No Time To Read Arif Ashraf

No Time To Read podcast

S3E2

The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula



Guest: Sonali Roy, Assistant Professor, Department of Agricultural and Environmental Sciences, Tennessee State University

Twitter/X: @SonaliRoy_



Host: Arif Ashraf, Assistant Professor, Department of Biology, Howard University

Twitter/X: @aribidopsis


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No Time To Read podcast

S3E1

Plant carbonic anhydrase-like enzymes in neuroactive alkaloid biosynthesis



Guest: Ryan Nett, Assistant Professor, Department of Molecular and cellular Biology, Harvard University

Twitter/X: @rnett42



Host: Arif Ashraf, Assistant Professor, Department of Biology, Howard University

Twitter/X: @aribidopsis


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Season 3 of the No Time To Read podcast is starting soon. Thanks for your support as an audience.


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Article: DNA methylation signatures of duplicate gene evolution in angiosperms

Journal: Plant Physiology

Year: 2023

Guest: Sunil Kenchanmane Raju

Host: Arif Ashraf



Abstract



Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomic approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole-genome duplicates were typically enriched for CG-only gene body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was a characteristic of more recent single-gene duplicates. Core angiosperm gene families were differentiated into those which preferentially retain paralogs and “duplication-resistant” families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence–absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.



Cover art design and audio editing: Ragib Anjum


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Article: Extensive embryonic patterning without cellular differentiation primes the plant epidermis for efficient post-embryonic stomatal activities

Journal: Developmental Cell

Year: 2023

Guest: Margot Smit

Host: Arif Ashraf



Abstract



Plant leaves feature epidermal stomata that are organized in stereotyped patterns. How does the pattern originate? We provide transcriptomic, imaging, and genetic evidence that Arabidopsis embryos engage known stomatal fate and patterning factors to create regularly spaced stomatal precursor cells. Analysis of embryos from 36 plant species indicates that this trait is widespread among angiosperms. Embryonic stomatal patterning in Arabidopsis is established in three stages: first, broad SPEECHLESS (SPCH) expression; second, coalescence of SPCH and its targets into discrete domains; and third, one round of asymmetric division to create stomatal precursors. Lineage progression is then halted until after germination. We show that the embryonic stomatal pattern enables fast stomatal differentiation and photosynthetic activity upon germination, but it also guides the formation of additional stomata as the leaf expands. In addition, key stomatal regulators are prevented from driving the fate transitions they can induce after germination, identifying stage-specific layers of regulation that control lineage progression during embryogenesis.




Cover art design and audio editing: Ragib Anjum


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Article: A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize

Journal: Plant Physiology

Year: 2023

Guest: Katie Murphy

Host: Arif Ashraf



Abstract


Two major groups of specialized metabolites in maize (Zea mays), termed kauralexins and dolabralexins, serve as known or predicted diterpenoid defenses against pathogens, herbivores, and other environmental stressors. To consider the physiological roles of the recently discovered dolabralexin pathway, we examined dolabralexin structural diversity, tissue-specificity, and stress-elicited production in a defined biosynthetic pathway mutant. Metabolomics analyses support a larger number of dolabralexin pathway products than previously known. We identified dolabradienol as a previously undetected pathway metabolite and characterized its enzymatic production. Transcript and metabolite profiling showed that dolabralexin biosynthesis and accumulation predominantly occur in primary roots and show quantitative variation across genetically diverse inbred lines. Generation and analysis of CRISPR-Cas9-derived loss-of-function Kaurene Synthase-Like 4 (Zmksl4) mutants demonstrated dolabralexin production deficiency, thus supporting ZmKSL4 as the diterpene synthase responsible for the conversion of geranylgeranyl pyrophosphate precursors into dolabradiene and downstream pathway products. Zmksl4 mutants further display altered root-to-shoot ratios and root architecture in response to water deficit. Collectively, these results demonstrate dolabralexin biosynthesis via ZmKSL4 as a committed pathway node biochemically separating kauralexin and dolabralexin metabolism, and suggest an interactive role of maize dolabralexins in plant vigor during abiotic stress.




Cover art design and audio editing: Ragib Anjum


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