Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings

An integration of physiology, transcriptomics, and proteomics reveals carbon and nitrogen metabolism responses in alfalfa (Medicago sativa L.) exposed to titanium dioxide nanoparticles

Nanoparticle (NP) pollution has negative impacts and is a major global environmental problem. However, the molecular response of alfalfa (Medicago sativa L.) to titanium dioxide nanoparticles (TiO2 NPs) is limited. Herein, the dual effects of TiO2 NPs (0-1000 mg L-1) on carbon (C) and nitrogen (N) metabolisms in alfalfa were investigated. The results showed that 500 mg L-1 TiO2 NPs (Ti-500) had the highest phytotoxicity in the C/N metabolizing enzymes; and it significantly increased total soluble sugar, starch, sucrose, and sucrose-phosphate synthase. Furthermore, obvious photosynthesis responses were found in alfalfa exposed to Ti-500. By contrast, 100 mg L-1 TiO2 NPs (Ti-100) enhanced N metabolizing enzymes. RNA-seq analyses showed 4265 and 2121 differentially expressed genes (DEGs) in Ti-100 and Ti-500, respectively. A total of 904 and 844 differentially expressed proteins (DEPs) were identified in Ti-100 and Ti-500, respectively. Through the physiological, transcriptional, and proteomic analyses, the DEGs and DEPs related to C/N metabolism, photosynthesis, chlorophyll synthesis, starch and sucrose metabolism, and C fixation in photosynthetic organisms were observed. Overall, TiO2 NPs at low doses improve photosynthesis and C/N regulation, but high doses can cause toxicity. It is valuable for the safe application of NPs in agriculture.

Integrated physiological and transcriptomic analyzes reveal the duality of TiO2 nanoparticles on alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is a feed crop due to its rich nutrition and high productivity. The utilization of titanium oxide nanoparticles (TiO2 NPs) brings benefits to agricultural production but also has potential hazards. To investigate the duality and related mechanism of TiO2 NPs on alfalfa, its different doses including 0, 50, 100, 200, 500, and 1000 mg L- 1 (CK, Ti-50, Ti-100, Ti-200, Ti-500, and Ti-1000) were sprayed on leaves. The results showed that greater doses of TiO2 NPs (500 and 1000 mg L-1) negatively affected the physiological parameters, including morphology, biomass, leaf ultrastructure, stomata, photosynthesis, pigments, and antioxidant ability. However, 100 mg L-1 TiO2 NPs revealed an optimal positive effect; compared with the CK, it dramatically increased plant height, fresh weight, and dry weight by 22%, 21%, and 41%, respectively. Additionally, TiO2 NPs at low doses significantly protected leaf tissue, promoted stomatal opening, and enhanced the antioxidant system; while higher doses had phytotoxicity. Hence, TiO2 NPs are dose-dependent on alfalfa. The transcriptomic analysis identified 4625 and 2121 differentially expressed genes (DEGs) in the comparison of CK vs. Ti-100 and CK vs. Ti-500, respectively. They were mainly enriched in photosynthesis, chlorophyll metabolism, and energy metabolism. Notably, TiO2 NPs-induced phytotoxicity on photosynthetic parameters happened concurrently with the alterations of the genes involved in the porphyrin and chlorophyll metabolism and carbon fixation in photosynthetic organisms in the KEGG analysis. Similarly, it affected the efficiency of alfalfa energy transformation processes, including pyruvate metabolism and chlorophyll synthesis. Several key related genes in these pathways were validated. Therefore, TiO2 NPs have positive and toxic effects by regulating morphology, leaf ultrastructure, stomata, photosynthesis, redox homeostasis, and genes related to key pathways. It is significant to understand the duality of TiO2 NPs and cultivate varieties resistant to nanomaterial pollution.

