The Oxidative Phosphorylation system of the mitochondria in plants

Unraveling the impact of PFOA toxicity on Zostera marina using a multi-omics approach: Insights from growth, physiological, transcriptomic, and metabolomic signatures

Perfluorooctanoic acid (PFOA), an anthropogenic organic pollutant known for its persistence, resistance to degradation, and toxicity, has raised significant concerns about its potential ecological impacts. Zostera marina, a common submerged seagrass species in temperate offshore areas, is highly vulnerable to pollutant stressors. However, the impact of PFOA on Z. marina remains unclear. In this study, Z. marina was exposed to different concentrations of PFOA (0, 0.5, 1, 5, 10, and 20 μg/L) for 14 days. We subsequently assessed survival rates, growth patterns, physiological indices, transcriptomic profiles, and metabolomic characteristics. The results revealed dose-dependent PFOA accumulation in Z. marina tissues and significant growth inhibition. Furthermore, exposure to PFOA resulted in a significant reduction in photosynthetic pigment content (IBRv2 indices: 2.78-10.29) and elevated enzyme activity (IBRv2 indices: 2.90-8.96). Transcriptomic analysis identified 1511 differentially expressed genes associated with 11 KEGG pathways predominantly affected by PFOA exposure. Weighted gene co-expression network analysis highlighted the crucial role of the hydroxyphenylpyruvate reductase (hppr) gene in antioxidant defense mechanisms and detoxification processes against PFOA-induced stress. Metabolomics identified 412 differentially expressed metabolites, mainly consisting of flavonoids, organic acids, and lipids. In summary, PFOA exposure resulted in the down-regulation of gene expression related to photosynthesis and energy metabolism while also affecting metabolite synthesis. The response of Z. marina to PFOA stress involves modulation of the cytoskeletal dynamics and signal transduction pathways, as well as activation of a suite of genes and metabolites to initiate defense mechanisms.

Transcriptome and DNA methylation analysis of the goat pineal gland during puberty

Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. To screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, we collected pineal glands from prepubertal and pubertal female goats, then, determined the DNA methylation profile by whole genome bisulfite sequencing and the transcriptome by RNA sequencing on Illumina HiSeqTM2500. We analyzed differentially expressed genes between the Pre group and Pub group using the DESeq2 software (version 1.20.0), and applied the Benjamini and Hochberg method for adjusting P-values. Genes with a P-value less than 0.05 and an absolute log2 fold change greater than 0 were considered differentially expressed genes. Results showed that there was no significant difference in the whole-genome methylation level of the pineal gland between prepubertal and pubertal goats, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland might play a role in regulating the initiation of goat puberty. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes remained unaffected by DNA methylation differences. Genes regulated by DNA methylation regulates genes primarily involved in metabolic processes, oxidative phosphorylation, and signaling pathways related to thermogenesis. Methylation significantly regulated the expression of genes such as ATP5F1D, CACNB2, and PTEN, while genes like LIN28B, GIP, OPN1SW, and DCC showed the most notable fold changes, which may indicate their involvement in the onset of puberty.

Cytochrome c levels link mitochondrial function to plant growth and stress responses through changes in SnRK1 pathway activity

Energy is required for growth as well as for multiple cellular processes. During evolution, plants developed regulatory mechanisms to adapt energy consumption to metabolic reserves and cellular needs. Reduced growth is often observed under stress, leading to a growth-stress trade-off that governs plant performance under different conditions. In this work, we report that plants with reduced levels of the mitochondrial respiratory chain component cytochrome c (CYTc), required for electron transport coupled to oxidative phosphorylation and ATP production, show impaired growth and increased global expression of stress-responsive genes, similar to those observed after inhibiting the respiratory chain or the mitochondrial ATP synthase. CYTc-deficient plants also show activation of the SnRK1 pathway, which regulates growth, metabolism, and stress responses under carbon starvation conditions, even though their carbohydrate levels are not significantly different from wild-type. Notably, loss-of-function of the gene encoding the SnRK1α1 subunit restores the growth of CYTc-deficient plants, as well as autophagy, free amino acid and TOR pathway activity levels, which are affected in these plants. Moreover, increasing CYTc levels decreases SnRK1 pathway activation, reflected in reduced SnRK1α1 phosphorylation, with no changes in total SnRK1α1 protein levels. Under stress imposed by mannitol, the growth of CYTc-deficient plants is relatively less affected than that of wild-type plants, which is also related to the activation of the SnRK1 pathway. Our results indicate that SnRK1 function is affected by CYTc levels, thus providing a molecular link between mitochondrial function and plant growth under normal and stress conditions.

Comparative transcriptome analysis provides novel insights into the seed germination of Panax japonicus, an endangered species in China

Panax japonicus, an endangered species in China, is usually used as a traditional medicine with functions of hemostasis, pain relief, and detoxify. However, the seeds of P. japonicus are hard to germinate in natural conditions, and the molecular events and systematic changes occurring in seed germination are still largely unknown. In this study, we compared the seeds in different germination stages in terms of morphological features, antioxidant enzyme activities, and transcriptomics. The results indicated that sand storage at 25℃ for 120 d effectively released the seed dormancy of P. japonicus and promoted the seed germination. Moreover, sand storage treatment increased the antioxidant capacity of P. japonicus seeds through increasing the activities of SOD, POD, and CAT. The RNA-seq identified 28,908 differentially expressed genes (DEGs) between different germination stages, of which 1697 DEGs significantly changed throughout the whole germination process. Functional annotations showed that the seed germination of P. japonicus was mainly regulated by the DEGs related to pathways of ROS-scavenging metabolism, plant hormonal signal transduction, starch and sucrose metabolism, energy supply (glycolysis, pyruvate metabolism, and oxidative phosphorylation), and phenylpropanoid biosynthesis, as well as the transcription factors such as bHLHs, MYBs, WRKYs, and bZIPs. This study provides a foundation for unveiling molecular mechanisms underlying the seed germination and is beneficial for accelerating the development of P. japonicus industry.

Changes in SWEET-mediated sugar partitioning affect photosynthesis performance and plant response to drought

Sugars, produced through photosynthesis, are at the core of all organic compounds synthesized and used for plant growth and their response to environmental changes. Their production, transport, and utilization are highly regulated and integrated throughout the plant life cycle. The maintenance of sugar partitioning between the different subcellular compartments and between cells is important in adjusting the photosynthesis performance and response to abiotic constraints. We investigated the consequences of the disruption of four genes coding for SWEET sugar transporters in Arabidopsis (SWEET11, SWEET12, SWEET16, and SWEET17) on plant photosynthesis and the response to drought. Our results show that mutations in both SWEET11 and SWEET12 genes lead to an increase of cytosolic sugars in mesophyll cells and phloem parenchyma cells, which impacts several photosynthesis-related parameters. Further, our results suggest that in the swt11swt12 double mutant, the sucrose-induced feedback mechanism on stomatal closure is poorly efficient. On the other hand, changes in fructose partitioning in mesophyll and vascular cells, measured in the swt16swt17 double mutant, positively impact gas exchanges, probably through an increased starch synthesis together with higher vacuolar sugar storage. Finally, we propose that the impaired sugar partitioning, rather than the total amount of sugars observed in the quadruple mutant, is responsible for the enhanced sensitivity upon drought. This work highlights the importance of considering SWEET-mediated sugar partitioning rather than global sugar content in photosynthesis performance and plant response to drought. Such knowledge will pave the way to design new strategies to maintain plant productivity in a challenging environment.

