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Mutation of a stromal C-terminal threonine residue of Photosystem II subunit S slows down NPQ induction and speeds up relaxation.

In order to prevent damage by excess light, light harvesting antennae can switch to an energy dissipative mode (termed non-photochemical quenching, NPQ). In higher plants, this switch is facilitated by the presence of Photosystem II subunit S (PsbS) protein, which was discovered 25 years ago. While the role of PsbS in induction of NPQ was soon found to require protonation of key glutamate residues facing the thylakoid lumen, a complete understanding of how NPQ is subsequently initiated is still lacking. Recent work on Norway spruce suggests that reversible phosphorylation at a few conserved residues of PsbS may affect its role in regulation of NPQ. Here we assessed PsbS phosphorylation changes in Arabidopsis thaliana plants, but these remained undetectable under control and combined chilling and high light stress conditions. We therefore used a genetic approach to assess potential functional implications of phosphorylation at threonine-259 (T259). Functional evaluation of point mutations at T259 in the background of PsbS knock-out mutant npq4 showed that neither phosphomimetic, phosphosubstitution, nor phosphonull substitutions could rescue NPQ activity to the level of the unperturbed protein, inconsistent with regulation via reversible phosphorylation. Instead, all residue substitutions at T259 gave rise to significantly impaired induction and accelerated NPQ recovery, while protein accumulation and thylakoid membrane localisation were not affected. We suggest that these results point to a role for the C-terminus in the propensity or stability of hydrophobic interactions between PsbS and LHCII antenna proteins to initiate the quenched state.

Photosystem II subunit S

The cold case of state transition 7 (stt7) mutants of Chlamydomonas reinhardtii, solved by whole-genome sequencing.

The process of State Transitions (ST) corresponds to an STT7 kinase-driven redistribution of the transmembrane LHCII antenna proteins between Photosystem II (PSII) and Photosystem I (PSI), which results from changes in their phosphorylation state. For the past two decades, two LHCII-kinase mutants, stt7-1 and stt7-9, have been instrumental in the study of STs in Chlamydomonas reinhardtii, the former being a null mutant for the kinase but quasi-sterile in crosses, while the latter, although fertile, has a leaky phenotype. Using long-read sequencing, this study further characterized the genetic lesions of the stt7 mutant strains through whole-genome reconstruction and de novo chromosome assembly. In addition, two new stt7 null mutants were generated, one derived by crosses from the original stt7-1 and one obtained by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (Cas9) technology. This work provides a comprehensive genomic characterization of the original stt7-1 null mutant, revealing extensive chromosomal rearrangements and high levels of aneuploidy, associated with increased cell size and meiotic dysfunction. Reassessment of their physiology and genetic backgrounds highlights the need for caution in interpreting genetic information. We thus produced more reliable null mutants for the LHCII-kinase, amenable to genetic crosses for the study of STs in a variety of genetic backgrounds.

Chlamydomonas reinhardtii

Alleviation of CO2-Induced Reductions in Tomato Photosynthesis Under Deficit Irrigation by Purple Nonsulfur Photosynthetic Bacteria.

