Functional characterization of a plastid-specific ribosomal protein PSRP2 in Arabidopsis thaliana under abiotic stress conditions

Function of plastid translation in plant temperature acclimation: Retrograde signalling or extraribosomal 'moonlighting' functions?

Specific components of the plastid ribosome could act as pivotal limiting factors in plant temperature acclimation. We endeavour to elucidate the molecular nexus between plastid translation and temperature acclimation by incorporating the concept of extraribosomal ‘moonlighting’ functions of plastid ribosome proteins.

Identification of the RRM1 gene family in rice (Oryza sativa) and its response to rice blast

To better understand RNA-binding proteins in rice, a comprehensive investigation was conducted on the RRM1 gene family of rice. It encompassed genome-wide identification and exploration of its role in rice blast resistance. The physicochemical properties of the rice OsRRM1 gene family were analyzed. There genes were also analyzed for their conserved domains, motifs, location information, gene structure, phylogenetic trees, collinearity, and cis-acting elements. Furthermore, alterations in the expression patterns of selected OsRRM1 genes were assessed using quantitative real-time PCR (qRT-PCR). A total of 212 members of the OsRRM1 gene family were identified, which were dispersed across 12 chromosomes. These genes all exhibit multiple exons and introns, all of which encompass the conserved RRM1 domain and share analogous motifs. This observation suggests a high degree of conservation within the encoded sequence domain of these genes. Phylogenetic analysis revealed the existence of five subfamilies within the OsRRM1 gene family. Furthermore, investigation of the promoter region identified cis-regulatory elements that are involved in nucleic acid binding and interaction with multiple transcription factors. By employing GO and KEGG analyses, four RRM1 genes were tentatively identified as crucial contributors to plant immunity, while the RRM1 gene family was also found to have a significant involvement in the complex of alternative splicing. The qRT-PCR results revealed distinct temporal changes in the expression patterns of OsRRM1 genes following rice blast infection. Additionally, gene expression analysis indicates that the majority of OsRRM1 genes exhibited constitutive expressions. These findings enrich our understanding of the OsRRM1 gene family. They also provide a foundation for further research on immune mechanisms rice and the management of rice blast.

Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves

Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development. Here, we studied leaf development in Populus Nanlin895 along a development gradient from the newly emerged leaf from the shoot apex to the sixth leaf (L1 to L6) using anatomical observations and RNA-seq analysis. It indicated that mesophyll cells possess obvious vascular, palisade, and spongy tissue with distinct intercellular spaces after L3. Additionally, vacuoles fuse while epidermal cells expand to form pavement cells. RNA-seq analysis indicated that genes highly expressed in L1 and L2 were related to cell division and differentiation, while those highly expressed in L3 were enriched in photosynthesis. Therefore, we selected L1 and L3 to integrate ATAC-seq and RNA-seq and identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility regions within their promoters, of which 87 were transcription factors (TFs), such as ABI3VP1, AP-EREBP, MYB, NAC, and GRF. Motif enrichment analysis revealed potential regulatory functions for the DEGs through upstream TFs including TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, our research provides a potential molecular foundation for regulatory network exploration in leaf development during photosynthesis establishment.

Identification of new potential molecular actors related to fiber quality in flax through Omics

