Including Carbon Metabolism Research Articles

Physiological and gene expression response mechanisms of dehydration process in Cinnamomum cassia (L.) J. Presl seeds.

A critical factor in the storability of recalcitrant seeds is their moisture content (MC), but its effect on the viability of Cinnamomum cassia (L.) J. Presl (C. cassia) seeds is not fully understood. Measured the germination rate, starch and soluble sugar content, and transcriptome of 8 seed samples with different MC obtained by low-temperature drying method. It was found that the germination rate was significantly negatively correlated with MC. The lethal MC was around 15.6%. During the dehydration process, there was a significant increase in the content of soluble sugars and starch. Transcriptome analysis was performed on CK, W3, W6 showed a total of 62.78 Gb of clean data. Among the 30,228 Unigenes, 28,195 were successfully annotated. In the three comparative groups (CK and W3, CK and W6, W3 and W6), 6,842, 7,640, and 11,628 differentially expressed genes (DEGs) were obtained, respectively. These DEGs were found to be involved in a variety of metabolic pathways, including carbon metabolism, amino acid biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and nucleotide and amino sugar metabolism. A total of 1,416 common genes were identified among all three comparison groups. Furthermore, among all the DEGs, a total of 71 transcription factor families were identified, with the C2H2 transcription factor family having the highest number of genes. This ground-breaking study sheds light on the physiological response and gene expression profiles of C. cassia seeds after undergoing dehydration treatment, which will provide valuable insights for further research and understanding of this process.

Genomic characterization and proteomic analysis of Bacillus amyloliquefaciens in response to lignin

This study examined the lignin degradation characteristics of Bacillus amyloliquefaciens MN-13. Specifically, whole-genome sequencing and comparative proteomic analysis were performed to investigate the responses of the MN-13 strain to lignin. A maximum lignin removal of 38.0 % was achieved after 36 h of inoculation in mineral salt medium with 0.2 g/L alkaline lignin, under the following conditions: the carbon to nitrogen ratio C/N = 1/1; inoculum size 6 %; addition of glucose as an exogenous carbon source. When the MN-13 strain was inoculated into mineral salt medium with and without lignin, respectively, 831 differentially expressed proteins were identified, 404 of which were up-regulated and 427 were down-regulated. Enrichment analysis revealed that up-regulated proteins were associated with microbial metabolism in diverse environment, biosynthesis of amino acids, and pathways related to energy production, including carbon metabolism, pyruvate metabolism, the TCA cycle etc. Genomic analysis revealed that the MN-13 strain possesses many ligninolytic enzymes and aromatics degradation pathway, including benzoate degradation and aminobenzoate degradation etc. Taken together, the proteomic and genomic analyses indicated that the meta-cleavage pathway of catechol, including benzoate degradation, etc., is the main lignin degradation pathway. These findings provide new insight into lignin degradation mediated by B. amyloliquefaciens.

Main metabolic pathways of Solanum nigrum L. hyperaccumulating cadmium except of copper simultaneously through differentially expressed proteins analysis

Determining the hyperaccumulation mechanism of Solanum nigrum L., which exclusively accumulates cadmium (Cd), presents significant challenges due to the difficulty in identifying its unique characteristics. While some metabolic pathways related to Cd accumulation can be explored, there are no methods to ascertain if other heavy metals may share the same pathways. Isobaric tags for relative and absolute quantitation (iTRAQ) were employed to investigate the metabolic pathways associated with Cd hyperaccumulation and Cu accumulation (non-Cu hyperaccumulator) by comparing differentially expressed proteins (DEPs). The results showed that 27 intersecting DEPs reflecting relative metabolic pathways related to Cd accumulation were identified by comparing DEPs in leaves and roots, including carbon metabolism, aminoacyl-tRNA biosynthesis, phagosome, peroxisome, as well as starch and sucrose metabolism. These pathways might be responsible for the values of Cd enrichment factor (EF) and translocation factor (TF) exceeding 1, associated with key proteins participated in phosphoenolpyruvate, carboxylase, chloroplastic catalytic activity, and granule-bound starch synthase I. The combined metabolic pathways identified by 2 intersecting DEPs related to Cu accumulation could result in Cu EF >1 in the 0.2 Cu mg kg−1 treatment, EF <1 in the 5 mg kg−1 treatment, and TF<1 in both treatments, associated with key proteins, which might concern photosynthesis-antenna proteins and hydroxymethylbilane synthase. No metabolic pathways related to simultaneous accumulation of Cd and Cu has been identified. The identified DEPs were validated using Western blotting with five key proteins. Additionally, Western blotting and yeast mutant confirmed the presence of proteins related to carbon fixation in photosynthetic organisms, carbon metabolism, peroxisome, as well as starch and sucrose metabolism. Photosynthetic, O2•−, H2O2 and non-enzymatic antioxidants indices reflecting protein-related differences indirectly supported the above results. These findings are crucial for further exploration of the Cd hyperaccumulation mechanism.