Mutations in nuclear genes encoding mitochondrial ribosome proteins restore pollen fertility in S male-sterile maize

The interaction of plant mitochondrial and nuclear genetic systems is exemplified by mitochondria-encoded cytoplasmic male sterility (CMS) under the control of nuclear restorer-of-fertility genes. The S type of CMS in maize is characterized by a pollen collapse phenotype and a unique paradigm for fertility restoration in which numerous nuclear restorer-of-fertility lethal mutations rescue pollen function but condition homozygous-lethal seed phenotypes. Two nonallelic restorer mutations recovered from Mutator transposon-active lines were investigated to determine the mechanisms of pollen fertility restoration and seed lethality. Mu Illumina sequencing of transposon-flanking regions identified insertion alleles of nuclear genes encoding mitochondrial ribosomal proteins RPL6 and RPL14 as candidate restorer-of-fertility lethal mutations. Both candidates were associated with lowered abundance of mitochondria-encoded proteins in developing maize pollen, and the rpl14 mutant candidate was confirmed by independent insertion alleles. While the restored pollen functioned despite reduced accumulation of mitochondrial respiratory proteins, normal-cytoplasm plants heterozygous for the mutant alleles showed a significant pollen transmission bias in favor of the nonmutant Rpl6 and Rpl14 alleles. CMS-S fertility restoration affords a unique forward genetic approach to investigate the mitochondrial requirements for, and contributions to, pollen and seed development.

What we know so far and what we can expect next: A molecular investigation of plant parasitism

The review explores parasitic plants' evolutionary success and adaptability, highlighting their widespread occurrence and emphasizing the role of an invasive organ called haustorium in nutrient acquisition from hosts. It discusses the genetic and physiological adaptations that facilitate parasitism, including horizontal gene transfer, and the impact of environmental factors like climate change on these relationships. It addresses the need for further research into parasitic plants' genomes and interactions with their hosts to better predict environmental changes' impacts.

Mitochondrial ß-Cyanoalanine Synthase Participates in flg22-Induced Stomatal Immunity

Plants regulate gas exchange with the environment and modulate transpirational water flow through guard cells, which set the aperture of the stomatal pores. External and internal stimuli are detected by guard cells and integrated into a signalling network that modulate turgor pressure and, hence, pore size. Pathogen-associated molecular patterns are among the stimuli that induce stomatal closure, to prevent pathogen entry through the pores, and this response, also referred to as stomatal immunity, is one of the hallmarks of PAMP-triggered immunity. While reactive oxygen species (ROS)-mediated signalling plays a key role in stomatal immunity, also the gasotransmitter hydrogen sulphide (H2S) interacts with key components of the guard cell signalling network to induce stomatal closure. While the role of H2S, produced by the main cytosolic source L-cysteine desulfhydrase 1, has been already investigated, there are additional enzymatic sources that synthesize H2S in different subcellular compartments. Their function has remained enigmatic, however. In this work, we elucidate the involvement of the mitochondrial H2S source, β-cyanoalanine synthase CAS-C1, on stomatal immunity induced by the bacterial PAMP flagellin (flg22). We show that cas-c1 plants are impaired to induce flg22-triggered stomatal closure and apoplastic ROS production, while they are more susceptible to bacterial surface inoculation. Moreover, mitochondrial H2S donor AP39 induced stomatal closure in an RBOHD-dependent manner, while depletion of endogenous H2S, impaired RBOHD-mediated apoplastic ROS production. In addition, pharmacological disruption of mitochondrial electron transport chain activity, affected stomatal closure produced by flg22, indicating its participation in the stomatal immunity response. Our findings add evidence to the emerging realization that intracellular organelles play a decisive role in orchestrating stomatal signalling and immune responses and suggest that mitochondrial-derived H2S is an important player of the stomatal immunity signalling network.

Plant supercomplex I + III2 structure and function: implications for the growing field

Mitochondrial respiration is major source of chemical energy for all free-living eukaryotes. Nevertheless, the mechanisms of the respiratory complexes and supercomplexes remain poorly understood. Here, I review recent structural and functional investigations of plant supercomplex I + III2 from Arabidopsis thaliana and Vigna radiata. I discuss commonalities, open questions and implications for complex I, complex III2 and supercomplexes in plants and non-plants. Studies across further clades will enhance our understanding of respiration and the potential universal mechanisms of its complexes and supercomplexes.

Effect of acute exposure of Hg on physiological parameters and transcriptome expression in silkworms (Bombyx mori)

Mercury (Hg) contamination poses a global threat to the environment, given its elevated ecotoxicity. Herein, we employed the lepidopteran model insect, silkworm (Bombyx mori), to systematically investigate the toxic effects of Hg-stress across its growth and development, histomorphology, antioxidant enzyme activities, and transcriptome responses. High doses of Hg exposure induced evident poisoning symptoms, markedly impeding the growth of silkworm larvae and escalating mortality in a dose-dependent manner. Under Hg exposure, the histomorphology of both the midgut and fat body exhibited impairments. Carboxylesterase (CarE) activity was increased in both midgut and fat body tissues responding to Hg treatment. Conversely, glutathione S-transferase (GST) levels increased in the fat body but decreased in the midgut. The transcriptomic analysis revealed that the response induced by Hg stress involved multiple metabolism processes. Significantly differently expressed genes (DEGs) exhibited strong associations with oxidative phosphorylation, nutrient metabolisms, insect hormone biosynthesis, lysosome, ribosome biogenesis in eukaryotes, and ribosome pathways in the midgut or the fat body. The findings implied that exposure to Hg might induce the oxidative stress response, attempting to compensate for impaired metabolism. Concurrently, disruptions in nutrient metabolism and insect hormone activity might hinder growth and development, leading to immune dysfunction in silkworms. These insights significantly advance our theoretical understanding of the potential mechanisms underlying Hg toxicity in invertebrate organisms.

Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica)

Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of Luffa cylindrica. The mt genome of L. cylindrica contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (ATP8, CCMFC, NAD4, RPL10, RPL5 and RPS4) showed positive selection. Phylogenetic analysis indicates that L. cylindrica is closely related to L. acutangula. The present results provide the mt genome of L. cylindrica, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. cylindrica.

