Fatty Acid Biosynthesis Pathway Research Articles

Screening the rate-limiting genes in the ω6 polyunsaturated fatty acid biosynthesis pathway in Nannochloropsis oceanica

The enrichment of polyunsaturated fatty acids has made Nannochloropsis sp. a promising candidate for the production of polyunsaturated fatty acids. Although most of the genes involved in polyunsaturated fatty acid biosynthesis have been cloned, the regulatory mechanism at the molecular level has not been elucidated. To target the rate-limiting genes in the ω6 polyunsaturated fatty acid biosynthesis pathway in Nannochloropsis oceanica, we performed the following experiments. The function of the Δ9 fatty acid desaturase gene of N. oceanica was verified in Saccharomyces cerevisiae with a substrate preference for stearic acid. With gas chromatography–mass spectrometry (GC–MS) analysis, the fatty acid profiles in N. oceanica under different stress conditions (high nitrogen, low nitrogen, high temperature, and low temperature) were measured. The results showed that high nitrogen and low temperature stresses played significant roles in promoting polyunsaturated fatty acid biosynthesis. In contrast, low nitrogen and high temperature stresses were beneficial for the accumulation of monounsaturated fatty acids. We further measured the transcriptional abundances of all six genes in the ω6 polyunsaturated fatty acid biosynthesis pathway in N. oceanica and found that the Δ6 fatty acid elongase and the Δ12, Δ5, and Δ17 fatty acid desaturase genes were more sensitive to the stresses set in this study. Pearson correlation analysis showed that the Δ9 fatty acid desaturase was significantly associated with monounsaturated fatty acid biosynthesis, while Δ12, Δ5, and Δ17 fatty acid desaturases were proposed to be the rate-limiting enzymes in polyunsaturated fatty acid biosynthesis. This study helps to thoroughly elucidate the responses of N. oceanica to nitrogen and temperature stresses and optimize cultivation for high yield and quality of polyunsaturated fatty acids. More importantly, the selected rate-limiting genes may benefit further genetic engineering in N. oceanica.

Sediment microbiota in polyculture of shrimp and fish pattern is distinctive from those in monoculture intensive shrimp or fish ponds

Sediment microbial community plays a crucial role in aquaculture ecosystem. In aquaculture practice, rather than monoculture intensive shrimp (IS) or intensive fish (IF) patterns, polyculture of shrimp and fish (PolySF) pattern leads to a more reliable production. However, knowledge is still limited about the characteristics of sediment microbiota and its potential functions in the PolySF ponds compared to monoculture patterns (IS and IF). Herein, we collected sediment samples from these three patterns in seven cities to evaluate microbial variations among patterns. The highest oxidation reduction potential (ORP), total phosphate (TP) and total organic carbon (TOC) were detected in the PolySF pattern, representing a relatively less anoxic environment, while the highest iron (Fe) was detected in IS pattern. Proteobacteria was the most abundant phylum among three patterns, followed by Bacteroidetes and Chloroflexi. The microbial alpha diversity in the PolySF was higher than those in the IF, but lower than those in the IS. Microbial communities of these three patterns were significantly distinct from each other, and 23 distinguished taxa for each pattern were further characterized. In additional, the relative abundances of genes involved in nitrogen metabolism, fatty acid biosynthesis and carbon fixation pathways were markedly shifted. Moreover, ORP, TOC and Fe were the shaping factors for sediment microbiota, which significantly varied among three patterns. Collectively, these findings demonstrated that sediment microbial communities in the PolySF were distinctive from those in the IS and IF, which enlarged our understanding for the underlying mechanism of advances in the PolySF pattern from ecological perspective.

