Biology subjects

Mazzella, M. A.

Publications and source records attributed to Mazzella, M. A..

4 recordsLinked to original sources

bioRxiv2025

Multi-Omics Meta-Analysis Provides Insights into Reversible Phosphorylation During Arabidopsis Skotomorphogenesis

We developed a pipeline to standardize and integrate publicly available transcriptomic, proteomic, and phosphoproteomic datasets from Arabidopsis thaliana etiolated seedlings. The pipeline is broadly adaptable, as its database schema and processing scripts can be applied to datasets from any organism or experimental condition. We applied it to etiolated seedlings to uncover protein kinases and protein phosphatases relevant to early skotomorphogenic development, a stage in which seedlings grow underground and rely on precisely regulated signaling networks to ensure survival and successful emergence. This multi-omics approach revealed a comprehensive landscape of protein expression at this developmental stage; however, we observed widespread discrepancies between transcript and protein abundance, pointing to post-transcriptional and/or post-translational regulation. This cross-study minimizes experimental bias and allows the detection of phosphorylation events that may have been overlooked in single-condition studies. A search of kinase specific motifs revealed that RxxS motifs were significantly enriched among phosphorylated peptides in protein phosphatases and microtubule-associated proteins, suggesting regulation by calcium dependent protein kinases (CPKs). CPK3 and CPK9 were identified as the most relevant isoforms in the proteome and phosphokinome, supporting their central role in skotomorphogenesis. Our results underscore the importance of phosphorylation-mediated signaling in coordinating early seedling development and provide a resource for dissecting regulatory networks and candidate genes involved in skotomorphogenesis.

plant biology↗

bioRxiv2025

PHYTOCHROME INTERACTING FACTORS are required to coordinate microtubule dynamics and differential cell growth during Arabidopsis apical hook opening

BackgroundDifferential cell growth is a key strategy that enables plants to adjust their morphology in response to internal and external cues. Apical hook opening in dark- grown Arabidopsis seedlings serves as an excellent model to study how coordinated cell expansion generates organ bending. Several works highlight the influence of hormone signaling, cell wall mechanics, and environmental cues on cortical microtubule (cMT) arrangement in bending tissues. However, the precise genetic hierarchy governing these processes remains largely unknown. ResultsHere, we reveal a two-step growth rate during apical hook opening, in which an initial phase of differential cell expansion is followed by a phase of more balanced growth. We show that cMT re-arrangement precedes and predicts cell expansion patterns, suggesting a central role in coordinating differential growth. Our findings indicate that PIF transcription factors regulate this process, as pifq mutants fail to align cMT reorganization with growth dynamics, resulting in premature hook opening. RNA- seq analysis further supports a role for PIFs in coordinating cell wall remodeling and microtubule-associated gene expression, including kinesins and cell wall-modifying enzymes. ConclusionsOur study uncovers a PIF-dependent regulatory mechanism that orchestrates cytoskeletal dynamics and cell expansion to control apical hook opening.

plant biology↗

bioRxiv2023

RADIP LIGHT-INDUCED PHOSPHORYLATION CHANGES IN MICROTUBULE RELATED PROTEINS IN ARABIDOPSIS

Rapid hypocotyl elongation allows buried seedlings to reach the surface, where light triggers de-etiolation and inhibits hypocotyl growth mainly by phytochromes A, B and cryptochromes 1, 2. Dynamic phosphorylation/dephosphorylation events provide a mechanism to rapidly transduce light signals. Only recently we have begun to uncover the earliest phospho-signaling responders to light. Here, we report a large-scale phosphoproteomic analysis and identify 20 proteins that change their phosphorylation pattern after 20 min of white light pulse compared to darkness. Microtubule-associated proteins (MAPs) were highly overrepresented in this group. Among them, we studied CIP7 (COP1-INTERACTING-PROTEIN-7), which presented microtubule (MT) localization, in contrast to what was previously described. Phosphorylated isoform in Serine 915 (Sp915) of CIP7 was detected in etiolated seedlings but undetectable after a light pulse in the presence of photoreceptors, while its expression decays with long light exposure. The short hypocotyl phenotype and rearrangement of MTs in etiolated cip7 mutants are complemented by CIP7-YFP and the phospho-mimetic CIP7S915D-YFP, but not the phospho-null CIP7S915A-YFP suggesting that Sp915CIP7 is the active isoform that promotes hypocotyl elongation thorough MT reorganisation in darkness. Our results reveal that the small repertory of proteins that changes the phosphorylation status after a rapid light signal is tightly focused on MAPs; suggesting that phospho-regulation of microtubule-base processes are early targets during de-etiolation. The evidence on Sp915CIP7 supports this idea.

plant biology↗

bioRxiv2018

Neighbor signals perceived by phytochrome B increase thermotolerance in Arabidopsis

Due to the preeminence of reductionist approaches, our understanding of plant responses to combined stresses is limited. We speculated that light-quality signals of neighboring vegetation might increase susceptibility to heat shocks because shade reduces tissue temperature and hence the likeness of heat shocks. In contrast, plants of Arabidopsis thaliana grown under low red / far-red ratios typical of shade were less damaged by heat stress than plants grown under simulated sunlight. Shade reduces the activity of phytochrome B (phyB) and the phyB mutant showed high tolerance to heat stress even under simulated sunlight. The enhanced heat tolerance under low red / far-red ratios failed in a multiple mutant of PHYTOCHROME INTERACTING FACTORs. The phyB mutant showed reduced expression of several fatty acid desaturase (FAD) genes, proportion of fully unsaturated fatty acids and electrolyte leakage of membranes exposed to a heat shock. Activation of phyB by red light also reduced thermotolerance of dark-grown (etiolated) seedlings but not via changes in FAD gene expression and membrane stability. We propose that the reduced photosynthetic capacity linked to thermotolerant membranes would be less costly under shade, where the light input itself limits photosynthesis.

plant biology↗