SIRT1-dependent PGC-1α deacetylation by SRT1720 rescues progression of atherosclerosis by enhancing mitochondrial function

Vascular smooth muscle cell (VSMC) senescence promotes atherosclerosis via lipid-mediated mitochondrial dysfunction and oxidative stress. However, the mechanisms of mitochondrial dysfunction and VSMC senescence in atherosclerosis have not been established. Here, we investigated the mechanisms whereby signaling pathways regulated by SRT1720 enhance or regulate mitochondrial functions in atherosclerotic VSMCs to suppress atherosclerosis. Initially, we examined the effect of SRT1720 on oleic acid (OA)-induced atherosclerosis. Atherosclerotic VSMCs exhibited elevated expressions of BODIPY and ADRP (adipose differentiation-related protein) and associated intracellular lipid droplet markers. In addition, the expression of collagen I was upregulated by OA, while the expressions of elastin and α-SMA were downregulated. mtDNA copy numbers, an ATP detection assay, transmission electron microscopy (TEM) imaging of mitochondria, mitochondria membrane potentials (assessed using JC-1 probe), and levels of mitochondrial oxidative phosphorylation (OXPHOS) were used to examine the effects of SRT1720 on OA-induced mitochondrial dysfunction. SRT1720 reduced mtDNA damage and accelerated mitochondria repair in VSMCs with OA-induced mitochondria dysfunction. In addition, mitochondrial reactive oxygen species (mtROS) levels were downregulated by SRT1720 in OA-treated VSMCs. Importantly, SRT1720 significantly increased SIRT1 and PGC-1α expression levels, but VSMCs senescence, inflammatory response, and atherosclerosis phenotypes were not recovered by treating cells with EX527 and SR-18292 before SRT1720. Mechanistically, the upregulations of SIRT1 and PGC-1α deacetylation by SRT1720 restored mitochondrial function, and consequently suppressed VSMC senescence and atherosclerosis-associated proteins and phenotypes. Collectively, this study indicates that SRT1720 can attenuate OA-induced atherosclerosis associated with VSMC senescence and mitochondrial dysfunction via SIRT1-mediated deacetylation of the PGC-1α pathway.

DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages

Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.

Mitochondrial complex I subunit NDUFS8.2 modulates responses to stresses associated with reduced water availability

Mitochondria are important sources of energy in plants and are implicated in coordination of a number of metabolic and physiological processes including stabilization of redox balance, synthesis and turnover of a number of metabolites, and control of programmed cell death. Mitochondrial electron transport chain (mETC) is the backbone of the energy producing process which can influence other processes as well. Accumulating evidence suggests that mETC can affect responses to environmental stimuli and modulate tolerance to extreme conditions such as drought or salinity. Screening for stress responses of 13 Arabidopsis mitochondria-related T-DNA insertion mutants, we identified ndufs8.2-1 which has an increased ability to withstand osmotic and oxidative stresses compared to wild type plants. Insertion in ndufs8.2-1 disrupted the gene that encodes the NADH dehydrogenase [ubiquinone] fragment S subunit 8 (NDUFS8) a component of Complex I of mETC. ndufs8.2-1 tolerated reduced water availability, retained photosynthetic activity and recovered from severe water stress with higher efficiency compared to wild type plants. Several mitochondrial functions were altered in the mutant including oxygen consumption, ROS production, ATP and ADP content as well as activities of genes encoding alternative oxidase 1A (AOX1A) and various alternative NAD(P)H dehydrogenases (ND). Our results suggest that in the absence of NDUFS8.2 stress-induced ROS generation is restrained leading to reduced oxidative damage and improved tolerance to water deficiency. mETC components can be implicated in redox and energy homeostasis and modulate responses to stresses associated with reduced water availability.

Recent progress in understanding the cellular and genetic basis of plant responses to low oxygen holds promise for developing flood-resilient crops

With recent progress in active research on flooding and hypoxia/anoxia tolerance in native and agricultural crop plants, vast knowledge has been gained on both individual tolerance mechanisms and the general mechanisms of flooding tolerance in plants. Research on carbohydrate consumption, ethanolic and lactic acid fermentation, and their regulation under stress conditions has been accompanied by investigations on aerenchyma development and the emergence of the radial oxygen loss barrier in some plant species under flooded conditions. The discovery of the oxygen-sensing mechanism in plants and unravelling the intricacies of this mechanism have boosted this very international research effort. Recent studies have highlighted the importance of oxygen availability as a signalling component during plant development. The latest developments in determining actual oxygen concentrations using minute probes and molecular sensors in tissues and even within cells have provided new insights into the intracellular effects of flooding. The information amassed during recent years has been used in the breeding of new flood-tolerant crop cultivars. With the wealth of metabolic, anatomical, and genetic information, novel holistic approaches can be used to enhance crop species and their productivity under increasing stress conditions due to climate change and the subsequent changes in the environment.

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family.

Copper and zinc interact significantly in their joint toxicity to Chlamydomonas reinhardtii: Insights from physiological and transcriptomic investigations

Copper (Cu) and zinc (Zn) often discharge simultaneously from industrial and agricultural sectors and cause stress to aquatic biota. Although microalgae have been extensively investigated for their responses to Cu or Zn exposure, how they cope with the mixtures of two metals, especially at transcriptomic level, remains largely unknown. In this study, Chlamydomonas reinhardtii was exposed to environmentally relevant concentrations of two metals. It was found that Zn promoted the entry of Cu into the algal cells. With the increase of combined toxicity, extracellular polymeric substances (EPS) and cell wall functional groups immobilized significant amounts of Cu and Zn. Furthermore, C. reinhardtii adjusted resistance strategies internally, including starch consumption and synthesis of chlorophyll and lipids. Upon high level of Cu and Zn coexistence, synergistic effects were observed in lipid peroxidation and catalase (CAT) activity. Under 1.05 mg/L Cu + 0.87 mg/L Zn, 256 differentially expressed genes (DEGs) were mainly involved in oxidative phosphorylation, ribosome, nitrogen metabolism; while 4294 DEGs induced by 4.21 mg/L Cu + 3.48 mg/L Zn were mainly related to photosynthesis, citric acid cycle, etc. Together, this study revealed a more comprehensive understanding of mechanisms of Cu/Zn detoxification in C. reinhardtii, emphasizing critical roles of photosynthetic carbon sequestration and energy metabolism in the metal resistance.

Microplastic size-dependent biochemical and molecular effects in alga Heterosigma akashiwo

Micro- and nano-plastics (MNPs) are increasingly prevalent contaminants in marine ecosystems and have a variety of negative impacts on marine organisms. While their toxic impact on freshwater microalgae has been well-documented, limited research has been conducted on the influence of MNPs on marine red tide algae, despite their significant implications for human health and coastal ecological stability. This study investigated the physiological, biochemical and molecular reactions of the common harmful algal species, Heterosigma akashiwo, when exposed to polystyrene (PS) MNPs of 80 nm and 1 µm in size with the concentrations of 0, 1, 10, and 20 mg L-1 in 12 days. The results showed that 80 nm-sized MNPs (at concentrations of 10 mg L-1 and 20 mg L-1) inhibited algal growth. Despite the increased superoxide dismutase (SOD) activity and up-regulation of glutathione metabolism, exposure-induced oxidative stress remained the main cause of the inhibition. Up-regulation of aminoacyl-tRNA biosynthesis and amino acid biosynthesis pathways provide the necessary amino acid feedstock for the synthesis of antioxidant enzymes such as SOD. 1 µm sized PS MNPs increased chlorophyll a (Chl-a) content without significant effects on other parameters. In addition, H. akashiwo have an effective self-regulation ability to defend against two sized MNPs stress at concentrations of 1 mg L-1 by upregulating gene expression related to endocytosis, biotin metabolism, and oxidative phosphorylation. These results provided evidence that H. akashiwo was able to resist exposure to 1 µm MPs, whereas 80 nm NPs exerted a toxic effect on H. akashiwo. This study deepens our understanding of the interaction between MNPs and marine harmful algal at the transcriptional level, providing valuable insights for further evaluating the potential impact of PS MNPs on harmful algal blooms in marine ecosystems.