Overexpression of DEFECTIVE IN ANTHER DEHISCENCE 1 increases rapeseed silique length through crosstalk between JA and auxin signaling

Rapeseed (Brassica napus) is the second largest oilseed crop worldwide. Silique length and seed weight are positively correlated with its yield. Here, a rapeseed gene DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1; Bna.A05DAD1) was isolated, and its overexpression could significantly increase the SL and SW in Arabidopsis and rapeseed through the enlargement of the silique pericarp cells. Bna.A05DAD1 expression is observed in the seeds and anthers specifically, and its associated protein is localized to the chloroplast. Transcriptomic analysis revealed that the fatty acid biosynthesis and phytohormone response pathways were influenced with Bna.A05DAD1 overexpression. Since the FATTY ACID DESATURASE 2/6 (FAD2/6) and FAD3/7/8 genes were significantly higher than the wild type, the concentrations of linoleic acid and linolenic acid were increased in the DAD1-overexpressing rapeseed plants. Besides, overexpression of Bna.A05DAD1 suppressed the negative regulation of AUXIN RESPONSE FACTOR 18 (ARF18) through upregulation of jasmonate acid (JA) biosynthesis genes (ALLENE OXIDE CYCLASE 4, AOC4; ALLENE OXIDE SYNTHASE, Bna.A02AOS and OXOPHYTODIENOATE-REDUCTASE, Bna.C03OPR), resulting in activating of auxin response genes, leading the auxin to accumulate and the SL and SW increase. Our results suggest new views about the role Bna.A05DAD1 played in regulating fatty acid composition and increasing yield in rapeseed, as well as reveal an important mechanism of the crosstalk between the JA and auxin signaling pathways in the breeding of high-yielding rapeseed.

Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes.

ABSTRACTThe existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations, efforts to identify microbial biomarkers have been limited due to a lack of appropriately matched controls, stratification of participants within the autism spectrum, and sample size. To overcome these limitations, we crowdsourced the recruitment of families with age-matched sibling pairs between 2 and 7 years old (within 2 years of each other), where one child had a diagnosis of ASD and the other did not. Parents collected stool samples, provided a home video of their ASD child’s natural social behavior, and responded online to diet and behavioral questionnaires. 16S rRNA V4 amplicon sequencing of 117 samples (60 ASD and 57 controls) identified 21 amplicon sequence variants (ASVs) that differed significantly between the two cohorts: 11 were found to be enriched in neurotypical children (six ASVs belonging to the Lachnospiraceae family), while 10 were enriched in children with ASD (including Ruminococcaceae and Bacteroidaceae families). Summarizing the expected KEGG orthologs of each predicted genome, the taxonomic biomarkers associated with children with ASD can use amino acids as precursors for butyragenic pathways, potentially altering the availability of neurotransmitters like glutamate and gamma aminobutyric acid (GABA).IMPORTANCE Autism spectrum disorder (ASD), which now affects 1 in 54 children in the United States, is known to have comorbidity with gut disorders of a variety of types; however, the link to the microbiome remains poorly characterized. Recent work has provided compelling evidence to link the gut microbiome to the autism phenotype in mouse models, but identification of specific taxa associated with autism has suffered replicability issues in humans. This has been due in part to sample size that sufficiently covers the spectrum of phenotypes known to autism (which range from subtle to severe) and a lack of appropriately matched controls. Our original study proposes to overcome these limitations by collecting stool-associated microbiome on 60 sibling pairs of children, one with autism and one neurotypically developing, both 2 to 7 years old and no more than 2 years apart in age. We use exact sequence variant analysis and both permutation and differential abundance procedures to identify 21 taxa with significant enrichment or depletion in the autism cohort compared to their matched sibling controls. Several of these 21 biomarkers have been identified in previous smaller studies; however, some are new to autism and known to be important in gut-brain interactions and/or are associated with specific fatty acid biosynthesis pathways.

