Biology subjects

Apelt, F.

Publications and source records attributed to Apelt, F..

5 recordsLinked to original sources

bioRxiv2024

Re-analysis of mobile mRNA datasets highlights challenges in the detection of mobile transcripts from short-read RNA-Seq data

Short-read RNA-Seq analyses of grafted plants have led to the proposal that large numbers of mRNAs move over long distances between plant tissues, acting as potential signals. The detection of transported transcripts by RNA-Seq is both experimentally and computationally challenging, requiring successful grafting, delicate harvesting, rigorous contamination controls and data processing approaches that can identify rare events in inherently noisy data. Here, we perform a meta-analysis of existing datasets and examine the associated bioinformatic pipelines. Our analysis reveals that technological noise, biological variation and incomplete genome assemblies give rise to features in the data that can distort the interpretation. Taking these considerations into account, we find that a substantial number of transcripts that are currently annotated as mobile are left without support from the available RNA-Seq data. Whilst several annotated mobile mRNAs have been validated, we cannot exclude that others may be false positives. The identified issues may also impact other RNA-Seq studies, in particular those using single nucleotide polymorphisms (SNPs) to detect variants.

plant biology↗

bioRxiv2024

Systemic mRNA transport depends on m5C methylation, nuclear mRNA export factors and developmental phase changes

In grafted plants mRNAs can be transported from shoot to root, however, how their mobility is regulated remains poorly understood. Recent work has shown that m5C methylation plays an essential role in systemic mRNA mobility in vegetative plants, but its role at later developmental stages remains unclear. To address this, we examined the mobility of three mobile mRNAs, TCTP1, HSC70.1 and GRP7 in mutants deficient in m5C mRNA methylation. By comparing vegetative and flowering stages, we found that in contrast to GRP7, the reduced mobility of TCTP1 and HSC70.1 observed in the vegetative growth phase is restored upon flowering, indicating that m5C-dependent regulation of RNA transport is developmentally controlled. We further identified two RNA-binding proteins, the nuclear mRNA export factors ALY2 and ALY4, as phloem mobile. ALY2 and ALY4 deficient plants show a similar developmental effect on mRNA mobility as m5C mRNA methylation mutants, suggesting that they contribute to the regulation of systemic mRNA transport. Notably, combined perturbation of m5C methylation and ALY2 or ALY4 results in reduced mRNA mobility even in flowering plants. Together, our findings reveal an unexpected developmental layer of control over mRNA transport and identify the nuclear mRNA export factors ALY2 and ALY4 as potential regulators of long-distance RNA movement. SIGNIFICANCE STATEMENTmRNA m5C methylation is essential for shoot-to-root mRNA transport during plant growth; however, whether and how mRNA mobility is regulated, and whether it changes during development remains unclear. We show that TCTP1 and HSC70.1 mRNA transport is reduced in vegetatively growing m5C-deficient mutants but remains unaffected upon flowering, and identify ALY2 and ALY4 proteins, two nuclear export factors, as additional regulators of long-distance mRNA transport, providing new layer of mRNA transport.

plant biology↗

bioRxiv2022

Transcription factor HSFA7b controls ethylene signaling and meristem maintenance at the shoot apical meristem during thermomemory

The shoot apical meristem (SAM) is responsible for overall shoot growth by generating all above-ground structures. Recent research identified that the SAM displays an autonomous heat stress (HS) memory of a previous non-lethal HS event. Considering the importance of the SAM for plant growth it is essential to unlock how its thermomemory is mechanistically controlled. Here, we report that HEAT SHOCK TRANSCRIPTION FACTOR A7b (HSFA7b) plays a crucial role in this process in Arabidopsis. We found that HSFA7b directly regulates ethylene response at the SAM by binding to promoters of key regulators of ethylene signaling including ETHYLENE-INSENSITIVE 3 to establish thermotolerance. Moreover, HSFA7b controls maintenance of the SAM stem cell pool during thermomemory by regulating the expression of the master regulator WUSCHEL through direct transcriptional activation of the SPLAYED chromatin remodelling factor.

plant biology↗

bioRxiv2020

Primary carbohydrate metabolism genes participate in heat stress memory at the shoot apical meristem of Arabidopsis thaliana

Although we have a good understanding of the development of shoot apical meristems (SAM) in higher plants, and the function of the stem cells (SCs) embedded in the SAM, there is surprisingly little known of its molecular responses to abiotic stresses. Here, we show that the SAM of Arabidopsis thaliana senses heat stress (HS) and retains an autonomous molecular memory of a previous non-lethal HS, allowing the SAM to regain growth after exposure to an otherwise lethal HS several days later. Using RNA-seq, we identified genes participating in establishing a SAM-specific HS memory. The genes include HEAT SHOCK TRANSCRIPTION FACTORs (HSFs), of which HSFA2 is essential, but not sufficient, for full HS memory in the SAM, the SC regulators CLAVATA1 (CLV1) and CLV3, and several primary carbohydrate metabolism genes, including FRUCTOSE-BISPHOSPHATE ALDOLASE 6 (FBA6). We found that expression of FBA6 during HS at the SAM complements that of FBA8 in the same organ. Furthermore, we show that sugar availability at the SAM is essential for survival at high-temperature HS. Collectively, plants have evolved a sophisticated protection mechanism to maintain SCs and, hence, their capacity to re-initiate shoot growth after stress release.

plant biology↗

bioRxiv2020

The mammalian CLU homolog FMT controls development and behavior in Arabidopsis

Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, comparative mitochondrial function among plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLU (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under salt stress and control conditions. FMT was found to regulate mitochondrial morphology and dynamics as well as germination, root length, and flowering time. Here, we show that it also affects leaf expansion growth, salt stress-responses and hyponasty. Strikingly, FMT impacted the speed of hyponasty with corresponding change in speed of locomotion of CLU heterozygous knockout mice. These observations indicate that homologous genes affect homologous functions in plants and animals offering the possibility to develop plant models for the study of mammalian behaviors.

plant biology↗