High expression of NADH Ubiquinone Oxidoreductase Subunit B11 induces catheter-associated venous thrombosis on continuous blood purification

Venous thromboembolism (VTE) is a common vascular disease of venous return disorders, including deep venous thrombosis and pulmonary embolism (PE), with high morbidity and high mortality. However, the relationship between oxidative phosphorylation and NDUFB11 and venous thromboembolism is still unclear. The venous thromboembolism datasets GSE48000 and GSE19151 were downloaded, and the differentially expressed Genes (DEGs) were screened. The protein-protein interaction (PPI) network was constructed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional enrichment analysis. The comparative toxicogenomics database (CTD) was used to identify the diseases most associated with the core genes. TargetScan was used to screen miRNA regulating central DEGs. Western blotting (WB) experiment and real-time quantitative PCR (RT-qPCR) experiment were performed. A total of 500 DEGs were identified. GO analysis showed that the DEGs were mainly enriched in ATP synthesis coupled electron transport, respiratory electron transport chain, cytoplasm, enzyme binding, nonalcoholic fatty liver disease, oxidative phosphorylation, and Alzheimer disease. Enrichment items were similar to GO and KEGG enrichment items of DEGs. The result of CTD showed that 12 genes (RPS24, FAU, RPLP0, RPS15A, RPS29, RPL9, RPL31, RPL27, NDUFB11, RPL34, COX7B, RPS27L) were associated with chemical and drug-induced liver injury, inflammation, kidney disease, and congenital pure red cell aplasia. WB and RT-qPCR results showed that the expression levels of 12 genes in venous thromboembolism were higher than normal whole blood tissue samples. NDUFB11 is highly expressed in catheter-related venous thromboembolism during continuous blood purification, which may lead to the formation of venous thrombosis through oxidative phosphorylation pathway.

Defense mechanisms of alfalfa against cyclic tetramethylene tetranitramine (HMX) stress

Much attention has been paid to the environmental toxicity and ecological risk caused by cyclic tetramethylene tetranitramine (HMX) pollution in military activity sites. In this study, the response mechanism of alfalfa plants to HMX was analyzed from the aspects of the photosynthetic system, micromorphology, antioxidant enzyme system, mineral metabolism, and secondary metabolism, in order to improve the efficiency of plant restoration. Exposure to 5 mg·L-1 HMX resulted in a significant increase in leaf N content and a significant increase and drift of the Fourier transform infrared protein peak area. Transmission electron microscopy images revealed damage to the root system subcellular morphology, but the plant leaves effectively resisted HMX pressure, and the photosynthetic parameters essentially maintained steady-state levels. The root proline content decreased significantly by 23.1-47.2 %, and the root reactive oxygen species content increased significantly by 1.66-1.80 fold. The roots regulate the transport/absorption of many elements that impart stress resistance, and Cu, Mn, and Na uptake is significantly associated with secondary metabolism. The metabolism of roots was upregulated in general by HMX exposure, with the main differences appearing in the content of lipids and lipid-like molecules, further confirming damage to the root biofilm structure. HMX causes an imbalance in the energy supply from oxidative phosphorylation in roots and generates important biomarkers in the form of pyrophosphate and dihydrogen phosphate. Interestingly, HMX had no significant effect on basic metabolic networks (i.e., glycolysis/gluconeogenesis and the tricarboxylic acid cycle), confirming that alfalfa has good stress resistance. Alfalfa plants apparently regulate multiple network systems to resist/overcome HMX toxicity. These findings provide a scientific basis for improving plant stress tolerance and understanding the HMX toxicity mechanism.

OXPHOS Organization and Activity in Mitochondria of Plants with Different Life Strategies

The study of the supramolecular organization of the mitochondrial oxidative phosphorylation system (OXPHOS) in various eukaryotes has led to the accumulation of a considerable amount of data on the composition, stoichiometry, and architecture of its constituent superstructures. However, the link between the features of system arrangement and the biological characteristics of the studied organisms has been poorly explored. Here, we report a comparative investigation into supramolecular and functional OXPHOS organization in the mitochondria of etiolated shoots of winter wheat (Triticum aestivum L.), maize (Zea mays L.), and pea (Pisum sativum L.). Investigations based on BN-PAGE, in-gel activity assays, and densitometric analysis revealed both similarities and specific OXPHOS features apparently related to the life strategies of each species. Frost-resistant winter wheat was distinguished by highly stable basic I1III2IVa/b respirasomes and V2 dimers, highly active complex I, and labile complex IV, which were probably essential for effective OXPHOS adaptation during hypothermia. Maize, a C4 plant, had the highly stable dimers IV2 and V2, less active complex I, and active alternative NAD(P)H dehydrogenases. The latter fact could contribute to successful chloroplast-mitochondrial cooperation, which is essential for highly efficient photosynthesis in this species. The pea OXPHOS contained detergent-resistant high-molecular respirasomes I1-2III2IVn, highly active complexes IV and V, and stable succinate dehydrogenase, suggesting an active energy metabolism in organelles of this plant. The results and conclusions are in good agreement with the literature data on the respiratory activity of mitochondria from these species and are summarized in a proposed scheme of organization of OXPHOS fragments.

ATP yield of plant respiration: potential, actual and unknown

BACKGROUND AND AIMS

The ATP yield of plant respiration (ATP/hexose unit respired) quantitatively links active heterotrophic processes with substrate consumption. Despite its importance, plant respiratory ATP yield is uncertain. The aim here was to integrate current knowledge of cellular mechanisms with inferences required to fill knowledge gaps to generate a contemporary estimate of respiratory ATP yield and identify important unknowns.

METHOD

A numerical balance sheet model combining respiratory carbon metabolism and electron transport pathways with uses of the resulting transmembrane electrochemical proton gradient was created and parameterized for healthy, non-photosynthesizing plant cells catabolizing sucrose or starch to produce cytosolic ATP.

KEY RESULTS

Mechanistically, the number of c subunits in the mitochondrial ATP synthase Fo sector c-ring, which is unquantified in plants, affects ATP yield. A value of 10 was (justifiably) used in the model, in which case respiration of sucrose potentially yields about 27.5 ATP/hexose (0.5 ATP/hexose more from starch). Actual ATP yield often will be smaller than its potential due to bypasses of energy-conserving reactions in the respiratory chain, even in unstressed plants. Notably, all else being optimal, if 25 % of respiratory O2 uptake is via the alternative oxidase - a typically observed fraction - ATP yield falls 15 % below its potential.

CONCLUSIONS

Plant respiratory ATP yield is smaller than often assumed (certainly less than older textbook values of 36-38 ATP/hexose) leading to underestimation of active-process substrate requirements. This hinders understanding of ecological/evolutionary trade-offs between competing active processes and assessments of crop growth gains possible through bioengineering of processes that consume ATP. Determining the plant mitochondrial ATP synthase c-ring size, the degree of any minimally required (useful) bypasses of energy-conserving reactions in the respiratory chain, and the magnitude of any 'leaks' in the inner mitochondrial membrane are key research needs.

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

Metabolite profiling and transcriptomic analyses demonstrate the effects of biocontrol agents on alkaloid accumulation in Fritillaria thunbergii

BACKGROUND

During Fritillaria thunbergii planting, pests and diseases usually invade the plant, resulting in reduced yield and quality. Previous studies have demonstrated that using biocontrol agents can effectively control grubs and affect the steroid alkaloids content in F. thunbergii. However, the molecular regulatory mechanisms underlying the differences in the accumulation of steroid alkaloids in response to biocontrol agents remain unclear.

