Biology subjects

Blomme, J.

Publications and source records attributed to Blomme, J..

5 recordsLinked to original sources

bioRxiv2026

A spatial atlas of the seaweed CO2-fixation machinery reveals a unique Rubisco condensation mechanism

Seaweeds (macroalgae) are important primary producers that sustain food webs in coastal ecosystems. Most algae accelerate inorganic carbon assimilation by actively concentrating CO2 in a Rubisco-rich specialized organelle called the pyrenoid. However, the molecular composition of this pathway is unknown in seaweeds. Here, we investigated the intracellular localization of 160 proteins associated with CO2 acquisition in the green seaweed Ulva (Sea lettuce). We assign 68 proteins to different pyrenoid subdomains and identify a consensus Ulva Rubisco binding motif revealing the molecular logic of the Ulva pyrenoid. We reveal Seaweed Ulva Pyrenoid Assembly 1 (SUPA1) as the core pyrenoid assembly factor. We show that Rubisco condensation is driven by a unique mechanism: the helical folding of SUPA1 motifs upon Rubisco binding, combined with steric hindrance that halves the available Rubisco binding sites from eight to four. Our data gives an unprecedented sub-cellular spatial understanding on seaweed carbon fixation and provides insights into the evolution of this important pathway in the global carbon cycle.

cell biology↗

bioRxiv2024

Consolidating Ulva functional genomics: Gene editing and new selection systems

The green seaweed Ulva compressa is a promising model for functional biology. In addition to historical research on growth and development, -omics data and molecular tools for stable transformation are available. However, more efficient tools are needed to study gene function. Here, we expand the molecular toolkit for Ulva. We screened the survival of Ulva and its mutualistic bacteria on 14 selective agents and establish that Blasticidin deaminases (BSD or bsr) can be used as selectable markers to generate stable transgenic lines. We show that Cas9 and Cas12a RNPs are suitable for targeted mutagenesis and can generate genomic deletions up to 20 kb using the marker gene ADENINE PHOSPHORIBOSYLTRANSFERASE (APT). We demonstrate that targeted insertion of a selectable marker via homology-directed repair or co-editing with APT is possible for non- marker genes. We evaluated 31 vector configurations and found that bicistronic fusion of Cas9 to a resistance marker or incorporation of introns in Cas9 led to the most mutants. We used this to generate mutants in three non-marker genes using a co-editing strategy. This expanded molecular toolkit now enables us to reliably make gain- and loss-of-function mutants, additional optimizations will be necessary to allow for vector-based multiplex genome editing in Ulva.

molecular biology↗

bioRxiv2022

Cell walls are dynamically O-acetylated in the green seaweed, Ulva compressa

We report that cell wall polymers in the chlorophyte algae may be modified by O-acetylation. The importance of cell wall modifications in the green algae is not well understood, although similar modifications play key roles in land plants by modulating the properties of cell wall carbohydrate polymers. Using a combination of biophysical (Fourier-transform infrared and cross-polarisation heteronuclear correlation nuclear magnetic resonance spectroscopy), biochemical (thin-layer chromatography) and molecular approaches (yellow fluorescent protein-tagged transgene localisation), we show that the extractable ulvan fractions of Ulva compressa cell walls contain O-acetyl sidechains, we demonstrate that acetylation is dynamic and decreases reversibly in response to metal-induced stress, we note interactions between acetyl and borate sidechains and we locate two candidate genes that, together, may encode an acetyltransferase. We therefore propose that O-acetylation of ulvan residues is involved in the normal cell wall physiology of at least some chlorophyte algae. To the best of our knowledge, this is the first demonstration of O-acetyl sidechains in green algal cell wall polymers, and of reversible changes in algal cell wall polymer modification in response to stress.

cell biology↗

bioRxiv2021

Gametogenesis in the green seaweed Ulva mutabilis coincides with massive transcriptional restructuring

The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Here, gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization. HighlightTranscriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in induction of sexual reproduction.

plant biology↗

bioRxiv2020

A molecular toolkit for the green seaweed Ulva mutabilis

The green seaweed Ulva is an ecologically-important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed Ulva mutabilis based on a Golden Gate cloning system. The toolkit presently contains 125 entry vectors, 26 destination vectors and 107 functionally validated expression vectors. We demonstrate the importance of endogenous regulatory sequences for transgene expression and characterize three endogenous promoters suitable to drive transgene expression. We describe two vector architectures to express transgenes via two expression cassettes or a bicistronic approach. The majority of selected transformants (50-80%) consistently give clear visual transgene expression. Furthermore, we made different marker lines for intracellular compartments after evaluating 13 transit peptides and 11 tagged endogenous Ulva genes. Our molecular toolkit enables the study of Ulva gain-of-function lines and paves the way for gene characterization and large-scale functional genomics studies in a green seaweed. One-sentence summaryMolecular cloning tools allow to generate gain-of-function seaweed lines that will help to study seaweed biology.

plant biology↗