Biology subjects

Pacak, A.

Publications and source records attributed to Pacak, A..

4 recordsLinked to original sources

bioRxiv2024

Barley miRNAs and their targets regulation in response to heat stress at the early stage of development

MiRNAs are key regulators of gene expression controlling plant development and response to environmental stresses. In this work we studied global dynamics of accumulation of conserved and identified novel barley miRNAs at early stage of plant development during heat stress (1h, 3h and 6h of heat stress). The majority of miRNAs responds to heat stress after 3h and 6h of heat stress duration (124 and 155, respectively). The comparison of heat-induced changes in mature miRNA accumulation to their cognate precursor levels allowed to indicate a smaller group of miRNAs that are controlled at transcriptional level and a larger group that is controlled posttranscriptionally in response to heat stress. For miRNAs with the significant accumulation changes during heat treatment, target mRNAs were identified. Moreover, novel targets have been experimentally assigned for selected miRNAs. mRNA of the effector protein of miRNA activity, AGO1B was found to be downregulated by increased miR168 during heat stress. Importantly, miRNA/mRNA target module miR399c/PHO2 responsible for the phosphorus uptake exhibits dynamic changes under heat stress conditions suggesting adaptation of plant development to stress conditions. This study provides new data for developing miRNA and their mRNA target-based strategies in barley breeding in response to heat stress. Keypoints- Involvement of small RNAs in response to the heat stress conditions have been studied in young barley plants. - The largest number of heat responsive miRNAs was found after 3h and 6h of heat duration. - Heat-induced mature miRNA accumulation and their precursor levels showed complex transcriptional or posttranscriptional regulation. - MiRNA-target modules responsive to heat stress were identified

molecular biology↗

bioRxiv2024

Toss GERALT into chloroplast to make it green: a new regulator of chloroplast biogenesis and chlorophyll biosynthesis

Proteins belonging into cryptochrome/photolyase family act as either blue light photoreceptors or as enzymes responsible for repair of pyrimidine dimers produced under UV. Surprisingly, the members of plant-specific photolyase/blue-light receptor 2 (PPL/PHR2) subclade of this family, are almost completely uncharacterized. Here, we focused on the physiological role of protein encoded by Arabidopsis At2g47590 gene. Our results demonstrate for the first time its crucial role in cotyledon greening and maintenance of plant fitness. Based on the phenotype of the mutant in At2g47590 gene i.e. albino cotyledons and pale green true leaves we named this gene GERALT (GERMINATION ALBINO TRANSIENT). Using different approach including analysis of plant phenotypes, chloroplast sizes and architecture, transcriptomes, photosynthetic pigments, maximum PSII quantum yield (FV/FM) we show that the proper plant functioning is the effect of co-operation of GERALT-dependent and -independent pathways with the role of the former diminishing with plant age. Lower levels of transcripts dependent on plastid encoded polymerase and higher levels of these dependent on nuclear encoded polymerase, smaller chloroplasts with large grana stacks and very weakly developed stromal thylakoids, lower levels of photosynthetic pigments with higher chlorophyll a/b ratio, are among characteristic features of geralt plants. We believe that these results encourage scientific community to study PPL/PHR2 proteins which seems to play a special role in plants.

plant biology↗

bioRxiv2023

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley

MicroRNAs are small, non-coding RNA molecules that regulate expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterized their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, by which functional and non-functional pri-miRNA444 isoforms are generated. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots, and a 5-fold reduced level of mature microRNA444c in roots. Taken together, our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

plant biology↗

bioRxiv2018

FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression

FUS is a multifunctional protein involved in many steps of RNA metabolism, including transcription, splicing, miRNA processing and replication-dependent histone gene expression. In this paper, we show for the first time that FUS binds and negatively regulates the levels of a subset of snoRNAs in cells. Scanning of available human small RNA databases revealed the existence of smaller RNA fragments that can be processed from FUS-dependent snoRNAs. Therefore, we suggest that FUS mediates the biogenesis of snoRNA-derived small RNAs, called sdRNAs. Further in silico approaches enabled us to predict putative targets of selected FUS-dependent sdRNAs. Our results indicate that sdRNAs may bind to different regions of target mRNAs as well as to noncoding transcripts and influence the posttranscriptional level or translation of these targets. SIGNIFICANCE STATEMENTRNA metabolism is orchestrated by a complex network of RNA-protein interactions and involves various classes of RNA molecules. Small nucleolar RNAs (snoRNAs) are commonly considered essential components of the ribosome biogenesis pathway. However, recent studies have revealed that snoRNAs can also be fragmented into small entities called snoRNA-derived RNAs (sdRNAs), which have been linked to multiple cancer types and thus may serve as next-generation prognostic or diagnostic biomarkers. In this paper, a multifunctional protein, FUS, was shown to be involved in the biogenesis of snoRNA-derived fragments. Furthermore, we combined bioinformatic analyses with complementary experimental approaches to elucidate the role of FUS-dependent sdRNAs in gene expression regulation. Our findings reveal the considerable regulatory potential of this new class of small noncoding RNAs.

molecular biology↗