Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain

Galván-Gordillo, Santiago Valentín; Martínez-Navarro, Angélica Concepción; Xoconostle‐Cázares, Beatriz; Ruíz-Medrano, Roberto

doi:10.1515/biolog-2016-0145

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…Another category of zinc finger proteins with a very high number of DEGs, but not included in the heat map, are the ZF-rvt (reverse transcriptase) domain-containing proteins. Some ZF-rvt domain-containing genes are thought to be derived from non-LTR retrotransposons that were endogenized in plants during evolution and have been proposed to modulate the expression of adjacent genes [32]. These were much more prevalent in the up-regulated DEGs and at the later stages of drought and heat stress, while the down-regulated ZF-rvt DEGs were less prevalent overall and peaked at the 24 h time point.…”

Section: Analysis Of Transcription Factors Differentially Regulated During Heat/drought Stressmentioning

confidence: 99%

Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress

Martin

Kronmiller

Dombrowski

2021

Plants

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Drought and heat are two major stresses predicted to increase in the future due to climate change. Plants exposed to multiple stressors elicit unique responses from those observed under individual stresses. A comparative transcriptome analysis of Lolium temulentum exposed to drought plus heat and non-stressed control plants revealed 20,221 unique up-regulated and 17,034 unique down-regulated differentially regulated transcripts. Gene ontology analysis revealed a strong emphasis on transcriptional regulation, protein folding, cell cycle/parts, organelles, binding, transport, signaling, oxidoreductase, and antioxidant activity. Differentially expressed genes (DEGs) encoding for transcriptional control proteins such as basic leucine zipper, APETALA2/Ethylene Responsive Factor, NAC, and WRKY transcription factors, and Zinc Finger (CCCH type and others) proteins were more often up-regulated, while DEGs encoding Basic Helix-Loop-Helix, MYB and GATA transcription factors, and C2H2 type Zinc Finger proteins were more often down-regulated. The DEGs encoding heat shock transcription factors were only up-regulated. Of the hormones, auxin-related DEGs were the most prevalent, encoding for auxin response factors, binding proteins, and efflux/influx carriers. Gibberellin-, cytokinin- and ABA-related DEGs were also prevalent, with fewer DEGs related to jasmonates and brassinosteroids. Knowledge of genes/pathways that grasses use to respond to the combination of heat/drought will be useful in developing multi-stress resistant grasses.

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Section: Analysis Of Transcription Factors Differentially Regulated During Heat/drought Stressmentioning

confidence: 99%

Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress

Martin

Kronmiller

Dombrowski

2021

Plants

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In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)

Choi

Wojciechowski

Ruhlman

et al. 2021

Molecular Phylogenetics and Evolution

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Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

Parakkunnel¹,

K²,

Girimalla³

et al. 2022

Front. Plant Sci.

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Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.

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Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain

Cited by 3 publications

References 31 publications

Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress

Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress

In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)

Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome

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