One of the biggest challenges for a more widespread utilization of plant fibers is to better understand the different molecular factors underlying the variability in fineness and mechanical properties of both elementary and scutched fibers. Accordingly, we analyzed genome-wide transcription profiling from bast fiber bearing tissues of seven different flax varieties (4 spring, 2 winter fiber varieties and 1 winter linseed) and identified 1041 differentially expressed genes between varieties, of which 97 were related to cell wall metabolism. KEGG analysis highlighted a number of different enriched pathways. Subsequent statistical analysis using Partial Least-Squares Discriminant Analysis showed that 73% of the total variance was explained by the first 3 X-variates corresponding to 56 differentially expressed genes. Calculation of Pearson correlations identified 5 genes showing a strong correlation between expression and morphometric data. Two-dimensional gel proteomic analysis on the two varieties showing the most discriminant and significant differences in morphometrics revealed 1490 protein spots of which 108 showed significant differential abundance. Mass spectrometry analysis successfully identified 46 proteins representing 32 non-redundant proteins. Statistical clusterization based on the expression level of genes corresponding to the 32 proteins showed clear discrimination into three separate clusters, reflecting the variety type (spring-/winter-fiber/oil). Four of the 32 proteins were also highly correlated with morphometric features. Examination of predicted functions for the 9 (5 + 4) identified genes highlighted lipid metabolism and senescence process. Calculation of Pearson correlation coefficients between expression data and retted fiber mechanical measurements (strength and maximum force) identified 3 significantly correlated genes. The genes were predicted to be connected to cell wall dynamics, either directly (Expansin-like protein), or indirectly (NAD(P)-binding Rossmann-fold superfamily protein). Taken together, our results have allowed the identification of molecular actors potentially associated with the determination of both in-planta fiber morphometrics, as well as ex-planta fiber mechanical properties, both of which are key parameters for elementary fiber and scutched fiber quality in flax.

Population Structure, Genetic Diversity and Candidate Genes for the Adaptation to Environmental Stress in Picea koraiensis

Picea koraiensis is major silvicultural and timber species in northeast China, and its distribution area is an important transition zone for genus spruce migration. The degree of intraspecific differentiation of P. koraiensis is high, but population structure and differentiation mechanisms are not clear. In this study, 523,761 single nucleotide polymorphisms (SNPs) were identified in 113 individuals from 9 populations of P. koraiensis by genotyping-by-sequencing (GBS). Population genomic analysis showed that P. koraiensis was divided into three geoclimatic regions: Great Khingan Mountains climatic region, Lesser Khingan Mountains climatic region, and Changbai Mountain climatic region. Mengkeshan (MKS) population on the northern edge of the distribution area and Wuyiling (WYL) population located in the mining area are two highly differentiated groups. Selective sweep analysis showed that MKS and WYL populations had 645 and 1126 selected genes, respectively. Genes selected in the MKS population were associated with flowering and photomorphogenesis, cellular response to water deficit, and glycerophospholipid metabolism; genes selected in the WYL population were associated with metal ion transport, biosynthesis of macromolecules, and DNA repair. Climatic factors and heavy metal stress drives divergence in MKS and WYL populations, respectively. Our findings provide insights into adaptive divergence mechanisms in Picea and will contribute to molecular breeding studies.

Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica

Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress-ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.

Unveiling the functions of plastid ribosomal proteins in plant development and abiotic stress tolerance

Translation of mRNAs into proteins is a universal process and ribosomes are the molecular machinery that carries it out. In eukaryotic cells, ribosomes can be found in the cytoplasm, mitochondria, and also in the chloroplasts of photosynthetic organisms. A number of genetic studies have been performed to determine the function of plastid ribosomal proteins (PRPs). Tobacco has been frequently used as a system to study the ribosomal proteins encoded by the chloroplast genome. In contrast, Arabidopsis thaliana and rice are preferentially used models to study the function of nuclear-encoded PRPs by using direct or reverse genetics approaches. The results of these works have provided a relatively comprehensive catalogue of the roles of PRPs in different plant biology aspects, which highlight that some PRPs are essential, while others are not. The latter ones are involved in chloroplast biogenesis, lateral root formation, leaf morphogenesis, plant growth, photosynthesis or chlorophyll synthesis. Furthermore, small gene families encode some PRPs. In the last few years, an increasing number of findings have revealed a close association between PRPs and tolerance to adverse environmental conditions. Sometimes, the same PRP can be involved in both developmental processes and the response to abiotic stress. The aim of this review is to compile and update the findings hitherto published on the functional analysis of PRPs. The study of the phenotypic effects caused by the disruption of PRPs from different species reveals the involvement of PRPs in different biological processes and highlights the significant impact of plastid translation on plant biology.

