Biology subjects

Mostafa, K.

Publications and source records attributed to Mostafa, K..

3 recordsLinked to original sources

bioRxiv2026

EPF/EPFL Peptide Signaling as a Regulatory Node Linking Stomatal Development to Drought and Heat Tolerance in Tomato (Solanum lycopersicum L.)

Stomatal development and function are tightly regulated by signaling peptides with distinct, overlapping, or antagonistic roles in gas exchange and water balance. EPIDERMAL PATTERNING FACTOR (EPF) / EPF-LIKE (EPF/EPFL) family is a founding member of the secreted peptide family that regulates stomatal patterning. The roles of EPF/EPFL genes in tomato responses to drought, heat, and combined drought-heat stress remain largely unexplored. To characterize the EPF/EPFL gene family and elucidate its potential regulatory roles in stomatal development, 15 family members were identified in S. lycopersicum L. All 15 candidate SlEPF proteins contained an EPF-type domain. Of these, 13 exhibited specific matches to the EPF domain, whereas SlEPF6 was classified within the EPF superfamily and SlEPF11 within the STOMAGEN-like superfamily. Phylogenetic analysis grouped EPF genes from diverse plant species into two major clades (A and B), each comprising distinct evolutionary subgroups. GO annotation indicated that most SlEPF genes were involved in stomatal complex development and guard cell differentiation, with molecular functions associated with MAP kinase activity, receptor serine/threonine kinase binding, and receptor ligand activity. Promoter analysis of SlEPF genes identified diverse cis-regulatory elements potentially involved in the regulation of environmental stress responses and plant development. Expression analysis of five putative stress-responsive genes (SlEPF5, SlEPF8, SlEPF9, SlEPF10, and SlEPF13) revealed distinct transcriptional patterns in the heat-tolerant drought-sensitive Money Maker (MM) and drought-tolerant Ailsa Craig (AC) tomato genotypes under drought, heat, and combined drought-heat stress. In MM, SlEPF5 and SlEPF13 were consistently downregulated across all stress conditions, whereas SlEPF8 was strongly induced under drought and combined stress. In contrast, AC showed broader transcriptional activation, particularly under heat and combined stress. Overall, these contrasting expression profiles suggest genotype- and stress-dependent regulation of SlEPF genes, highlighting their potential involvement in tomato abiotic stress responses.

plant biology↗

bioRxiv2026

Gene identity, not variant effect, dominates ClinVar benchmarks of missense pathogenicity predictors

Missense pathogenicity predictors are routinely benchmarked against ClinVar, whose labels are strongly structured by gene: genes under diagnostic scrutiny accumulate pathogenic submissions while incidentally sequenced genes accumulate benign ones. We asked how much of a benchmark score this structure alone can produce. On 197,904 ClinVar missense variants validated against UniProt canonical sequences, a null model using no variant-level information, scoring each variant only by the pathogenic fraction of its own gene, reaches an area under the receiver operating characteristic curve (AUROC) of 0.921 under a random 10-fold split. On a common intersection of 169,989 variants, four current predictors exceed it by only 0.036 to 0.044. The inflation is not uniform, so it does not cancel when predictors are compared: under within-gene evaluation the ranking inverts, AlphaMissense rising from third to first and gMVP falling to third (p < 0.0001). The inversion survives removal of ceiling genes and replicates on an independently curated benchmark. Because both rankings derive from the same ClinVar labels, we arbitrated between them using data with no gene-level structure: agreement with 47 human deep mutational scanning assays matches the within-gene ranking and inverts the conventional one (p = 0.027, 0.0023). Across twenty-two dbNSFP predictors scored on one common intersection of 112,248 variants, with each tool's exposure to clinical labels registered before any score was extracted, predictors never trained on such labels sit 0.051 AUROC behind supervised ones globally but only 0.026 behind within genes (difference +0.025 [+0.023, +0.027], p < 0.0001). Leave-one-out correction, the standard remedy, is worth 0.002 AUROC. Much of ClinVar benchmark performance reflects gene identity rather than variant effect, and the distortion changes which predictor a benchmark ranks first, in a direction experimental data contradicts. We release genenull, a single-file implementation, so reporting this baseline costs one function call.

bioinformatics↗

bioRxiv2023

GATA transcription factor in common bean: a comprehensive genome-wide functional characterization, identification, and abiotic stress response evaluation.

The GATA transcription factor has been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance to abiotic stress has not yet been studied in the common bean, a popular and commercially important crop affected by the intensifying climate change. This study analyzed the functional identity of the GATA gene family in the P. vulgaris genome under different abiotic and phytohormonal stress. The GATA gene family was systematically investigated in the P. vulgaris genome, and 31 PvGATA TFs were identified. The collinearity between the common bean, rice, and Arabidopsis was studied, and collinearity with Arabidopsis was higher than in rice. Among the 31 PvGATAs, 18 showed duplicated events, which suggests the importance of gene duplication in contribution to GATA gene expansion. Furthermore, all the PvGATA genes were classified into four major subfamilies, with eight, three, six, and 13 members in each subfamily (subfamilies I, II, III, and IV), respectively. A single GATA domain was also present in all PvGATA protein sequences, however, members of subfamily II contained additional domains like CCT and tify domains. The study also predicted and analyzed the promoter cis-regulatory elements (CREs). A total of 799 CREs was predicted in the PvGATAs, categorized into three categories, namely growth and development regulatory elements, stress-responsive elements, and phytohormone-responsive elements. The growth and development regulatory elements had the largest share of CREs in the promoter region of PvGATA genes. Additionally, we used qRT-PCR to investigate the expression profiles of five PvGATA genes in the common bean roots under abiotic and phytohormone treatments. The results suggest that PvGATA1/10/25/28 may play crucial roles in regulating plant resistance against salt and drought stress at 24 hours and may be involved in phytohormone-mediated stress signaling pathways. This study provides a comprehensive analysis of the PvGATA gene family, which can serve as a foundation for future research on the function of GATA Tfs in abiotic stress tolerance in common bean plants.

genomics↗