Chloroplast- or Mitochondria-Targeted DEAD-Box RNA Helicases Play Essential Roles in Organellar RNA Metabolism and Abiotic Stress Responses

Comparative proteomic analysis of resistant and susceptible cotton genotypes in response to leaf hopper infestation

The cotton leaf hopper is a major pest in cotton, causing a hopper burn in leaves. In this study, a comparative proteomic analysis of NDLH2010 (Resistant) and LRA5166 (Susceptible), infected with leaf hopper, was employed using a nano LC-MS/MS approach. A total of 1402 proteins varied significantly between leaf hopper-infected and control plants. The resistant and susceptible genotypes had differentially expressed proteins (DEPs) of 743 and 659, respectively. Functional annotation of DEPs revealed that the DEPs were primarily associated with stress response, hormone synthesis, photosynthesis, cell wall, and secondary metabolites. Notably, DEPs such as polyphenol oxidase, carboxypeptidase, heat shock proteins, protein BTR1-like isoform X2, chaperone protein ClpB1, and β glucosidase factors associated with environmental stress response were also detected. Quantitative real-time PCR (qRT-PCR) analysis confirmed a positive correlation between protein abundances and transcripts for all genes. Collectively, this study provides the molecular mechanisms associated with cotton defense responses against leaf hopper. SIGNIFICANCE STATEMENT: Cotton, a natural fiber, assumes a pivotal role as a raw material for textile industries, thereby bearing significant importance in the global economy. The cotton production sector is considerably affected by both biotic and abiotic stresses. The cotton leaf hopper (Amrasca biguttula biguttula (Ishida)) stands as a polyphagous insect, emerging as a dominant sap-feeding pest of the cotton crop. The continuous onslaught of sap-feeding insects on cotton plants has a detrimental impact, with leaf hoppers potentially causing yield reductions of up to 50%. Therefore, comprehending the molecular interplay between cotton and leaf hopper, elucidated at the proteome level, holds promise for more effective pest management strategies. This approach holds the potential to offer insights that contribute to the development of leaf hopper-resistant cotton varieties.

Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression

Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both 'cis'- and 'trans'-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.

Chloroplast Ribosome Biogenesis Factors

The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.

DEAD-Box RNA Helicase Family in Physic Nut (Jatropha curcas L.): Structural Characterization and Response to Salinity

Helicases, motor proteins present in both prokaryotes and eukaryotes, play a direct role in various steps of RNA metabolism. Specifically, SF2 RNA helicases, a subset of the DEAD-box family, are essential players in plant developmental processes and responses to biotic and abiotic stresses. Despite this, information on this family in the physic nut (Jatropha curcas L.) remains limited, spanning from structural patterns to stress responses. We identified 79 genes encoding DEAD-box RNA helicases (JcDHX) in the J. curcas genome. These genes were further categorized into three subfamilies: DEAD (42 genes), DEAH (30 genes), and DExH/D (seven genes). Characterization of the encoded proteins revealed a remarkable diversity, with observed patterns in domains, motifs, and exon-intron structures suggesting that the DEAH and DExH/D subfamilies in J. curcas likely contribute to the overall versatility of the family. Three-dimensional modeling of the candidates showed characteristic hallmarks, highlighting the expected functional performance of these enzymes. The promoter regions of the JcDHX genes revealed potential cis-elements such as Dof-type, BBR-BPC, and AP2-ERF, indicating their potential involvement in the response to abiotic stresses. Analysis of RNA-Seq data from the roots of physic nut accessions exposed to 150 mM of NaCl for 3 h showed most of the JcDHX candidates repressed. The protein-protein interaction network indicated that JcDHX proteins occupy central positions, connecting events associated with RNA metabolism. Quantitative PCR analysis validated the expression of nine DEAD-box RNA helicase transcripts, showing significant associations with key components of the stress response, including RNA turnover, ribosome biogenesis, DNA repair, clathrin-mediated vesicular transport, phosphatidyl 3,5-inositol synthesis, and mitochondrial translation. Furthermore, the induced expression of one transcript (JcDHX44) was confirmed, suggesting that it is a potential candidate for future functional analyses to better understand its role in salinity stress tolerance. This study represents the first global report on the DEAD-box family of RNA helicases in physic nuts and displays structural characteristics compatible with their functions, likely serving as a critical component of the plant's response pathways.

Genome-wide systematic survey and analysis of the RNA helicase gene family and their response to abiotic stress in sweetpotato

Sweetpotato (Ipomoea batatas (L.) Lam.) holds a crucial position as one of the staple foods globally, however, its yields are frequently impacted by environmental stresses. In the realm of plant evolution and the response to abiotic stress, the RNA helicase family assumes a significant role. Despite this importance, a comprehensive understanding of the RNA helicase gene family in sweetpotato has been lacking. Therefore, we conducted a comprehensive genome-wide analysis of the sweetpotato RNA helicase family, encompassing aspects such as chromosome distribution, promoter elements, and motif compositions. This study aims to shed light on the intricate mechanisms underlying the stress responses and evolutionary adaptations in sweetpotato, thereby facilitating the development of strategies for enhancing its resilience and productivity. 300 RNA helicase genes were identified in sweetpotato and categorized into three subfamilies, namely IbDEAD, IbDEAH and IbDExDH. The collinearity relationship between the sweetpotato RNA helicase gene and 8 related homologous genes from other species was explored, providing a reliable foundation for further study of the sweetpotato RNA helicase gene family's evolution. Furthermore, through RNA-Seq analysis and qRT-PCR verification, it was observed that the expression of eight RNA helicase genes exhibited significant responsiveness to four abiotic stresses (cold, drought, heat, and salt) across various tissues of ten different sweetpotato varieties. Sweetpotato transgenic lines overexpressing the RNA helicase gene IbDExDH96 were generated using A.rhizogenes-mediated technology. This approach allowed for the preliminary investigation of the role of sweetpotato RNA helicase genes in the response to cold stress. Notably, the promoters of RNA helicase genes contained numerous cis-acting elements associated with temperature, hormone, and light response, highlighting their crucial role in sweetpotato abiotic stress response.