Proteomic characterization of peripheral leukocytes in variant carriers of CDKAL1 associated with cholesterol efflux capacity

Abstract Background Genetic variations near CDKAL1 (CDK5 regulatory subunit-associated protein 1-like 1) gene recently showed association with individual’s cholesterol efflux capacity. The aim of this study was to compare the proteomes of peripheral leukocytes in CDKAL1 variant carriers and controls to identify evidence of biological impact caused by these variants. Methods Peripheral blood leukocytes were isolated from five individuals with any of four CDKAL1 variants (rs117835232, rs117252933, rs118064592, and rs150434350) and five controls. Cell lysates were digested to peptides and Q Exactive Orbitrap Plus mass spectrometry was applied for comparative proteomics analysis. Protein identification and quantification were performed with MaxQuant software. Results In total, 2,387 proteins were identified at false discovery rate 1% level, of which 176 proteins were differently abundant between CDKAL1 variant and control groups (p &amp;lt;0.05, fold-difference &amp;gt;1.5). Among them, 39 upregulated and 137 downregulated proteins were identified in the variant group (p &amp;lt;0.05; fold change&amp;gt;1.5) (Figure 1). The upregulated included docosahexaenoic acid omega hydroxylase, resistin, and apoA1, whereas the downregulated included NADH ubiquinone oxidoreductase. The functional enrichment and KEGG pathway analysis showed 20 associated pathways including carbon metabolism, synthesis of antibiotics, and RNA transport. Conclusions Differential expression of proteins regulating lipid metabolism and RNA transport in CDKAL1 variant carriers indicates differences in corresponding biological function in these individuals. Detailed contribution of the reported proteins remains to be clarified.

MiR-3200 accelerates the growth of liver cancer cells by enhancing Rab7A

Researches indicate miR-3200 is closely related to tumorigenesis, However, the role of miR-3200 in human hepatocarcinogenesis is still unclear. In this study, we clearly demonstrate that miR-3200 accelerates the growth of liver cancer cells in vivo and in vitro. Obviously, these findings are noteworthy that miR-3200 affects the transcriptional regulation for several genes, including DSP，BABAM2, Rab7A,SQSTM1,PRKAG2,CDK1,ABCE1,BECN1,PTEN,UPRT. And miR-3200 affects the transcriptional ability of several genes, such as, upregulating CADPS, DSP,FBXO32, PPCA,SGK1, PATXN7L1, PLK2,ITGB5,FZD3,HOXC8,HSPA1A,C-Myc,CyclnD1,CyclinE,PCNA and down –regulating SUV39H1, MYO1G, OLFML3, CBX5, PPDE2A, HOXA7, RAD54L, CDC45,SHMT7,MAD2L1,P27,IQGAP3,PTEN,P57,SCAMP3,etc...On the other hand, it is obvious that miR-3200 affects the translational ability of several genes, such as, upregulating GNS,UPRT,EIFAD,YOS1,SGK1,K-Ras,PKM2,C-myc,Pim1,CyclinD1,mTOR,erbB-2,CyclinE,PCNA,RRAS,ARAF,RAPH1,etc.. and down-regulating KDM2A, AATF, TMM17B, RAB8B, MYO1G,P21WAF1/Cip1,GADD45,PTEN,P27,P18,P57,SERBP1,RPL34,UFD1,Bax,ANXA6,GSK3β. Strikingly, miR-3200 affects some signaling pathway in liver cancer, including carbon metabolism signaling pathway, DNA replication pathway, FoxO signaling pathway, Hippo signaling pathway, serine and threonine metabolism signaling pathway, mTOR signaling pathway, Fatty acid biosynthesis signaling pathway, carcinogenesis-receptor activation signaling pathway, autophagy signaling pathway. Furthermore, our results suggest that miR-3200 enhances expression of RAB7A, and then Rab7A regulates the carcinogenic function of miR-3200 by increasing telomere remodeling in human liver cancer. These results are of great significance for the prevention and treatment of human liver cancer.

