Carbon Metabolic Pathways Research Articles

Heterotrophic origin and diverse sources of branched glycerol monoalkyl glycerol tetraethers (brGMGTs) in peats and lignites

The branched glycerol monoalkyl glycerol tetraether lipids of bacteria (brGMGTs, sometimes referred to as H-brGDGTs) are found in marine, lacustrine, and terrestrial mesophilic environments. The abundance of brGMGTs relative to their dialkyl analogues (brGDGTs) has been proposed as a proxy for past continental air and lake water temperature. However, the source(s) of brGMGTs remain unknown. brGDGT production has been described in multiple cultivated Acidobacteria, but so far no brGMGT producer has been identified. We hypothesize that the stable carbon isotopic composition (δ13C) of brGMGTs, as a tracer of carbon source and metabolic pathway, could be used to elucidate the source(s) of brGMGTs relative to brGDGTs. However, the large monoalkyl moiety of these compounds impedes carbon isotopic analysis using conventional techniques based on gas chromatography. Here, we used spooling-wire microcombustion to analyse the stable carbon isotopic composition of brGMGTs and brGDGTs found in peats and lignites. We show that the δ13C of brGMGTs is within ∼2‰ similar to that of brGDGTs from the same samples, as well as the δ13C of the total organic carbon. This suggests that the source organisms use heterotrophic metabolism. However, offsets in the δ13C of brGDGTs and brGMGTs in some samples suggest that not all brGDGT producers also produce brGMGTs. Further, in modern peats we observe downcore increases in brGMGT relative abundance and decreases in the carbon isotopic offsets with brGDGTs, which indicates that brGMGT producers occur throughout the oxic-anoxic continuum and may metabolize different organic carbon pools. Based on this indirect evidence for diverse brGMGT sources, we suggest that in addition to homeostatic responses to temperature, brGMGT relative abundances may be influenced by changes in bacterial community composition in response to additional environmental and biogeochemical parameters.

Inhibition of invasive plant Mikania micrantha rapid growth by host-specific rust (Puccinia spegazzinii).

Mikania micrantha Kunth is a fast-growing global invasive weed species that causes severe damage to natural ecosystems and very large economic losses of forest and crop production. Although Puccinia spegazzinii can effectively inhibit the growth of M. micrantha and is used as a biological control strain in many countries, the mechanism of inhibiting the growth in Mikania micrantha is not clear. Here, we used a combination of phenotypic, enzyme activity, transcriptomic and metabolomic approaches to study the response of M. micrantha after infection by P. spegazzinii. In the early stages of rust infection, JA, JA-Ile and SA levels in infected leaves were significantly lower than that in uninfected leaves. In teliospore initial and developed stages of P. spegazzinii, JA and JA-Ile levels substantially increased by more than 6 times, which resulted in a significant decrease in accumulation of defense hormone SA in infected leaves of M. micrantha. The contents of plant growth-promoting hormones were significantly reduced in the infected plants as a result of substantial downregulation of expression of key genes related to hormone biosynthesis. Furthermore, rust infection led to high levels of ROS in chloroplasts and the destruction of chlorophyll structure, which also led to decreased photosynthetic gene expression, net photosynthetic rate, activity of Rubisco and levels of important organic acids in the Calvin cycle. We hypothesised that after P. spegazzinii infection, JA or JA-Ile accumulation not only inhibited SA levels to promote rust infection and development, but also impeded the rapid growth of M. micrantha by affecting plant growth hormones, carbon, and nitrogen metabolic pathways.

Transcriptional Self-Regulation of the Master Nitrogen Regulator GlnR in Mycobacteria.

