Biology subjects

Kearly, A.

Publications and source records attributed to Kearly, A..

3 recordsLinked to original sources

bioRxiv2025

RBP47 family members are negative regulators of heat stress tolerance in Arabidopsis thaliana

Stress granules (SGs) are liquid-liquid phase-separated condensates that sequester RNA, proteins, and metabolites to modulate cellular physiology under stress. In Arabidopsis, the RNA-binding protein RBP47b is a canonical SG marker, yet its functional contribution to thermotolerance remains unresolved. Here, we combined mTurboID proximity labeling with multi-omics profiling to define the RBP47b interactome and its physiological impact. mTurboID identified a stress-specific enrichment of 40S ribosomal subunits within RBP47b SGs, implicating these condensates in translational control. Surprisingly, quadruple mutant plants lacking all four RBP47 paralogues (rbp47abcc') displayed enhanced survival, attenuated growth delay, and faster recovery of photosynthetic efficiency after severe heat stress. Integrated transcriptome, proteome, and metabolome analyses revealed that this gain of thermotolerance is associated with (i) accelerated re-initiation of translation, (ii) constitutively elevated jasmonate and oxylipin pools, and (iii) reduced ROS accumulation during heat and recovery. We conclude that the RBP47 family acts as a negative regulator of heat tolerance by sequestering 40S subunits and limiting translational restart; loss of these SG scaffolds pre-primes jasmonate-dependent detoxification pathways and expedites proteome rebuilding, thereby conferring superior thermotolerance.

plant biology↗

bioRxiv2024

Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells

The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1.

genetics↗

bioRxiv2023

Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying [~]0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the dark proteome. This dark proteome is highly enriched for certain (e.g. CLE, CEP, IDA, PSY) but not other (e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life (e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.

plant biology↗