Arabidopsis MDN1 Is Involved in the Establishment of a Normal Seed Proteome and Seed Germination

Unravelling the Significance of Seed Proteomics: Insights into Seed Development, Function, and Agricultural Applications

Seeds are essential for plant reproduction, ensuring species survival and dispersal while adapting to diverse environments throughout a plant's life. Proteomics has emerged as a powerful tool for deciphering the complexities of seed growth, germination, and stress responses. Advanced proteomic technologies enable the analysis of protein changes during germination, dormancy, and ageing, enhancing our understanding of seed lifespan and vitality. Recent studies have revealed detailed insights into metabolic processes and storage protein profiles across various plant species. This knowledge is crucial for improving seed storage, conserving quality, and maintaining viability. Additionally, it contributes to sustainable agriculture by identifying stress-responsive proteins and signalling pathways that can mitigate stress and enhance farming practices. This review highlights significant advancements in seed proteomics over the past decade, discussing critical discoveries related to storage proteins, protein interactions, and proteome modifications due to stress. It illustrates how these insights transform seed biology, boosting productivity, food security, and environmentally friendly practices. The review also identifies existing knowledge gaps and provides direction for future research, underscoring the need for continued interdisciplinary collaboration in this dynamic field.

FLOWERING REPRESSOR AAA+ ATPase 1 is a novel regulator of perennial flowering in Arabis alpina

Arabis alpina is a polycarpic perennial, in which PERPETUAL FLOWERING1 (PEP1) regulates flowering and perennial traits in a vernalization-dependent manner. Mutagenesis screens of the pep1 mutant established the role of other flowering time regulators in PEP1-parallel pathways. Here we characterized three allelic enhancers of pep1 (eop002, 085 and 091) which flower early. We mapped the causal mutations and complemented mutants with the identified gene. Using quantitative reverse transcriptase PCR and reporter lines, we determined the protein spatiotemporal expression patterns and localization within the cell. We also characterized its role in Arabidopsis thaliana using CRISPR and in A. alpina by introgressing mutant alleles into a wild-type background. These mutants carried lesions in an AAA⁺ ATPase of unknown function, FLOWERING REPRESSOR AAA⁺ ATPase 1 (AaFRAT1). AaFRAT1 was detected in the vasculature of young leaf primordia and the rib zone of flowering shoot apical meristems. At the subcellular level, AaFRAT1 was localized at the interphase between the endoplasmic reticulum and peroxisomes. Introgression lines carrying Aafrat1 alleles required less vernalization to flower and reduced number of vegetative axillary branches. By contrast, A. thaliana CRISPR lines showed weak flowering phenotypes. AaFRAT1 contributes to flowering time regulation and the perennial growth habit of A. alpina.

Mutation of an Essential 60S Ribosome Assembly Factor MIDASIN 1 Induces Early Flowering in Arabidopsis

Ribosome biogenesis is tightly associated with plant growth and reproduction. Mutations in genes encoding ribosomal proteins (RPs) or ribosome biogenesis factors (RBFs) generally result in retarded growth and delayed flowering. However, the early-flowering phenotype resulting from the ribosome biogenesis defect is rarely reported. We previously identified that the AAA-ATPase MIDASIN 1 (MDN1) functions as a 60S RBF in Arabidopsis. Here, we found that its weak mutant mdn1-1 is early-flowering. Transcriptomic analysis showed that the expression of FLOWERING LOCUS C (FLC) is down-regulated, while that of some autonomous pathway genes and ABSCISIC ACID-INSENSITIVE 5 (ABI5) is up-regulated in mdn1-1. Phenotypic analysis revealed that the flowering time of mdn1-1 is severely delayed by increasing FLC expression, suggesting that the early flowering in mdn1-1 is likely associated with the downregulation of FLC. We also found that the photoperiod pathway downstream of CONSTANTS (CO) and FLOWERING LOCUS T (FT) might contribute to the early flowering in mdn1-1. Intriguingly, the abi5-4 allele completely blocks the early flowering in mdn1-1. Collectively, our results indicate that the ribosome biogenesis defect elicited by the mutation of MDN1 leads to early flowering by affecting multiple flowering regulation pathways.