Phenotypic and microarray analysis reveals salinity stress-induced oxidative tolerance in transgenic rice expressing a DEAD-box RNA helicase, OsDB10

Helicases are the motor proteins not only involved in the process of mRNA metabolism but also played a significant role in providing abiotic stresses tolerance. In this study, a DEAD-box RNA helicase OsDB10 was cloned and functionally characterized. The transcript levels of OsDB10 were increased both in shoot and root upon salt, heat, cold, and ABA application and was more prominent in shoot compared to root. Genomic integration of OsDB10 in transgenic rice was confirmed by PCR, Southern blot and qRT-PCR analysis. The transgenic plants showed quicker seed germination, reduced necrosis, higher chlorophyll, more survival rate, better seedling growth, and produced more grain yield under salinity stress. Furthermore, transgenic lines also accumulated less Na+ and high K+ ions and salinity tolerance of the transgenic were also assayed by measuring different bio-physiological indices. Moreover, the OsDB10 transgenic plants showed enhanced tolerance to salinity-induced oxidative stress by scavenging ROS and increased activity of antioxidants enzymes. Microarray analysis showed upregulation of transcriptional regulations and metabolic reprogramming as OsDB10 overexpression modulates the expression of many other genes. Altogether, our results confirmed that OsDB10 is a functional DEAD-box RNA helicase and played vital roles in plant defence response against salinity stress.

Comparative analysis of wild-type and chloroplast MCU-deficient plants reveals multiple consequences of chloroplast calcium handling under drought stress

Introduction

Chloroplast calcium homeostasis plays an important role in modulating the response of plants to abiotic and biotic stresses. One of the greatest challenges is to understand how chloroplast calcium-permeable pathways and sensors are regulated in a concerted manner to translate specific information into a calcium signature and to elucidate the downstream effects of specific chloroplast calcium dynamics. One of the six homologs of the mitochondrial calcium uniporter (MCU) was found to be located in chloroplasts in the leaves and to crucially contribute to drought- and oxidative stress-triggered uptake of calcium into this organelle.

Methods

In the present study we integrated comparative proteomic analysis with biochemical, genetic, cellular, ionomic and hormone analysis in order to gain an insight into how chloroplast calcium channels are integrated into signaling circuits under watered condition and under drought stress.

Results

Altogether, our results indicate for the first time a link between chloroplast calcium channels and hormone levels, showing an enhanced ABA level in the cmcu mutant already in well-watered condition. Furthermore, we show that the lack of cMCU results in an upregulation of the calcium sensor CAS and of enzymes of chlorophyll synthesis, which are also involved in retrograde signaling upon drought stress, in two independent KO lines generated in Col-0 and Col-4 ecotypes.

Conclusions

These observations point to chloroplasts as important signaling hubs linked to their calcium dynamics. Our results obtained in the model plant Arabidopsis thaliana are discussed also in light of our limited knowledge regarding organellar calcium signaling in crops and raise the possibility of an involvement of such signaling in response to drought stress also in crops.

Plant organellar RNA maturation

Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.

Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response

Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3'-UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and downregulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.

Utilizing Proteomic Approach to Analyze Potential Antioxidant Proteins in Plant against Irradiation

Gamma-ray irradiation is an effective and clean method of sterilization by inactivating microorganisms. It can also be applied to induce anti-oxidants for future application. In this study, the mung bean (Vigna radiata) was exposed to gamma-ray irradiation under the dose of 0, 5 or 10 kGy. With increasing irradiation doses, the concentrations of malondiadehyde decreased while the levels of total flavonoids and DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity increased. It has been shown that consuming flavonoids can provide protective effects. In addition, proteomic analysis identified several proteins having anti-oxidant activities in the 5 kGy irradiated group. These proteins are Apocytochrome f, Systemin receptor SR 160, DELLA protein DWARF8, DEAD-box ATP-dependent RNA helicase 9, ζ-carotene desaturase (ZDS), and Floral homeotic protein AGAMOUS. Our findings indicate that plants contain a variety of phytochemicals and antioxidant proteins which may effectively prevent oxidative stress caused by irradiated peroxidation.

Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior

BACKGROUND

Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw.

RESULTS

A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO.

CONCLUSIONS

Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.

Genome-Wide Identification and Characterization of the Soybean DEAD-Box Gene Family and Expression Response to Rhizobia

DEAD-box proteins are a large family of RNA helicases that play important roles in almost all cellular RNA processes in model plants. However, little is known about this family of proteins in crops such as soybean. Here, we identified 80 DEAD-box family genes in the Glycine max (soybean) genome. These DEAD-box genes were distributed on 19 chromosomes, and some genes were clustered together. The majority of DEAD-box family proteins were highly conserved in Arabidopsis and soybean, but Glyma.08G231300 and Glyma.14G115100 were specific to soybean. The promoters of these DEAD-box genes share cis-acting elements involved in plant responses to MeJA, salicylic acid (SA), low temperature and biotic as well as abiotic stresses; interestingly, half of the genes contain nodulation-related cis elements in their promoters. Microarray data analysis revealed that the DEAD-box genes were differentially expressed in the root and nodule. Notably, 31 genes were induced by rhizobia and/or were highly expressed in the nodule. Real-time quantitative PCR analysis validated the expression patterns of some DEAD-box genes, and among them, Glyma.08G231300 and Glyma.14G115100 were induced by rhizobia in root hair. Thus, we provide a comprehensive view of the DEAD-box family genes in soybean and highlight the crucial role of these genes in symbiotic nodulation.