Transcriptomic analysis of \u03b1-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds

BackgroundPaeonia ostii is a potentially important oilseed crop because its seed yield is high, and the seeds are rich in α-linolenic acid (ALA). However, the molecular mechanisms underlying ALA biosynthesis during seed kernel, seed testa, and fruit pericarp development in this plant are unclear. We used transcriptome data to address this knowledge gap.ResultsGas chromatograph-mass spectrometry indicated that ALA content was highest in the kernel, moderate in the testa, and lowest in the pericarp. Therefore, we used RNA-sequencing to compare ALA synthesis among these three tissues. We identified 227,837 unigenes, with an average length of 755 bp. Of these, 1371 unigenes were associated with lipid metabolism. The fatty acid (FA) biosynthesis and metabolism pathways were significantly enriched during the early stages of oil accumulation in the kernel. ALA biosynthesis was significantly enriched in parallel with increasing ALA content in the testa, but these metabolic pathways were not significantly enriched during pericarp development. By comparing unigene transcription profiles with patterns of ALA accumulation, specific unigenes encoding crucial enzymes and transcription factors (TFs) involved in de novo FA biosynthesis and oil accumulation were identified. Specifically, the bell-shaped expression patterns of genes encoding SAD, FAD2, FAD3, PDCT, PDAT, OLE, CLE, and SLE in the kernel were similar to the patterns of ALA accumulation in this tissue. Genes encoding BCCP, BC, KAS I– III, and FATA were also upregulated during the early stages of oil accumulation in the kernel. In the testa, the upregulation of the genes encoding SAD, FAD2, and FAD3 was followed by a sharp increase in the concentrations of ALA. In contrast, these genes were minimally expressed (and ALA content was low) throughout pericarp development.ConclusionsWe used three tissues with high, moderate, and low ALA concentrations as an exemplar system in which to investigate tissue-specific ALA accumulation mechanisms in P. ostii. The genes and TFs identified herein might be useful targets for future studies of ALA accumulation in the tree peony. This study also provides a framework for future studies of FA biosynthesis in other oilseed plants.

Proteomic Study Reveals Major Pathways Regulating the Development of Black Soldier Fly.

Nowadays, biodegrading organic waste, as a solution to confront environmental challenges, has attracted wide attention. A dipteran insect, black soldier fly (BSF), exhibits outstanding capability to convert organic waste into proteins and lipid resources, and thus, much interest has been shown in it. However, information of fundamental biology of BSF is still limited besides its recycling efficiency. In this work, we present a complete proteomic database of BSF at all instars (before prepupa). We further formulated the pathways corresponding to BSF development and built a relationship with the current genetic database. To achieve this, we investigated the proteomics of BSF during different periods. We identified 5036 proteins, and among them, 3905 proteins were annotated in the protein function database. illustrated three pathways related to major physiological processes including the insulin signaling pathway for feeding and growth, fatty acid biosynthesis pathway for fatty acid using, and toll/immune deficiency pathway for immune behavior. The proteins in these three pathways were matched with a published genetic database, and this reference library could be used for future BSF genetic engineering. In conclusion, this work provided a comprehensive protein library of BSF and expands the basic knowledge of BSF for future research.

TILLING-by-Sequencing+ to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis.

Reverse genetic approaches have been widely applied to study gene function in crop species; however, these techniques, including gel-based TILLING, present low efficiency to characterize genes in soybeans due to genome complexity, gene duplication, and the presence of multiple gene family members that share high homology in their DNA sequence. Chemical mutagenesis emerges as a genetically modified-free strategy to produce large-scale soybean mutants for economically important traits improvement. The current study uses an optimized high-throughput TILLING by target capture sequencing technology, or TILLING-by-Sequencing+ (TbyS+), coupled with universal bioinformatic tools to identify population-wide mutations in soybeans. Four ethyl methanesulfonate mutagenized populations (4032 mutant families) have been screened for the presence of induced mutations in targeted genes. The mutation types and effects have been characterized for a total of 138 soybean genes involved in soybean seed composition, disease resistance, and many other quality traits. To test the efficiency of TbyS+ in complex genomes, we used soybeans as a model with a focus on three desaturase gene families, GmSACPD, GmFAD2, and GmFAD3, that are involved in the soybean fatty acid biosynthesis pathway. We successfully isolated mutants from all the six gene family members. Unsurprisingly, most of the characterized mutants showed significant changes either in their stearic, oleic, or linolenic acids. By using TbyS+, we discovered novel sources of soybean oil traits, including high saturated and monosaturated fatty acids in addition to low polyunsaturated fatty acid contents. This technology provides an unprecedented platform for highly effective screening of polyploid mutant populations and functional gene analysis. The obtained soybean mutants from this study can be used in subsequent soybean breeding programs for improved oil composition traits.

