Biology subjects

Whitcomb, S. J.

Publications and source records attributed to Whitcomb, S. J..

4 recordsLinked to original sources

bioRxiv2025

SNRK3.15 is a crucial component of the sulfur deprivation response in Arabidopsis thaliana

Sulfate deprivation (-S) results in numerous metabolic and phenotypic alterations in plants. Kinases are often key players in transducing nutrient status signals to molecular components involved in metabolic and developmental program regulation, but despite the physiological importance of sulfur, to date, no signaling kinases have been identified in sulfur-deficiency signaling response programs. Here we show that the serine/threonine protein kinase CIPK14/SNRK3.15 plays a regulatory role in the -S response in Arabidopsis thaliana seedlings. Multiple molecular and physiological responses to -S are attenuated in snrk3.15 mutants, including both early adaptive responses and later emergency salvage processes including nutrient deficiency induced senescence. When grown in soil with sufficient sulfur supply, snrk3.15 mutants showed no clear phenotypes, including no difference in seed sulfur content. Lastly, the proteome dataset generated from Col-0 and snrk3.15.1 Arabidopsis seedlings under -S conditions for this project is the first of its kind and will be a valuable research resource. Proteomics data are available via ProteomeXchange with identifier PXD046612.

plant biology↗

bioRxiv2025

Development and quality assessment of low-cost benchtop malting protocol for laboratory-scale malt quality evaluation

High-quality malt is influenced by three primary factors: barley genotype, environmental conditions, and malting process. To effectively evaluate malting barley breeding material and assess how environmental changes influence malt quality, it is essential to have laboratory- scale malting methods that can produce malt approximating that produced by commercial malting operations. However, existing laboratory-scale malting procedures often demand large quantities of grain, rely on specialized equipment, and are costly. To overcome these challenges, we developed a small sample-scale benchtop malting method utilizing standard laboratory equipment and components available at hardware stores. We validated the method by conducting standard malt quality tests including diastatic power, -amylase activity, total malt protein, and wort composition (soluble protein, wort soluble/total malt protein, {beta}-glucan, free amino nitrogen, and malt extract). Our findings indicate that the benchtop malting method yields quality metrics comparable to those obtained from established small-scale and full-scale malting protocols. Furthermore, a key innovation of this system is the use of separate Erlenmeyer flasks for malting each sample. Unlike conventional shared malting systems, this design enables precise measurement and comparison of treatment effects across samples malted simultaneously. This reliable, low-cost, and efficient method provides a valuable tool for screening malt quality traits in breeding lines with limited sample sizes and for testing malting regimes aimed at improving malt quality and efficiency. Additionally, it offers an accessible solution for producing high-quality, research-scale malt in laboratories without dedicated quality assurance facilities.

biochemistry↗

bioRxiv2024

Integrative LC-MS and GC-MS Metabolic Profiling Unveils Dynamic Changes during Barley Malting

Malting, a crucial process for beer production, involves complex biochemical transformations affecting sensory attributes and product quality. Despite extensive research on storage carbohydrates and proteins involved in malting, a detailed understanding of metabolic alterations during this process remains elusive, limiting our ability to assess and enhance malt quality. Our study employed untargeted GC-MS and LC-MS metabolite profiling to elucidate these changes across six malting stages: dry seed, post-steeping (DOG0), germination (DOG1, DOG3, DOG5), and kilning. We identified a total of 4980 known metabolites, with approximately 82% exhibiting significant changes. Statistical analysis revealed stage-dependent metabolic shifts, with most significant shifts occurring from DOG1 to DOG3 and during kilning. Dynamic changes in various chemical classes and metabolic pathways provide insights into processes critical for malt quality and beer production. Additionally, metabolites associated with antimicrobial properties and stress responses were identified, underscoring the interplay between barley and microbial metabolic processes during malting. HighlightsO_LIGC-MS and LC-MS profiling were performed to track metabolic changes during malting. C_LIO_LIIdentified 4980 known compounds belonging to 346 chemical classes during malting. C_LIO_LIMany microbial metabolites demonstrated increased abundance in finished malt. C_LIO_LIThe most significant metabolic shifts occurred during early germination and kilning. C_LI

biochemistry↗

bioRxiv2021

In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2

A. thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency and their transcription is strongly induced by this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. To identify potential transcription factors and DNA sequence element regulators of SDI expression we performed a comparative in silico analysis of their promoter sequences cataloguing known and potentially new cis-elements. We further screened an arrayed library of Arabidopsis transcription factors (TF) for binding to the SDI1 and SDI2 promoters. In total 14 candidate TF regulators of SDIs were identified with yeast-one-hybrid analyses, of which five bound to both promoters, 4 were specific to SDI1, and 5 were specific SDI2. Direct association between particular cis-elements in these promoter regions and specific TFs was established via electrophoretic mobility shift assays. SLIM1 was shown to bind SURE cis-element(s) in the proximal promoter region of both SDI1 and SDI2. The bZIP core cis-element in the proximal promoter region of SDI2 was shown to be important for bZIP16, bZIP44, and HYH binding. GBF1 was shown to bind the E-box in the proximal promoter region of SDI2. Additionally, we performed a meta-analysis of expression changes of these 14 TF candidates in a variety of conditions that alter SDI expression. These data will allow for more detailed future analysis of the molecular factors required for transcriptional regulation of SDIs under a range of physiological and metabolic conditions, apart from sulfur deficiency.

plant biology↗