Transcriptomic analysis of poco1, a mitochondrial pentatricopeptide repeat protein mutant in Arabidopsis thaliana

Abstract

Background: Flowering is a crucial stage during plant development. Plants may respond to unfavorable conditions by accelerating reproductive processes like flowering. In a recent study, we showed that PRECOCIOUS1 (POCO1) is a mitochondrial pentatricopeptide repeat (PPR) protein involved in flowering time and abscisic acid (ABA) signaling in Arabidopsis thaliana. Here, we use RNA-seq data to investigate global gene expression alteration in the poco1 mutant. Results: RNA-seq analysis was performed during different developmental stages for wild-type and poco1 plants. The most profound differences in gene expression were found when wild-type and poco1 plants of the same developmental stage were compared. Coverage analysis confirmed the T-DNA insertion in POCO1, which was concomitant with truncated transcripts. Many biological processes were found to be enriched. Several floweringrelated genes such as FLOWERING LOCUS T (FT), which may be involved in the early-flowering phenotype of poco1, were differentially regulated. Numerous ABA-associated genes, including the core components of ABA signaling such as ABA receptors, protein phosphatases, protein kinases, and ABA-responsive element (ABRE) binding proteins (AREBs)/ABRE-binding factors (ABFs) as well as important genes for stomatal function, were mostly down-regulated in poco1. Drought and oxidative stress-related genes, including ABA-induced stress genes, were differentially regulated. RNA-seq analysis also uncovered differentially regulated genes encoding various classes of transcription factors and genes involved in cellular signaling. Furthermore, the expression of stress-associated nuclear genes encoding mitochondrial proteins (NGEMPs) was found to be altered in poco1. Redox-related genes were affected, suggesting that the redox state in poco1 might be altered. Conclusion: The identification of various enriched biological processes indicates that complex regulatory mechanisms underlie poco1 development. Differentially regulated genes associated with flowering may contribute to the early-flowering phenotype of poco1. Our data suggest the involvement of POCO1 in the early ABA signaling process. The down-regulation of many ABA-related genes suggests an association of poco1 mutation with the ABA signaling deficiency. This condition further affects the expression of many stress-related, especially droughtassociated genes in poco1, consistent with the drought sensitivity of poco1. poco1 mutation also affects the expression of genes associated with the cellular regulation, redox, and mitochondrial perturbation.

Cytochrome c and the transcription factor ABI4 establish a molecular link between mitochondria and ABA‐dependent seed germination

“…Our results showing that mutation of CYTC‐2 affected ABA sensitivity, but not respiratory activity, are in agreement with this proposal. It is also noteworthy that mutants in other genes encoding mitochondrial components showed decreased ABA sensitivity during germination (Wang et al ., 2014; Yao et al ., 2015; Liu et al ., 2016; Emami & Kempken, 2019). In summary, available evidence indicated that signals derived from mitochondria influence ABA transduction pathways and the response to this hormone.…”

“…Our results showing that mutation of CYTC-2 affected ABA sensitivity, but not respiratory activity, are in agreement with this proposal. It is also noteworthy that mutants in other genes encoding mitochondrial components showed decreased ABA sensitivity during germination (Wang et al, 2014;Yao et al, 2015;Liu et al, 2016;Emami & Kempken, 2019) New Phytologist transduction pathways and the response to this hormone. Recent evidence also linked the positive effect of ethylene on dormancy breaking to changes in mitochondrial ROS production and induction of the MRR (Jurdak et al, 2021), implying that mitochondrial function affects different hormonal pathways during seed germination.…”

Functions of PPR Proteins in Plant Growth and Development

“…GUN1 is a chloroplast-located PPR protein, the gun1 mutant is defective in response to norflurazon, lincomycin, and high-light treatments [29], and it also exhibits a more susceptible phenotype to photooxidative stress caused during the de-etiolation [30]. In addition, nine mitochondria-located PPR proteins, MED11/LOI1 [31], PPR40 [32], ABO5 [33], PGN [34], AHG11 [35], SLG1 [36], SLO2 [37], PPR96 [38], and POCO1 [39] were reported to participate in responses to many abiotic or biotic stresses. In rice, two chloroplast-located PPR proteins, OsV4 and TCD10, are required for chloroplast development at early seedling stage under cold stress [40,41].…”

“…OsNBL3 takes part in the splicing of mitochondrial nad5 [43]. Although POCO1 encodes a mitochondrialocalized P-class PPR protein, multiple RNA editing defects were identified in poco1 mutant, which suggest that POCO1 may be required for RNA editing [39].…”

Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview

“…Under cold stress, TCD10 is essential for chloroplast development in rice [16]. Similarly, drought sensitivity was found to be increased in PRECOCIOUS1 (POCO1) Arabidopsis mutant (poco1) plants [55]. The mitochondrial PRECOCIOUS1 (POCO1) is generally involved in ABA signaling and flowering time regulation.…”