Metabolic pathways engineering for drought or/and heat tolerance in cereals.

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments.

The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.

The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress.

Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO2 fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.

Global proteomic analysis reveals lysine succinylation contributes to the pathogenesis of aortic aneurysm and dissection

Protein lysine succinylation is a recently discovered posttranslational modification. This study examined the role of protein lysine succinylation in the pathogenesis of aortic aneurysm and dissection (AAD). 4D label-free LC-MS/MS analysis was used to perform the global profiles of succinylation in aortas obtained from 5 heart transplant donors, 5 patients with thoracic aortic aneurysm (TAA), and 5 patients with thoracic aortic dissection (TAD). In comparison to normal controls, we detected 1138 succinylated sites from 314 proteins in TAA, and 1499 sites from 381 proteins in TAD. Among these, 120 differentially succinylated sites from 76 proteins overlapped between TAA and TAD (|log2FC| > 0.585, p < 0.05). These differentially modified proteins were mainly localized in the mitochondria and cytoplasm, and were primarily involved in diverse energy metabolic processes, including carbon metabolism, amino acid catabolism, and β-oxidation of fatty acids. By establishing an in vitro model of lysine succinylation in vascular smooth muscle cells, we observed changes in the activities of three key metabolic enzymes (PKM, LDHA, and SDHA). These findings suggest that succinylation potentially contributes to the pathogenesis of aortic diseases, and presents a valuable resource for investigating the functional roles and regulatory mechanisms of succinylation in AAD. SignificanceAAD are interrelated life-threatening diseases associated with high morbidity and mortality. Although we discovered that lysine succinylation was significantly up-regulated in the aorta tissues of patients with AAD, its role in the progression of aortic diseases is largely unknown. We conducted a 4D label-free LC-MS/MS analysis and identified 120 differentially succinylated sites on 76 proteins that overlapped between TAA and TAD as compared to normal controls. Lysine succinylation may contribute to the pathogenesis of AAD by regulating energy metabolism pathways. The proteins containing succinylated sites could be served as potential diagnostic markers and therapeutic targets for aortic diseases.

Microplastics trigger the Matthew effect on nitrogen assimilation in marine diatoms at an environmentally relevant concentration

Microplastics (MPs, diameter <5 mm) are widely distributed on Earth, especially in the oceans. Diatoms account for ∼40% of marine primary productivity and affect the global biogeochemical cycles of macroelements. However, the effects of MPs on marine nitrogen cycling remain poorly understood, particularly comparisons between nitrogen-replete and nitrogen-limited conditions. We found that MPs trigger the Matthew effect on nitrogen assimilation in diatoms, where MPs inhibited nitrogen assimilation under nitrogen-limited conditions while enhancing nitrogen metabolism under nitrogen-replete conditions in Phaeodactylum tricornutum. Nitrate reductase (NR) and nitrite reductase (NIR) are upregulated, but nitrate transporter (NRT) and glutamine synthetase (GS) are downregulated by MPs under nitrogen-limited conditions. In contrast, NR, NIR, and GS are all upregulated by MPs under nitrogen-replete conditions. MPs accelerate nitrogen anabolic processes with an increase in the accumulation of carbohydrates by 80.7 ± 7.9% and enhance the activities of key nitrogen-metabolizing enzymes (8.20–44.90%) under nitrogen-replete conditions. In contrast, the abundance of carbohydrates decreases by 22.0–34.4%, and NRT activity is inhibited by 79.0–86.5% in nitrogen-limited algae exposed to MPs. Metabolomic and transcriptomic analyses were performed to further explore the molecular mechanisms of reprogrammed nitrogen assimilation, including carbon metabolism, nitrogen transport and ammonia assimilation. The aforementioned spatial redistribution (e.g., the Matthew effect between nitrogen-replete and -limited conditions) of nitrogen assimilation highlights the potential risks of MP contamination in the ocean.