RESULTS

Combined transcriptomic and metabolic analyses were performed by treating the bulbs of F. thunbergii treated with biocontrol agents during planting. Otherwise, 48 alkaloids including 32 steroid alkaloids, 6 indole alkaloids, 2 scopolamine-type alkaloids, 1 isoquinoline alkaloid, 1 furoquinoline alkaloid, and 6 other alkaloids were identified. The content of steroidal alkaloids particularly peimine, peiminine, and veratramine, increased significantly in the group treated with the biocontrol agents. Transcriptome sequencing identified 929 differential genes using biocontrol agents, including 589 upregulated and 340 downregulated genes. Putative biosynthesis networks of steroid alkaloids have been established and combined with differentially expressed structural unigenes, such as acetyl-CoA C-acetyl-transferase, acelyl-CoAC-acetyltransferase3-hydroxy-3-methylglutaryl-coenzyme A synthase, 1-deoxy-D-xylulose-5-phosphate reductor-isomerase, 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase. In addition, biological processes such as amino acid accumulation and oxidative phosphorylation were predicted to be related to the synthesis of steroid alkaloids. Cytochrome P450 enzymes also play crucial roles in the steroid alkaloid synthesis. The transcription factor families MYB and bHLH were significantly upregulated after using biocontrol agents.

CONCLUSIONS

Biocontrol agents increased the steroid alkaloids accumulation of steroid alkaloids by affecting key enzymes in the steroid alkaloid synthesis pathway, biological processes of oxidative phosphorylation and amino acid synthesis, cytochrome P450 enzymes, and transcription factors. This study revealed the mechanism underlying the difference in steroidal alkaloids in F. thunbergii after using biocontrol agents, laying the groundwork for future industrial production of steroid alkaloids and ecological planting of medicinal materials in the future.

Informing the Cannabis Conjecture: From Life's Beginnings to Mitochondria, Membranes and the Electrome-A Review

Before the late 1980s, ideas around how the lipophilic phytocannabinoids might be working involved membranes and bioenergetics as these disciplines were "in vogue". However, as interest in genetics and pharmacology grew, interest in mitochondria (and membranes) waned. The discovery of the cognate receptor for tetrahydrocannabinol (THC) led to the classification of the endocannabinoid system (ECS) and the conjecture that phytocannabinoids might be "working" through this system. However, the how and the "why" they might be beneficial, especially for compounds like CBD, remains unclear. Given the centrality of membranes and mitochondria in complex organisms, and their evolutionary heritage from the beginnings of life, revisiting phytocannabinoid action in this light could be enlightening. For example, life can be described as a self-organising and replicating far from equilibrium dissipating system, which is defined by the movement of charge across a membrane. Hence the building evidence, at least in animals, that THC and CBD modulate mitochondrial function could be highly informative. In this paper, we offer a unique perspective to the question, why and how do compounds like CBD potentially work as medicines in so many different conditions? The answer, we suggest, is that they can modulate membrane fluidity in a number of ways and thus dissipation and engender homeostasis, particularly under stress. To understand this, we need to embrace origins of life theories, the role of mitochondria in plants and explanations of disease and ageing from an adaptive thermodynamic perspective, as well as quantum mechanics.

Enhancement of carbon sequestration via MIL-100(Fe)@PUS in bacterial-algal symbiosis treating municipal wastewater

Bacterial-algal symbiosis (BAS) is a promising carbon neutrality technology to treat municipal wastewater. However, there are still non-trivial CO₂ emissions in BAS due to the slow diffusion and biosorption of CO₂. Aiming to reduce CO₂ emissions, the inoculation ratio of aerobic sludge to algae was further optimized at 4:1 on the base of favorable carbon conversion. MIL-100(Fe) served as CO₂ adsorbents was immobilized on polyurethane sponge (PUS) to increase the interaction with microbes. When MIL-100(Fe)@PUS was added to BAS in the treatment of municipal wastewater, zero CO₂ emission was achieved and the carbon sequestration efficiency was increased from 79.9% to 89.0%. Most genes related to metabolic function were derived from Proteobacteria and Chlorophyta. The mechanism of enhanced carbon sequestration in BAS could be attributed to both enrichment of algae (Chlorella and Micractinium) and increased abundance of functional genes related to PS I, PS II and Calvin cycle in photosynthesis.

The Viscum album Gene Space database

The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on 'Benchmarking Universal Single-Copy Orthologs' (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).

The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae)

Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.

Mitochondrial H2S donor AP39 induces stomatal closure by modulating guard cell mitochondrial activity

Hydrogen sulfide (H2S) is a gaseous signaling molecule involved in numerous physiological processes in plants, including gas exchange with the environment through the regulation of stomatal pore width. Guard cells (GCs) are pairs of specialized epidermal cells that delimit stomatal pores and have a higher mitochondrial density and metabolic activity than their neighboring cells. However, there is no clear evidence on the role of mitochondrial activity in stomatal closure induction. In this work, we showed that the mitochondrial-targeted H2S donor AP39 induces stomatal closure in a dose-dependent manner. Experiments using inhibitors of the mitochondrial electron transport chain (mETC) or insertional mutants in cytochrome c (CYTc) indicated that the activity of mitochondrial CYTc and/or complex IV are required for AP39-dependent stomatal closure. By using fluorescent probes and genetically encoded biosensors we reported that AP39 hyperpolarized the mitochondrial inner potential (Δψm) and increased cytosolic ATP, cytosolic hydrogen peroxide levels, and oxidation of the glutathione pool in GCs. These findings showed that mitochondrial-targeted H2S donors induce stomatal closure, modulate guard cell mETC activity, the cytosolic energetic and oxidative status, pointing to an interplay between mitochondrial H2S, mitochondrial activity, and stomatal closure.

An inosine triphosphate pyrophosphatase safeguards plant nucleic acids from aberrant purine nucleotides

In plants, inosine is enzymatically introduced in some tRNAs, but not in other RNAs or DNA. Nonetheless, our data show that RNA and DNA from Arabidopsis thaliana contain (deoxy)inosine, probably derived from nonenzymatic adenosine deamination in nucleic acids and usage of (deoxy)inosine triphosphate (dITP and ITP) during nucleic acid synthesis. We combined biochemical approaches, LC-MS, as well as RNA-Seq to characterize a plant INOSINE TRIPHOSPHATE PYROPHOSPHATASE (ITPA) from A. thaliana, which is conserved in many organisms, and investigated the sources of deaminated purine nucleotides in plants. Inosine triphosphate pyrophosphatase dephosphorylates deaminated nucleoside di- and triphosphates to the respective monophosphates. ITPA loss-of-function causes inosine di- and triphosphate accumulation in vivo and an elevated inosine and deoxyinosine content in RNA and DNA, respectively, as well as salicylic acid (SA) accumulation, early senescence, and upregulation of transcripts associated with immunity and senescence. Cadmium-induced oxidative stress and biochemical inhibition of the INOSINE MONOPHOSPHATE DEHYDROGENASE leads to more IDP and ITP in the wild-type (WT), and this effect is enhanced in itpa mutants, suggesting that ITP originates from ATP deamination and IMP phosphorylation. Inosine triphosphate pyrophosphatase is part of a molecular protection system in plants, preventing the accumulation of (d)ITP and its usage for nucleic acid synthesis.