As a master nitrogen regulator in most actinomycetes, GlnR both governs central nitrogen metabolism and regulates many carbon, phosphate, and secondary metabolic pathways. To date, most studies have been focused on the GlnR regulon, while little is known about the transcriptional regulator for glnR itself. It has been observed that glnR transcription can be upregulated in Mycobacterium smegmatis under nitrogen-limited growth conditions; however, the detailed regulatory mechanism is still unclear. Here, we demonstrate that the glnR gene in M. smegmatis is transcriptionally activated by its product GlnR in response to nitrogen limitation. The precise GlnR binding site was successfully characterized in its promoter region using the electrophoretic mobility shift assay and the DNase I footprinting assay. Site mutagenesis and genetic analyses confirmed that the binding site was essential for in vivo self-activation of glnR transcription. Moreover, based on bioinformatic analyses, we discovered that most of the mycobacterial glnR promoter regions (144 out of 147) contain potential GlnR binding sites, and we subsequently proved that the purified M. smegmatis GlnR protein could specifically bind 16 promoter regions that represent 119 mycobacterial species, including Mycobacterium tuberculosis. Together, our findings not only elucidate the transcriptional self-regulation mechanism of glnR transcription in M. smegmatis but also indicate the ubiquity of the mechanism in other mycobacterial species. IMPORTANCE In actinomycetes, the nitrogen metabolism not only is essential for the construction of life macromolecules but also affects the biosynthesis of secondary metabolites and even virulence (e.g., Mycobacterium tuberculosis). The transcriptional regulation of genes involved in nitrogen metabolism has been thoroughly studied and involves the master nitrogen regulator GlnR. However, the transcriptional regulation of glnR itself remains elusive. Here, we demonstrated that GlnR functions as a transcriptional self-activator in response to nitrogen starvation in the fast-growing model Mycobacterium species Mycobacterium smegmatis. We further showed that this self-regulation mechanism could be widespread in other mycobacteria, which might be beneficial for those slow-growing mycobacteria to adapt to the nitrogen-starvation environments such as within human macrophages for M. tuberculosis.

A natural variation in the promoter of GRA117 affects carbon assimilation in rice.

GRA117 is crucial in the process of carbon assimilation in rice as it regulates the development of chloroplasts, which in turn facilitates the Calvin-Benson cycle. Carbon assimilation is a critical process for plant growth, and despite numerous relevant studies, there are still unknown constraints. In this study, we isolated a rice mutant, gra117, which exhibited seedling albinism, delayed chloroplast development, decreased chlorophyll content, reduced yield, and seedling stress susceptibility, as compared to WT. Our further investigations revealed that gra117 had a significantly lower net photosynthetic carbon assimilation rate, as well as reduced levels of Rubisco enzyme activity, RUBP, PGA, carbohydrate, protein content, and dry matter accumulation. These findings provide evidence for decreased carbon assimilation in gra117. By mapping cloning, we discovered a 665bp insertion in the GRA117 promoter region that decreases GRA117 transcriptional activity and causes the gra117 phenotype. GRA117 encodes PfkB-type fructokinase-like 2, which is subcellularly localized in chloroplasts and is widely expressed in various rice tissues, particularly at high levels in leaf tissues. GRA117 transcription is regulated by the core region 1029bp before the start codon. Our quantitative RT-PCR and Western blot assays showed that GRA117 promotes the expression and translation of photosynthetic genes. RNA-Seq analysis revealed that GRA117 plays a significant role in photosynthetic carbon fixation, carbon metabolism, and chloroplast ribosome-related pathways. Our study supports that GRA117 promotes the Calvin-Benson cycle by regulating chloroplast development, ultimately leading to enhanced carbon assimilation in rice.

Niche-mediated bacterial community composition in continental glacier alluvial valleys under cold and arid environments.

Bacteria are an essential component of glacier-fed ecosystems and play a dominant role in driving elemental cycling in the hydrosphere and pedosphere. However, studies of bacterial community composition mechanisms and their potential ecological functions from the alluvial valley of mountain glaciers are extremely scarce under cold and arid environments. Here, we analyzed the effects of major physicochemical parameters related to soil on the bacterial community compositions in an alluvial valley of the Laohugou Glacier No. 12 from the perspective of core, other, and unique taxa and explored their functional composition characteristics. The different characteristics of core, other, and unique taxa highlighted the conservation and difference in bacterial community composition. The bacterial community structure of the glacial alluvial valley was mainly affected by the above sea level, soil organic carbon, and water holding capacity. In addition, the most common and active carbon metabolic pathways and their spatial distribution patterns along the glacial alluvial valley were revealed by FAPTOTAX. Collectively, this study provides new insights into the comprehensive assessment of glacier-fed ecosystems in glacial meltwater ceasing or glacier disappearance.