Late Embryogenesis Abundant (LEA)5 Regulates Translation in Mitochondria and Chloroplasts to Enhance Growth and Stress Tolerance

The late embryogenesis abundant (LEA)5 protein is predominantly expressed in Arabidopsis leaves in the dark, the levels of LEA5 transcripts decreasing rapidly upon illumination. LEA5 is important in plant responses to environmental stresses but the mechanisms involved have not been elucidated. We therefore explored LEA5 functions in Arabidopsis mutants (lea5) and transgenic Arabidopsis plants constitutively expressing LEA5 (OEX 2-5), as well as in transgenic barley lines expressing the Arabidopsis LEA5 gene. The OEX 2-5 plants grew better than controls and lea5 mutants in the presence of the prooxidants methyl viologen and menadione. Confocal microscopy of Arabidopsis mesophyll protoplasts expressing a LEA5-YFP fusion protein demonstrated that LEA5 could be localized to chloroplasts as well as mitochondria in Arabidopsis protoplasts. Tandem affinity purification (TAP) analysis revealed LEA5 interacts with the chloroplast DEAD-box ATP-dependent RNA helicase 22 (RH22) in Arabidopsis cells. Split YFP analysis confirmed the interaction between RH22 and LEA5 in chloroplasts. The abundance of translated protein products in chloroplasts was decreased in transgenic Arabidopsis plants and increased in lea5 knockout mutants. Conversely, the abundance of translated mitochondrial protein products was increased in OEX 2-5 plants and decreased in lea5 mutants. Mitochondrial electron transport rates were higher in the OEX 2-5 plants than the wild type. The transformed barley lines expressing the Arabidopsis LEA5 had increased seed yields, but they showed a greater drought-induced inhibition of photosynthesis than controls. Taken together, these data demonstrate that LEA5 regulates organellar translation, in order to enhance respiration relative to photosynthesis in response to stress.

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

RNA helicases play crucial functions in RNA biology. In plants, RNA helicases are encoded by large gene families, performing roles in abiotic stress responses, development, the post-transcriptional regulation of gene expression as well as house-keeping functions. Several of these RNA helicases are targeted to the organelles, mitochondria and chloroplasts. Cyanobacteria are the direct evolutionary ancestors of plant chloroplasts. The cyanobacterium Synechocystis 6803 encodes a single DEAD-box RNA helicase, CrhR, that is induced by a range of abiotic stresses, including low temperature. Though the ΔcrhR mutant exhibits a severe cold-sensitive phenotype, the physiological function(s) performed by CrhR have not been described. To identify transcripts interacting with CrhR, we performed RNA co-immunoprecipitation with extracts from a Synechocystis crhR deletion mutant expressing the FLAG-tagged native CrhR or a K57A mutated version with an anticipated enhanced RNA binding. The composition of the interactome was strikingly biased towards photosynthesis-associated and redox-controlled transcripts. A transcript highly enriched in all experiments was the crhR mRNA, suggesting an auto-regulatory molecular mechanism. The identified interactome explains the described physiological role of CrhR in response to the redox poise of the photosynthetic electron transport chain and characterizes CrhR as an enzyme with a diverse range of transcripts as molecular targets.

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

Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.

Acclimation in plants - the Green Hub consortium

Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.

Linking the plant stress responses with RNA helicases

RNA helicases are omnipresent plant proteins across all kingdoms and have been demonstrated to play an essential role in all cellular processes involving nucleic acids. Currently, these proteins emerged as a new tool for plant molecular biologists to modulate plant stress responses. Here, we review the crucial role of RNA helicases triggered by biotic, abiotic, and multiple stress conditions. In this review, the emphasis has been given on the role of these proteins upon viral stress. Further, we have explored RNA helicase mediated regulation of RNA metabolism, starting from ribosome biogenesis to its decay upon stress induction. We also highlighted the cross-talk between RNA helicase, phytohormones, and ROS. Different overexpression and transgenic studies have been provided in the text to indicate the stress tolerance abilities of these proteins.

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment.

Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance

Plastid gene expression (PGE) must adequately respond to changes in both development and environmental cues. The transcriptional machinery of plastids in land plants is far more complex than that of prokaryotes. Two types of DNA-dependent RNA polymerases transcribe the plastid genome: a multimeric plastid-encoded polymerase (PEP), and a monomeric nuclear-encoded polymerase (NEP). A single NEP in monocots (RPOTp, RNA polymerase of the T3/T7 phage-type) and two NEPs in dicots (plastid-targeted RPOTp, and plastid- and mitochondrial-targeted RPOTmp) have been hitherto identified. To unravel the role of PGE in plant responses to abiotic stress, we investigated if Arabidopsis RPOTp could function in plant salt tolerance. To this end, we studied the sensitivity of T-DNA mutants scabra3-2 (sca3-2) and sca3-3, defective in the RPOTp gene, to salinity, osmotic stress and the phytohormone abscisic acid (ABA) required for plants to adapt to abiotic stress. sca3 mutants were hypersensitive to NaCl, mannitol and ABA during germination and seedling establishment. Later in development, sca3 plants displayed reduced sensitivity to salt stress. A gene ontology (GO) analysis of the nuclear genes differentially expressed in the sca3-2 mutant (301) revealed that many significantly enriched GO terms were related to chloroplast function, and also to the response to several abiotic stresses. By quantitative RT-PCR (qRT-PCR), we found that genes LHCB1 (LIGHT-HARVESTING CHLOROPHYLL a/b-BINDING1) and AOX1A (ALTERNATIVE OXIDASE 1A) were respectively down- and up-regulated in the Columbia-0 (Col-0) salt-stressed plants, which suggests the activation of plastid and mitochondria-to-nucleus retrograde signaling. The transcript levels of genes RPOTp, RPOTmp and RPOTm significantly increased in these salt-stressed seedlings, but this enhanced expression did not lead to the up-regulation of the plastid genes solely transcribed by NEP. Similar to salinity, carotenoid inhibitor norflurazon (NF) also enhanced the RPOTp transcript levels in Col-0 seedlings. This shows that besides salinity, inhibition of chloroplast biogenesis also induces RPOTp expression. Unlike salt and NF, the NEP genes were significantly down-regulated in the Col-0 seedlings grown in ABA-supplemented media. Together, our findings demonstrate that RPOTp functions in abiotic stress tolerance, and RPOTp is likely regulated positively by plastid-to-nucleus retrograde signaling, which is triggered when chloroplast functionality is perturbed by environmental stresses, e.g., salinity or NF. This suggests the existence of a compensatory mechanism, elicited by impaired chloroplast function. To our knowledge, this is the first study to suggest the role of a nuclear-encoded plastid-RNA polymerase in salt stress tolerance in plants.

The res (restored cell structure by salinity) tomato mutant reveals the role of the DEAD-box RNA helicase SlDEAD39 in plant development and salt response

Increasing evidences highlight the importance of DEAD-box RNA helicases in plant development and stress responses. In a previous study, we characterized the tomato res mutant (restored cell structure by salinity), showing chlorosis and development alterations that reverted under salt-stress conditions. Map-based cloning demonstrates that RES gene encodes SlDEAD39, a chloroplast-targeted DEAD-box RNA helicase. Constitutive expression of SlDEAD39 complements the res mutation, while the silencing lines had a similar phenotype than res mutant, which is also reverted under salinity. Functional analysis of res mutant proved SlDEAD39 is involved in the in vivo processing of the chloroplast, 23S rRNA, at the hidden break-B site, a feature also supported by in vitro binding experiments of the protein. In addition, our results show that other genes coding for chloroplast-targeted DEAD-box proteins are induced by salt-stress, which might explain the rescue of the res mutant phenotype. Interestingly, salinity restored the phenotype of res adult plants by increasing their sugar content and fruit yield. Together, these results propose an unprecedented role of a DEAD-box RNA helicase in regulating plant development and stress response through the proper ribosome and chloroplast functioning, which, in turn, represents a potential target to improve salt tolerance in tomato crops.

Roles of Organellar RNA-Binding Proteins in Plant Growth, Development, and Abiotic Stress Responses

Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation of post-transcriptional RNA metabolism in organelles. Although the functional roles of nCMRBPs have been studied in plants, their cellular and physiological functions remain largely unknown. Nevertheless, existing studies that have characterized the functions of nCMRBP families, such as chloroplast ribosome maturation and splicing domain (CRM) proteins, pentatricopeptide repeat (PPR) proteins, DEAD-Box RNA helicase (DBRH) proteins, and S1-domain containing proteins (SDPs), have begun to shed light on the role of nCMRBPs in plant growth, development, and stress responses. Here, we review the latest research developments regarding the functional roles of organellar RBPs in RNA metabolism during growth, development, and abiotic stress responses in plants.

OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival

BACKGROUND

The large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice.

RESULTS

In this study, we raised a mutant from tissue-culture-derived plants of Oryza sativa subsp. japonica 'Zhonghua 11', which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designated seedling-lethal chlorosis 1 (slc1). The slc1 mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning of OsSLC1 revealed that a single base (G) deletion was detected in the first exon of Os06g0710800 in the slc1 mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed that OsSLC1 is responsible for the seedling-lethal chlorosis phenotype in the slc1 mutant. OsSLC1 was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function of OsSLC1 affected the intron splicing of multiple group II introns, and especially precluded the intron splicing of rps16, and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes.

CONCLUSION

We characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially the rps16 intron, and is essential for early chloroplast development and seedling survival in rice.

Investigation of a Novel Salt Stress-Responsive Pathway Mediated by Arabidopsis DEAD-Box RNA Helicase Gene AtRH17 Using RNA-Seq Analysis

Previously, we reported that overexpression of AtRH17, an Arabidopsis DEAD-box RNA helicase gene, confers salt stress-tolerance via a pathway other than the well-known salt stress-responsive pathways. To decipher the salt stress-responsive pathway in AtRH17-overexpressing transgenic plants (OXs), we performed RNA-Sequencing and identified 397 differentially expressed genes between wild type (WT) and AtRH17 OXs. Among them, 286 genes were upregulated and 111 genes were downregulated in AtRH17 OXs relative to WT. Gene ontology annotation enrichment and KEGG pathway analysis showed that the 397 upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4-5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4-5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition. Taken together, our results suggest that a high AtRH17 expression confers salt stress-tolerance through a novel salt stress-responsive pathway involving nine genes, other than the well-known ABA-dependent and ABA-independent pathways.

