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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.

Numerous attempts have been made to identify and engineer sequence-specific RNA endonucleases, as these would allow for efficient RNA manipulation. However, no natural RNA endonuclease that recognizes RNA in a sequence-specific manner has been described to date. Here, we report that SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an Arabidopsis pentatricopeptide repeat (PPR) protein with a small MutS-related (SMR) domain, has RNA endonuclease activity. We show that the SMR moiety of SOT1 performs the endonucleolytic maturation of 23S and 4.5S rRNA through the PPR domain, specifically recognizing a 13-nucleotide RNA sequence in the 5′ end of the chloroplast 23S–4.5S rRNA precursor. In addition, we successfully engineered the SOT1 protein with altered PPR motifs to recognize and cleave a predicted RNA substrate. Our findings point to SOT1 as an exciting tool for RNA manipulation.

Chloroplast development, maintenance and function depend on the coordinated expression of chloroplast and nuclear genes. The retrograde chloroplast signals are essential in coordinating nuclear gene expression. Although the sources of signals in chloroplasts have been identified and the associated transcription factors in the nucleus extensively studied, the molecular mechanism that relays chloroplast signals to the nucleus remains a mystery. Here we show that PTM, a chloroplast envelope-bound plant homeodomain (PHD) transcription factor with transmembrane domains, functions in multiple retrograde signal pathways. The proteolytic cleavage of PTM occurs in response to retrograde signals and amino-terminal PTM accumulates in the nucleus, where it activates ABI4 transcription in a PHD-dependent manner associated with histone modifications. These results provide a molecular basis for the critical function of PTM in retrograde chloroplast signaling and shed new light on the mechanism whereby chloroplast signals are transmitted to the nucleus through the cytosol. Retrograde chloroplast signals are essential in coordinating nuclear gene expression, but the mechanism that relays chloroplast signals to the nucleus remains elusive. In this study, a chloroplast envelope-bound transcription factor PTM is shown to transmit chloroplast signals to the nucleus.

The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C‐terminal small MutS‐related (SMR) domain. Although there are relatively few PPR‐SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid‐to‐nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR‐SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR‐SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted. Pentatricopeptide repeat‐small MutS‐related (PPR‐SMR) proteins play essential roles in embryo development, chloroplast biogenesis and gene expression, and retrograde signaling. The PPR motifs and SMR domain of the PPR‐SMR protein SOT1 confer RNA sequence specificity and endonucleolytic activity, respectively. SOT1 could be used as a tool for RNA manipulation, particularly in studies of chloroplast and mitochondrial biology and RNA viral defense.

The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts, transcribing over 80% of all primary plastid transcripts. This polymerase consists of a prokaryotic-like core enzyme known as the plastid-encoded RNA polymerase core, and is supplemented by newly evolved associated proteins known as PAPs. However, the architecture of the plastid-encoded RNA polymerase and the possible functions of PAPs remain unknown. Here, we present the cryo-electron microscopy structure of a 19-subunit plastid-encoded RNA polymerase complex derived from spinach ( Spinacia oleracea ). The structure shows that the plastid-encoded RNA polymerase core resembles bacterial RNA polymerase. Twelve PAPs and two additional proteins (FLN2 and pTAC18) bind at the periphery of the plastid-encoded RNA polymerase core, forming extensive interactions that may facilitate complex assembly and stability. PAPs may also protect the complex against oxidative damage and has potential functions in transcriptional regulation. This research offers a structural basis for future investigations into the functions and regulatory mechanisms governing the transcription of plastid genes. The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts. Here, the authors present the cryo-electron microscopy structure of a 19-subunit plastid-encoded RNA polymerase complex derived from spinach.

During growth and development, cells experience both internal and external stresses, which can exert harmful impacts if they are poorly managed. Endoplasmic reticulum (ER) stress is an internal stress that is induced when protein misfolding or perturbations occur at excess rates, and the conventional response pathways from the ER to the nucleus are activated to address the stress. However, the involvement of the plasma membrane (PM) system in response to this internal stress has been insufficiently investigated. Here, a PM sensor, MoPh1, was observed to perceive stress through ER-PM contact sites and target the autophagosome and vacuole, consequently stimulating the autophagy process and supporting stress relief. The PM-to-vacuole pathway mediated by MoPh1 is independent of the classical ER-to-nucleus pathway and might be highly important in both fungi and plants, as it plays a crucial role in alleviating ER stress and promoting cellular adaptation for cell survival. The unfolded protein response is activated at the ER due to protein misfolding. Here the authors show that in Magnaporthe oryzae , the plasma membrane localized MoPh1 protein perceives stress through ER-PM contact sites and stimulates autophagy to support stress relief.