Cell damage repair mechanism in a desert green algae Chlorella sp. against UV-B radiation

The protective ozone layer is continually depleting owing to an increase in the levels of solar UV-B radiation, which has harmful effects on organisms. Algae in desert soil can resist UV-B radiation, but most research on the radiation resistance of desert algae has focused on cyanobacteria. In this study, we found that desert green algae, Chlorella sp., could maintain high photosynthetic activity under UV-B stress. To examine the tolerance mechanism of the desert green algae photosystem, we observed the physiological and transcriptome-level responses of Chlorella sp. to high doses of UV-B radiation. The results showed that the reactive oxygen species (ROS) content first increased and then decreased, while the malondialdehyde (MDA) content revealed no notable lipid peroxidation during the UV-B exposure period. These results suggested that Chlorella sp. may have strong system characteristics for scavenging ROS. The antioxidant enzyme system showed efficient alternate coordination, which exhibited a protective effect against enhanced UV-B radiation. DNA damage and the chlorophyll and soluble protein contents had no significant changes in the early irradiation stage; UV-B radiation did not induce extracellular polysaccharides (EPS) synthesis. Transcriptomic data revealed that a strong photosynthetic system, efficient DNA repair, and changes in the expression of genes encoding ribosomal protein (which aid in protein synthesis and improve resistance) are responsible for the high UV-B tolerance characteristics of Chlorella sp. In contrast, EPS synthesis was not the main pathway for UV-B resistance. Our results revealed the potential cell damage repair mechanisms within Chlorella sp. that were associated with high intensity UV-B stress, thereby providing insights into the underlying regulatory adaptations of desert green algae.

Maize Seed Germination Under Low-Temperature Stress Impacts Seedling Growth Under Normal Temperature by Modulating Photosynthesis and Antioxidant Metabolism

Spring maize is usually subjected to low-temperature stress during seed germination, which retards seedling growth later even under a suitable temperature. However, the mechanism underlying maize seed germination under low-temperature stress impacting seedling growth is still ambiguous. In this study, we used one low-temperature sensitive maize (SM) and one low-temperature resistance maize (RM) to investigate the mechanism. The results showed that the SM line had higher malondialdehyde content and lower total antioxidant capacity (TAC) and germination percentage than the RM line under low-temperature stress, indicating the vulnerability of SM line to low-temperature stress. Further transcriptome analysis revealed that seed germination under low-temperature stress caused the down-regulation of photosynthesis-related gene ontology terms in two lines. Moreover, the SM line displayed down-regulation of ribosome and superoxide dismutase (SOD) related genes, whereas genes involved in SOD and vitamin B6 were up-regulated in the RM line. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that photosynthesis and antioxidant metabolism-related pathways played essential roles in response to low-temperature stress during seed germination. The photosynthetic system displayed a higher degree of damage in the SM line. Both qRT-PCR and physiological characteristics experiments showed similar results with transcriptome data. Taken together, we propose a model for maize seed germination in response to low-temperature stress.

ZmmiR190 and its target regulate plant responses to drought stress through an ABA-dependent pathway

MicroRNAs (miRNAs) are small, non-coding regulatory RNAs that regulate gene expression by facilitating target mRNA cleavage in plants. They are crucial for responses to diverse stresses. The novel drought-responsive miRNA ZmmiR190 was previously identified during an analysis of the maize transcriptome. In this study, we revealed that transgenic Arabidopsis thaliana overexpressing ZmmiR190 is more sensitive to drought than the wild-type control. The transcript of a nuclear-localized gene, ZmCRP04, was identified as a likely target of ZmmiR190. Moreover, ZmmiR190 and ZmCRP04 had the opposite expression profiles following drought and salt treatments. Additionally, 5' RACE and coexpression analyses in A. thaliana provided evidence of the in vivo targeting of the ZmCRP04 transcript by ZmmiR190. Furthermore, the overexpression of ZmCRP04 in A. thaliana and rice significantly enhanced drought tolerance, with lower malonaldehyde contents and relative electrolyte leakage in the transgenic A. thaliana and rice plants than in the wild-type control. Transgenic plants overexpressing ZmmiR190 or ZmCRP04 were hypersensitive to abscisic acid. These results suggest that the ZmCRP04 transcript is targeted by ZmmiR190 and may encode a protein that positively regulates drought stress tolerance via an abscisic acid-dependent pathway. These findings may be relevant for future molecular breeding aimed at improving crop drought tolerance.

Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean

BACKGROUND

Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage.

RESULTS

In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation.

CONCLUSIONS

Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.

The acidic domain of the chloroplast RNA-binding protein CP31A supports cold tolerance in Arabidopsis thaliana

The processing of chloroplast RNA requires a large number of nuclear-encoded RNA-binding proteins (RBPs) that are imported post-translationally into the organelle. The chloroplast ribonucleoprotein 31A (CP31A) supports RNA editing at 13 sites and also supports the accumulation of multiple chloroplast mRNAs. In cp31a mutants it is the ndhF mRNA (coding for a subunit of the NDH complex) that is most strongly affected. CP31A becomes particularly important at low temperatures, where it is essential for chloroplast development in young tissue. Next to two RNA-recognition motifs (RRMs), CP31A has an N-terminal acidic domain that is phosphorylated at several sites. We investigated the function of the acidic domain in the role of CP31A in RNA metabolism and cold resistance. Using point mutagenesis, we demonstrate that the known phosphorylation sites within the acidic domain are irrelevant for any of the known functions of CP31A, both at normal and at low temperatures. Even when the entire acidic domain is removed, no effects on RNA editing were observed. By contrast, loss of the acidic domain reduced the ability of CP31A to stabilize the ndhF mRNA, which was associated with reduced NDH complex activity. Most importantly, acidic domain-less CP31A lines displayed bleached young tissue in the cold. Together, these data show that the different functions of CP31A can be assigned to different regions of the protein: the RRMs are sufficient to maintain RNA editing and to allow the accumulation of basal amounts of ndhF mRNA, while chloroplast development under cold conditions critically depends on the acidic domain.

QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing

Improvement in sesame drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. In this study, three traits and their relative values, including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and osmotic conditions in a recombinant inbred line (RIL) population derived from cross of Zhushanbai and Jinhuangma. Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through whole genome re-sequencing (WGS) strategy. Quantitative trait loci (QTL) mapping was performed for all the traits. A total of 34 QTLs were detected on 10 chromosomes. Among them, 13 stable QTLs were revealed in two independent experiments, eight of them were associated with traits under water stress condition. One region on chromosome 12 related to RL under osmotic condition and relative RL had the highest LOD value and explained the largest phenotypic variation among all the QTLs detected under water stress condition. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.

iTRAQ and PRM-based comparative proteomic profiling in gills of white shrimp Litopenaeus vannamei under copper stress

Crustaceans are particularly sensitive to heavy metal pollution. Copper (Cu) is one of typical heavy metal pollutants in aquatic ecosystems. However, limited attention has been paid on the proteomic responses of shrimp under Cu stress. White shrimp Litopenaeus vannamei held in 5‰ seawater were exposed to 5 mg L^-1 Cu for 3 h, and the regulatory mechanism in the gills was elucidated using iTRAQ-based quantitative proteomics. The results showed that a total of 5034 proteins were identified, 385 differentially expressed proteins (DEPs), including 147 differentially up-regulated proteins (DUPs) and 238 differentially down-regulated proteins (DDPs) were found. Bioinformatics analysis indicated the DEPs responding to Cu stress mainly involved in cytoskeleton, immune response, stress response, protein synthesis, detoxification, ion homeostasis and apoptosis. Furthermore, we still performed PRM analysis on sarcoplasmic calcium binding protein (SCP), serine proteinase inhibitor B3 (SPIB3), C-type lectin 4 (CTL4), cathepsin L (CATHL), JHE-like carboxylesterase 1 (CXE1) and paramyosin (PMY), and biochemical analysis on Cu/Zn-superoxide dismutase (Cu/Zn-SOD) to validate the iTRAQ results, respectively. The present proteome analysis revealed that Cu stress disrupted the ion homeostasis and protein synthesis, and L.vannamei mainly regulates a series of molecular pathways which contained many key proteins involved in the immune process to protect the organism from Cu stress. Our data provides more insight about the underlying mechanisms that related to the stress response of Cu exposure in crustacean.