Pentatricopeptide repeat protein MID1 modulates nad2 intron 1 splicing and Arabidopsis development

As one of the best-studied RNA binding proteins in plant, pentatricopeptide repeats (PPRs) protein are mainly targeted to mitochondria and/or chloroplasts for RNA processing to regulate the biogenesis and function of the organelles, but its molecular mechanism and role in development remain to be further revealed. Here, we identified a mitochondria-localized P-type small PPR protein, MITOCHONDRION-MEDIATED GROWTH DEFECT 1 (MID1) that is crucial for Arabidopsis development. Mutation in MID1 causes retarded embryo development and stunted plant growth with defects in cell expansion and proliferation. Molecular experiments showed that MID1 is required for the splicing of the nad2 intron 1 in mitochondria. Consistently, mid1 plants display significant reduction in the abundance and activity of mitochondrial respiration complex I, accompanied by abnormal mitochondrial morphology and energy metabolism. Furthermore, MID1 is associated with other trans-factors involved in NICOTINAMIDE ADENINE DINUCLEOTIDE HYDROGEN (NADH) DEHYDROGENASE SUBUNIT 2 (nad2) intron 1 splicing, and interacts directly with itself and MITOCHONDRIAL STABILITY FACTOR 1 (MTSF1). This suggests that MID1 most likely functions as a dimer for nad2 intron 1 splicing. Together, we characterized a novel PPR protein MID1 for nad2 intron 1 splicing.

Translocation of Drought-Responsive Proteins from the Chloroplasts

Some chloroplast proteins are known to serve as messengers to transmit retrograde signals from chloroplasts to the nuclei in response to environmental stresses. However, whether particular chloroplast proteins respond to drought stress and serve as messengers for retrograde signal transduction are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) to monitor the proteomic changes in tobacco (Nicotiana benthamiana) treated with drought stress/re-watering. We identified 3936 and 1087 differentially accumulated total leaf and chloroplast proteins, respectively, which were grouped into 16 categories. Among these, one particular category of proteins, that includes carbonic anhydrase 1 (CA1), exhibited a great decline in chloroplasts, but a remarkable increase in leaves under drought stress. The subcellular localizations of CA1 proteins from moss (Physcomitrella patens), Arabidopsis thaliana and rice (Oryza sativa) in P. patens protoplasts consistently showed that CA1 proteins gradually diminished within chloroplasts but increasingly accumulated in the cytosol under osmotic stress treatment, suggesting that they could be translocated from chloroplasts to the cytosol and act as a signal messenger from the chloroplast. Our results thus highlight the potential importance of chloroplast proteins in retrograde signaling pathways and provide a set of candidate proteins for further research.

Genetic mapping of green curd gene Gr in cauliflower

Gr5.1 is the major locus for cauliflower green curd color and mapped to an interval of 236 Kbp with four most likely candidate genes. Cauliflower with colored curd enhances not only the visual appeal but also the nutritional value of the crop. Green cauliflower results from ectopic development of chloroplasts in the normal white curd. However, the underlying genetic basis is unknown. In this study, we employed QTL-seq analysis to identify the loci that were associated with green curd phenotype in cauliflower. A F2 population was generated following a cross between a white curd (Stovepipe) and a green curd (ACX800) cauliflower plants. By whole-genome resequencing and SNP analysis of green and white F2 bulks, two QTLs were detected on chromosomes 5 (Gr5.1) and 7 (Gr7.1). Validation by traditional genetic mapping with CAPS markers suggested that Gr5.1 represented a major QTL, whereas Gr7.1 had a minor effect. Subsequent high-resolution mapping of Gr5.1 in the second large F2 population with additional CAPS markers narrowed down the target region to a genetic and physical distance of 0.3 cM and 236 Kbp, respectively. This region contained 35 genes with four of them representing the best candidates for the green curd phenotype in cauliflower. They are LOC106295953, LOC106343833, LOC106345143, and LOC106295954, which encode UMP kinase, DEAD-box RNA helicase 51-like, glutathione S-transferase T3-like, and protein MKS1, respectively. These findings lay a solid foundation for the isolation of the Gr gene and provide a potential for marker-assisted selection of the green curd trait in cauliflower breeding. The eventual isolation of Gr will also facilitate better understanding of chloroplast biogenesis and development in plants.

Genome-wide expression of low temperature response genes in Rosa hybrida L

Plants respond to low temperature stress during cold acclimation, a complex process involving changes in physiological and biochemical modifications. The rose serves as a good model to investigate low temperature responses in perennial ornamentals. In this study, a heterologous apple microarray is used to investigate genome-wide expression profiles in Rosa hybrida subjected to low temperature dark treatment. Transcriptome profiles are determined in floral buds at 0h, 2h, and 12h of low temperature treatment (4 °C). It is observed that a total of 134 transcripts are up-regulated and 169 transcripts are down-regulated in response to low temperature. Interestingly, a total of eight up-regulated genes, including those coding for two cytochrome P450 proteins, two ankyrin repeat family proteins, two metal ion binding proteins, and two zinc finger protein-related transcription factors, along with a single down-regulated gene, coding for a dynamin-like protein, are detected. Transcript profiles of 12 genes known to be involved in cold stress response are also validated using qRT-PCR. Furthermore, expression patterns of the AP2/ERF gene family of transcription factors are investigated in both floral buds and leaves. Overall, AP2/ERFs genes are more rapidly induced in leaves than in floral buds. Moreover, differential expression of several AP2/ERF genes are detected earlier in vegetative rather than in reproductive tissues. These findings highlight important roles of various low temperature response genes in mediating cold acclimation, thereby allowing roses to adapt to low temperatures, but without adversely affecting flower bud development and subsequent flowering, while vegetative tissues undergo early adaptation to low temperatures.