Evolution of m6A-related genes in insects and the function of METTL3 in silkworm embryonic development.

N6-methyladenosine (m6A) plays a key role in many biological processes. However, the function and evolutionary relationship of m6A-related genes in insects remain largely unknown. Here we analysed the phylogeny of m6A-related genes among 207 insect species and found that m6A-related genes are evolutionarily conserved in insects. Subcellular localization experiments of m6A-related proteins in BmN cells confirmed that BmYTHDF3 was localized in the cytoplasm, BmMETTL3, BmMETTL14, and BmYTHDC were localized in the nucleus, and FL2D was localized to both the nucleus and cytoplasm. We examined the expression patterns of m6A-related genes during the embryonic development of Bombyx mori. To elucidate the function of BmMETTL3 during the embryonic stage, RNA sequencing was performed to measure changes in gene expression in silkworm eggs after BmMETTL3 knockdown, as well as in BmN cells overexpressing BmMETTL3. The global transcriptional pattern showed that knockdown of BmMETTL3 affected multiple cellular processes, including oxidoreductase activity, transcription regulator activity, and the cation binding. In addition, transcriptomic data revealed that many observed DEGs were associated with fundamental metabolic processes, including carbon metabolism, purine metabolism, amino acid biosynthesis, and the citrate cycle. Interestingly, we found that knockdown of BmMETTL3 significantly affected Wnt and Toll/Imd pathways in embryos. Taken together, these results suggest that BmMETTL3 plays an essential role in the embryonic development of B. mori, and deepen our understanding of the function of m6A-related genes in insects.

Metabolic and molecular mechanisms underlying the foliar Zn application induced increase of 2-acetyl-1-pyrroline conferring the 'taro-like' aroma in pumpkin leaves.

Fresh pumpkin leaf is popular vegetable for its rich nutrition. The pleasant taro-like odour is important aroma quality of crops, and mostly contributed by 2-acetyl-1-pyrroline in pumpkin. Element Zn can impact metabolite biosynthesis in plants, including aroma formation. However, Zn-induced biochemical responses, especially 2-acetyl-1-pyrroline formation in pumpkin, haven't been elucidated. This study integrated metabolome and transcriptome to explore molecular fluctuations in pumpkin leaves at different time intervals after foliar Zntreatment. We first identified more than one thousand metabolites from pumpkin leaves by integrating different mass spectrometry methods according to the form in which a metabolite exists. Comparative metabolomic analysis revealed there were separately 25 out of 50 and 286 out of 963 metabolites that were respectively identified by gas chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry, differentially regulated by Zn treatment. Our findings revealed that 50mg/L of Zn significantly enhanced 2-acetyl-1-pyrroline production by more than 38%, which was contributed by increased biosynthesis of its precursors, including ornithine and proline. The following transcriptome analysis discovered 30,574 genes, including 953 novel genes. Zn treatment induced the differential expression of 41.6% of identified genes which were supposed to regulate the downstream metabolite changes in a time-dependent manner. Pathway analysis indicated that alternations in primary metabolism, including carbon metabolism and biosynthesis of amino acids, were vital to the fluctuated aromatic compound generation. Phytohormones and transcription factors may regulate the expression of gene P5CS and proline biosynthesis, which, therefore, affect 2-acetyl-1-pyrroline production. This research reveals molecular mechanisms of 2-acetyl-1-pyrroline formation in pumpkin, which will provide the molecular basis for desired aroma compound production through metabolite engineering.