The Murine Oral Metatranscriptome Reveals Microbial and Host Signatures of Periodontal Disease

Periodontal disease is accompanied by alterations to cellular profiles and biological activities of both the subgingival microbiome and host tissues. Although significant progress has been made in describing the molecular basis of the homeostatic balance of host–commensal microbe interactions in health compared to the destructive imbalance in disease, particularly with respect to immune and inflammatory systems, few studies have attempted a comprehensive analysis in diverse host models. Here, we describe the development and application of a metatranscriptomic approach to analysis of host–microbe gene transcription in a murine periodontal disease model, based on oral gavage infection using Porphyromonas gingivalis in C57BL6/J mice. We generated 24 metatranscriptomic libraries from individual mouse oral swabs, representing health and disease. On average, 76% ± 11.7% reads in each sample belonged to the murine host genome and the remainder to the microbes. We found 3,468 (2.4% of the total) murine host transcripts differentially expressed between health and disease, of which 76% were overexpressed in periodontitis. Predictably, there were prominent alterations to genes and pathways linked with the host immune compartment in disease—the CD40 signaling pathway being the top enriched biological process in this data set. However, in addition, we observed significant alterations to other biological processes in disease, particularly cellular/metabolic processes and biological regulation. The number of differentially expressed microbial genes particularly indicated shifts in carbon metabolism pathways in disease with potential consequences for metabolic end-product formation. Together, these metatranscriptome data reveal marked changes between the gene expression patterns in both the murine host and microbiota, which may represent signatures of health and disease, providing the basis for future functional studies of prokaryotic and eukaryotic cellular responses in periodontal disease. In addition, the noninvasive protocol developed in this study will enable further longitudinal and interventionist studies of host–microbe gene expression networks.

Changes in the Histology of Walnut (Juglans regia L.) Infected with Phomopsis capsici and Transcriptome and Metabolome Analysis

Phomopsis capsici (P. capsici) causes branch blight of walnuts, which leads to significant economic loss. The molecular mechanism behind the response of walnuts remains unknown. Paraffin sectioning and transcriptome and metabolome analyses were performed to explore the changes in tissue structure, gene expression, and metabolic processes in walnut after infection with P. capsici. We found that P. capsici caused serious damage to xylem vessels during the infestation of walnut branches, destroying the structure and function of the vessels and creating obstacles to the transport of nutrients and water to the branches. The transcriptome results showed that differentially expressed genes (DEGs) were mainly annotated in carbon metabolism and ribosomes. Further metabolome analyses verified the specific induction of carbohydrate and amino acid biosynthesis by P. capsici. Finally, association analysis was performed for DEGs and differentially expressed metabolites (DEMs), which focused on the synthesis and metabolic pathways of amino acids, carbon metabolism, and secondary metabolites and cofactors. Three significant metabolites were identified: succinic semialdehyde acid, fumaric acid, and phosphoenolpyruvic acid. In conclusion, this study provides data reference on the pathogenesis of walnut branch blight and direction for breeding walnut to enhance its disease resistance.

