Biology subjects

Sterck, L.

Publications and source records attributed to Sterck, L..

7 recordsLinked to original sources

bioRxiv2024

Warm temperature modifies cell fates to reduce stomata production in Arabidopsis

O_LIStomatal abundance decrease in Arabidopsis triggered by warm-temperature is attributed to PIF4-mediated repression of SPEECHLESS (SPCH) expression. We identified the unknown developmental and transcriptional basis of this adaptive response. C_LIO_LIWe traced stomatal lineages in vivo using cell-identity marker lines and mutants, quantified epidermal traits and conducted RNA sequencing under oscillating temperatures. C_LIO_LIProlonged warm-temperature or PIF4-overexpression altered cell-fates, inducing diverted stomatal precursors (DPs) that lacked stomatal fate, accounting for stomata reduction. DPs originated from meristemoids that lost SPCH expression, lacked MUTE expression and exited the cell cycle. Short warm-temperature pulses allowed later recovery of SPCH expression, and did not induce DPs or stomata reduction. Comparison of transcriptomes obtained during warm-temperature pulses with stomatal lineage cell-specific profiles identified gene expression changes and contrasted their reversibility. Though warm-temperature silenced key stomatal drivers, most lineages formed stomata through partly modified transcriptional landscapes that promoted uncommitted cell identities and included alternative pathways. C_LIO_LIExpression changes in stomatal regulators and cell-fate changes explain lineage progression under fluctuating temperatures. Since short-term temperature oscillations prevail in natural conditions, the requirement of long warm-temperature exposure to trigger DPs would prevent stomata reduction by occasional temperature rises. Promoting uncommitted lineage stages provides flexibility to stomatal development under environmental changes. C_LI

plant biology↗

bioRxiv2024

The spliceosomal component GAMETOPHYTIC FACTOR 1 (GFA1) regulates a key photoperiodic switch

Plants have evolved sophisticated mechanisms to perceive and interpret daytime in order to flower at an optimal time point. Here we show that the spliceosomal component GAMETOPHYTIC FACTOR 1 (GFA1) constitutes a previously unrecognized key photoperiodic switch, that is essential for flowering in long days. We show that gfa1 hypomorphic (gfa1hyp) plants fail to initiate flowering in long-days (LD), which correlates with ectopic activation of the short-day (SD) flowering repressor ARABIDOPSIS THALIANA CENTRORADIALIS (ATC). Accordingly, flowering is restored upon inactivation of ATC in gfa1hyp mutants. A novel tissue-specific in-planta splice assay and comprehensive RNAseq profiling of gfa1hyp mutants indicate that GFA1 mediated pre-mRNA splicing is substrate specific, as previously suggested for GFA1 orthologs. Furthermore, we show that gfa1hyp mutants accumulate nonsense transcripts of the photoreceptor components PHYB and RRC1, suggesting inappropriate photoreceptor signaling as a potential cause for the ectopic activation of the SD characteristic profile in gfa1hyp. In fact, known downstream targets of the phytochrome system such as RS31, SR34a, SRp30 accumulate reduced amounts of light-dependent splice isoforms. Together, our data reveal a link between spliceosome composition and long-day flowering, based on complex transcriptional readouts in response to day length.

developmental biology↗

bioRxiv2021

GPI anchor remodeling by the plant PGAP1 ortholog HLD1 is essential for Papaver self-incompatibility

In eukaryotes, glycosylphosphatidylinositol anchored proteins (GPI-APs) are tethered to the outer leaflet of the plasma membrane where they function as key regulators of a plethora of biological processes. Self-incompatibility (SI) plays a pivotal role regulating fertilization in higher plants through recognition and rejection of self pollen. Here we used Arabidopsis thaliana lines engineered to be self-incompatible by expression of Papaver SI determinants for an SI suppressor screen. We identify HLD1, an ortholog of human GPI-inositol deacylase PGAP1, whose mutation completely abolishes the SI response. We show that HLD1 functions as a GPI-inositol deacylase and that this GPI-remodeling activity is essential for SI. Using GFP-SKU5 as a representative GPI-AP, we show that HLD1 mutation does not affect GPI-AP production and targeting, but alters the configuration of mature GPI-APs. This prevents GPI-AP release from the plasma membrane, suggesting that this process plays a critical role in the regulation of SI. Our data not only identify GPI anchoring as a new pathway of SI providing new directions to investigate SI mechanisms, but identifies for the first time a function for GPI-AP remodeling by inositol deacylation in plants. One sentence summaryThe Papaver self-incompatibility response requires GPI-anchor modification by HLD1, an ortholog of the mammalian PGAP1.

plant biology↗

bioRxiv2020

ABCB-mediated auxin transport in outer root tissues regulates lateral root spacing in Arabidopsis

Root branching is an important strategy to explore efficiently large volumes of soil. To economize this process, lateral roots (LR) are formed along the growing root at discrete positions that are instructed by oscillating auxin signals derived from the lateral root cap (LRC). This assumes that auxin moves from the LRC across multiple layers to accumulate in the pericycle. Here, we identified, using gene silencing and CRISPR based approaches, a group of five genetically linked, closely related ABCBs that control LR spacing by modulating the amplitude of the auxin oscillation. The transporters localize to the plasma membrane and reveal significant auxin export activity. These ABCBs are mainly expressed in the LRC and epidermis where they contribute to auxin transport towards the root oscillation zone. Our findings highlight the importance of auxin transport in the outer tissues of the root meristem to regulate LR spacing.

plant biology↗

bioRxiv2020

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer new insights on the genetic diversity and gene functions in benthic diatoms.

bioinformatics↗

bioRxiv2019

Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder

Hi-C has become a popular technique in recent genome assembly projects. Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs in draft genomes, resulting in chromosome-level assemblies. However, application of this approach is currently hampered by a lack of robust programs that are capable of effectively treating this type of data, particularly open source programs. We developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes. Both GRAAL, and instaGRAAL use a Markov Chain Monte Carlo algorithm to perform Hi-C scaffolding, but instaGRAAL features a number of improvements including a modular polishing approach that optionally integrates independent data. To validate the program, we used it to generate chromosome-level assemblies for two brown algae, Desmarestia herbacea and the model Ectocarpus sp., and quantified improvements compared to the initial draft for the latter. Overall, instaGRAAL is a program able to generate, using default parameters with minimal human intervention, near-complete assemblies.

genomics↗

bioRxiv2019

Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic background often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we found that several coding loci contribute to local adaptation. We also discovered a very large (ca. 300 Mbp) putative inversion with a signal of local adaptation, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out to the need for more attention towards multi-locus analysis of polygenic adaptation.

genomics↗