Biology subjects

Mutte, S.

Publications and source records attributed to Mutte, S..

10 recordsLinked to original sources

bioRxiv2026

Systematic proteomics identifies a conserved mechanism for polar targeting of plant cortical proteins

Multicellular development is tightly coupled to the polarization of individual cells, which partitions polar proteins along the cell cortex and can control asymmetric cell division, anisotropic growth, local differentiation or physiology. Mechanisms driving cell polarization have been described in fungi and animals, but these lack counterparts in plants. While several polarized proteins have been identified in plants, the overall mechanisms guiding their polar localization are poorly characterized. Through iterative affinity proteomics on the recently identified SOSEKI polar proteins, we discovered a network of polar proteins that is conserved in the flowering plant Arabidopsis and the liverwort Marchantia. We next used this collection of novel polarized proteins for systematic proximity ligation proteomics in these two species to map their global polar proteome. We identified a subfamily of polarized Protein S-acyl transferase (PAT) enzymes that are required for membrane targeting of Arabidopsis SOSEKI proteins. Using human and fruit fly models, we showed that PAT19 is sufficient for membrane targeting of SOSEKI1, likely through direct palmitoylation. This work demonstrates a conserved mechanism for polar protein targeting in plants and offers a resource for studying polar protein localization.

plant biology↗

bioRxiv2025

Genetic diversity, predictive protein structures, and interaction networks of Cysteine-Rich Receptor-Like Kinases in Arabidopsis thaliana

Cysteine-rich receptor-like kinases (CRKs) are a large subfamily of plant receptor-like kinases (RLKs) implicated in immunity and development, yet their ligands, interaction partners, and mechanistic roles remain poorly defined. We combined population-genetic analyses and AlphaFold-based structural prediction to characterise the Arabidopsis thaliana CRK family. Phylogenetic reconstruction from 69 natural accessions resolved five well-supported CRK clades. Nucleotide diversity ({pi}) and neutrality tests revealed heterogeneous diversity across loci, with evidence of both positive and negative selection pressure acting on different CRKs. AlphaFold models of CRK extracellular domains (ECDs) recapitulate the DUF26 structure observed in Plasmodesmata Localizing Protein (PDLP)5/PDLP8 and ginkbilobin-2 but display distinct biochemical properties and disulfide-bond topologies. Pairwise AlphaFold dimer modelling of all 780 CRK-ECD combinations produced 145 high-confidence interaction models; [~]78% of these adopt a shared dimer conformation characterized by an extended intermolecular {beta}-sheet at the interface. Integrating evolutionary and structural approaches reveals clade-specific selective regimes and conserved structural features of CRK ECDs that likely underpin receptor-receptor interactions. Predicted high-confidence dimer interfaces suggest a general mode of CRK-ECD association that can guide targeted biochemical and genetic validation, accelerating functional dissection of this important receptor family.

bioinformatics↗

bioRxiv2024

Auxin and tryptophan trigger common responses in the streptophyte alga Penium margaritaceum

Auxin is a signaling molecule that regulates multiple processes in the growth and development of land plants. Research gathered from model species, particularly Arabidopsis thaliana, has revealed that the nuclear auxin pathway controls many of these processes through transcriptional regulation. Recently, a non-transcriptional pathway based on rapid phosphorylation mediated by kinases has been described, complementing the understanding of the complexity of auxin-regulated processes. Phylogenetic inferences of both pathways indicate that only some of the components are conserved beyond land plants. This raises fundamental questions about the evolutionary origin of auxin responses and whether algal sisters share mechanistic features with land plants. Here we explore auxin responses in the unicellular streptophyte alga Penium margaritaceum. By assessing physiological, transcriptomic and cellular responses we found that auxin triggers cell proliferation, gene regulation and acceleration of cytoplasmic streaming. Notably, all these responses are also triggered by the structurally related tryptophan. These results identify shared auxin response features among land plants and algae, and suggest that less chemically specific responses preceded the emergence of auxin-specific regulatory networks in land plants.

plant biology↗

bioRxiv2024

ETTIN-mediated auxin signalling is an angiosperm-specific neofunctionalization for carpel development