Microbial cell factories

<p indent="0mm">Microbial cell factories are among the key subjects in synthetic biology research. Microbial cell factories produce bulk chemicals and natural products through renewable biomass resources. These green and clean biological manufacturing routes can supplement nonrenewable petrochemical resources and rare plant resources; thus, these routes can partially replace petrochemical manufacturing and plant extraction routes, which consume high amounts of energy and generate high pollution levels. The green routes provide an important method for society to address resource, energy and environmental problems. To successfully commercialize microbial cell factories, the regulatory mechanisms that microorganisms use to efficiently produce chemicals were investigated from two perspectives, including carbon metabolism and energy metabolism. Regarding carbon metabolism, a synthetic biology platform for enzyme mining was established, and the synthetic pathways of several triterpenoids were characterized using this platform. Furthermore, some cell factories that produce triterpenoids, such as hawthorn acid, corosolic acid and trichoparic acid, were created by <italic>Saccharomyces cerevisiae</italic>. In addition, precision pathway regulation technologies, including simultaneous modulation of multiple genes in chromosomes and glycosylase base editor (GBE), were developed and could improve the rate of xylose utilization by 3-fold compared with that of the control. The rate-limiting steps of the synthetic pathways for a series of chemicals were identified, and the rate-limiting enzymes were activated to increase the rate of chemical production by 2.5- to 600-fold; thus, the adaptation problems between enzyme parts and synthetic pathways were solved. When considering energy metabolism, four new modules of generating energy through glucose metabolism were designed according to the requirements of synthetic products; thus, the imbalance problems between the supply and the necessity of reducing equivalents in the synthetic pathway were solved. Based on the knowledge of the regulatory mechanisms for synthetic metabolism, efficient microbial cell factories were constructed by our research team to produce a series of chemicals. Technologies to microbially produce 14 chemicals have been licensed. Among these chemicals, four have been successfully commercialized, and the annual production of each chemical can reach over <sc>10000 t.</sc> In addition, one company realized IPO. All these factors have promoted the industrial application of microbial cell factories. The future directions of research on microbial cell factories are discussed at the end of this paper. Most of the synthetic pathways of these cell factories are based on existing biosynthetic pathways in nature. However, for the vast majority of chemicals, the biosynthetic pathways are often unknown or do not occur in nature. How to microbially synthesize these chemicals is among the difficulties encountered when constructing a microbial cell factory. The principle of designing new pathways and new enzymes, the regulation of energy metabolism based on nonnatural coenzymes and the mechanism of chemical stress on cells can be studied in substance metabolism, energy metabolism, and physiological metabolism, respectively.

Identification of Key Genes during Ethylene-Induced Adventitious Root Development in Cucumber (Cucumis sativus L.).