Metabolic Markers Demonstrate the Heterogeneity of Myosteatosis in Community-Dwelling Older Black Men from the Health ABC Study.

Myosteatosis is a complex condition, associated with aging and diverse pathological conditions (e.g., diabetes), that contributes to mobility disability. Improved characterization of myosteatosis is required to develop targeted interventions to maintain muscle health in aging. We first determined the associations between plasma metabolites and intermuscular fat (IMF) in a cross-sectional analysis of 313 older Black men from Health ABC Study. Using partial correlation analysis, 34/350 metabolites were associated with IMF, the majority of which were lipids and organic acids. Next, we used Homeostasis Model Assessment of Insulin Resistance (HOMA-IR), as an indicator of metabolic health to delineate the anthropometric, functional, and metabolic heterogeneity of myosteatosis in a case-control matching analysis. We categorized participants based on their IMF and HOMA-IR levels into: Low-IMF with Low- versus High-HOMA, as well as High-IMF with Low- versus High-HOMA. Among participants with similar levels of IMF, those who were metabolically unhealthy, i.e., with High HOMA-IR, had higher fat and lean mass, muscle strength, and had hyperglycemia, hypertriglyceridemia, hyperinsulinemia, and higher levels of plasma metabolites belonging to diacylglycerols, triacylglycerols, fatty acid and aminoacyl-tRNA biosynthesis pathways versus those with Low HOMA-IR. In summary, HOMA-IR delineates the heterogeneity of myosteatosis by distinguishing metabolically healthy versus unhealthy individuals.

Transcriptome-based analysis of the effects of salicylic acid and high light on lipid and astaxanthin accumulation in Haematococcus pluvialis

BackgroundThe unicellular alga Haematococcus pluvialis has achieved considerable interests for its capacity to accumulate large amounts of triacylglycerol and astaxanthin under various environmental stresses. To our knowledge, studies focusing on transcriptome research of H. pluvialis under exogenous hormones together with physical stresses are rare. In the present study, the change patterns at transcriptome level were analyzed to distinguish the multiple defensive systems of astaxanthin and fatty acid metabolism against exogenous salicylic acid and high light (SAHL) stresses.ResultsBased on RNA-seq data, a total of 112,463 unigenes and 61,191 genes were annotated in six databases, including NR, KEGG, Swiss-Prot, PFAM, COG and GO. Analysis of differentially expressed genes (DEGs) in KEGG identified many transcripts that associated with the biosynthesis of primary and secondary metabolites, photosynthesis, and immune system responses. Furthermore, 705 unigenes predicted as putative transcription factors (TFs) were identified, and the most abundant TFs families were likely to be associated with the biosynthesis of astaxanthin and fatty acid in H. pluvialis upon exposure to SAHL stresses. Additionally, majority of the fifteen key genes involved in astaxanthin and fatty acid biosynthesis pathways presented the same expression pattern, resulting in increased accumulation of astaxanthin and fatty acids in single celled H. pluvialis, in which astaxanthin content increased from 0.56 ± 0.05 mg·L−1 at stage Control to 0.89 ± 0.12 mg·L−1 at stage SAHL_48. And positive correlations were observed among these studied genes by Pearson Correlation (PC) analysis, indicating the coordination between astaxanthin and fatty acid biosynthesis. In addition, protein–protein interaction (PPI) network analysis also demonstrated that this coordination might be at transcriptional level.ConclusionThe results in this study provided valuable information to illustrate the molecular mechanisms of coordinate relations between astaxanthin and fatty acid biosynthesis. And salicylic acid might play a role in self-protection processes of cells, helping adaption of H. pluvialis to high light stress.

