Cold-induced inhibition of photosynthesis-related genes integrated by a TOP6 complex in rice mesophyll cells

Integrative analysis of transcriptome and metabolism reveals functional roles of redox homeostasis in low light and salt combined stress in Leymus chinensis

Salt stress is one of the major limiting factors of Leymus chinensis (named sheepgrass) growth, which accelerates inhibitive effects that are particularly concomitant with low light regimes (LL-Salt). However, little is known about physiological and molecular mechanisms under such LL-Salt in sheepgrass. This study aims to uncover the key reprogrammed metabolic pathways induced by LL-Salt through an integrated analysis of transcriptome and metabolism. Results suggested that the growth of sheepgrass seedlings was dramatically inhibited with a ranging of 8 to 20% reduction in Fv/Fm in LL-Salt combined treatments. Catalase activities were increased by 40% in LL but significantly decreased in salt stress, ranging from 15 to 46%. Both transcriptome and metabolism analysis reveal that carbon metabolism pathways were significantly enriched in the differentially expressed genes with downregulation by both LL and salt stress treatment. Metabolites involved in the photorespiration pathway, including serine and glycolate, were downregulated in LL while upregulated in salt stress treatment, with the same pattern of expression levels of a photorespiration regulatory gene, glycolate oxidase. Collectively, we found that serval antioxidant redox pathways, including photorespiration, GSG/GSSH redox, and ABA signaling, participated in response to LL and salt combined events and highlighted the roles of cellular redox homeostasis in LL-Salt response in sheepgrass.

Combined analysis of proteomics and metabolism reveals critical roles of oxidoreductase activity in mushrooms stimulated by wolfberry and sea buckthorn substrates

Background

Cultivating edible fungi, particularly Lentinula edodes, efficiently transforms agroforestry byproducts into valuable products. However, the mechanism of the promotive effects of those substrates was largely unknown. This study used wolfberry (WB) and sea buckthorn (SBK) substrates to investigate mushroom fruiting bodies' physiological, proteomics, and metabolism profiling.

Results

Results show that compared to apple wood (AW), the crude protein and fatty acids were substantially enhanced by both WB and SBK treatment. We identified 1409 and 1190 upregulated and downregulated differentially abundant proteins (DAPs) for the SBK versus AW group and observed 929 overlapped DAPs with upregulation patterns. Of these DAPs, carbohydrates and oxidoreductase activity pathways were significantly enriched. Moreover, the enhanced expression of nine genes by WB and SBK was confirmed by qPCR. Metabolism suggests that 66 differentially abundant metabolites overlapped in the list of two comparison groups (WB versus AW and SBK versus AW).

Conclusion

Collectively, we summarized that both WB and SBK stimulate glucose degradation, enhance the expression of gene-related oxidoreductase activity, and promote protein biosynthesis by coordinating with amino acid metabolism. This study highlights the importance of oxidoreductase activity in promoting nutritional value in mushroom fruiting bodies induced by WB and SBK substrates.

Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton

BACKGROUND

Cold stress significantly challenges cotton growth and productivity, yet the genetic and molecular mechanisms underlying cold tolerance remain poorly understood.

RESULTS

We employed RNA-seq and iterative weighted gene co-expression network analysis (WGCNA) to investigate gene and transposable element (TE) expression changes at six cold stress time points (0 h, 2 h, 4 h, 6 h, 12 h, 24 h). Thousands of differentially expressed genes (DEGs) were identified, exhibiting time-specific patterns that highlight a phase-dependent transcriptional response. While the A and D subgenomes contributed comparably to DEG numbers, numerous homeologous gene pairs showed differential expression, indicating regulatory divergence. Iterative WGCNA uncovered 125 gene co-expression modules, with some enriched in specific chromosomes or chromosomal regions, suggesting localized regulatory hotspots for cold stress response. Notably, transcription factors, including MYB73, ERF017, MYB30, and OBP1, emerged as central regulators within these modules. Analysis of 11 plant hormone-related genes revealed dynamic expression, with ethylene (ETH) and cytokinins (CK) playing significant roles in stress-responsive pathways. Furthermore, we documented over 15,000 expressed TEs, with differentially expressed TEs forming five distinct clusters. TE families, such as LTR/Copia, demonstrated significant enrichment in these expression clusters, suggesting their potential role as modulators of gene expression under cold stress.

CONCLUSIONS

These findings provide valuable insights into the complex regulatory networks underlying cold stress response in cotton, highlighting key molecular components involved in cold stress regulation. This study provides potential genetic targets for breeding strategies aimed at enhancing cold tolerance in cotton.

DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis

It has been hypothesized that DNA damage has the potential to induce DNA hypermethylation, contributing to carcinogenesis in mammals. However, there is no sufficient evidence to support that DNA damage can cause genome-wide DNA hypermethylation. In this study, we demonstrated that DNA single-strand breaks with 3' blocked ends (DNA 3' blocks) not only can reinforce DNA methylation at normally methylated loci but also can induce DNA methylation at normally nonmethylated loci in plants. The CG and CHG hypermethylation tend to localize within gene bodies, with a significant proportion being de novo generated. In contrast, the CHH hypermethylation is concentrated in centromeric and pericentromeric regions, primarily being reinforced methylation. Mechanistically, DNA 3' blocks regulate the DREAM complex to induce CG and CHG methylation. Moreover, they utilize the RdDM pathway to induce CHH hypermethylation. Intriguingly, repair of DNA damage or blocking the DNA damage response can fully abolish CHH hypermethylation and partially rescue CHG hypermethylation but rarely alter CG hypermethylation, indicating that DNA damage-induced symmetric DNA methylation can serve as a form of genetic imprinting. Collectively, these results suggest that DNA damage is an important force driving the emergence and evolution of genomic DNA methylation levels and patterns in plants.

Identifications of Genes Involved in ABA and MAPK Signaling Pathways Positively Regulating Cold Tolerance in Rice

Cold stress (CS) significantly impacts rice (Oryza sativa L.) growth during seedling and heading stages. Based on two-year field observations, this study identified two rice lines, L9 (cold stress-sensitive) and LD18 (cold stress-tolerant), showing contrasting CS responses. L9 exhibited a 38% reduction in photosynthetic efficiency, whereas LD18 remained unchanged, correlating with seed rates. Transcriptome analysis identified differentially expressed genes (DEGs) with LD18 showing enriched pathways (carbon fixation, starch/sucrose metabolism, and glutathione metabolism). LD18 displayed dramatically enhanced expression of MAPK-related genes (LOC4342017, LOC9267741, and LOC4342267) and increased ABA signaling genes (LOC4333690, LOC4345611, and LOC4335640) compared with L9 exposed to CS. Results from qPCR confirmed the enhanced expression of the three MAPK-related genes in LD18 with a dramatic reduction in L9 under CS relative to that under CK. We also observed up to 66% reduction in expression levels of the three genes related to the ABA signaling pathway in L9 relative to LD18 under CS. Consistent with the results of photosynthetic efficiency, metabolic analysis suggests pyruvate metabolism, TCA cycle, and carbon metabolism enrichment in LD18 under CS. The study reveals reprogramming of the carbon assimilation metabolic pathways, emphasizing the critical roles of the key DEGs involved in ABA and MAPK signaling pathways in positive regulation of LD18 response to CS, offering the foundation toward cold tolerance breeding through targeted gene editing.

Enhancement of cold tolerance in tea plants (Camellia sinensis) by glycine betaine accumulation through CsBADH overexpression

Cold stress significantly limits the growth and yield of tea plants (Camellia sinensis (L.) O. Kuntze), particularly in northern China, may lead to huge economic losses. Glycine betaine (GB), an osmotic regulator, is widely applied in crop resistance to abiotic stress. This study investigates the role of GB and its biosynthetic enzyme CsBADH in enhancing cold tolerance in tea plants. Two cultivars, 'Shuchazao' (cold-resistant) and 'Baiye 1' (cold-sensitive), were subjected to low temperature stress (0 °C). GB accumulation was measured, revealing that 'Shuchazao' exhibited 1.4-fold higher GB levels than 'Baiye 1', suggesting a link between higher GB accumulation and cold tolerance. Exogenous GB treatment improved cold resistance, especially in the cold-sensitive cultivar 'Baiye 1'. The CsBADH gene, a key enzyme in GB biosynthesis, was cloned and expressed in Escherichia coli, confirming its activity. Transgenic Arabidopsis thaliana, Nicotiana tabacum, and C. sinensis plants overexpressing CsBADH showed increased GB levels (1.5- to 2.4-fold), proline content, peroxidase (POD) activities, and enhanced cold tolerance, while silencing CsBADH decreased GB accumulation and cold resistance. These findings demonstrate that CsBADH plays a critical role in cold stress response by promoting GB accumulation, offering potential strategies for improving the resilience of tea and other leaf crops to cold stress.