Quantitative proteomics reveals reduction in central carbon and energy metabolisms contributes to gentamicin resistance in Staphylococcus aureus

The emergence of antibiotic resistance greatly increases the difficulty of treating bacterial infections. In order to develop effective treatments, the underlying mechanisms of antibiotic resistance must be understood. In this study, Staphylococcus aureus ATCC6538 strain was passaged in medium with and without gentamicin and obtained lab-evolved gentamicin-resistant S. aureus (RGEN) and gentamicin-sensitive S. aureus (SGEN) strains, respectively. Data-Independent Acquisition (DIA)-based proteomics approach was applied to compare the two strains. A total of 1426 proteins were identified, of which 462 were significantly different: 126 were upregulated and 336 were downregulated in RGEN compared to SGEN. Further analysis found that reduced protein biosynthesis was a characteristic feature in RGEN, related to metabolic suppression. The most differentially expressed proteins were involved in metabolic pathways. In RGEN, central carbon metabolism was dysregulated and energy metabolism decreased. After verification, it was found that the levels of NADH, ATP, and reactive oxygen species (ROS) decreased, and superoxide dismutase and catalase activities increased. These findings suggest that inhibition of central carbon and energy metabolic pathways may play an important role in the resistance of S. aureus to gentamicin, and that gentamicin resistance is associated with oxidative stress.Significance: The overuse and misuse of antibiotics have led to bacterial antibiotic resistance, which is a serious threat to human health. Understanding the mechanisms of antibiotic resistance will help better control these antibiotic-resistant pathogens in the future. The present study characterized the differential proteome of gentamicin-resistant Staphylococcus aureus using the most advanced DIA-based proteomics technology. Many of the differential expressed proteins were related to metabolism, specifically, reduced central carbon and energy metabolism. Lower levels of NADH, ROS, and ATP were detected as a consequence of the reduced metabolism. These results reveal that downregulation of protein expression affecting central carbon and energy metabolisms may play an important role in the resistance of S. aureus to gentamicin.

Exogenous addition of putrescine enhanced lipid accumulation in Tetradesmus obliquus for increased biodiesel productivity

Microalgae can continuously convert carbon dioxide into biofuels as a typical organism of biological carbon fixation. This study investigated the effects of exogenous putrescine on lipid accumulation, algal growth, and transcriptional metabolism of Tetradesmus obliquus. The results showed that the content of neutral lipids increased by 2.26-fold after short-term stress of putrescine, and the total lipids increased to 355.51 mg/g. Furthermore, the transcriptomic analysis reveals that putrescine treatment plays a dramatic role in photosynthetic electron transport, carbon metabolism, and signal transduction pathways, and the purpose of lipid accumulation was achieved by influencing the changes in cell carbon flux and physiological functions. Altogether, this study demonstrates for the first time that putrescine treatment has a positive effect on lipid accumulation through unprecedented regulation of key metabolic nodes and provides theoretical support for the industrial biodiesel production of microalgae.

Cyclic di-GMP Modulates a Metabolic Flux for Carbon Utilization in Salmonella enterica Serovar Typhimurium.

Salmonella enterica serovar Typhimurium is an enteric pathogen spreading via the fecal-oral route. Transmission across humans, animals, and environmental reservoirs has forced this pathogen to rapidly respond to changing environments and adapt to new environmental conditions. Cyclic di-GMP (c-di-GMP) is a second messenger that controls the transition between planktonic and sessile lifestyles, in response to environmental cues. Our study reveals the potential of c-di-GMP to alter the carbon metabolic pathways in S. Typhimurium. Cyclic di-GMP overproduction decreased the transcription of genes that encode components of three phosphoenolpyruvate (PEP):carbohydrate phosphotransferase systems (PTSs) allocated for the uptake of glucose (PTSGlc), mannose (PTSMan), and fructose (PTSFru). PTS gene downregulation by c-di-GMP was alleviated in the absence of the three regulators, SgrS, Mlc, and Cra, suggesting their intermediary roles between c-di-GMP and PTS regulation. Moreover, Cra was found to bind to the promoters of ptsG, manX, and fruB. In contrast, c-di-GMP increased the transcription of genes important for gluconeogenesis. However, this effect of c-di-GMP in gluconeogenesis disappeared in the absence of Cra, indicating that Cra is a pivotal regulator that coordinates the carbon flux between PTS-mediated sugar uptake and gluconeogenesis, in response to cellular c-di-GMP concentrations. Since gluconeogenesis supplies precursor sugars required for extracellular polysaccharide production, Salmonella may exploit c-di-GMP as a dual-purpose signal that rewires carbon flux from glycolysis to gluconeogenesis and promotes biofilm formation using the end products of gluconeogenesis. This study sheds light on a new role for c-di-GMP in modulating carbon flux, to coordinate bacterial behavior in response to hostile environments. IMPORTANCE Cyclic di-GMP is a central signaling molecule that determines the transition between motile and nonmotile lifestyles in many bacteria. It stimulates biofilm formation at high concentrations but leads to biofilm dispersal and planktonic status at low concentrations. This study provides new insights into the role of c-di-GMP in programming carbon metabolic pathways. An increase in c-di-GMP downregulated the expression of PTS genes important for sugar uptake, while simultaneously upregulating the transcription of genes important for bacterial gluconeogenesis. The directly opposing effects of c-di-GMP on sugar metabolism were mediated by Cra (catabolite repressor/activator), a dual transcriptional regulator that modulates the direction of carbon flow. Salmonella may potentially harness c-di-GMP to promote its survival and fitness in hostile environments via the coordination of carbon metabolic pathways and the induction of biofilm formation.