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.

Functional analysis of mTERF5 and mTERF9 contribution to salt tolerance, plastid gene expression and retrograde signalling in Arabidopsis thaliana

We previously showed that Arabidopsis mda1 and mterf9 mutants, defective in the chloroplast-targeted mitochondrial transcription termination factors mTERF5 and mTERF9, respectively, display altered responses to abiotic stresses and abscisic acid (ABA), as well as perturbed development, likely through abnormal chloroplast biogenesis. To advance the functional analysis of mTERF5 and mTERF9, we obtained and characterized overexpression (OE) lines. Additionally, we studied genetic interactions between sca3-2, affected in the plastid-RNA polymerase RpoTp, and the mda1-1 and mterf9 mutations. We also investigated the role of mTERF5 and mTERF9 in plastid translation and plastid-to-nucleus signalling. We found that mTERF9 OE reduces salt and ABA tolerance, while mTERF5 or mTERF9 OE alter expression of nuclear and plastid genes. We determined that mda1-1 and mterf9 mutations genetically interact with sca3-2. Further, plastid 16S rRNA levels were reduced in mda1-1 and mterf9 mutants, and mterf9 was more sensitive to chemical inhibitors of chloroplast translation. Expression of the photosynthesis gene LHCB1, a retrograde signalling marker, was differentially affected in mda1-1 and/or mterf9 compared to wild-type Col-0, after treatments with inhibitors of carotenoid biosynthesis (norflurazon) or chloroplast translation (lincomycin). Moreover, mterf9, but not mda1-1, synergistically interacts with gun1-1, defective in GUN1, a central integrator of plastid retrograde signals. Our results show that mTERF9, and to a lesser extent mTERF5, are negative regulators of salt tolerance and that both genes are functionally related to RpoTp, and that mTERF9 is likely required for plastid ribosomal stability and/or assembly. Furthermore, our findings support a role for mTERF9 in retrograde signalling.

Complementary analyses of the transcriptome and iTRAQ proteome revealed mechanism of ethylene dependent salt response in bread wheat (Triticum aestivum L.)

In order to clarify the ethylene dependent salt response mechanism in wheat, 2-week-old wheat seedlings of cultivar 'Qingmai 6' treated with water, sodium chloride (NaCl), NaCl and ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), and NaCl and ethylene signaling inhibitor 1-methylcyclopropene (1-MCP) were collected and analyzed by transcriptional sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) proteomics. At least 1140 proteins and 73,401 genes were identified, and proteins including ribosomal proteins (RPs), nucleoside diphosphate kinases (CDPKs), transaldolases (TALs), beta-glucosidases (BGLUs), phosphoenlpyruvate carboxylases (PEPCs), superoxide dismutases (SODs), and 6-phosphogluconate dehydrogenases (6-PGDHs) were significantly differently expressed. These genes and proteins revealed that ethylene dependent salt response through RPs activation, chaperones synthesis, the reactive oxygen species (ROS) scavenging, and carbohydrate metabolites pathway. Our results provided transcriptomics and proteomics information with respect to the molecular mechanisms of ethylene regualted salt response.

The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA

Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with the vast majority of the psbA transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B's preference for psbA, suggesting that there are other determinants of specificity in vivo.

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.

