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.

Fusarium oxysporum f. sp. radicis-lycopersici (Forl) is a destructive soil-borne phytopathogenic fungus that causes Fusarium crown and root rot (FCRR) of tomato, leading to considerable field yield losses. In this study, we explored the antifungal capability of linalool, a natural plant volatile organic component, against Forl and its role in controlling FCRR symptoms in tomatoes. Our results showed that Forl mycelial growth was inhibited by the linalool treatment and that the linalool treatment damaged cell membrane integrity, enhanced reactive oxygen species levels, depleted glutathione, and reduced the activities of many antioxidant enzymes in Forl. Transcriptomic and proteomic analyses demonstrated that linalool also downregulated metabolic biosynthetic pathways at the transcript and protein levels, including redox, transporter activity, and carbohydrate metabolism in Forl. Moreover, linalool significantly decreased the expression of many Forl pathogenic genes, such as cell wall degrading enzymes (CWDEs) and G proteins, which is likely how a Forl infection was prevented. Importantly, exogenously applied linalool activated the salicylic acid (SA) and jasmonic acid (JA) defensive pathways to improve disease resistance and relieved the negative effects of Forl on plant growth. Taken together, we report that linalool is an effective fungicide against Forl and will be a promising green chemical agent for controlling FCRR.

Gray mold is a disease that often occurs in postharvest tomato fruits, leading to a significant decline in the fruits’ quality. In production, pesticides are mostly used to control gray mold, which negatively affect both the environment and food safety. The purpose of this article is to study the effects of linalool fumigation on controlling gray mold in tomato fruits and to further investigate the mechanism of linalool function, so as to provide technical support and a theoretical basis for the application of linalool in the green control of tomato gray mold. The results of the in vitro experiments showed that linalool fumigation had a strong inhibitory effect on the mycelial growth of Botrytis cinerea and that the fumigation of linalool inhibited the expansion of pathogens on tomato fruits. The disease index of tomato fruits in the linalool treatment was always lower than that of the control within 72 h after inoculation with Botrytis cinerea; at the end of experiment, the disease index of the control reached 100.0, which was only 8.0 with the 30 μL/L linalool treatment. Linalool fumigation increased the antioxidant capacity of the tomato fruits under Botrytis cinerea infection through regulating activities of SOD, POD and CAT as well as the ascorbic acid (AsA) content, which could be responsible for the lower malondialdehyde (MDA) accumulation. Linalool fumigation increased the activities of polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) in tomato fruits, indicating that secondary metabolism was involved in the function of linalool in the regulation of tomato fruit resistance to pathogens. As the main enzymes related to cell structure, polygalacturonase (PG), cellulase (CL) and β-galactosidase (β-GAL) were inhibited by linalool, which could protect cell wall structures from damage, and strengthened the mechanical barrier against pathogen access to fruit flesh.

Paclobutrazol Resistance (PRE) genes encode atypical basic helix–loop–helix (bHLH) transcription factor family. Typical bHLH proteins contain a bifunctional structure with a basic region involved in DNA binding and an adjacent helix–loop–helix domain involved in protein–protein interaction. PRE members lack the basic region but retain the HLH domain, which interacts with other typical bHLH proteins to suppress or enhance their DNA-binding activity. PRE proteins are involved in phytohormone responses, light signal transduction, and fruit pigment accumulation. However, apple (Malus domestica) PRE protein functions have not been studied. In this study, nine MdPRE genes were identified from the apple GDDH13 v1.1 reference genome and were mapped to seven chromosomes. The cis-acting element analysis revealed that MdPRE promoters possessed various elements related to hormones, light, and stress responses. Expression pattern analysis showed that MdPRE genes have different tissue expression profiles. Hormonal and abiotic stress treatments can induce the expression of several MdPRE genes. Moreover, we provide molecular and genetic evidence showing that MdPRE4.3 increases the apple’s sensitivity to NaCl, abscisic acid (ABA), and indoleacetic acid (IAA) and improves tolerance to brassinosteroids (BR); however, it does not affect the apple’s response to gibberellin (GA). Finally, the protein interaction network among the MdPRES proteins was predicted, which could help us elucidate the molecular and biological functions of atypical bHLH transcription factors in the apple.

Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5′ ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.

Bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato (Pst), is a globally significant disease leading to substantial yield losses. This study demonstrated that methyl caffeate (MC), a plant‐derived phenolic acid, exhibited dual functionality against Pst strain DC3000 through direct antibacterial action and indirect host resistance priming. In vitro assays revealed MC's potent inhibitory activity against bacterial growth, characterised by disruption of membrane integrity, leading to intracellular content leakage and reactive oxygen species (ROS) accumulation. Transcriptomic analysis identified 434 upregulated and 326 downregulated genes, with differentially expressed genes primarily enriched in pathways related to flagellar assembly, motility, quorum sensing, chemotaxis and the type III secretion system (T3SS), thereby impairing bacterial motility and virulence. Concurrently, MC enhances plant defence responses by inducing the transcriptional expression of defence hormone signalling pathway‐related genes and increasing the activities of defence enzymes such as phenylalanine ammonia‐lyase (PAL) and polyphenol oxidase (PPO). This modulation helps maintain ROS homeostasis and alleviates oxidative damage caused by Pst infection, thereby attenuating disease progression. These findings established MC as a multifunctional agent combining direct bactericidal effects with plant immunity induction, providing a sustainable strategy for bacterial speck management.