Characterization of a Potential Probiotic Lactiplantibacillus plantarum LRCC5310 by Comparative Genomic Analysis and its Vitamin B6 Production Ability.

Safety assessment and functional analysis of probiotic candidates are important for their industrial applications. Lactiplantibacillus plantarum is one of the most widely recognized probiotic strains. In this study we aimed to determine the functional genes of L. plantarum LRCC5310, isolated from kimchi, using next-generation, whole-genome sequencing analysis. Genes were annotated using the Rapid Annotations using Subsystems Technology (RAST) server and the National Center for Biotechnology Information (NCBI) pipelines to establish the strain's probiotic potential. Phylogenetic analysis of L. plantarum LRCC5310 and related strains showed that LRCC5310 belonged to L. plantarum. However, comparative analysis revealed genetic differences between L. plantarum strains. Carbon metabolic pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database showed that L. plantarum LRCC5310 is a homofermentative bacterium. Furthermore, gene annotation results indicated that the L. plantarum LRCC5310 genome encodes an almost complete vitamin B6 biosynthetic pathway. Among five L. plantarum strains, including L. plantarum ATCC 14917T, L. plantarum LRCC5310 detected the highest concentration of pyridoxal 5'-phosphate with 88.08 ± 0.67 nM in MRS broth. These results indicated that L. plantarum LRCC5310 could be used as a functional probiotic for vitamin B6 supplementation.

Transcriptome analysis reveals that yeast extract inhibits synthesis of prodigiosin by Serratia marcescens SDSPY-136

Prodigiosin (2-methyl-3-pentyl-6-methoxyprodiginine) is a valuable medicinal and edible natural pigment derived from Serratia marcescens. How prodigiosin synthesis is suppressed by environmental factors has not been investigated. Previous studies described a low level of prodigiosin production in the presence of yeast extracts. However, we have observed that S. marcescens SDSPY-136 did not synthesize prodigiosin in yeast extract culture. In this study, transcriptome sequencing of yeast extract cultures was used to estimate the metabolic control of the synthetic prodigiosin pathway in S. marcescens. Key phosphorylation enzymes in the glycolysis pathway, 6-phosphofructokinase, and glyceraldehyde 3-phosphate dehydrogenase, were downregulated by yeast extract and other carbon metabolism pathway genes were enhanced. Genes related to ribosomes, amino acid metabolism, and aminoacyl-tRNA biosynthesis were also highly up-regulated. The presence of metal ions in yeast extracts and the accumulation of fermentation metabolites alter the two-component signaling system, which regulated metabolism to various degrees. The results of metal ion testing suggested that prodigiosin inhibition could be caused by metal ions, such as zinc ion. The findings indicate that yeast extract may affect metabolism through multiple pathways in S. marcescens. This research sheds light on the mechanism of prodigiosin regulatory inhibition.