Cre-miR914-regulated RPL18 is involved with UV-B adaptation in Chlamydomonas reinhardtii

UV radiation is a serious threat to life, and algae have developed highly efficient adaptations to UV radiation through the course of evolution. To date, studies investigating the mechanisms of UV adaptation in algae have focused on physiological regulation and associated protein coding genes, with only a few reports on associated protein non-coding genes. In a previous study, we found that Cre-miR914 was significantly down-regulated in Chlamydomonas reinhardtii in response to heat shock. In the present study, we aimed to determine whether Cre-miR914 plays a role in response to UV-B radiation. Our bioinformatics analysis indicated that the potential target gene of Cre-miR914 is ribosomal protein L18 (RPL18). We also measured the expression of Cre-miR914 and RPL18 in response to UV-B radiation through qPCR analysis. Then, we constructed cell lines overexpressing Cre-miR914 or RPL18, and performed survival experiments under UV-B stress. The results showed that Cre-miR914 overexpression decreased resistance while RPL18 overexpression enhanced tolerance to UV-B radiation. These results indicate that Cre-miR914 and its potential target gene RPL18 are involved in the adaptation to UV-B in C. reinhardtii.

Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation

Chloroplastic translation is mediated by a bacterial-type 70S chloroplast ribosome. During the evolution, chloroplast ribosomes have acquired five plastid-specific ribosomal proteins or PSRPs (cS22, cS23, bTHXc, cL37 and cL38) which have been suggested to play important regulatory roles in translation. However, their exact locations on the chloroplast ribosome remain elusive due to lack of a high-resolution structure, hindering our progress to understand their possible roles. Here we present a cryo-EM structure of the 70S chloroplast ribosome from spinach resolved to 3.4 Å and focus our discussion mainly on the architecture of the 30S small subunit (SSU) which is resolved to 3.7 Å. cS22 localizes at the SSU foot where it seems to compensate for the deletions in 16S rRNA. The mRNA exit site is highly remodeled due to the presence of cS23 suggesting an alternative mode of translation initiation. bTHXc is positioned at the SSU head and appears to stabilize the intersubunit bridge B1b during thermal fluctuations. The translation factor plastid pY binds to the SSU on the intersubunit side and interacts with the conserved nucleotide bases involved in decoding. Most of the intersubunit bridges are conserved compared to the bacteria, except for a new bridge involving uL2c and bS6c.

Functional diversity of Arabidopsis organelle-localized RNA-recognition motif-containing proteins

RNA-Binding Proteins (RBPs) play key roles in plant gene expression and regulation. RBPs contain a variety of RNA-binding motifs, the most abundant and most widespread one in eukaryotes is the RNA recognition motif (RRM). Many nucleus-encoded RRM-containing proteins are transported into chloroplasts and/or mitochondria, and participate in various RNA-related processes in plant organelles. Loss of these proteins can have a detrimental effect on some critical processes such as photosynthesis and respiration, sometimes leading to lethality. Progress has been made in the last few years in understanding the function of particular organelle-localized RRM-containing proteins. Members of the Organelle RRM protein (ORRM, some also characterized as Glycine-Rich RNA-Binding Proteins) family and the Chloroplast RiboNucleoProtein (cpRNP) family, are involved in various types of RNA metabolism, including RNA editing, RNA stability and RNA processing. Organelle-localized RRM proteins also function in plant development and stress responses, in some conditions acting as protein or RNA chaperones. There has been recent progress in characterizing the function of organelle-localized RRM proteins in RNA-related processes and how RRM proteins contribute to the normal growth and development of plants. WIREs RNA 2017, 8:e1420. doi: 10.1002/wrna.1420 For further resources related to this article, please visit the WIREs website.

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY

Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo‐EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid‐specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid‐specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light‐ and temperature‐dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A‐site and P‐site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non‐rotated state, in which the intersubunit bridges to the large subunit are stabilized.