Ethylene (ETH), as a key plant hormone, plays critical roles in various processes of plant growth and development. ETH has been reported to induce adventitious rooting. Moreover, our previous studies have shown that exogenous ETH may induce plant adventitious root development in cucumber (Cucumis sativus L.). However, the key genes involved in this process are still unclear. To explore the key genes in ETH-induced adventitious root development, we employed a transcriptome technique and revealed 1415 differentially expressed genes (DEGs), with 687 DEGs up-regulated and 728 DEGs down-regulated. Using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we further identified critical pathways that were involved in ETH-induced adventitious root development, including carbon metabolism (starch and sucrose metabolism, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis, and fatty acid degradation), secondary metabolism (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction. In carbon metabolism, ETH reduced the content of sucrose, glucose, starch, the activity of sucrose synthase (SS), sucrose-phosphate synthase (SPS) and hexokinase (HK), and the expressions of CsHK2, pyruvate kinase2 (CsPK2), and CsCYP86A1, whereas it enhanced the expressions of β-amylase 1 (CsBAM1) and β-amylase 3 (CsBAM3). In secondary metabolism, the transcript levels of phenylalanine ammonia-lyase (CsPAL) and flavonoid 3'-monooxygenase (CsF3'M) were negatively regulated, and that of primary-amine oxidase (CsPAO) was positively regulated by ETH. Additionally, the indole-3-acetic acid (IAA) content and the expressions of auxin and ETH signaling transduction-related genes (auxin transporter-like protein 5 (CsLAX5), CsGH3.17, CsSUAR50, and CsERS) were suppressed, whereas the abscisic acid (ABA) content and the expressions of ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, BRI1-associated kinase 1 (CsBAK1), and CsXTH3) were promoted by ETH. Furthermore, the mRNA levels of these genes were confirmed by real-time PCR (RT-qPCR). These results indicate that genes related to carbon metabolism, secondary metabolite biosynthesis, and plant hormone signaling transduction are involved in ETH-induced adventitious root development. This work identified the key pathways and genes in ETH-induced adventitious rooting in cucumber, which may provide new insights into ETH-induced adventitious root development and will be useful for investigating the molecular roles of key genes in this process in further studies.

Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq.

Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were obtained. Two bulks of progenies were then constructed, one consisted of 27 highly smut resistant progenies and the other 24 smut susceptible progenies. Total RNAs of the progenies of each bulk, were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). These DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions. Besides, 45,946 high-quality, credible SNPs, a 1.27 Mb region at Saccharum spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Among them, twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. RT-qPCR analysis demonstrated that they played a positive role in smut resistance. Finally, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane.

Deciphering microbial syntrophic mechanisms for simultaneous removal of nitrate and Cr(VI) by Mn@Corn cob immobilized bioreactor: Performance, enhancement mechanisms and community assembly

When bioremediation is applied to Cr(VI) and NO3−-N contaminated groundwater, the lack of carbon sources and weak physiological activity dramatically affect the treatment efficacy. Hence, a bioreactor consisting of cellulose degradation-manganese (Mn) cycling bilayer carrier and two core strains was established. After 270 operating days, the experimental group (EG) achieved 96.34 and 95.37% of NO3−-N and Cr(VI) removal efficiency, respectively. When the C/N ratio was reduced to 1.0, cellulose-degrading strain CDZ9 produced significantly hydrolyzed cellulose from the corn cob substrate. Meanwhile, the balance between microbial metabolic activity and carbon supply was manipulated by the dissimilatory Mn-reducing strain MFG10. Dissolved organic matter response in EG provided evidence for enhanced carbon utilization and electron transfer processes. The syntrophic relationship between EG core strains significantly enhanced bioreactor metabolism and bioactivity. It drove the coupling of different elemental cycles with contaminant removal including carbon metabolism, nitrogen metabolism, Mn cycle and Cr(VI) reduction.

Improvement of the growth performance, intestinal health, and water quality in juvenile crucian carp (Carassius auratus gibelio) biofortified system with the bacteria-microalgae association

Aquaculture, as one of the largest food production sectors, is a candidate industry to solve the worldwide food shortage. Nitrogenous compounds from uneaten feed and excretion continually destroy the rearing water quality during the breeding which causes slow growth, production reduction, and even death. Thus, alleviating water contamination can improve fish welfare and prevent disease occurrence. In the present study, a stable bacteria-microalgae association was used to construct a biofortified crucian carps culture system without water exchange. During the 8-week experiments, the water quality, fish production, and intestinal health were assessed. In this biofortified system, water quality was significantly improved and the content of total ammonia-N and nitrite-N was finally in a state of dynamic equilibrium at a lower concentration compared with that in blank control. The final body weight of crucian carps in the bacteria-microalgae groups was significantly improved by 10.52%. The crucian carps intestinal health including amylase and lipase activities, villus length and width, and muscle thickness was also significantly increased by 56.33%, 63.89%, 347.25%, 98.48%, and 129.53%, respectively, in bacteria-microalgae groups. Intestinal microbiota was improved significantly by changing the microbiota composition and LEfSe analysis demonstrated that some genera frequently found in the intestines of stressed and dying animals were enriched in crucian carps intestine in blank control. The KEGG prediction proved that metabolisms including carbon metabolism, pyruvate metabolism, and fatty acid metabolism were significantly improved. In summary, the bacteria-microalgae association biofortified culture system improved the rearing water quality, and then improved the intestinal health of crucian carp, eventually increased the production of crucian carp.