The coordinated action of PPR4 and EMB2654 on each intron half mediates trans-splicing of rps12 transcripts in plant chloroplasts

The pentatricopeptide repeat proteins PPR4 and EMB2654 have been shown to be required for the trans-splicing of plastid rps12 transcripts in Zea mays (maize) and Arabidopsis, respectively, but their roles in this process are not well understood. We investigated the functions of the Arabidopsis and Oryza sativa (rice) orthologs of PPR4, designated AtPPR4 (At5g04810) and OsPPR4 (Os4g58780). Arabidopsis atppr4 and rice osppr4 mutants are embryo-lethal and seedling-lethal 3 weeks after germination, respectively, showing that PPR4 is essential in the development of both dicot and monocot plants. Artificial microRNA-mediated mutants of AtPPR4 displayed a specific defect in rps12 trans-splicing, with pale-green, yellowish or albino phenotypes, according to the degree of knock-down of AtPPR4 expression. Comparison of RNA footprints in atppr4 and emb2654 mutants showed a similar concordant loss of extensive footprints at the 3' end of intron 1a and at the 5' end of intron 1b in both cases. EMB2654 is known to bind within the footprint region in intron 1a and we show that AtPPR4 binds to the footprint region in intron 1b, via its PPR motifs. Binding of both PPR4 and EMB2654 is essential to juxtapose the two intron halves and to maintain the RNAs in a splicing-competent structure for the efficient trans-splicing of rps12 intron 1, which is crucial for chloroplast biogenesis and plant development. The similarity of EMB2654 and PPR4 orthologs and their respective binding sites across land plant phylogeny indicates that their coordinate function in rps12 trans-splicing has probably been conserved for 500 million years.

CFM9, a Mitochondrial CRM Protein, Is Crucial for Mitochondrial Intron Splicing, Mitochondria Function and Arabidopsis Growth and Stress Responses

Although the importance of chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins has been established for chloroplast RNA metabolism and plant development, the functional role of CRM proteins in mitochondria remains largely unknown. Here, we investigated the role of a mitochondria-targeted CRM protein (At3g27550), named CFM9, in Arabidopsis thaliana. Confocal analysis revealed that CFM9 is localized in mitochondria. The cfm9 mutant exhibited delayed seed germination, retarded growth and shorter height compared with the wild type under normal conditions. The growth-defect phenotypes were more manifested upon high salinity, dehydration or ABA application. Complementation lines expressing CFM9 in the mutant background fully recovered the wild-type phenotypes. Notably, the mutant had abnormal mitochondria, increased hydrogen peroxide and reduced respiration activity, implying that CFM9 is indispensable for normal mitochondrial function. More important, the splicing of many intron-containing genes in mitochondria was defective in the mutant, suggesting that CFM9 plays a crucial role in the splicing of mitochondrial introns. Collectively, our results provide clear evidence emphasizing that CFM9 is an essential factor in the splicing of mitochondrial introns, which is crucial for mitochondrial biogenesis and function and the growth and development of Arabidopsis.

Disruption of a Upf1-like helicase-encoding gene OsPLS2 triggers light-dependent premature leaf senescence in rice

The OsPLS2 locus was isolated and cloned by map-based cloning that encodes a Upf1-like helicase. Disruption of OsPLS2 accelerated light-dependent leaf senescence in the rice mutant of ospls2. Leaf senescence is a very complex physiological process controlled by both genetic and environmental factors, however its underlying molecular mechanisms remain elusive. In this study, we report a novel Oryza sativa premature leaf senescence mutant (ospls2). Through map-based cloning, a G-to-A substitution was determined at the 1st nucleotide of the 13th intron in the OsPLS2 gene that encodes a Upf1-like helicase. This mutation prompts aberrant splicing of OsPLS2 messenger and consequent disruption of its full-length protein translation, suggesting a negative role of OsPLS2 in regulating leaf senescence. Wild-type rice accordingly displayed a progressive drop of OsPSL2 protein levels with age-dependent leaf senescence. Shading and light filtration studies showed that the ospls2 phenotype, which was characteristic of photo-oxidative stress and reactive oxygen species (ROS) accumulation, was an effect of irritation by light. When continuously exposed to far-red light, exogenous H₂O₂ and/or abscisic acid (ABA), the ospls2 mutant sustained hypersensitive leaf senescence. In consistence, light and ROS signal pathways in ospls2 were activated by down-regulation of phytochrome genes, and up-regulation of PHYTOCHROME-INTERACTING FACTORS (PIFs) and WRKY genes, all promoting leaf senescence. Together, these data indicated that OsPLS2 played an essential role in leaf senescence and its disruption triggered light-dependent leaf senescence in rice.

Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression (OGE) and Its Roles in Plant Salt Tolerance

Given their endosymbiotic origin, chloroplasts and mitochondria genomes harbor only between 100 and 200 genes that encode the proteins involved in organellar gene expression (OGE), photosynthesis, and the electron transport chain. However, as the activity of these organelles also needs a few thousand proteins encoded by the nuclear genome, a close coordination of the gene expression between the nucleus and organelles must exist. In line with this, OGE regulation is crucial for plant growth and development, and is achieved mainly through post-transcriptional mechanisms performed by nuclear genes. In this way, the nucleus controls the activity of organelles and these, in turn, transmit information about their functional state to the nucleus by modulating nuclear expression according to the organelles' physiological requirements. This adjusts organelle function to plant physiological, developmental, or growth demands. Therefore, OGE must appropriately respond to both the endogenous signals and exogenous environmental cues that can jeopardize plant survival. As sessile organisms, plants have to respond to adverse conditions to acclimate and adapt to them. Salinity is a major abiotic stress that negatively affects plant development and growth, disrupts chloroplast and mitochondria function, and leads to reduced yields. Information on the effects that the disturbance of the OGE function has on plant tolerance to salinity is still quite fragmented. Nonetheless, many plant mutants which display altered responses to salinity have been characterized in recent years, and interestingly, several are affected in nuclear genes encoding organelle-localized proteins that regulate the expression of organelle genes. These results strongly support a link between OGE and plant salt tolerance, likely through retrograde signaling. Our review analyzes recent findings on the OGE functions required by plants to respond and tolerate salinity, and highlights the fundamental role that chloroplast and mitochondrion homeostasis plays in plant adaptation to salt stress.

Rice OsRH58, a chloroplast DEAD-box RNA helicase, improves salt or drought stress tolerance in Arabidopsis by affecting chloroplast translation

BACKGROUND

Despite increasing characterization of DEAD-box RNA helicases (RHs) in chloroplast gene expression regulation at posttranscriptional levels in plants, their functional roles in growth responses of crops, including rice (Oryza sativa), to abiotic stresses are yet to be characterized. In this study, rice OsRH58 (LOC_Os01g73900), a chloroplast-localized DEAD-box RH, was characterized for its expression patterns upon stress treatment and its functional roles using transgenic Arabidopsis plants under normal and abiotic stress conditions.

RESULTS

Chloroplast localization of OsRH58 was confirmed by analyzing the expression of OsRH58-GFP fusion proteins in tobacco leaves. Expression of OsRH58 in rice was up-regulated by salt, drought, or heat stress, whereas its expression was decreased by cold, UV, or ABA treatment. The OsRH58-expressing Arabidopsis plants were taller and had more seeds than the wild type under favorable conditions. The transgenic plants displayed faster seed germination, better seedling growth, and a higher survival rate than the wild type under high salt or drought stress. Importantly, levels of several chloroplast proteins were increased in the transgenic plants under salt or dehydration stress. Notably, OsRH58 harbored RNA chaperone activity.

CONCLUSIONS

These findings suggest that the chloroplast-transported OsRH58 possessing RNA chaperone activity confers stress tolerance by increasing translation of chloroplast mRNAs.

Molecular and Functional Diversity of RNA Editing in Plant Mitochondria

RNA editing is a fundamental biochemical process relating to the modification of nucleotides in messenger RNAs of functional genes in cells. RNA editing leads to re-establishment of conserved amino acid residues for functional proteins in nuclei, chloroplasts, and mitochondria. Identification of RNA editing factors that contributes to target site recognition increases our understanding of RNA editing mechanisms. Significant progress has been made in recent years in RNA editing studies for both animal and plant cells. RNA editing in nuclei and mitochondria of animal cells and in chloroplast of plant cells has been extensively documented and reviewed. RNA editing has been also extensively documented on plant mitochondria. However, functional diversity of RNA editing factors in plant mitochondria is not overviewed. Here, we review the biological significance of RNA editing, recent progress on the molecular mechanisms of RNA editing process, and function diversity of editing factors in plant mitochondrial research. We will focus on: (1) pentatricopeptide repeat proteins in Arabidopsis and in crop plants; (2) the progress of RNA editing process in plant mitochondria; (3) RNA editing-related RNA splicing; (4) RNA editing associated flower development; (5) RNA editing modulated male sterile; (6) RNA editing-regulated cell signaling; and (7) RNA editing involving abiotic stress. Advances described in this review will be valuable in expanding our understanding in RNA editing. The diverse functions of RNA editing in plant mitochondria will shed light on the investigation of molecular mechanisms that underlies plant development and abiotic stress tolerance.

Overexpression of the DEAD-Box RNA Helicase Gene AtRH17 Confers Tolerance to Salt Stress in Arabidopsis

Plants adapt to abiotic stresses by complex mechanisms involving various stress-responsive genes. Here, we identified a DEAD-box RNA helicase (RH) gene, AtRH17, in Arabidopsis, involved in salt-stress responses using activation tagging, a useful technique for isolating novel stress-responsive genes. AT895, an activation tagging line, was more tolerant than wild type (WT) under NaCl treatment during germination and seedling development, and AtRH17 was activated in AT895. AtRH17 possesses nine well-conserved motifs of DEAD-box RHs, consisting of motifs Q, I, Ia, Ib, and II-VI. Although at least 12 orthologs of AtRH17 have been found in various plant species, no paralog occurs in Arabidopsis. AtRH17 protein is subcellularily localized in the nucleus. AtRH17-overexpressing transgenic plants (OXs) were more tolerant to high concentrations of NaCl and LiCl compared with WT, but no differences from WT were detected among seedlings exposed to mannitol and freezing treatments. Moreover, in the mature plant stage, AtRH17 OXs were also more tolerant to NaCl than WT, but not to drought, suggesting that AtRH17 is involved specifically in the salt-stress response. Notably, transcriptions of well-known abscisic acid (ABA)-dependent and ABA-independent stress-response genes were similar or lower in AtRH17 OXs than WT under salt-stress treatments. Taken together, our findings suggest that AtRH17, a nuclear DEAD-box RH protein, is involved in salt-stress tolerance, and that its overexpression confers salt-stress tolerance via a pathway other than the well-known ABA-dependent and ABA-independent pathways.