Porcine reproductive and respiratory syndrome virus infection manipulates central carbon metabolism

The metabolic pathways of central carbon metabolism (CCM), glycolysis and the tricarboxylic acid (TCA) cycle, are important host factors determining the outcome of viral infection. Thus, it is not surprising that viruses easily manipulate CCM for optimized replication. Porcine reproductive and respiratory syndrome virus (PRRSV) is an Arterivirus that has devastated the swine industry worldwide for over 30 years. However, whether PRRSV reprograms CCM is still unclear. In this study, we found that PRRSV infection increased the intensity of cellular uptake of glucose and glutamine, two main carbon sources for mammalian cells. Deprivation of glucose and/or glutamine significantly reduced PRRSV replication; restricted entry of glucose and glutamine into CCM inhibited PRRSV proliferation. We further found that PRRSV infection elevated glycolysis and maintained the TCA cycle flux. Furthermore, preventing the flow of glycolysis or the TCA cycle led to a reduction in PRRSV proliferation. The anaplerotic usage of glutamine in the TCA cycle partially rescued PRRSV growth by replacing glutamine with α-ketoglutarate (α-KG), an intermediate of the TCA cycle. Interestingly, the addition of α-KG in replete medium also promoted PRRSV proliferation. Taken together, these results reveal that PRRSV infection promotes cellular uptake of glucose and glutamine to provide the energy and macromolecules required for PRRSV replication, and optimal PRRSV replication occurs in cells dependent on glycolysis and the TCA cycle.

Impacts of dibutyl phthalate on bacterial community composition and carbon and nitrogen metabolic pathways in a municipal wastewater treatment system

Dibutyl phthalate (DBP) is a typical toxic and hazardous pollutant in pharmaceutical wastewater, affecting the metabolism of microbial flora, leading to decreased treatment efficiency, and deteriorated effluent quality in municipal wastewater treatment plants (WWTPs). This study conducted a long-term experiment with 6 operational stages in a pilot-scale A2O-MBR system, analyzing the effect of DBP on the bacterial community and their carbon and nitrogen metabolic pathways. 16S rRNA gene amplicon sequencing analysis and principal components analysis (PCA) showed that DBP at 8 mg/L significantly influenced the structure of bacterial community (P < 0.05), resulting in reduced bacterial community diversity. Metagenomic analysis was used to explore the embedded carbon and nitrogen metabolic pathways. At the presence of DBP, the metabolism of saccharides, lipids, and aromatic compounds were blocked owing to the vanishment of key enzyme (such as acetylaminohexosyltransferase (EC 2.4.1.92) and UDP-sugar pyro phosphorylase (EC 2.7.7.64)) encoding genes, resulting in weakened carbon metabolism, and thus reduced COD removal performance. The resultant deficiency of the genes such as those encoding hydroxyproline dehydrogenase (EC 1.5.5.3) gave rise to interrupted metabolic pathways of amino acid (arginine, proline, tyrosine, and tryptophan), resulting in declined function of nitrogen metabolism and thus reduced TN removal efficiency. The uncovery of the mechanisms by which DBP affects wastewater treatment system efficiency and microbial metabolism is of theoretical importance for the efficient operation of municipal and pharmaceutical wastewater treatment systems.

Integrated metabolomic and transcriptomic study unveils the gene regulatory mechanisms of sugarcane growth promotion during interaction with an endophytic nitrogen-fixing bacteria