ABI5 binding protein2 inhibits ABA responses during germination without ABA-INSENSITIVE5 degradation

Overexpression of ABA-INSENSITIVE5 binding proteins (AFPs) results in extreme ABA resistance of seeds and failure to acquire desiccation tolerance, at least in part through effects on chromatin modification. We tested the hypothesis that AFPs promote germination in Arabidopsis (Arabidopsis thaliana) by also functioning as adapters for E3 ligases that ubiquitinate ABI5, leading to its degradation. Interactions between AFPs and two well-characterized classes of E3 ligases targeting ABI5, DWD HYPERSENSITIVE TO ABA (DWA)s and KEEP ON GOING, were analyzed by yeast two-hybrid, bimolecular fluorescence complementation, and genetic assays. Although weak direct interactions were detected between AFPs and E3 ligases, loss of function for these E3 ligases did not impair ABA-resistance conferred by overexpression of the YFP-AFP2 fusion. Comparison of ABI5 and AFP2 levels in these lines showed that AFP2 accumulation increased during germination, but that ABI5 degradation followed germination, demonstrating that AFP2 overexpression reduces ABA sensitivity, thereby permitting germination prior to ABI5 degradation. Surprisingly, AFP2 overexpression in the dwa1 dwa2 mutant background produced the unusual combination of extreme ABA resistance and desiccation tolerance, creating an opportunity to separate the underlying biochemical characteristics of ABA sensitivity and desiccation tolerance. Our quantitative proteomics analysis identified at least three-fold more differentially accumulated seed proteins than previous studies. Comparison of dry seed proteomes of wild-type or dwa1 dwa2 mutants with or without AFP2 overexpression allowed us to separate and refine the changes in protein accumulation patterns associated with desiccation tolerance independently of ABA sensitivity, or vice versa, to a subset of cold-induced and defense stress-responsive proteins and signaling regulators.

Coordination between MIDASIN 1-mediated ribosome biogenesis and auxin modulates plant development

Ribosomes are required for plant growth and development, and ribosome biogenesis-deficient mutants generally display auxin-related phenotypes. Although the relationship between ribosome dysfunction and auxin is known, many aspects of this subject remain to be understood. We previously reported that MIDASIN 1 (MDN1) is an essential pre-60S ribosome biogenesis factor (RBF) in Arabidopsis. In this study, we further characterized the aberrant auxin-related phenotypes of mdn1-1, a weak mutant allele of MDN1. Auxin response is disturbed in both shoots and roots of mdn1-1, as indicated by the DR5:GUS reporter. By combining transcriptome profiling analysis and reporter gene detection, we found that expression of genes involved in auxin biosynthesis, transport, and signaling is changed in mdn1-1. Furthermore, MDN1 deficiency affects the post-transcriptional regulation and protein distribution of PIN-FORMED 2 (PIN2, an auxin efflux facilitator) in mdn1-1 roots. These results indicate that MDN1 is required for maintaining the auxin system. More interestingly, MDN1 is an auxin-responsive gene, and its promoter can be targeted by multiple AUXIN RESPONSE FACTORs (ARFs), including ARF7 and ARF19, in vitro. Indeed, in arf7 arf19, the auxin sensitivity of MDN1 expression is significantly reduced. Together, our results reveal a coordination mechanism between auxin and MDN1-dependent ribosome biogenesis for regulating plant development.

Identification of Low-Abundance Lipid Droplet Proteins in Seeds and Seedlings

The developmental program of seed formation, germination, and early seedling growth requires not only tight regulation of cell division and metabolism, but also concerted control of the structure and function of organelles, which relies on specific changes in their protein composition. Of particular interest is the switch from heterotrophic to photoautotrophic seedling growth, for which cytoplasmic lipid droplets (LDs) play a critical role as depots for energy-rich storage lipids. Here, we present the results of a bottom-up proteomics study analyzing the total protein fractions and LD-enriched fractions in eight different developmental phases during silique (seed) development, seed germination, and seedling establishment in Arabidopsis (Arabidopsis thaliana). The quantitative analysis of the LD proteome using LD-enrichment factors led to the identification of six previously unidentified and comparably low-abundance LD proteins, each of which was confirmed by intracellular localization studies with fluorescent protein fusions. In addition to these advances in LD protein discovery and the potential insights provided to as yet unexplored aspects in plant LD functions, our data set allowed for a comparative analysis of the LD protein composition throughout the various developmental phases examined. Among the most notable of the alterations in the LD proteome were those during seedling establishment, indicating a switch in the physiological function(s) of LDs after greening of the cotyledons. This work highlights LDs as dynamic organelles with functions beyond lipid storage.

Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis

AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.