The stimulatory effect of elevated CO2 (eCO2) on photosynthesis in most C3 crops under water deficit often declines over time due to photosynthetic acclimation. An exception occurs in plants inoculated with symbiotic nitrogen-fixing bacteria. Photosynthetic bacteria (PSB), specifically anoxygenic purple nonsulfur bacteria (Rhodopseudomonas palustris in this study), a group of nitrogen-fixing bacteria, are effective in enhancing crop photosynthesis. Therefore, this study investigated the synergistic effects of PSB and eCO2 in alleviating the effects of deficit irrigation and enhancing photosynthetic capacity in tomato plants during prolonged exposure. Our results showed that photosynthetic efficiency was significantly reduced in noninoculated plants under eCO2, and this reduction was more pronounced under water deficit. Proteomic analysis revealed that in eCO2-treated plants, the downregulation of cell wall proteins increased mesophyll resistance to CO2 diffusion, while the suppression of the photosynthetic apparatus impaired electron transport capacity, ultimately reducing CO2 assimilation efficiency. In contrast, these negative effects were alleviated by PSB inoculation. PSB promoted the upregulation of proteins involved in photosynthesis under deficit irrigation, as well as proteins related to chlorophyll biosynthesis, components of photosystem I and II, and light-harvesting complex proteins. These proteins contributed to improved photosynthetic efficiency during deficit irrigation and photosynthetic acclimation. Physiological analyses further confirmed that PSB inoculation enhanced nitrogen content, electron transport capacity, chlorophyll biosynthesis, and overall photosynthetic performance under eCO2 and deficit irrigation, resulting in improved plant growth. These findings suggest that PSB inoculation is a promising strategy to sustain and enhance the CO2 fertilization effect on crop productivity under water-limited conditions.

Photosynthesis

Effects of light on chloroplast translation in Marchantia polymorpha are similar to those in angiosperms and are not influenced by light-independent chlorophyll synthesis.

Translation of the chloroplast psbA mRNA in angiosperms is activated by photodamage of its gene product, the D1 subunit of photosystem II (PSII), providing nascent D1 for PSII repair. The involvement of chlorophyll in the regulatory mechanism has been suggested due to the regulatory roles of proteins proposed to mediate chlorophyll/D1 transactions and the fact that chlorophyll is synthesized only in the light in angiosperms. We used ribosome profiling and RNA-seq to address whether the effects of light on chloroplast translation are conserved in the liverwort Marchantia (Marchantia polymorpha), which synthesizes chlorophyll in both the dark and the light. As in angiosperms, ribosome occupancy on psbA mRNA decreased rapidly upon shifting plants to the dark and was rapidly restored upon a transfer back to the light, whereas ribosome occupancy on other chloroplast mRNAs changed very little. The results were similar in a Marchantia mutant unable to synthesize chlorophyll in the dark. Those results, in conjunction with pulse-labeling data, suggest that light elicits a plastome-wide activation of translation elongation and a specific increase in psbA translation initiation in Marchantia, as in angiosperms. These findings show that light regulates chloroplast translation similarly in vascular and non-vascular plants, and that constitutive chlorophyll synthesis does not affect light-regulated psbA translation initiation. Additionally, the translational outputs of chloroplast genes are similar in Marchantia and angiosperms but result from differing contributions of mRNA abundance and translational efficiencies. This adds to the evidence that chloroplast mRNA abundance and translational efficiencies co-evolve under selection to maintain protein outputs.

Chloroplasts

Preliminary mapping of wheat (Triticum aestivum L.) tolerance genes to the English grain aphid (Sitobion avenae Fabricius) by genome-wide association study.

Six Sitobion avenae-tolerant wheat accessions, mapped 110 associated SNPs and six candidate genes were identified, providing valuable genetic resources for breeding wheat with tolerance to S. avenae. Wheat tolerance to the English grain aphid (Sitobion avenae) is rarely incorporated into integrated pest management strategies for wheat fields. The scarcity of tolerant accession and insufficient mapping of tolerance-related gene are key limiting factors. To address these gaps, 640 wheat accessions were evaluated for S. avenae tolerance, combined with genome-wide association study (GWAS) and qPCR validation. Six wheat accessions with stable tolerance were identified: Lerma Rojo 64, AC Vista, Hanxuan 10, Zimai, Ningnuomai 1, Louguding. A total of 110 single nucleotide polymorphism (SNP) loci associated with tolerance to S. avenae were mapped, and six candidate genes (TraesCS2D03G0041800, TraesCS2Dnew048215, TraesCS2D03G0046300, TraesCS6B03G0655800, TraesCS2Dnew048223, TraesCS2D03G0040800) were examined for transcriptional responses following aphid infestation via qRT-PCR. These genes are involved in cellular redox homeostasis, ADP-binding-mediated defense, and photosystem II (PSII) functionality. This study provides valuable genetic resources for breeding wheat with tolerance to S. avenae and lays a foundation for subsequent functional validation of these tolerance genes and its molecular mechanism exploration.