WD40 protein OsTTG1 promotes anthocyanin accumulation and CBF transcription factor-dependent pathways for rice cold tolerance

Temperature is a critical abiotic factor affecting rice (Oryza sativa L.) yields, and cold stress at the seedling stage can inhibit plant growth or even be fatal. Antioxidants such as anthocyanins accumulate in a variety of plants during cold stress, but the underlying mechanisms are not well understood. Here, we report that rice TRANSPARENT TESTA GLABRA 1 (OsTTG1), a major regulator of anthocyanin biosynthesis in rice, responds to short- and long-term cold stress at both the transcriptional and protein levels. Metabolomic and transcriptomic data indicate that OsTTG1 activates the expression of anthocyanidin synthase (OsANS) genes under cold stress. Our data also suggest that OsTTG1 forms a MYB-bHLH-WD (MBW) complex with Basic helix-loop-helix 148 (OsbHLH148) and Myb-related S3 (OsMYBS3), and this complex activates the expression of Dehydration-responsive element-binding protein 1 (OsDREB1) and OsANS genes. Together, our findings reveal the mechanisms by which OsTTG1 coordinates both anthocyanin biosynthesis and the expression of cold-responsive genes in colored rice, providing genetic resources for future cold resistance breeding in rice.

Integrating Proteomics and Metabolomics Approaches to Elucidate the Mechanism of Responses to Combined Stress in the Bell Pepper (Capsicum annuum)

Bell pepper plants are sensitive to environmental changes and are significantly affected by abiotic factors such as UV-B radiation and cold, which reduce their yield and production. Various approaches, including omics data integration, have been employed to understand the mechanisms by which this crop copes with abiotic stress. This study aimed to find metabolic changes in bell pepper stems caused by UV-B radiation and cold by integrating omic data. Proteome and metabolome profiles were generated using liquid chromatography coupled with mass spectrometry, and data integration was performed in the plant metabolic pathway database. The combined stress of UV-B and cold induced the accumulation of proteins related to photosynthesis, mitochondrial electron transport, and a response to a stimulus. Further, the production of flavonoids and their glycosides, as well as affecting carbon metabolism, tetrapyrrole, and scopolamine pathways, were identified. We have made the first metabolic regulatory network map showing how bell pepper stems respond to cold and UV-B stress. We did this by looking at changes in proteins and metabolites that help with respiration, photosynthesis, and the buildup of photoprotective and antioxidant compounds.

The Molecular Mechanism of Cold-Stress Tolerance: Cold Responsive Genes and Their Mechanisms in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.

The MRE11-ATM-SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae

Plants are constantly exposed to microbial pathogens in the environment. One branch of innate plant immunity is mediated by cell-membrane-localized receptors, but less is known about associations between DNA damage and plant immune responses. Here, we show that rice (Oryza sativa) mesophyll cells are prone to DNA double-stranded breaks (DSBs) in response to ZJ173, a strain of Xanthomonas oryzae pv. oryzae (Xoo). The DSB signal transducer ataxia telangiectasia mutated (ATM), but not the ATM and Rad3-related branch, confers resistance against Xoo. Mechanistically, the MRE11-ATM module phosphorylates suppressor of gamma response 1 (SOG1), which activates several phenylpropanoid pathway genes and prompts downstream phytoalexin biosynthesis during Xoo infection. Intriguingly, overexpression of the topoisomerase gene TOP6A3 causes a switch from the classic non-homologous end joining (NHEJ) pathway to the alternative NHEJ and homologous recombination pathways at Xoo-induced DSBs. The enhanced ATM signaling of the alternative NHEJ pathway strengthens the SOG1-regulated phenylpropanoid pathway and thereby boosts Xoo-induced phytoalexin biosynthesis in TOP6A3-OE1 overexpression lines. Overall, the MRE11-ATM-SOG1 pathway serves as a prime example of plant-pathogen interactions that occur via host non-specific recognition. The function of TOP6-facilitated ATM signaling in the defense response makes it a promising target for breeding of rice germplasm that exhibits resistance to bacterial blight disease without a growth penalty.

Effects of exogenous glycine betaine on growth and development of tomato seedlings under cold stress

Low temperature is a type of abiotic stress affecting the tomato (Solanum lycopersicum) growth. Understanding the mechanisms and utilization of exogenous substances underlying plant tolerance to cold stress would lay the foundation for improving temperature resilience in this important crop. Our study is aiming to investigate the effect of exogenous glycine betaine (GB) on tomato seedlings to increase tolerance to low temperatures. By treating tomato seedlings with exogenous GB under low temperature stress, we found that 30 mmol/L exogenous GB can significantly improve the cold tolerance of tomato seedlings. Exogenous GB can influence the enzyme activity of antioxidant defense system and ROS levels in tomato leaves. The seedlings with GB treatment presented higher Fv/Fm value and photochemical activity under cold stress compared with the control. Moreover, analysis of high-throughput plant phenotyping of tomato seedlings also supported that exogenous GB can protect the photosynthetic system of tomato seedlings under cold stress. In addition, we proved that exogenous GB significantly increased the content of endogenous abscisic acid (ABA) and decreased endogenous gibberellin (GA) levels, which protected tomatoes from low temperatures. Meanwhile, transcriptional analysis showed that GB regulated the expression of genes involved in antioxidant capacity, calcium signaling, photosynthesis activity, energy metabolism-related and low temperature pathway-related genes in tomato plants. In conclusion, our findings indicated that exogenous GB, as a cryoprotectant, can enhance plant tolerance to low temperature by improving the antioxidant system, photosynthetic system, hormone signaling, and cold response pathway and so on.