BackgroundSugarcane growth and yield are complex biological processes influenced by endophytic nitrogen-fixing bacteria, for which the molecular mechanisms involved are largely unknown. In this study, integrated metabolomic and RNA-seq were conducted to investigate the interaction between an endophytic bacterial strain, Burkholderia GXS16, and sugarcane tissue culture seedlings.ResultsDuring treatment, the colonization of GXS16 in sugarcane roots were determined, along with the enhanced activities of various antioxidant enzymes. Accordingly, 161, 113, and 37 differentially accumulated metabolites (DAMs) were found in the pairwise comparisons of adjacent stages. In addition, transcriptomic analyses obtained 1,371 (IN-vs-CN), 1,457 (KN-vs-IN), and 365 (LN-vs-KN) differentially expressed genes (DEGs), which were mainly involved in the pathways of glutathione metabolism and carbon metabolism. We then assessed the pattern of metabolite accumulation and gene expression in sugarcane during GXS16 colonization. The results showed that both DAMs and DGEs in the upregulated expression profiles were involved in the flavonoid biosynthesis pathway. Overall, p-coumaroyl-CoA in sugarcane roots transferred into homoeriodictyol chalcone and 5-deoxyleucopelargonidin due to the upregulation of the expression of genes shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), and phlorizin synthase (PGT1).ConclusionsThis study provides insights into the gene regulatory mechanisms involved in the interaction between GXS16 and sugarcane roots, which will facilitate future applications of endophytic nitrogen-fixing bacteria to promote crop growth.

Effect of different drying techniques on rose (Rosa rugosa cv. Plena) proteome based on label-free quantitative proteomics

To explore the molecular mechanisms of different processing technologies on rose tea (Rosa rugosa cv. Plena), we investigated the rose tea proteome (fresh rose tea [CS], vacuum freeze-drying rose tea [FD], and vacuum microwave rose tea [VD]) using label-free quantification proteomics (LFQ). A total of 2187 proteins were identified, with 1864, 1905, and 1660 proteins identified in CS, FD, and VD, respectively. Of those, 1500 proteins were quantified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and enrichment analysis of differential expression proteins (DEPs) in VD vs. CS, FD vs. CS, and FD vs. VD showed that these pathways were associated with energy metabolism, the metabolic breakdown of energy substances and protein biosynthesis, such as oxidative phosphorylation, citrate cycle, carbon metabolism pathways, and ribosome and protein processing in endoplasmic reticulum. FD could ensure the synthesis of protein translation and energy metabolism, thereby maintaining the high quality of rose tea.

Knocking out central metabolism genes to identify new targets and alternating substrates to improve lipid synthesis in Y. lipolytica.

Introduction: Systematic gene knockout studies may offer us novel insights on cell metabolism and physiology. Specifically, the lipid accumulation mechanism at the molecular or cellular level is yet to be determined in the oleaginous yeast Y. lipolytica. Methods: Herein, we established ten engineered strains with the knockout of important genes involving in central carbon metabolism, NADPH generation, and fatty acid biosynthetic pathways. Results: Our result showed that NADPH sources for lipogenesis include the OxPP pathway, POM cycle, and a trans-mitochondrial isocitrate-α-oxoglutarate NADPH shuttle in Y. lipolytica. Moreover, we found that knockout of mitochondrial NAD+ isocitrate dehydrogenase IDH2 and overexpression of cytosolic NADP+ isocitrate dehydrogenase IDP2 could facilitate lipid synthesis. Besides, we also demonstrated that acetate is a more favorable carbon source for lipid synthesis when glycolysis step is impaired, indicating the evolutionary robustness of Y. lipolytica. Discussion: This systematic investigation of gene deletions and overexpression across various lipogenic pathways would help us better understand lipogenesis and engineer yeast factories to upgrade the lipid biomanufacturing platform.

Insights into the core bacterial consortia of root endophytes in two cultivated varieties of rice in West Bengal

Root endophytes are considered to be one of the potent environment-friendly substitutes for chemical fertilizers, as they possess an ability to induce crosstalk inside the hosts for growth promotion, nitrogen fixation, phosphate solubilization and iron sequestration. This study aimed to explore and evaluate the key root endophytic bacterial consortia of two widely cultivated varieties of rice (Oryza sativa L.), cv. ‘Saraswati’ (OS01) and cv. ‘Kunti’ (OS04). Detailed comparative metagenome data were generated for endophytes of OS01 and OS04 and the species richness was calculated. OS01 showed higher endophyte species richness than OS04, with alpha diversity values of 3.10 and 2.40, respectively. Bacillus, Magnetospirillum, Methanocystis, Desulfomicrobium and Pantoea were identified as common endophyte members for both cultivars. Solibacillus, Paenibacillus, Candidatus, and Melospira were unique members of OS01, and Herbaspirillum, Pandoraea, Anabaenopsis for OS04. Considerable occurrence of nitrogen fixing bacteria and methanogenic bacteria in the cultivars confirmed biological nitrogen fixation, which can contribute to plant development. Core homeotic pathways of amino acid biosynthesis and carbon metabolism were also reflected in endophytes from both cultivars, indicating a supportive environment for microorganisms. Sulfur metabolism pathways were likewise predicted to be active in the niche under study, which may be attributed as a response to arsenic stress. Furthermore, the most abundant genera identified may potentially serve as crucial consortium candidates for host plant development and contribute to better yield in a sustainable manner.