Gene expression variation explains maize seed germination heterosis

BackgroundHeterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis.ResultsIn this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc.ConclusionOur results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.

Xanthomonas oryzae Pv. oryzicola Response Regulator VemR Is Co-opted by the Sensor Kinase CheA for Phosphorylation of Multiple Pathogenicity-Related Targets

Two-component systems (TCSs) (cognate sensor histidine kinase/response regulator pair, HK/RR) play a crucial role in bacterial adaptation, survival, and productive colonization. An atypical orphan single-domain RR VemR was characterized by the non-vascular pathogen Xanthomonas oryzae pv. oryzicola (Xoc) is known to cause bacterial leaf streak (BLS) disease in rice. Xoc growth and pathogenicity in rice, motility, biosynthesis of extracellular polysaccharide (EPS), and the ability to trigger HR in non-host tobacco were severely compromised in the deletion mutant strain RΔvemR as compared to the wild-type strain RS105. Site-directed mutagenesis and phosphotransfer experiments revealed that the conserved aspartate (D56) residue within the stand-alone phosphoacceptor receiver (REC) domain is essential for phosphorelay and the regulatory activity of Xoc VemR. Yeast two-hybrid (Y2H) and co-immunoprecipitation (co-IP) data identified CheA as the HK co-opting the RR VemR for phosphorylation. Affinity proteomics identified several downstream VemR-interacting proteins, such as 2-oxoglutarate dehydrogenase (OGDH), DNA-binding RR SirA, flagellar basal body P-ring formation protein FlgA, Type 4a pilus retraction ATPase PilT, stress-inducible sensor HK BaeS, septum site-determining protein MinD, cytoskeletal protein CcmA, and Type III and VI secretion system proteins HrpG and Hcp, respectively. Y2H and deletion mutant analyses corroborated that VemR interacted with OGDH, SirA, FlgA, and HrpG; thus, implicating multi-layered control of diverse cellular processes including carbon metabolism, motility, and pathogenicity in the rice. Physical interaction between VemR and HrpG suggested cross-talk interaction between CheA/VemR- and HpaS/HrpG-mediated signal transduction events orchestrating the hrp gene expression.

The Interaction Between CitMYB52 and CitbHLH2 Negatively Regulates Citrate Accumulation by Activating CitALMT in Citrus Fruit.

Citric acid plays significant roles in numerous physiological processes in plants, including carbon metabolism, signal transduction, and tolerance to environmental stress. For fruits, it has a major effect on fruit organoleptic quality by directly influencing consumer taste. Citric acid in citrus is mainly regulated by the balance between synthesis, degradation, and vacuolar storage. The genetic and molecular regulations of citric acid synthesis and degradation have been comprehensively elucidated. However, the transporters for citric acid in fruits are less well understood. Here, an aluminum-activated malate transporter, CitALMT, was characterized. Transient overexpression and stable transformation of CitALMT significantly reduced citrate concentration in citrus fruits and transgenic callus. Correspondingly, transient RNA interference-induced silencing of CitALMT and increased citrate significantly, indicating that CitALMT plays an important role in regulating citrate concentration in citrus fruits. In addition, dual-luciferase assays indicated that CitMYB52 and CitbHLH2 could trans-activate the promoter of CitALMT. EMSA analysis showed that CitbHLH2 could physically interact with the E-box motif in the CitALMT promoter. Bimolecular fluorescence complementation assays, yeast two-hybrid, coimmunoprecipitation and transient overexpression, and RNAi assay indicated that the interaction between CitMYB52 and CitbHLH2 could synergistically trans-activate CitALMT to negatively regulate citrate accumulation.