Metabolomics reveals arbuscular mycorrhizal fungi-mediated tolerance of walnut to soil drought

BACKGROUND

Arbuscular mycorrhizal fungi (AMF) have a positive effect on drought tolerance of plants after establishing reciprocal resymbiosis with roots, while the underlying mechanism is not deciphered. Metabolomics can explain the mechanism of plant response to environmental stress by analyzing the changes of all small molecular weight metabolites. The purpose of this study was to use Ultra High Performance Liquid Chromatography Q Exactive Mass Spectrometer to analyze changes in root metabolites of walnut (Juglans regia) after inoculation with an arbuscular mycorrhizal fungus Diversispora spurca under well-watered (WW) and drought stress (DS).

RESULTS

Sixty days of soil drought significantly inhibited root mycorrhizal colonization rate, shoot and root biomass production, and leaf water potential in walnut, while AMF inoculation significantly increased biomass production and leaf water potential, accompanied by a higher increase magnitude under DS versus under WW. A total of 3278 metabolites were identified. Under WW, AMF inoculation up-regulated 172 metabolites and down-regulated 61 metabolites, along with no changes in 1104 metabolites. However, under DS, AMF inoculation up-regulated 49 metabolites and down-regulated 116 metabolites, coupled with no changes in 1172 metabolites. Among them, juglone (a quinone found in walnuts) as the first ranked differential metabolite was up-regulated by AMF under WW but not under DS; 2,3,5-trihydroxy-5-7-dimethoxyflavanone as the first ranked differential metabolite was increased by AMF under DS but not under WW. The KEGG annotation showed a large number of metabolic pathways triggered by AMF, accompanied by different metabolic pathways under WW and DS. Among them, oxidative phosphorylation and phenylalanine metabolism and biosynthesis were triggered by AMF in response to WW and DS, where N-acetyl-L-phenylalanine was induced by AMF to increase under DS, while decreasing under WW.

CONCLUSION

This study provides new insights into the metabolic mechanisms of mycorrhiza-enhanced drought tolerance in walnuts.

Nectary development in Cleome violacea

Nectaries are a promising frontier for plant evo-devo research, and are particularly fascinating given their diversity in form, position, and secretion methods across angiosperms. Emerging model systems permit investigations of the molecular basis for nectary development and nectar secretion across a range of taxa, which addresses fundamental questions about underlying parallelisms and convergence. Herein, we explore nectary development and nectar secretion in the emerging model taxa, Cleome violacea (Cleomaceae), which exhibits a prominent adaxial nectary. First, we characterized nectary anatomy and quantified nectar secretion to establish a foundation for quantitative and functional gene experiments. Next, we leveraged RNA-seq to establish gene expression profiles of nectaries across three key stages of development: pre-anthesis, anthesis, and post-fertilization. We then performed functional studies on five genes that were putatively involved in nectary and nectar formation: CvCRABSCLAW (CvCRC), CvAGAMOUS (CvAG), CvSHATTERPROOF (CvSHP), CvSWEET9, and a highly expressed but uncharacterized transcript. These experiments revealed a high degree of functional convergence to homologues from other core Eudicots, especially Arabidopsis. CvCRC, redundantly with CvAG and CvSHP, are required for nectary initiation. Concordantly, CvSWEET9 is essential for nectar formation and secretion, which indicates that the process is eccrine based in C. violacea. While demonstration of conservation is informative to our understanding of nectary evolution, questions remain. For example, it is unknown which genes are downstream of the developmental initiators CvCRC, CvAG, and CvSHP, or what role the TCP gene family plays in nectary initiation in this family. Further to this, we have initiated a characterization of associations between nectaries, yeast, and bacteria, but more research is required beyond establishing their presence. Cleome violacea is an excellent model for continued research into nectary development because of its conspicuous nectaries, short generation time, and close taxonomic distance to Arabidopsis.

Cryo-EM structure of the respiratory I + III2 supercomplex from Arabidopsis thaliana at 2 Å resolution

Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III₂ with a co-purified ubiquinone in the Q_O site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.

From dynamin related proteins structures and oligomers to membrane fusion mediated by mitofusins

Mitochondria assemble in a highly dynamic network where interconnected tubules evolve in length and size through regulated cycles of fission and fusion of mitochondrial membranes thereby adapting to cellular needs. Mitochondrial fusion and fission processes are mediated by specific sets of mechano-chemical large GTPases that belong to the Dynamin-Related Proteins (DRPs) super family. DRPs bind to cognate membranes and auto-oligomerize to drive lipid bilayers remodeling in a nucleotide dependent manner. Although structural characterization and mechanisms of DRPs that mediate membrane fission are well established, the capacity of DRPs to mediate membrane fusion is only emerging. In this review, we discuss the distinct structures and mechanisms of DRPs that trigger the anchoring and fusion of biological membranes with a specific focus on mitofusins that are dedicated to the fusion of mitochondrial outer membranes. In particular, we will highlight oligomeric assemblies of distinct DRPs and confront their mode of action against existing models of mitofusins assemblies with emphasis on recent biochemical, structural and computational reports. As we will see, the literature brings valuable insights into the presumed macro-assemblies mitofusins may form during anchoring and fusion of mitochondrial outer membranes.

Transcriptomic and metabolic analyses reveal the potential mechanism of increasing steroidal alkaloids in Fritillaria hupehensis through intercropping with Magnolia officinalis

Fritillaria hupehensis, a well-known medicinal perennial herb, is used as an antitussive and an expectorant. Continuous cropping and monoculture cultivation usually negativly affect the growth of F. hupehensis. Compared with the monoculture system, the F. hupehensis-Magnolia officinalis intercropping system significantly increases the yield of F. hupehensis. However, changes in steroidal alkaloid metabolites (the most important bioactive components) and their molecular regulatory mechanisms in F. hupehensis intercropping system remain unclear. We performed comparative transcriptomic and metabolomic analyses of F. hupehensis bulbs grown in monocropping and intercropping systems. A total of 40 alkaloids were identified, including 26 steroidal alkaloids, 4 plumeranes, 3 phenolamines, 1 pyridine alkaloid, and 6 other alkaloids. The results showed that intercropping significantly increased the levels of peimine, peiminine, hupehenine, korseveridine, verticinone N-oxide, delafrine, tortifoline, pingbeinone, puqienine B, puqienine E, jervine, ussuriedine, hydroxymandelonitrile, N-feruloylputrescine, and N-benzylmethylene isomethylamine in F. hupehensis, but decreased the levels of indole, p-coumaroylputrescine, and N-benzylformamide. Transcriptome sequencing identified 11,466 differentially expressed unigenes in F. hupehensis under the intercropping system, of which 5,656 genes were up-regulated and 5,810 genes were down-regulated. We proposed a possible steroidal alkaloid biosynthesis pathway, in which 12 differentially expressed genes were identified. The higher expressions of these genes in the intercropping system positively correlated with the high accumulation of peimine, peiminine, and hupehenine, further validating our proposal. Moreover, the biological processes of oxidative phosphorylation and plant hormone signal transduction, cytochrome P450 enzymes, ATP-binding cassette transporters, and transcription factors may play pivotal roles in the regulation of steroidal alkaloid biosynthesis. This study revealed the underlying molecular mechanisms of intercropping in improving steroidal alkaloids in F. hupehensis at the transcriptome and metabolome levels. These findings provided a theoretical foundation for sustainable development of this ecological planting method.