Chimeric deletion mutation of rpoC2 underlies the leaf-patterning of Clivia miniata var. variegata

KEY MESSAGE

The deletion mutated rpoC2 leads to yellow stripes of Clivia miniata var. variegata by down regulating the transcription of 28 chloroplast genes and disturbing chloroplast biogenesis and thylakoid membrane development. Clivia miniata var. variegata (Cmvv) is a common mutant of Clivia miniata but its genetic basis is unclear. Here, we found that a 425 bp deletion mutation of chloroplast rpoC2 underlies the yellow stripes (YSs) of Cmvv. Both RNA polymerase PEP and NEP coexist in seed-plant chloroplasts and the β″ subunit of PEP is encoded by rpoC2. The rpoC2 mutation changed the discontinuous cleft domain required to form the PEP central cleft for DNA binding from 1103 to 59 aa. RNA-Seq revealed that 28 chloroplast genes (cpDEGs) were all down-regulated in YSs, of which, four involved in chloroplast protein translation and 21 of photosynthesis system (PS)I, PSII, cytochrome b6/f complex and ATP synthase are crucial for chloroplast biogenesis/development. The accuracy and reliability of RNA-Seq was verified by qRT-PCR. Moreover, the chlorophyll (Chl) a/b content, ratio of Chla/Chlb and photosynthetic rate (Pn) of YS decreased significantly. Meanwhile, chloroplasts of the YS mesophyll cells were smaller, irregular in shape, contain almost no thylakoid membrane, and even proplastid was found in YS. These findings indicate that the rpoC2 mutation down-regulated expression of the 28 cpDEGs, which disturb chloroplast biogenesis and its thylakoid membrane development. Thus, there are not enough PSI and II components to bind Chl, so that the corresponding areas of the leaf are yellow and show a low Pn. In this study, the molecular mechanism of three phenotypes of F1 (Cmvv ♀ × C. miniata ♂) was revealed, which lays a foundation for the breeding of variegated plants.

Transcriptome reveals the exposure effects of CeO2 nanoparticles on pakchoi (Brassica chinensis L.) photosynthesis

In this study, soil-grown pakchoi after 2 weeks seedling cultivation were exposed to CeO₂ nanoparticles (CeO₂ NPs) at 0.7, 7, 70, and 350 mg kg^-1 for 30 days. Results showed that chlorophyll content and photosynthetic assimilation rate were decreased significantly under all treatments with the largest decrease of 34.16% (0.7 mg kg^-1 CeO₂ NPs), however, sub-stomatal CO₂ was increased dramatically under low dose of CeO₂ NPs (0.7 mg kg^-1). There were 4576, 3548, 2787, and 2514 genes up/down regulated significantly by 0.7, 7, 70, and 350 mg kg^-1 CeO₂ NPs, respectively, and 767 genes affected under all treatments. In addition, 0.7 mg kg^-1 CeO₂ NPs up-regulated 10 chlorophyll synthesis genes, 20 photosynthesis genes, and 10 carbon fixation enzyme genes; while 350 mg kg^-1 CeO₂ NPs down-regulated 5 photosynthesis genes and 28 auxin-activated genes. Among the key genes of photosynthesis, Ferredoxin-NADP reductase (PetH) was upregulated in 0.7, 7 and 70 mg kg^-1 treatments, while Photosystem II lipoprotein (Psb27) was downregulated under 7, 70 and 350 mg kg^-1 treatments. Top 20 metabolic pathways affected by CeO₂ NPs including plant hormone, amino acids, and glutathione, and carbon metabolism These results provide information about utilizing CeO₂ NPs more safely and effectively in the future.

Transcriptomic analysis reveals biosynthesis genes and transcription factors related to leaf anthocyanin biosynthesis in Aglaonema commutatum

BACKGROUND

Aglaonema commutatum 'Red Valentine', as a foliage ornamental plant, is widely used for interior and exterior decoration because of its easy cultivation and management. However, reduced proportion of red foliage during large-scale production of A. commutatum seedlings is a frequent occurrence, which has considerable implications on the plant's ornamental and market value. However, the molecular mechanisms underlying this phenomenon remain unclear.

