↗