Insights into growth-promoting effect of nanomaterials: Using transcriptomics and metabolomics to reveal the molecular mechanisms of MWCNTs in enhancing hyperaccumulator under heavy metal(loid)s stress

Carbon nanotubes present potential applications in soil remediation, particularly in phytoremediation. Yet, how multi-walled carbon nanotubes (MWCNTs) induced hyperaccumulator growth at molecular level remains unclear. Here, physio-biochemical, transcriptomic, and metabolomic analyses were performed to determine the effect of MWCNTs on Solanum nigrum L. (S. nigrum) growth under cadmium and arsenic stresses. 500 mg/kg MWCNTs application significantly promoted S. nigrum growth, especially for root tissues. Specially, MWCNTs application yields 1.38-fold, 1.56-fold, and 1.37-fold enhancement in the shoot length, root length, and fresh biomass, respectively. Furthermore, MWCNTs significantly strengthened P and Fe absorption in roots, as well as the activities of antioxidative enzymes. Importantly, the transcriptomic analysis indicated that S. nigrum gene expression was sensitive to MWCNTs, and MWCNTs upregulated advantageous biological processes under heavy metal(loid)s stress. Besides, MWCNTs reprogramed metabolism that related to defense system, leading to accumulation of 4-hydroxyphenylpyruvic acid (amino acid), 4-hydroxycinnamic acid (xenobiotic), and (S)-abscisic acid (lipid). In addition, key common pathways of differentially expressed metabolites and genes, including "tyrosine metabolism" and "isoquinoline alkaloid biosynthesis" were selected via integrating transcriptome and metabolome analyses. Combined omics technologies, our findings provide molecular mechanisms of MWCNTs in promoting S. nigrum growth, and highlight potential application of MWCNTs in soil remediation.

Synthesis, Antibacterial Activity, and Action Mechanism of Novel Sulfonamides Containing Oxyacetal and Pyrimidine

Bacterial leaf blight (BLB) and bacterial leaf streak (BLS) are two serious bacterial diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively. However, the control of these diseases by conventional pesticides remains challenging due to development of resistances. We aimed to address this pending problem and developed a series of novel pyrimidine sulfonamide derivatives. Structurally, title compounds bear a unique oxyacetal group, which has a proven immune-activating effect. Compound E35 designed based on the 3D-QSAR model was demonstrated as the optimal in vitro activity against Xoo and Xoc, with EC₅₀ values of 26.7 and 30.8 mg/L, respectively, which were higher than the positive controls bismerthiazol (29.9 and 32.7 mg/L) and thiodiazole copper (30.5 and 36.4 mg/L). On the prevention level, the biological activity test showed compound E35 had superior protective activity (43.7%) on BLS to thiodiazole copper (32.1%). The defense enzymes and proteomics results suggested that compound E35 could be a versatile candidate as it improved plant's resistance to disease.

Structural insights into the assembly and the function of the plant oxidative phosphorylation system

One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. We also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.

Transcriptome Analysis of the Accumulation of Astaxanthin in Haematococcus pluvialis Treated with White and Blue Lights as well as Salicylic Acid

Haematococcus pluvialis is the most commercially valuable microalga for the production of natural astaxanthin, showing enhanced production of astaxanthin with the treatments of high-intensity light and hormones. The molecular mechanisms regulating the biosynthesis of astaxanthin in H. pluvialis treated with white light, blue light, and blue light with salicylic acid (SA) were investigated based on the transcriptome analysis. Results showed that the combined treatment with both blue light and SA generated the highest production of astaxanthin. A total of 109,443 unigenes were identified to show that the genes involved in the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway (PPP), and the astaxanthin biosynthesis were significantly upregulated to increase the production of the substrates for the synthesis of astaxanthin, i.e., pyruvate and glyceraldehyde-3-phosphate generated in the TCA cycle and PPP, respectively. Results of transcriptome analysis were further verified by the quantitative real-time PCR (qRT-PCR) analysis, showing that the highest content of astaxanthin was obtained with the expression of the bkt gene significantly increased. Our study provided the novel insights into the molecular mechanisms regulating the synthesis of astaxanthin and an innovative strategy combining the exogenous hormone and physical stress to increase the commercial production of astaxanthin by H. pluvialis.

The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): Structure and evolutionary aspects

Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.

Native and foreign mitochondrial and nuclear encoded proteins conform the OXPHOS complexes of a holoparasitic plant

The intimate contact between the holoparasitic plant Lophophytum mirabile (Balanophoraceae) and its host plant (Fabaceae) facilitates the exchange of genetic information, increasing the frequency of horizontal gene transfer (HGT). Lophophytum stands out because it acquired a large number of mitochondrial genes (greater than 20) from its legume host that replaced the majority of the native homologs. These foreign genes code for proteins that form multisubunit enzyme complexes, such as those in the oxidative phosphorylation system (OXPHOS) and cytochrome c maturation (ccm) system, together with dozens of nuclear-encoded subunits. However, the existence and the origin of the nuclear subunits that form the major part of the OXPHOS and ccm system in Lophophytum remain unknown. It was proposed that nuclear-encoding genes whose products interact with foreign mitochondrial proteins are also foreign, minimizing the incompatibilities that could arise in the assembly and functioning of these multiprotein complexes. We identified a nearly complete set of OXPHOS and ccm system subunits evolving under selective constraints in the transcriptome of Lophophytum, indicating that OXPHOS is functional and resembles that of free-living angiosperms. Maximum Likelihood phylogenetic analyses revealed a single case of HGT in the nuclear genes, which results in mosaic OXPHOS and ccm system in Lophophytum. These observations raise new questions about the evolution and physiology of this parasitic plant. A putative case of cooperation between two foreign (one mitochondrial and one nuclear) genes is presented.

Defense Mechanism of Capsicum annuum L. Infected with Pepper Mild Mottle Virus Induced by Vanisulfane

Pepper mild mottle virus (PMMoV), an RNA virus, is one of the most devastating pathogens in pepper crops and has a significant influence on global crop yields. PMMoV poses a major threat to the global shortage of pepper plants and other Solanaceae crops due to the lack of an effective antiviral agent. In this study, we have developed a plant immune inducer (vanisulfane), as a "plant vaccine" that boosts plant immunity against PMMoV, and studied its resistance mechanism. The protective activity of vanisulfane against PMMoV was 59.4%. Vanisulfane can enhance the activity of defense enzymes and improve the content of chlorophyll, flavonoids, and total phenols for removing harmful free radicals from plants. Furthermore, vanisulfane was found to enhance defense genes. Label-free quantitative proteomics would tackle disease resistance pathways of vanisulfane. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, differentially abundant proteins (DAPs) are mainly involved in starch and sucrose metabolism, photosynthesis, MAPK signaling pathway, and oxidative phosphorylation pathway. These results are crucial for the discovery of new pesticides, understanding the improvement of plant immunity and the antiviral activity of plant immune inducers.