RESULTS

To explore the molecular basis of the variation in leaf color of A. commutatum Red Valentine, we performed transcriptome sequencing with the Illumina platform using two different varieties of A. commutatum, namely Red Valentine and a green mutant, at three different stages of leaf development. We annotated 63,621 unigenes and 14,186 differentially expressed genes by pairwise comparison. Furthermore, we identified 26 anthocyanin biosynthesis structural genes. The transcript per million (TPM) values were significantly higher for Red Valentine than for the green mutant in all three developmental stages, consistent with the high anthocyanin content of Red Valentine leaves. We detected positive transcription factors that may be involved in the regulation of anthocyanin biosynthesis using BLAST and through correlation analysis. Downregulation of these transcription factors may downregulate the expression of anthocyanin genes. We obtained full-length cDNA of the anthocyanin biosynthesis and regulatory genes and constructed phylogenetic trees to ensure accuracy of the analysis.

CONCLUSIONS

Our study provides insights into the molecular mechanisms underlying leaf variation in A. commutatum Red Valentine and may be used to facilitate the breeding of ornamental cultivars with high anthocyanin levels.

Black carbon and humic acid alleviate the toxicity of antibiotics to a cyanobacterium Synechocystis sp

Natural organic matters (NOMs), omnipresent in natural water, challenge the toxicity assessment of pollutants to aquatic organisms due to their complex interactions with chemicals and organisms. Here, we investigated the combined toxicity of one solid NOM (black carbon, BC) or one soluble NOM (humic acid, HA) with antibiotics, roxithromycin (RTM) or gatifloxacin (GAT), to the cyanobacterium Synechocystis sp.. The NOMs alleviated the toxicity of RTM and GAT to Synechocystis sp., and BC had greater alleviation effects than HA due to its stronger adsorption to antibiotics. Antibiotics disturbed the photosynthesis of Synechocystis sp. significantly, which were also mitigated by BC and HA. Proteomic analysis showed that BC up-regulated the pathway of ribosome and photosynthetic antenna protein. GAT down-regulated the pathways of ABC transporter and oxidative phosphorylation. RTM interfered the pathway of porphyrin and chlorophyll metabolism. Furthermore, the addition of BC reduced the number of differentially expressed proteins caused by antibiotics, corroborating its mitigation effects on the toxicity of antibiotics. The disturbance of HA on the pathway of ABC transporters inhibited the internalization of RTM, thus decreasing its toxicity. This study underscores the significance of NOMs in mediating the toxicity of organic pollutants to aquatic organisms in natural waters.

Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.)

Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

Label-free quantitative proteomics analysis of jujube (Ziziphus jujuba Mill.) during different growth stages

Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.

Effects of exogenous methyl jasmonate on the synthesis of endogenous jasmonates and the regulation of photosynthesis in citrus

Methyl jasmonate (MeJA) is an airborne signaling phytohormone that can induce changes in endogenous jasmonates (JAs) and cause photosynthetic responses. However, the response of these two aspects of citrus plants at different MeJA concentrations is still unclear. Four MeJA concentrations were used in two citrus varieties, Huangguogan (C. reticulata × C. sinensis) and Shiranuhi [C. reticulata × (C. reticulata × C. sinensis)], to investigate the effects of MeJA dose on the endogenous JAs pathway and photosynthetic capacity. We observed that MeJA acted in a dose-dependent manner, and its stimulation in citrus leaves showed a bidirectional character at different concentrations. This work demonstrates that MeJA at only a concentration of 2.2 mM or less contributed to the activation of magnesium protoporphyrin IX methyltransferase (ChlM, EC 2.1.1.11) and protochlorophyllide oxidoreductase (POR, EC 1.3.1.11) and the simultaneous accumulation of Chl a and Chl b, which in turn contributed to an improved photosynthetic capacity and PSII photochemistry efficiency of citrus. Meanwhile, the inhibition of endogenous JAs synthesis by exogenous MeJA was observed. This was achieved by reducing the ratio of monogalactosyl diacylglycerol (MGDG) to diagalactosyl diacylglycerol (DGDG) and inhibiting the activities of key enzymes in JAs synthesis, especially 12-oxo-phytodienoic acid reductase (OPR, EC 1.3.1.42). Another noteworthy finding is that there may exist a JA-independent pathway that could regulate 12-oxo-phytodienoic acid (OPDA) synthesis. This study jointly analyzed the internal hormone regulation mechanism and the external physiological response, as well as revealed the effects of exogenous MeJA on promoting the photosynthesis and inhibiting the endogenous JAs synthesis.