Animals

Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress.

The ERF-VII gene family, a critical branch of the AP2/ERF superfamily, is central to plant stress adaptation. However, its evolutionary history and function in tea plant (Camellia sinensis) remain unclear. Here, we performed integrated evolutionary, genomic, and functional analyses of ERF-VII genes across 14 plant lineages and 20 tea plant cultivars. The phylogenetic analysis revealed that ERF-VII proteins originated after vascular plant divergence, coinciding with the emergence of the N-terminal MCGGA/I motif linked to the oxygen-dependent N-degron pathway. Gymnosperms retained few conserved members, whereas angiosperms exhibited lineage-specific expansion-extensive in monocots via whole-genome duplication, moderate in eudicots with functional diversification. Pan-genome analysis across 20 tea plant cultivars further revealed varietal differences in ERF-VII gene distribution. Transcriptome profiling via the Tea Plant Information Archive identified CsRAP2.2 as a cold-inducible ERF-VII member with sustained expression under low-temperature stress. Functional assays demonstrated that silencing CsRAP2.2 reduced cold tolerance, while overexpression in tea leaves and heterologous expression in Arabidopsis thaliana enhanced cold tolerance by maintaining photosystem II efficiency, reducing membrane lipid peroxidation, and improving antioxidant capacity. Weighted gene co-expression network analysis positioned CsRAP2.2 as a regulatory hub integrating cold, hormone, and oxygen-sensing pathways. These results clarify the evolutionary trajectory of ERF-VII genes and establish CsRAP2.2 as a core cold-tolerance regulator in tea plant. These findings may inform future breeding of cold-resilient tea cultivars.

Camellia sinensis

Comparative Responses of Invasive and Native Plant Species to Combined Cd and Microplastic Pollution.

The co-occurrence of heavy metal contamination and biodegradable microplastic (polylactic acid, PLA) pollution poses increasing risks to terrestrial plant communities and soil functioning, yet species-specific responses to combined stress remain poorly understood. Cd and microplastics frequently co-occur in agricultural soils, where microplastics can alter cadmium mobility, bioavailability, and transport pathways, potentially modifying metal toxicity and plant stress responses compared with single-pollutant exposure. We investigated the responses of the invasive Bidens pilosa and the native Solanum nigrum grown in monoculture and mixed culture under combined cadmium (Cd) and biodegradable microplastic (PLA) stress by integrating plant growth, photosynthetic performance, oxidative physiology, and rhizosphere biochemical processes. Combined Cd-MP exposure markedly reduced plant growth, chlorophyll content (SPAD), photosystem II efficiency (Fv/Fm), nitrogen accumulation, biomass production, and rhizosphere enzyme activities associated with carbon, nitrogen, and phosphorus cycling. However, B. pilosa maintained greater physiological stability under stress, characterized by higher antioxidant enzyme activities (SOD, CAT, POD), lower reactive oxygen species (H2O2, O2˙-) accumulation, and reduced lipid peroxidation (MDA), whereas S. nigrum exhibited stronger oxidative damage and functional impairment. Multivariate analyses further revealed that root antioxidant capacity was closely associated with rhizosphere microbial enzyme activity, suggesting a root-centered regulatory mechanism linking plant stress tolerance to soil functioning. Overall, the invasive species showed greater tolerance to combined contamination and maintained relatively higher rhizosphere functional activity than the native species, indicating that multi-pollutant stress may alter competitive interactions between invasive and native plants in contaminated environments.

Cadmium

Bundle sheath cell-specific expression of chloroplast genes encoding subunits of the NADH dehydrogenase-like complex in maize.

