Biology subjects

Bayer, T.

Publications and source records attributed to Bayer, T..

8 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

Local Adaptation and Transcriptomic Plasticity of the Copepod Acartia tonsa Under Low Salinity Stress

Salinity--an essential factor shaping marine species distributions--is rapidly shifting due to global change, yet the mechanisms of salinity tolerance and adaptation remain poorly understood. We investigated local adaptation in the calanoid copepod Acartia tonsa, a broadly distributed marine species that thrives in the brackish Baltic Sea. Using a common-garden design, we compared physiological and transcriptomic responses to low salinity between populations from the North Sea (>25 PSU) and the Baltic Sea (<15 PSU). Baltic copepods exhibited significantly higher survival under low salinity, indicating local adaptation. While both populations shared a core osmoregulatory strategy involving active ion transport and regulation of amino acids, transcriptomic profiles revealed population-specific differences. Baltic individuals showed a reduced overall gene expression response, yet maintained higher relative expression of osmoregulatory genes--suggesting higher plasticity and a primed response. In contrast, North Sea copepods exhibited broader transcriptional shifts, including downregulation of metabolic and developmental pathways after prolonged stress exposure, possibly reflecting energy conservation mechanisms. These findings reveal that A. tonsa possesses both a plastic osmoregulatory strategy and population-level adaptation that enable survival in extreme salinity conditions. While both populations tolerate short-term exposure to low salinity, local adaptation has enhanced the Baltic populations resilience. This suggests that A. tonsa is broadly tolerant of moderate climate-driven salinity declines across most of its distribution. However, our data also indicate potential range contractions in the lowest salinity zones of the Baltic Sea, underscoring the importance of identifying physiological and genetic thresholds in climate resilience studies.

molecular biology↗

bioRxiv2024

Consistent long-distance foraging flights across years and seasons at colony level in a Neotropical bat

All foraging animals face a trade-off: how much time should they invest in exploitation of known resources versus exploration to discover new resources? For group-living central place foragers, balancing these competing goals poses particular challenges. The availability of social information may discourage individuals from investing in risky, expensive but possibly rewarding exploration. We GPS-tracked groups of greater spear-nosed bats (Phyllostomus hastatus) from three colonies on Isla Colon in Panama. In the dry season, when these omnivores forage on the nectar of ephemeral balsa flowers (Ochroma pyramidale), bats consistently travelled long distances to remote, colony-specific foraging areas, bypassing flowering trees closer to their roosts. They continued to use these same areas in the wet season, when feeding on a diverse, presumably ubiquitously distributed diet, but also visited other, similarly distant foraging areas. Foraging areas were shared within, but not always between colonies. Our longitudinal dataset suggests that bats from each colony invest in long-distance commutes to socially learned shared foraging areas, bypassing other available food patches. Rather than investing in exploration to find nearby resources or engaging in a win-stay lost-shift foraging strategy, these bats follow colony specific behaviours consistent with the existence of culturally transmitted preferences for specific feeding grounds.

animal behavior and cognition↗

bioRxiv2024

The chromosome-level genome of the ctenophore Mnemiopsis leidyi A. Agassiz, 1865 reveals a unique immune gene repertoire

Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one of the most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly of M. leidyi with a focus on its immune gene repertoire. The genome was 247.97 Mb, with N50 16.84 Mb, and 84.7% completeness. Its karyotype was 13 chromosomes. In this genome and that of two other ctenophores, Bolinopsis microptera and Hormiphora californensis, we detected a high number of protein domains related to potential immune receptors. Among those, proteins containing Toll/interleukin-1(TIR2) domain, NACHT domain, Scavenger Receptor Cystein-Rich (SRCR) domain, or C-type Lectin domain (CTLD) were abundant and presented unique domain architectures in M. leidyi. M. leidyi seems to lack bona fide Toll like Receptors, but it does possess a repertoire of 15 TIR2-domain containing genes. Besides, we detected a bona fide NOD-like receptor and 38 NACHT-domain containing genes. In order to verify the function of those domain containing genes, we exposed M. leidyi to the pathogen Vibrio coralliilyticus. Among the differentially expressed genes, we identified potential immune receptors, including four TIR2-domain containing genes, all of which were upregulated in response to pathogen exposure. To conclude, many common immune receptor domains, highly conserved across metazoans, are already present in Ctenophora. These domains have large expansions and unique architectures in M. leidyi, findings consistent with the basal evolutionary position of this group, but still might have conserved functions in immunity and host-microbe interaction.

genomics↗

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

Zetaproteobacteria pan-genome reveals candidate gene cluster for twisted stalk biosynthesis and export

Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The "stalk formation in Zetaproteobacteria" (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologues, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point towards a c-di-GMP regulated surface attachment function of stalks during sessile growth.

microbiology↗

bioRxiv2019

Somatic genetic drift and multi-level selection in modular species

Cells in multicellular organisms are genetically heterogeneous owing to somatic mutations. The accumulation of somatic genetic variation in species undergoing asexual (or clonal) reproduction (termed modular species) may lead to phenotypic heterogeneity among modules. However, abundance and dynamics of somatic genetic variation under clonal growth, a widespread life history in nature, remain poorly understood. Here we show that branching events in a seagrass clone or genet leads to population bottlenecks at the cellular level and hence the evolution of genetically differentiated modules. Studying inter-module somatic genetic variation, we uncovered thousands of SNPs that segregated among modules. The strength of purifying selection on mosaic genetic variation was greater at the intra-module comparing with the inter-module level. Our study provides evidence for the operation of selection at multiple levels, of cell population and modules. Somatic genetic drift leads to the emergence of genetically unique modules; hence, modules in long-lived clonal species constitute an appropriate elementary level of selection and individuality.

evolutionary biology↗

bioRxiv2016

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering

Riboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components. This is due to several limitations including sensitivity to changes in genetic context, low tunability, and variability in performance. To overcome the associated difficulties with riboswitches, we have designed and introduced a novel genetic element called a Ribo-attenuator in Bacteria. This genetic element allows for predictable tuning, insulation from contextual changes, and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as truly modular and tunable components, and thus increases their reliability for a wide range of applications.

synthetic biology↗