Faculty Opinions recommendation of Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana.

It is well established among interdisciplinary researchers that there is an urgent need to address the negative impacts that accompany climate change. One such negative impact is the increased prevalence of unfavorable environmental conditions that significantly contribute to reduced agricultural yield. Plant microRNAs (miRNAs) are key gene expression regulators that control development, defense against invading pathogens and adaptation to abiotic stress. Arabidopsis thaliana (Arabidopsis) can be readily molecularly manipulated, therefore offering an excellent experimental system to alter the profile of abiotic stress responsive miRNA/target gene expression modules to determine whether such modification enables Arabidopsis to express an altered abiotic stress response phenotype. Towards this goal, high throughput sequencing was used to profile the miRNA landscape of Arabidopsis whole seedlings exposed to heat, drought and salt stress, and identified 121, 123 and 118 miRNAs with a greater than 2-fold altered abundance, respectively. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) was next employed to experimentally validate miRNA abundance fold changes, and to document reciprocal expression trends for the target genes of miRNAs determined abiotic stress responsive. RT-qPCR also demonstrated that each miRNA/target gene expression module determined to be abiotic stress responsive in Arabidopsis whole seedlings was reflective of altered miRNA/target gene abundance in Arabidopsis root and shoot tissues post salt stress exposure. Taken together, the data presented here offers an excellent starting platform to identify the miRNA/target gene expression modules for future molecular manipulation to generate plant lines that display an altered response phenotype to abiotic stress.

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Evaluation of copy number polymorphism of microRNA genes in Arabidopsis thaliana

10.46678/pb.20.1052993 ◽

2020 ◽

Author(s):

Anna Samelak-Czajka

Keyword(s):

Arabidopsis Thaliana ◽

Copy Number ◽

Copy Number Polymorphism ◽

Microrna Genes

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Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences

10.1101/682591 ◽

2019 ◽

Cited By ~ 1

Author(s):

Lydia Gramzow ◽

Dajana Lobbes ◽

Sophia Walter ◽

Nathan Innard ◽

Günter Theißen

Keyword(s):

Transcription Factors ◽

Target Gene ◽

Target Genes ◽

Mirna Biogenesis ◽

Mads Box ◽

Mads Box Genes ◽

Developmental Processes ◽

Inverted Duplication ◽

The Future ◽

Transcribed Sequences

AbstractSome microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC-group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that in both cases the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a new model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies.

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The receptor-like cytoplasmic kinase MAZZA and CLAVATA-family receptors interact in vivo, together mediating developmental processes in Arabidopsis thaliana

10.1101/2020.11.12.379859 ◽

2020 ◽

Author(s):

Patrick Blümke ◽

Jenia Schlegel ◽

Sabine Becher ◽

Karine Pinto ◽

Rüdiger Simon

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Plasma Membrane ◽

Root Development ◽

Target Gene ◽

Size Control ◽

Receptor Complexes ◽

Cle Peptide ◽

Developmental Contexts

AbstractThe receptor-like kinases (RLKs) CLAVATA1 (CLV1) and BARELY ANY MERISTEMs (BAM1 – 3) form the CLV-family (CLVf), which perceives peptides of the CLV3/EMBRYO SURROUNDING REGION (ESR)-related (CLE) family within various signaling pathways of Arabidopsis thaliana. CLE peptide signaling, which is required for meristem size control, vascular development, or pathogen responses, involves the formation of receptor complexes at the plasma membrane (PM). These complexes comprise RLKs and co-receptors in varying compositions depending on the signaling context and regulate target gene expression, such as WUSCHEL (WUS). How the CLE signal is transmitted intracellularly after perception at the PM is not known.Here, we found that the membrane-associated receptor-like cytoplasmic kinase (RLCK) MAZZA (MAZ) MAZ and additional members of the Pti1-like protein family interact in vivo with CLVf receptors. MAZ, which is widely expressed throughout the plant, localizes to the PM via posttranslational palmitoylation potentially enabling stimulus-triggered protein re-localization. We identified a role for a CLV1/MAZ signaling module during stomatal and root development, and redundancy could potentially mask other phenotypes of maz-1 mutants. We propose that RLCKs such as MAZ mediate CLVf signaling in a variety of developmental contexts, paving the way towards understanding the intracellular processes after CLE peptide perception.

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Control of vein-forming, striped gene expression by auxin signaling

BMC Biology ◽

10.1186/s12915-021-01143-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Anmol Krishna ◽

Jason Gardiner ◽

Tyler J. Donner ◽

Enrico Scarpella

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Acetic Acid ◽

Target Gene ◽

Target Genes ◽

Auxin Signaling ◽

Plant Leaves ◽

Vein Formation ◽

Indole 3 Acetic Acid ◽

Differential Affinity

Abstract Background Activation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target gene ARABIDOPSIS THALIANA HOMEOBOX FACTOR8 (ATHB8). Results We find that ATHB8 promotes vein formation and that such vein-forming function depends on both levels of ATHB8 expression and width of ATHB8 expression domains. We further find that ATHB8 expression is activated in striped domains by a combination of (1) activation of ATHB8 expression through binding of peak levels of MP to a low-affinity MP-binding site in the ATHB8 promoter and (2) repression of ATHB8 expression by MP target genes of the AUXIN/INDOLE-3-ACETIC-ACID-INDUCIBLE family. Conclusions Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity.

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Control of Vein-Forming, Striped Gene-Expression by Auxin Signaling

10.1101/2020.09.28.317644 ◽

2020 ◽

Author(s):

Anmol Krishna ◽

Jason Gardiner ◽

Tyler J. Donner ◽

Enrico Scarpella

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Acetic Acid ◽

Target Gene ◽

Target Genes ◽

Auxin Signaling ◽

Plant Leaves ◽

Vein Formation ◽

Indole 3 Acetic Acid ◽

Differential Affinity

ABSTRACTActivation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target gene ARABIDOPSIS THALIANA HOMEOBOX FACTOR8 (ATHB8). We find that ATHB8 promotes vein formation and that such vein-forming function depends on both levels of ATHB8 expression and width of ATHB8 expression domains. We further find that ATHB8 expression is activated in striped domains by a combination of (1) activation of ATHB8 expression through binding of peak levels of MP to a low-affinity MP-binding site in the ATHB8 promoter and (2) repression of ATHB8 expression by MP target genes of the INDOLE-3-ACETIC-ACID-INDUCIBLE family such as BODENLOS. Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity.

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