Transcriptome analyses reveal photosynthesis-related genes involved in photosynthetic regulation under low temperature stress in Lavandula angustifolia Mill

In order to reveal the mechanisms of photosynthetic regulation of Lavandula angustifolia Mill. under low temperature stress, photosynthesis-related genes were screened and the molecular mechanism were analyzed for this species growing in Harbin, northeast of China. RNA-seq technique and photosynthetic physiology measurement were performed under 20°C, 10°C, and 0°C in this study. The results showed that the observing modified rectangular hyperbola mode could accurately reflect the light-response processes under low temperature stress and the low temperature reduced the light energy utilization of L. angustifolia. The stomatal conductance decreased with the temperature dropping, which was associated with the up-regulation of LaBAM1s, LaMPK4-1 and LaMMK2. The up-regulation of LaMPK4-1 and LaMMK2 was beneficial for ROS scavenging. The improvement of cold resistance in L. angustifolia was related to the up-regulated expression of LaFBA and LaOMTs and down-regulated expression of LaGAPAs, LaGOX, and LaTKL1s with the temperature decreasing. The up-expression of LaPSY at 10°C than it at 20°C could protect the photosynthetic organs from oxidative damage. Moreover, the photosynthetic rates at 10°C and 0°C were close to the measured values, which was related to the interactions of RCA with SBPase and Rubisco with SBPase. These findings could provide a theoretical reference for further exploring the cold tolerance mechanism of L. angustifolia, as an important aromatic plant resource, and promoting its cultivation and distribution in the northeast of China.

Effect of gibberellic acid on photosynthesis and oxidative stress response in maize under weak light conditions

Gibberellin (GA) is an important endogenous hormone involved in plant responses to abiotic stresses. Experiments were conducted at the Research and Education Center of Agronomy, Shenyang Agricultural University (Shenyang, China) in 2021.We used a pair of near-isogenic inbred maize lines comprising, SN98A (light-sensitive inbred line) and SN98B (light-insensitive inbred line) to study the effects of exogenous gibberellin A3 (GA₃) application on different light-sensitive inbred lines under weak light conditions. The concentration of GA₃ was selected as 20, 40 and 60 mg L^-1. After shade treatment, the photosynthetic physiological indexes of SN98A were always lower than SN98B, and the net photosynthetic rate of SN98A was 10.12% lower than SN98B on the 20th day after shade treatment. GA₃ treatments significantly reduced the barren stalk ratios in SN98A and improved its seed setting rates by increasing the net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs), photosynthetic pigment contents, photochemical efficiency of photosystem II (PS II) (Fv/Fm), photochemical quenching coefficient (qP), effective quantum yield of PSII photochemistry (Φ_PSII), and antioxidant enzyme activities, where the most effective treatment was 60 mg L^-1GA₃. Compared with CK group, the seed setting rate increased by 33.87%. GA₃ treatment also regulated the metabolism of reactive oxygen species (ROS) and reduced the superoxide anion ( O 2 - ) production rate, H₂O₂ content, and malondialdehyde content. The superoxide anion ( O 2 - ) production rate, H₂O₂ content and malondialdehyde content of SN98A sprayed with 60 mg L^-1 GA₃ decreased by 17.32%,10.44% and 50.33% compared with CK group, respectively. Compared with the control, GA₃ treatment significantly (P < 0.05) increased the expression levels of APX and GR in SN98A, and APX, Fe-SOD, and GR in SN98B. Weak light stress decreased the expression of GA20ox2, which was related to gibberellin synthesis, and the endogenous gibberellin synthesis of SN98A. Weak light stress accelerated leaf senescence, and exogenous GA₃ application inhibited the ROS levels in the leaves and maintained normal physiological functions in the leaves. These results indicate that exogenous GA₃ enhances the adaptability of plants to low light stress by regulating photosynthesis, ROS metabolism and protection mechanisms, as well as the expression of key genes, which may be an economical and environmentally friendly method to solve the low light stress problem in maize production.