Reductive stress triggers ANAC017-mediated retrograde signaling to safeguard the endoplasmic reticulum by boosting mitochondrial respiratory capacity

Redox processes are at the heart of universal life processes, such as metabolism, signaling, or folding of secreted proteins. Redox landscapes differ between cell compartments and are strictly controlled to tolerate changing conditions and to avoid cell dysfunction. While a sophisticated antioxidant network counteracts oxidative stress, our understanding of reductive stress responses remains fragmentary. Here, we observed root growth impairment in Arabidopsis thaliana mutants of mitochondrial alternative oxidase 1a (aox1a) in response to the model thiol reductant dithiothreitol (DTT). Mutants of mitochondrial uncoupling protein 1 (ucp1) displayed a similar phenotype indicating that impaired respiratory flexibility led to hypersensitivity. Endoplasmic reticulum (ER) stress was enhanced in the mitochondrial mutants and limiting ER oxidoreductin capacity in the aox1a background led to synergistic root growth impairment by DTT, indicating that mitochondrial respiration alleviates reductive ER stress. The observations that DTT triggered nicotinamide adenine dinucleotide (NAD) reduction in vivo and that the presence of thiols led to electron transport chain activity in isolated mitochondria offer a biochemical framework of mitochondrion-mediated alleviation of thiol-mediated reductive stress. Ablation of transcription factor Arabidopsis NAC domain-containing protein17 (ANAC017) impaired the induction of AOX1a expression by DTT and led to DTT hypersensitivity, revealing that reductive stress tolerance is achieved by adjusting mitochondrial respiratory capacity via retrograde signaling. Our data reveal an unexpected role for mitochondrial respiratory flexibility and retrograde signaling in reductive stress tolerance involving inter-organelle redox crosstalk.

High Doses of Pesticides Induce mtDNA Damage in Intact Mitochondria of Potato In Vitro and Do Not Impact on mtDNA Integrity of Mitochondria of Shoots and Tubers under In Vivo Exposure

It is well known that pesticides are toxic for mitochondria of animals. The effect of pesticides on plant mitochondria has not been widely studied. The goal of this research is to study the impact of metribuzin and imidacloprid on the amount of damage in the mtDNA of potato (Solanum tuberosum L.) in various conditions. We developed a set of primers to estimate mtDNA damage for the fragments in three chromosomes of potato mitogenome. We showed that both metribuzin and imidacloprid considerably damage mtDNA in vitro. Imidacloprid reduces the rate of seed germination, but does not impact the rate of the growth and number of mtDNA damage in the potato shoots. Field experiments show that pesticide exposure does not induce change in aconitate hydratase activity, and can cause a decrease in the rate of H2O2 production. We can assume that the mechanism of pesticide-induced mtDNA damage in vitro is not associated with H2O2 production, and pesticides as electrophilic substances directly interact with mtDNA. The effect of pesticides on the integrity of mtDNA in green parts of plants and in crop tubers is insignificant. In general, plant mtDNA is resistant to pesticide exposure in vivo, probably due to the presence of non-coupled respiratory systems in plant mitochondria.

Electrophysiological, Morphologic, and Transcriptomic Profiling of the Ogura-CMS, DGMS and Maintainer Broccoli Lines

To better serve breeding of broccoli, the electrophysiological, morphological and transcriptomic profiling of the isogenic Ogura-CMS, DGMS and their maintainer fertile lines, were carried out by scanning electron microscopy, investigation of agronomic traits and RNA-sequencing analysis. The agronomic traits of plant height, length of the largest leaf, plant spread angle, single head weight, head width and stem diameter showed stronger performance in Ogura-CMS broccoli than in DGMS line or maintainer fertile line. However, the Ogura-CMS broccoli was poorer in the seed yield and seed germination than in the DGMS line and maintainer fertile line. Additionally, the DGMS broccoli had longer maturation and flowering periods than the Ogura-CMS and maintainer fertile lines. There were obvious differences in the honey gland, happening in the male sterility and fertile lines of broccoli. Additionally, the mechanism regulating Ogura-CMS and DGMS in broccoli was investigated using florets transcriptome analyses of the Ogura-CMS, DGMS and maintainer fertile lines. As a result, a total of 2670 differentially expressed genes (DEGs) were detected, including 1054 up- and 1616 downregulated genes in the Ogura-CMS and DGMS lines compared to the maintainer fertile line. A number of functionally known genes involved in plant hormones (auxin, salicylic acid and brassinosteroid), five Mitochondrial Oxidative Phosphorylation (OXPHOS) genes of atp8, LOC106319879, LOC106324734, LOC106314622 and LOC106298585, and three upregulated genes (Lhcb1, Lhcb3 and Lhcb5) associated with the photosynthesis-antenna protein pathway, were obviously detected to be highly associated with reproductive development including flowering time, maturity and reproductive period in the Ogura-CMS and DGMS broccoli comparing to their maintainer fertile line. Our research would provide a comprehensive foundation for understanding the differences of electrophysiological, morphological and transcriptomic profiles in the Ogura-CMS, DGMS and maintainer broccoli, and as well as being beneficial to exploring the mechanism of male sterility in Brassica crops.

A glossary of plant cell structures: Current insights and future questions

In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

Long-distance control of pumpkin rootstock over cucumber scion under drought stress as revealed by transcriptome sequencing and mobile mRNAs identifications

Grafting with pumpkin rootstock is commonly used not only to improve the quality of cucumber fruits but also to confer biotic or abiotic stress tolerance. However, the molecular mechanism of grafted cucumbers to drought stress and the possible roles of mobile mRNAs to improve stress tolerance have remained obscure. Hence, we conducted transcriptome sequencing and combined it with morpho-physiological experiments to compare the response of homografts (cucumber as scion and rootstock) (C) and heterografts (cucumber as scion and pumpkin as rootstock) (P) to drought stress. After applying drought stress, homografts and heterografts expressed 2960 and 3088 genes in response to drought stress, respectively. The identified DEGs in heterografts under drought stress were categorized into different stress-responsive groups, such as carbohydrate metabolism (involved in osmotic adjustment by sugar accumulation), lipid and cell wall metabolism (involved in cell membrane integrity by a reduction in lipid peroxidation), redox homeostasis (increased antioxidant enzymes activities), phytohormone (increased ABA content), protein kinases and transcription factors (TFs) using MapMan software. Earlier and greater H2O2 accumulation in xylem below the graft union was accompanied by leaf ABA accumulation in heterografts in response to drought stress. Greater leaf ABA helped heterografted cucumbers to sense and respond to drought stress earlier than homografts. The timely response of heterografts to drought stress led to maintain higher water content in the leaves even in the late stage of drought stress. The identified mobile mRNAs (mb-mRNAs) in heterografts were mostly related to photosynthesis which would be the possible reason for improved chlorophyll content and maximum photochemical efficiency of PSII (Fv/Fm). The existence of some stress-responsive pumpkin (rootstock) mRNAs in cucumber (scion), such as heat shock protein (HSP70, a well-known stress-responsive gene), led to the higher proline accumulation than homografts. The expression of the mobile and immobile stress-responsive mRNAs and timely response of heterografts to drought stress could improve drought tolerance in pumpkin-rooted plants.

Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Background

Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance.

Results

The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF.

Conclusions

The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08286-7.