RNA editing is a posttranscriptional process that covalently alters the sequence of RNA molecules and plays important biological roles in both animals and land plants. In flowering plants, RNA editing converts specific cytidine residues to uridine in both plastid and mitochondrial transcripts. Previous studies identified pentatricopeptide repeat (PPR) motif-containing proteins as site-specific recognition factors for cytidine targets in RNA sequences. However, the regulatory mechanism underlying RNA editing was largely unknown. Here, we report that protoporphyrinogen IX oxidase 1 (PPO1), an enzyme that catalyzes protoporphyrinogen IX into protoporphyrin IX in the tetrapyrrole biosynthetic pathway, plays an unexpected role in editing multiple sites of plastid RNA transcripts, most of which encode subunits of the NADH dehydrogenase-like complex (NDH), in the reference plant Arabidopsis thaliana. We identified multiple organellar RNA editing factors (MORFs), including MORF2, MORF8, and MORF9, that interact with PPO1. We found that two conserved motifs within the 22-aa region at the N terminus of PPO1 are essential for its interaction with MORFs, its RNA editing function, and subsequently, its effect on NDH activity. However, transgenic plants lacking key domains for the tetrapyrrole biosynthetic activity of PPO1 exhibit normal RNA editing. Furthermore, MORF2 and MORF9 interact with three PPRs or related proteins required for editing of ndhB and ndhD sites. These results reveal that the tetrapyrrole biosynthetic enzyme PPO1 is required for plastid RNA editing, acting as a regulator that promotes the stability of MORF proteins through physical interaction.

Soil salinization threatens global food security, necessitating the development of saline–alkaline-tolerant crops. This study investigated the molecular mechanisms of alkali stress tolerance in maize. Screening 369 inbred lines identified two alkali-resistant and two alkali-sensitive varieties. Systematic analysis revealed that resistant varieties rapidly lowered rhizosphere pH and maintained root architecture, whereas sensitive varieties suffered reduced lateral roots and severe biomass loss. Metabolomic profiling showed that all varieties secreted malonic acid via the pyrimidine pathway to modulate rhizosphere pH, with resistant varieties exhibiting stronger accumulation. Transcriptome and RT-qPCR analysis identified two key genes: Zm00001eb396990 (asparagine synthetase), upregulated in resistant varieties and linked to organic acid synthesis, and Zm00001eb370000 (cytokinin dehydrogenase), downregulated in resistant varieties, potentially aiding root maintenance. Multi-omics correlation confirmed the association between Zm00001eb396990 expression and malonic acid content. This study demonstrates that maize roots can alleviate alkali stress through the secretion of malonic acid and the regulation of related genes, providing potential genetic targets and a theoretical basis for cultivating alkali-tolerant maize.

Chloroplast retrograde signals play important roles in coordinating the plastid and nuclear gene expression and are critical for proper chloroplast biogenesis and for maintaining optimal chloroplast functions in response to environmental changes in plants. Until now, the signals and the mechanisms for retrograde signalling remain poorly understood. Here we identify factors that allow the nucleus to perceive stress conditions in the chloroplast and to respond accordingly by inducing or repressing specific nuclear genes encoding plastid proteins. We show that ABI4, which is known to repress the LHCB genes during retrograde signalling, is activated through phosphorylation by the MAP kinases MPK3/MPK6 and the activity of these kinases is regulated through 14-3-3ω-mediated Ca 2+ -dependent scaffolding depending on the chloroplast calcium sensor protein CAS. These findings uncover an additional mechanism in which chloroplast-modulated Ca 2+ signalling controls the MAPK pathway for the activation of critical components of the retrograde signalling chain. Retrograde signalling co-ordinates nuclear gene expression in response to stress perceived in the chloroplast. Here Guo et al. show that a MAPK cascade acting downstream of a plastid derived Ca 2+ signal contributes to the regulation of nuclear gene expression by phosphorylation of ABI4 during retrograde signalling.