Chemical profiling and metabolic mechanism of Pixian doubanjiang, a famous condiment in Chinese cuisine

Pixian doubanjiang (PXDB) is a famous fermentation condiment in China and throughout the world. However, detailed information regarding its metabolic mechanism remains scarce. This paper presents a comprehensive chemical profiling of PXDB during fermentation, to obtain a global understanding of the metabolite variations based on the untargeted metabolomics approach through ultra-performance liquid chromatography coupled with quadruple-time-of flight mass spectrometry (UHPLC-Q-TOF). Ninety-nine metabolites, including amino acids, small peptides, organic acids, fatty acids and phospholipids were proposed as key chemical markers for the first time. Meanwhile, the pathways’ analysis revealed that the transformation of these metabolites was primarily associated with arginine biosynthesis, alanine, aspartic acid and glutamate metabolism, glycerol phospholipid metabolism, unsaturated fatty acid biosynthesis and citric acid cycle pathways. The comprehensive analysis of the metabolite changes is expected to help us explore the formation of the taste and flavor components in PXDB production.

Weighted gene co-expression network analysis to identify key modules and hub genes related to hyperlipidaemia

BackgroundThe purpose of this study was to explore the potential molecular targets of hyperlipidaemia and the related molecular mechanisms.MethodsThe microarray dataset of GSE66676 obtained from patients with hyperlipidaemia was downloaded. Weighted gene co-expression network (WGCNA) analysis was used to analyse the gene expression profile, and the royal blue module was considered to have the highest correlation. Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were implemented for the identification of genes in the royal blue module using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool (version 6.8; http://david.abcc.ncifcrf.gov). A protein–protein interaction (PPI) network was established by using the online STRING tool. Then, several hub genes were identified by the MCODE and cytoHubba plug-ins in Cytoscape software.ResultsThe significant module (royal blue) identified was associated with TC, TG and non-HDL-C. GO and KEGG enrichment analyses revealed that the genes in the royal blue module were associated with carbon metabolism, steroid biosynthesis, fatty acid metabolism and biosynthesis pathways of unsaturated fatty acids. SQLE (degree = 17) was revealed as a key molecule associated with hypercholesterolaemia (HCH), and SCD was revealed as a key molecule associated with hypertriglyceridaemia (HTG). RT-qPCR analysis also confirmed the above results based on our HCH/HTG samples.ConclusionsSQLE and SCD are related to hyperlipidaemia, and SQLE/SCD may be new targets for cholesterol-lowering or triglyceride-lowering therapy, respectively.

Adipose-specific knockout of Protein Kinase D1 suppresses de novo lipogenesis in mice via SREBP1c-dependent signaling

Having healthy adipose tissue is essential for metabolic health, as excessive adipose tissue in the body can cause its dysregulation and driving chronic metabolic diseases. Protein kinase D1 (PKD1) is considered to be a key kinase in signal transduction, which regulates multiple cellular functions, but its physiological functions in adipose are still not fully understood. This study aimed at elucidating the function of adipocyte PKD1 on lipogenesis. From RNA-Sequencing data, we found that the fatty acid biosynthesis pathway in white adipose tissue lacking PKD1 was significantly affected. Critical rate-limiting enzymes for de novo lipogenesis in adipocytes, such as FASN, ACCα, and SCD1, were significantly repressed after deleting PKD1 in vivo and in vitro. Further studies revealed that blockade of PKD1 significantly increased phosphorylation of SREBP1c at serine 372 site. Co-immunoprecipitation analysis showed that PKD1 interacts with SREBP1c in vitro and in vivo. Importantly, overexpression of SREBP1c reversed the inhibition of FASN and ACCα expression caused by PKD1 silencing. Together, adipocyte PKD1 promotes de novo lipogenesis via SREBP1c-dependent manner in visceral white adipose tissue and might provide a new target for the development of anti-obesity therapies.

Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids

BackgroundCystic fibrosis (CF) affects >70,000 people worldwide, yet the microbiologic trigger for pulmonary exacerbations (PExs) remains unknown. The objective of this study was to identify changes in bacterial metabolic pathways associated with clinical status.MethodsRespiratory samples were collected at hospital admission for PEx, end of intravenous (IV) antibiotic treatment, and follow-up from 27 hospitalized children with CF. Bacterial DNA was extracted and shotgun DNA sequencing was performed. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance, while DESeq2 was used to evaluate differential abundance based on clinical status.ResultsThe mean age of study participants was 10 years; 85% received combination IV antibiotic therapy (beta-lactam plus a second agent). Long-chain fatty acid (LCFA) biosynthesis pathways were upregulated in follow-up samples compared to end of treatment: gondoate (p = 0.012), oleate (p = 0.048), palmitoleate (p = 0.043), and pathways of fatty acid elongation (p = 0.012). Achromobacter xylosoxidans and Escherichia sp. were also more prevalent in follow-up compared to PEx (p < 0.001).ConclusionsLCFAs may be associated with persistent infection of opportunistic pathogens. Future studies should more closely investigate the role of LCFA production by lung bacteria in the transition from baseline wellness to PEx in persons with CF.ImpactIncreased levels of LCFAs are found after IV antibiotic treatment in persons with CF.LCFAs have previously been associated with increased lung inflammation in asthma.This is the first report of LCFAs in the airway of persons with CF.This research provides support that bacterial production of LCFAs may be a contributor to inflammation in persons with CF.Future studies should evaluate LCFAs as predictors of future PExs.

Biochemical variances through metabolomic profile analysis of Capsicum chinense Jacq. during fruit development

Abstract Capsicum chinense Jacq. is classified under the Solanaceae family, which is an extensively consumed spice and vegetable globally. Therefore, to gain more knowledge and insight into the diversity of Capsicum chinense Jacq. metabolites, a total of 18 placental tissues from various development stages were collected and untargeted metabolomics was conducted by means of ultra-performance liquid chromatography (UPLC) and mass spectrometry (MS). Principal component analysis (PCA) analysis established the existence of distinct metabolite distribution patterns as observed at 16 days post anthesis (DPA), compared with the metabolites at 36 and 48 DPA groups, whereas there was a difference in metabolites between the orange ripening period (B) and the red ripening period (C), which intersected with each other. Furthermore, several pathways including metabolic pathways, biosynthesis of phenylpropanoids, ABC transporters, alanine, aspartate and glutamate metabolism, fatty acid biosynthesis, pentose and glucoronate pathways, secondary metabolites biosynthesis, cutin, biosynthesis of suberine and wax were significantly enriched across the fruit ripening stages. The capsaicin content was observed to be less in the early ripening stages, but gradually increased to a high concentration during the late ripening stages. In conclusion, our study findings submit a suitable approach for interpreting the biochemical variances of non-targeted metabolomics in hot pepper developmental stages, as well as offer new findings that can be applied in the development strategies in breeding of Capsicum chinense Jacq.

H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the most intractable and devastating malignant tumors. Epigenetic modifications such as DNA methylation and histone modification regulate tumor initiation and progression. However, the contribution of histone variants in PDAC is unknown. Here, we demonstrated that the histone variant H2A.Z is highly expressed in PDAC cell lines and PDAC patients and that its overexpression correlates with poor prognosis. Moreover, all three H2A.Z isoforms (H2A.Z.1, H2A.Z.2.1, and H2A.Z.2.2) are highly expressed in PDAC cell lines and PDAC patients. Knockdown of these H2A.Z isoforms in PDAC cell lines induces a senescent phenotype, cell cycle arrest in phase G2/M, increased expression of cyclin-dependent kinase inhibitor CDKN2A/p16, SA-β-galactosidase activity and interleukin 8 production. Transcriptome analysis of H2A.Z-depleted PDAC cells showed altered gene expression in fatty acid biosynthesis pathways and those that regulate cell cycle and DNA damage repair. Importantly, depletion of H2A.Z isoforms reduces the tumor size in a mouse xenograft model in vivo and sensitizes PDAC cells to gemcitabine. Overexpression of H2A.Z.1 and H2A.Z.2.1 more than H2A.Z.2.2 partially restores the oncogenic phenotype. Therefore, our data suggest that overexpression of H2A.Z isoforms enables cells to overcome the oncoprotective barrier associated with senescence, favoring PDAC tumor grow and chemoresistance. These results make H2A.Z a potential candidate as a diagnostic biomarker and therapeutic target for PDAC.