Regulation of Chloroplast Protein Import by the Ubiquitin E3 Ligase SP1 Is Important for Stress Tolerance in Plants

Chloroplasts are the organelles responsible for photosynthesis in plants [1, 2]. The chloroplast proteome comprises ∼3,000 different proteins, including components of the photosynthetic apparatus, which are highly abundant. Most chloroplast proteins are nucleus-encoded and imported following synthesis in the cytosol. Such import is mediated by multiprotein complexes in the envelope membranes that surround each organelle [3, 4]. The translocon at the outer envelope membrane of chloroplasts (TOC) mediates client protein recognition and early stages of import. The TOC apparatus is regulated by the ubiquitin-proteasome system (UPS) in a process controlled by the envelope-localized ubiquitin E3 ligase SUPPRESSOR OF PPI1 LOCUS1 (SP1) [5, 6]. Previous work showed that SP1-mediated regulation of chloroplast protein import contributes to the organellar proteome changes that occur during plant development (e.g., during de-etiolation). Here, we reveal a critical role for SP1 in plant responses to abiotic stress, which is a major and increasing cause of agricultural yield losses globally [7]. Arabidopsis plants lacking SP1 are hypersensitive to salt, osmotic, and oxidative stresses, whereas plants overexpressing SP1 are considerably more stress tolerant than wild-type. We present evidence that SP1 acts to deplete the TOC apparatus under stress conditions to limit the import of photosynthetic apparatus components, which may attenuate photosynthetic activity and reduce the potential for reactive oxygen species production and photo-oxidative damage. Our results indicate that chloroplast protein import is responsive to environmental cues, enabling dynamic regulation of the organellar proteome, and suggest new approaches for improving stress tolerance in crops.

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Levels of the chloroplast E3 ligase SP1 influence plant abiotic stress tolerance

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Effects of SP1 on stress tolerance are linked to reactive oxygen species levels

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SP1 acts to deplete the chloroplast protein import (TOC) machinery under stress

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TOC depletion by SP1 is linked to reduced plastid import of photosynthesis proteins

The translational apparatus of plastids and its role in plant development

Chloroplasts (plastids) possess a genome and their own machinery to express it. Translation in plastids occurs on bacterial-type 70S ribosomes utilizing a set of tRNAs that is entirely encoded in the plastid genome. In recent years, the components of the chloroplast translational apparatus have been intensely studied by proteomic approaches and by reverse genetics in the model systems tobacco (plastid-encoded components) and Arabidopsis (nucleus-encoded components). This work has provided important new insights into the structure, function, and biogenesis of chloroplast ribosomes, and also has shed fresh light on the molecular mechanisms of the translation process in plastids. In addition, mutants affected in plastid translation have yielded strong genetic evidence for chloroplast genes and gene products influencing plant development at various levels, presumably via retrograde signaling pathway(s). In this review, we describe recent progress with the functional analysis of components of the chloroplast translational machinery and discuss the currently available evidence that supports a significant impact of plastid translational activity on plant anatomy and morphology.

Abiotic stress resistance, a novel moonlighting function of ribosomal protein RPL44 in the halophilic fungus Aspergillus glaucus

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily involved in the translation of mRNA leading to protein synthesis. However, certain ribosomal proteins moonlight in the development and differentiation of organisms. In this study, the ribosomal protein L44 (RPL44), associated with salt resistance, was screened from the halophilic fungus Aspergillus glaucus (AgRPL44), and its activity was investigated in Saccharomyces cerevisiae and Nicotiana tabacum. Sequence alignment revealed that AgRPL44 is one of the proteins of the large ribosomal subunit 60S. Expression of AgRPL44 was upregulated via treatment with salt, sorbitol, or heavy metals to demonstrate its response to osmotic stress. A homologous sequence from the model fungus Magnaporthe oryzae, MoRPL44, was cloned and compared with AgRPL44 in a yeast expression system. The results indicated that yeast cells with overexpressed AgRPL44 were more resistant to salt, drought, and heavy metals than were yeast cells expressing MoRPL44 at a similar level of stress. When AgRPL44 was introduced into M. oryzae, the transformants displayed obviously enhanced tolerance to salt and drought, indicating the potential value of AgRPL44 for genetic applications. To verify the value of its application in plants, tobacco was transformed with AgRPL44, and the results were similar. Taken together, we conclude that AgRPL44 supports abiotic stress resistance and may have value for genetic application.