CHLOROPLAST RIBOSOME ASSOCIATED Supports Translation under Stress and Interacts with the Ribosomal 30S Subunit

Chloroplast ribosomes, which originated from cyanobacteria, comprise a large subunit (50S) and a small subunit (30S) containing ribosomal RNAs (rRNAs) and various ribosomal proteins. Genes for many chloroplast ribosomal proteins, as well as proteins with auxiliary roles in ribosome biogenesis or functioning, reside in the nucleus. Here, we identified Arabidopsis (Arabidopsis thaliana) CHLOROPLAST RIBOSOME ASSOCIATED (CRASS), a member of the latter class of proteins, based on the tight coexpression of its mRNA with transcripts for nucleus-encoded chloroplast ribosomal proteins. CRASS was acquired during the evolution of embryophytes and is localized to the chloroplast stroma. Loss of CRASS results in minor defects in development, photosynthetic efficiency, and chloroplast translation activity under controlled growth conditions, but these phenotypes are greatly exacerbated under stress conditions induced by the translational inhibitors lincomycin and chloramphenicol or by cold treatment. The CRASS protein comigrates with chloroplast ribosomal particles and coimmunoprecipitates with the 16S rRNA and several chloroplast ribosomal proteins, particularly the plastid ribosomal proteins of the 30S subunit (PRPS1 and PRPS5). The association of CRASS with PRPS1 and PRPS5 is independent of rRNA and is not detectable in yeast two-hybrid experiments, implying that either CRASS interacts indirectly with PRPS1 and PRPS5 via another component of the small ribosomal subunit or that it recognizes structural features of the multiprotein/rRNA particle. CRASS plays a role in the biogenesis and/or stability of the chloroplast ribosome that becomes critical under certain stressful conditions when ribosomal activity is compromised.

A chloroplast-targeted cabbage DEAD-box RNA helicase BrRH22 confers abiotic stress tolerance to transgenic Arabidopsis plants by affecting translation of chloroplast transcripts

Although the roles of many DEAD-box RNA helicases (RHs) have been determined in the nucleus as well as in cytoplasm during stress responses, the importance of chloroplast-targeted DEAD-box RHs in stress response remains largely unknown. In this study, we determined the function of BrRH22, a chloroplast-targeted DEAD-box RH in cabbage (Brassica rapa), in abiotic stress responses. The expression of BrRH22 was markedly increased by drought, heat, salt, or cold stress and by ABA treatment, but was largely decreased by UV stress. Expression of BrRH22 in Arabidopsis enhanced germination and plantlet growth under high salinity or drought stress. BrRH22-expressing plants displayed a higher cotyledon greening and better plantlet growth upon ABA treatment due to decreases in the levels of ABI3, ABI4, and ABI5. Further, BrRH22 affected translation of several chloroplast transcripts under stress. Notably, BrRH22 had RNA chaperone function. These results altogether suggest that chloroplast-transported BrRH22 contributes positively to the response of transgenic Arabidopsis to abiotic stress by affecting translation of chloroplast genes via its RNA chaperone activity.

Identification of a locus conferring dominant resistance to maize rough dwarf disease in maize

Maize rough dwarf disease (MRDD) is a severe viral disease of maize that occurs worldwide, particularly in the summer maize-growing areas in China, resulting in yield losses and quality deterioration in susceptible maize varieties. An effective solution to control MRDD is to use resistance genes to improve the behavior of susceptible genotypes. Here, we employed maize F₂ populations derived from a cross between susceptible line S221 and resistant line K36 for the deep sequencing of the two DNA pools containing extremely resistant and susceptible F₂ individuals, and used traditional linkage analysis to locate the resistance-related genomic region. The results showed that MRDD resistance in K36 was controlled by a single dominant locus, and an associated region was identified within the genomic interval of 68,396,487 bp and 69,523,478 bp on chromosome 6. Two simple sequence repeat (SSR) markers 6F29R29 and 6F34R34 were tightly linked to the MRDD resistance locus. The findings of the present study improve our understanding of the inheritance patterns of MRDD resistance, and should inform MRDD-resistant maize breeding programs.

The DEAD-box RNA Helicase RH50 Is a 23S-4.5S rRNA Maturation Factor that Functionally Overlaps with the Plastid Signaling Factor GUN1

DEAD-box RNA helicases (DBRHs) modulate RNA secondary structure, allowing RNA molecules to adopt the conformations required for interaction with their target proteins. RH50 is a chloroplast-located DBRH that colocalizes and is coexpressed with GUN1, a central factor in chloroplast-to-nucleus signaling. When combined with mutations that impair plastid gene expression (prors1-1, prpl11-1, prps1-1, prps21-1, prps17-1, and prpl24-1), rh50 and gun1 mutations evoke similar patterns of epistatic effects. These observations, together with the synergistic growth phenotype of the double mutant rh50-1 gun1-102, suggest that RH50 and GUN1 are functionally related and that this function is associated with plastid gene expression, in particular ribosome functioning. However, rh50-1 itself is not a gun mutant, although-like gun1-102-the rh50-1 mutation suppresses the down-regulation of nuclear genes for photosynthesis induced by the prors1-1 mutation. The RH50 protein comigrates with ribosomal particles, and is required for efficient translation of plastid proteins. RH50 binds to transcripts of the 23S-4.5S intergenic region and, in its absence, levels of the corresponding rRNA processing intermediate are strongly increased, implying that RH50 is required for the maturation of the 23S and 4.5S rRNAs. This inference is supported by the finding that loss of RH50 renders chloroplast protein synthesis sensitive to erythromycin and exposure to cold. Based on these results, we conclude that RH50 is a plastid rRNA maturation factor.