Effects of lysine 2-hydroxyisobutyrylation on bacterial FabI activity and resistance to triclosan

Lysine 2-hydroxyisobutyrylation (Khib) is a novel protein posttranslational modification conserved in eukaryotes and prokaryotes. However, the biological significance of Khib remains largely unknown. Here, through screening the proteome-wide Khib modification sites in bacteria using a bioinformatic method, we identified a potential Khib site (K201hib) targeted by de-2-hyroxyisobutyrylase CobB at the substrate-binding site of FabI, an enoyl-acyl carry protein reductase (EnvM or FabI) in fatty acid biosynthesis pathway. First, we confirmed that the previously identified de-2-hyroxyisobutyrylase CobB can remove Khib of FabI in an in vitro experiment. To investigate the biological effects of the Khib on FabI’s activity, amino acid substitutes were introduced to the modification sites of the protein of E. coli origin to mimic modified/unmodified status. We found that the mutant mimicking K201hib reduced FabI activity with decreased Michaelis constant (Km) and catalytic turnover number (kcat), while the mutant mimicking the unmodified form and the recombinant wild-type protein treated with CobB exhibited increased activity. However, the dissociation constant (KD) between FabI and NADH was not affected by the mutation mimicking the modification, suggesting that K201hib didn’t alter the binding between NADH and FabI. We also found that K201hib tended to increase the resistance of E. coli to triclosan (TCL), a widely-used antibiotics targeting FabI. Taken together, this study identified the regulatory role of Khib on FabI activity and pointed to a novel mechanism related to antibiotic resistance.

Revealing the Mechanism of Biochar Enhancing the Production of Medium Chain Fatty Acids from Waste Activated Sludge Alkaline Fermentation Liquor

In this work, the effectiveness of biochar with distinctively different particle sizes (i.e., 2000–5000 and 75–150 μm) derived from anaerobically digested sludge was comprehensively evaluated in the production of enhancing MCFAs (medium chain fatty acids) using waste activated sludge alkaline fermentation liquor as feedstock with ethanol as the electron donor. The results showed that fine biochar (i.e., 75–150 μm) was more favorable for enhancing the production of MCFAs with an increased electron transfer efficiency reaching 92.6%. Metagenomic analysis revealed that the total microbial taxonomic composition shifted in favor of the production of MCFAs (e.g., Clostridium kluyveri sp., Clostridium magnum sp., and Clostridium botulinum sp.). The increased relative abundance of functional enzymes associated with the production of MCFAs confirmed that both the reverse β-oxidation pathway and the fatty acid biosynthesis pathway were enhanced by biochar. Mechanistic studies revealed that the biochar had high redox-active properties due to the functional groups (mainly quinones and hydroquinone) on its surface and an important ability to charge and/or discharge, which thus promoted the transfer of electrons for the production of MCFAs during the CE process.

Ampicillin used in aseptic processing influences the production of pigments and fatty acids in Chlorella sorokiniana.

