Biology subjects

Palatnik, J. F.

Publications and source records attributed to Palatnik, J. F..

4 recordsLinked to original sources

bioRxiv2025

The WRC domain of GRF transcription factors. Structure and DNA recognition

Growth-regulating factors (GRFs) belong to a plant-specific family of transcription factors which display important roles in plant growth and development. GRF transcriptional activity is finely tuned by regulatory processes involving post-transcriptional silencing exerted by miRNA396, and protein-protein interactions involving a family of co-transcriptional regulators known as GRF-interacting factors (GIFs). In this way, expression of GRF target genes is modulated by a highly complex interplay between GRF/GIF isoform diversity and expression patterns along with miR396 and GIF gradients throughout plant tissues. At the protein level, GRFs are composed of two highly conserved domains known as QLQ and WRC and a less conserved C-terminal trans-activation domain. Whereas QLQ mediates GRF-GIF interaction by forming a complex with SNH domains found in GIFs, the WRC has been proposed as a putative zinc finger domain responsible for target DNA recognition and nuclear import. However, the structural aspects governing GRF transcriptional activity and target recognition remain unknown. In this work, we applied bioinformatic and biophysical analysis to comprehensively characterize the structural features that modulate the biological function of this protein family with a focus on the WRC domain. We provide insights into the structure of the WRC domain in GRFs and explore the WRC features driving GRFs:DNA complex formation. These findings offer new insights into how WRC domains modulate the biological functions of GRFs, laying the groundwork for future studies on their structure-function relationship in gene regulation and development of plants.

biophysics↗

bioRxiv2020

A chimera including a GROWTH-REGULATING FACTOR (GRF) and its cofactor GRF-INTERACTING FACTOR (GIF) increases transgenic plant regeneration efficiency

Genome editing allows precise DNA manipulation, but its potential is limited in many crops by low regeneration efficiencies and few transformable genotypes. Here, we show that expression of a chimeric protein including wheat GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) dramatically increases the efficiency and speed of regeneration in wheat, triticale and rice and expands the number of transformable wheat genotypes. Moreover, GRF4-GIF1 induces efficient wheat regeneration in the absence of exogenous cytokinins, which facilitates selection of transgenic plants without selectable markers. By combining GRF4-GIF1 and CRISPR-Cas9 technologies, we were able to generate large numbers of edited wheat plants. The GRF4-GIF1 transgenic plants were fertile and without obvious developmental defects, likely due to post-transcriptional regulatory mechanisms operating on GRF4 in adult tissues. Finally, we show that a dicot GRF-GIF chimera improves regeneration efficiency in citrus suggesting that this strategy can be expanded to dicot crops.

plant biology↗

bioRxiv2019

Specific Regulation of TCP genes by miR319

MicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. Many of the evolutionarily conserved miRNAs in plants are encoded by small gene families. The miR159/miR319 family has six members of similar sequences sharing 17 nucleotides in Arabidopsis thaliana. The members of this miRNA family regulate genes encoding TCP (TEOSINTE BRANCHED1, CYCLOIDEA and PCF1/2) and MYB transcription factors. However, despite their sequence similarities, genetic evidence indicates that miR159 and miR319 fulfil different roles in vivo. Here, we confirm previous findings showing that TCP genes are not targeted by miR159. Thus, specific small sequence differences between the miRNAs allow for the specific regulation of TCP transcription factors by miR319 miRNAs.

plant biology↗

bioRxiv2017

Evolutionary footprints reveal insights into plant microRNA biogenesis

MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity. They are processed from longer precursors that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing machinery in different ways. However, ancient miRNAs and their binding sites in target genes are conserved during evolution. Here, we designed a strategy to systematically analyze MIRNAs from different species generating a graphical representation of the conservation of the primary sequence and secondary structure. We found that plant MIRNAs have evolutionary footprints that go beyond the small RNA sequence itself, yet, their location along the precursor depends on the specific MIRNA. We show that these conserved regions correspond to structural determinants recognized during the biogenesis of plant miRNAs. Furthermore, we found that the members of the miR166 family have unusual conservation patterns and demonstrated that the recognition of these precursors in vivo differs from other known miRNAs. Our results describe a link between the evolutionary conservation of plant MIRNAs and the mechanisms underlying the biogenesis of these small RNAs, and show that the MIRNA pattern of conservation can be used to infer the mode of miRNA biogenesis.

plant biology↗