C4 photosynthesis alleviates the limitation caused by the oxygenase activity of Rubisco by partitioning photosynthetic functions between two distinct cell types: bundle sheath cells (BSCs) and mesophyll cells (MCs). These cell types perform different steps of photosynthesis using specialized machinery, accompanied by differential expression of chloroplast genes. To uncover the underlying molecular mechanisms for this differentiation, we isolated BSCs and MCs and compared their chloroplast transcriptomes, focusing on the chloroplast NADH dehydrogenase-like (NDH) complex, which is enriched in BSCs. To investigate whether RNA stabilization contributes to differential gene expression, we analyzed RNA footprints that reflect the binding of pentatricopeptide repeat (PPR) proteins to their RNA targets. We could not detect cell-type-specific accumulation of footprint RNAs. We then focused on transcriptional regulation, specifically on an operon that starts with the rps15 gene. The operon includes six ndh genes and the psaC gene encoding a photosystem I subunit. Transcript levels of all genes in this operon were higher in BSCs than in MCs, suggesting coordinated regulation as a transcriptional unit. Based on the genomic location of the rps15 gene within inverted repeats near the junctions on both sides of the small single copy region, we demonstrated that rps15, through two distinct promoters, is sufficient to drive preferential accumulation of downstream transcripts in BSCs.

Zea mays

Integrative analysis of transcriptome and chromatin accessibility reveals promoter-proximal regulation and identifies candidate ABC transporters associated with cold stress responses in maize.

BACKGROUND: Low-temperature stress is a formidable environmental constraint that severely limits the growth and productivity of maize (Zea mays L.), particularly during the highly vulnerable early seedling stage. While cold tolerance is a critical agronomic objective, the integrated transcriptional and epigenetic regulatory mechanisms that govern this trait remain largely elusive. Characterizing these coordinated molecular networks is fundamental to the genetic enhancement of cold resilience in maize. METHODS: Using two maize inbred lines contrasting in chilling response (ZHB12 tolerant, B73 sensitive), we performed integrative time‑course RNA‑seq and ATAC‑seq to thoroughly and systematically characterize the precise dynamic interplay between gene expression and chromatin accessibility under cold stress conditions at the seedling stage. RESULTS: Physiological assessments confirmed that ZHB12 possesses superior cold tolerance, manifested by significantly attenuated electrolyte leakage and reduced foliar damage compared to B73. Transcriptomic profiling revealed a massive, time-dependent divergence in gene expression between the two genotypes, with a major regulatory transition identified at 24 h of cold exposure. Functional enrichment analysis demonstrated that ZHB12 preferentially activates a robust defense repertoire, including Photosystem II electron transport, diterpenoid biosynthesis, and ATP biosynthetic pathways. Notably, multiple ATP-binding cassette (ABC) transporter genes were coordinately upregulated under chilling, suggesting their potential involvement in cellular homeostasis. ATAC-seq analysis indicated that cold stress is associated with chromatin remodeling in ZHB12, with increased accessibility observed in proximal promoter regions. Integrative analysis identified a core set of dual-responsive genes, in which increased promoter accessibility coincided with transcriptional upregulation. These genes were predominantly enriched in transporter activity and transcriptional regulation, suggesting potential epigenetic link to the superior stress response of ZHB12. CONCLUSION: Our findings reveal extensive transcriptional and chromatin accessibility changes in ZHB12 under cold stress. The observed associations between promoter accessibility and gene activation, particularly in genes involved in transport processes, highlight candidate regulators potentially contributing to cold tolerance. This study provides a molecular framework and identifies high-value candidate genes that may inform future efforts in breeding cold-tolerant maize, pending functional validation.

Zea mays

The Elements of Life, Photosynthesis and Genomics.

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute's efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets - focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors - that are well-used and appreciated by the community. A new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true "green yeast" and as a platform for engineering algae to produce useful bioproducts.

Photosynthesis