Ampicillin sodium salt (AMP) is commonly and effectively used to prevent bacterial infection in algal culture, but the response of algal strains to AMP has not been investigated. In this study, Chlorella sorokiniana was selected to evaluate the influence of AMP on algae. AMP enhanced the contents of chlorophyll and two fatty acids, myristic acid (C22:1N9) and tetracosanoic acid (C6:0), but inhibited the growth, carotenoid production, and contents of 16 fatty acids in C. sorokiniana. A global transcriptome analysis from experimental data identified 3 825 upregulated and 1 432 downregulated differentially expressed genes (DEGs) in C. sorokiniana. The upregulated DEGs, such as hemB/alaD, mmaB/pduO, cox15/ctaA, fxN, cpoX/hemF, and earS/gltX, were enriched in the porphyrin and chlorophyll metabolism pathways, whereas the downregulated DEGs, including lcyB (crtL1), crtY (lcyE, crtL2), lut1 (CYP97C1), z-isO, crtZ and crtisO (crtH), were enriched in the carotenoid biosynthesis pathway, and the downregulated DEGs, abH, fadD, fabF, acsL, fabG, and accD were enriched in the fatty acid biosynthesis pathway. Thus, the use of AMP to obtain an axenic strain revealed that AMP might affect the regulatory dynamics and the results of the metabolic process in C. sorokiniana. The data obtained in the study provide foundational information for algal purification and aseptic processing.

Hepatic deletion of Mboat7 (LPIAT1) causes activation of SREBP-1c and fatty liver

AbstractGenetic variants that increase the risk of fatty liver disease and cirrhosis have recently been identified in the proximity of membrane-bound O-acyltransferase domain-containing 7 (MBOAT7). To elucidate the link between these variants and fatty liver disease, we characterized Mboat7 liver-specific KO mice (Mboat7 LSKO). Chow-fed Mboat7 LSKO mice developed fatty livers and associated liver injury. Lipidomic analysis of liver using MS revealed a pronounced reduction in 20-carbon PUFA content in phosphatidylinositols (PIs) but not in other phospholipids. The change in fatty acid composition of PIs in these mice was associated with a marked increase in de novo lipogenesis because of activation of SREBP-1c, a transcription factor that coordinates the activation of genes encoding enzymes in the fatty acid biosynthesis pathway. Hepatic removal of both SREBP cleavage-activating protein (Scap) and Mboat7 normalized hepatic triglycerides relative to Scap-only hepatic KO, showing that increased SREBP-1c processing is required for Mboat7-induced steatosis. This study reveals a clear relationship between PI fatty acid composition and regulation of hepatic fat synthesis and delineates the mechanism by which mutations in MBOAT7 cause hepatic steatosis.

Comprehensive analysis of lncRNA expression profiles in cytopathic biotype BVDV-infected MDBK cells provides an insight into biological contexts of host–BVDV interactions

ABSTRACT Bovine viral diarrhea virus (BVDV) is the causative agent of bovine viral diarrhea-mucosal disease, which significantly affects the production performance of cattle, causing serious economic losses to the cattle industries worldwide. Up to now, some mechanisms involved in host–BVDV interaction are still not fully understood. The discovery of long non-coding RNAs (lncRNAs) has provided a new perspective on gene regulation in diverse biological contexts, particularly in viral infection and host immune responses. However, little is known about the profiles and functions of lncRNAs in host cells in response to BVDV infection. Here, we utilized Illumina sequencing to explore lncRNAs profiles in cytopathic (CP) biotype BVDV-infected MDBK cells to further reveal the potential roles of lncRNAs in BVDV infection and host–BVDV interaction with integrated analysis of lncRNAs and mRNA expression profiles. A total of 1747 significantly differentially expressed genes, DEGs (156 lncRNAs and 1591 mRNAs) were obtained via RNA-seq in BVDV-infected MDBK cells compared to mock-infected cells. Next, these DE lncRNAs and mRNAs were subjected to construct lncRNAs-mRNAs co-expression network followed by the prediction of potential functions of the DE lncRNAs. Co-expression network analysis elucidated that DE lncRNAs were significant enrichment in NOD-like receptor, TNF, NF-ĸB, ErbB, Ras, apoptosis, and fatty acid biosynthesis pathways, indicating that DE lncRNAs play important roles in host–BVDV interactions. Our data give an overview of changes in transcriptome and potential roles of lncRNAs, providing molecular biology basis for further exploring the mechanisms of host–BVDV interaction.