The phytohormone auxin affects processes throughout plant growth and development. While auxin signalling has been mainly attributed to a repressor degradation-based pathway, numerous alternative mechanisms for how auxin mediates its effect have been revealed in recent years. One such mechanism involves a direct auxin-induced switch in the transcriptional regulatory activity of the Auxin Response Factor (ARF) ETTIN (ETT). ETT lacks a conserved C-terminus domain involved in canonical pathway interactions but contains a middle region domain mediating auxin binding. As the ETT clade only exists in the angiosperms, it remains unknown when the pathway evolved. Here we provide evidence for a two-step origin of the ETT clade and its neofunctionalisation through the gain of auxin perception in gynoecium patterning. Phylogenetic analyses reveal the structural divergence of ETT and its paralogue ARF4 after their duplication from an ancestral euphyllophyte ARF3/4 clade. Auxin sensitivity was identified as an ETT-specific innovation that likely originated in the last common angiosperm ancestor. Furthermore, in planta complementation experiments demonstrated the full genetic redundancy of ETT and ARF4 in leaf and ovary development, but a specialised role for the ETT-mediated auxin signalling pathway in style development. Our work thus provides evidence that ETT was recruited from an ancestral role in leaf development and subsequently underwent neofunctionalisation through the acquisition of direct auxin sensing for a novel role in gynoecium patterning.

evolutionary biology↗

bioRxiv2022

An ultra-fast, proteome-wide response to the plant hormone auxin

The plant signaling molecule auxin controls growth and development through a simple nuclear pathway that regulates gene expresion. There are however several cellular and physiological responses to auxin that occur within seconds, far too rapid to be mediated by transcriptional changes, for which no molecular mechanism has yet been identified. Using a phosphoproteomic strategy in Arabidopsis thaliana roots, we identify an ultra-rapid auxin response system that targets over 1700 proteins, many within 30 seconds. Auxin response is chemically specific, requires known auxin-binding proteins, and targets various pathways. Through exploring its temporal dynamics, we infer auxin-triggered kinase-substrate networks and identify apoplastic pH changes as a target of signaling and as part of a relay mechanism. By generating a variety of phosphoproteomic datasets, integrated with structural information in a web-app, and by demonstrating analysis and inference strategies, we offer a resource to explore rapid and dynamic signaling in plants.

plant biology↗

bioRxiv2022

A RAF-like kinase mediates a deeply conserved, ultra-rapid auxin response

The plant signaling molecule auxin triggers both fast and slow cellular responses across the plant kingdom, including both land plants and algae. A nuclear response pathway mediates auxin-dependent gene expression, and controls a range of growth and developmental processes in land plants. It is unknown what mechanisms underlie both the physiological responses occurring within seconds, and the responses in algae, that lack the nuclear auxin response pathway. We discovered an ultra-fast proteome-wide phosphorylation response to auxin across 5 land plant and algal species, converging on a core group of shared target proteins. We find conserved rapid physiological responses to auxin in the same species and identified a RAF-like protein kinase as a central mediator of auxin-triggered phosphorylation across species. Genetic analysis allowed to connect this kinase to both auxin-triggered protein phosphorylation and a rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.

plant biology↗

bioRxiv2020

Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes

Protein oligomerization is a fundamental process to build complex functional modules. Domains that facilitate the oligomerization process are diverse and widespread in nature across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is functionally (relatively) well understood in the animal kingdom. However, beyond animals, neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. While PB1 domain proteins have been found in other kingdoms, including plants, it is unclear how these relate to animal PB1 proteins. To address this question, we utilized large transcriptome datasets along with the proteomes of a broad range of species. We discovered eight PB1 domain-containing protein families in plants, along with three each in Protozoa and Chromista and four families in Fungi. Studying the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. Tertiary structural models of these plant PB1 families, combined with Random Forest based classification, indicated family-specific differences attributed to the length of PB1 domain and the proportion of {beta}-sheets. This study identifies novel PB1 families and reveals considerable complexity in the protein oligomerization potential at the origin of eukaryotes. The newly identified relationships provide an evolutionary basis to understand the diverse functional interactions of key regulatory proteins carrying PB1 domains across eukaryotic life.

evolutionary biology↗

bioRxiv2019

Design principles of a minimal auxin response system

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1-3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development2-4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. Expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned, or prevented. This fundamental design likely represents the ancestral system, and formed the basis for inflated, complex systems.

plant biology↗

bioRxiv2019

Evolution of vascular plants through redeployment of ancient developmental regulators

Vascular plants provide most of the biomass, food and feed on earth; yet the molecular innovations that led to the evolution of their conductive tissues are unknown. Here, we reveal the evolutionary trajectory for the heterodimeric TMO5/LHW transcription factor complex, which is rate-limiting for vascular cell proliferation in Arabidopsis thaliana. Both regulators have origins predating vascular tissue emergence, and even terrestrialization. We further show that TMO5 evolved its modern function, including dimerization with LHW, at the origin of land plants. A second innovation in LHW, coinciding with vascular plant emergence, conditioned obligate heterodimerization and generated the critical function in vascular development. In summary, our results suggest that division potential of vascular cells may have been a major driver in the evolution of vascular plants.

plant biology↗

bioRxiv2017

Origin and evolution of the nuclear auxin response system

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

genomics↗