Foliar Selenium Nanoparticles Application Promotes the Growth of Maize (Zea mays L.) Seedlings by Regulating Carbon, Nitrogen and Oxidative Stress Metabolism

Current understanding of selenium (Se) nanoparticles (SeNPs) effects on growth of C4 cereals is deeply scarce, and thus a hydroponic experiment was conducted to explore the physiological, biochemical, and metabolites variations in maize following foliar application of SeO32- and SeNPs each at 2 and 20 mg/L. The results demonstrated that fresh weight of Se foliar-applied leaves (Se-leaves) significantly increased by 27% after foliar application of SeNPs at 20 mg/L, which was mainly attributed to the improved photosynthetic efficiency (50%–78%) and stomatal conductance (46%–60%) of Se-leaves. Foliar-applied SeNPs and SeO32- both increased the Se concentration of each part of maize, while SeNPs was more efficient in improving the Se concentration, and Se was mainly accumulated in the cell wall. Significant increase was observed in GSH (14%–64%), POD (6%–24%), SOD (2%–11%), CAT (55%–73%), APX (50%–90%) at SeNPs application in comparison with control. Metabolomic results indicated that foliar application of 20 mg/L SeNPs significantly up-regulated 42 metabolites, which were mainly carbohydrates, amino acids, ketone and phenol, vitamin, and ten metabolic pathways (2 metabolic pathways related with carbon metabolism, 5 related with nitrogen metabolism, and 1 related with oxidative stress metabolism) was improved. Therefore, SeNPs mainly enhanced the antioxidant capacity by improving metabolic pathways of glutathione metabolism, carbon metabolism, and nitrogen metabolism and finally improved various physiological indexes of maize to boost the growth of maize.

Identification of Novel Pathways Regulated by APE1/Ref-1 in Human Retinal Endothelial Cells.

APE1/Ref-1 (apurinic/apyrimidinic endonuclease 1, APE1 or APEX1; redox factor-1, Ref-1) is a dual-functional enzyme with crucial roles in DNA repair, reduction/oxidation (redox) signaling, and RNA processing and metabolism. The redox function of Ref-1 regulates several transcription factors, such as NF-κB, STAT3, HIF-1α, and others, which have been implicated in multiple human diseases, including ocular angiogenesis, inflammation, and multiple cancers. To better understand how APE1 influences these disease processes, we investigated the effects of APEX1 knockdown (KD) on gene expression in human retinal endothelial cells. This abolishes both DNA repair and redox signaling functions, as well as RNA interactions. Using RNA-seq analysis, we identified the crucial signaling pathways affected following APEX1 KD, with subsequent validation by qRT-PCR. Gene expression data revealed that multiple genes involved in DNA base excision repair, other DNA repair pathways, purine or pyrimidine metabolism signaling, and histidine/one carbon metabolism pathways were downregulated by APEX1 KD. This is in contrast with the alteration of pathways by APEX1 KD in human cancer lines, such as pancreatic ductal adenocarcinoma, lung, HeLa, and malignant peripheral nerve sheath tumors. These results highlight the unique role of APE1/Ref-1 and the clinical therapeutic potential of targeting APE1 and pathways regulated by APE1 in the eye. These findings provide novel avenues for ocular neovascularization treatment.