Citric Acid Cycle Genes Research Articles

Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

BackgroundFilamentous fungal cell factories are used to produce numerous proteins, enzymes, and organic acids. Protein secretion and filamentous growth are tightly coupled at the hyphal tip. Additionally, both these processes require ATP and amino acid precursors derived from the citric acid cycle. Despite this interconnection of organic acid production and protein secretion/filamentous growth, few studies in fungi have identified genes which may concomitantly impact all three processes.ResultsWe applied a novel screen of a global co-expression network in the cell factory Aspergillus niger to identify candidate genes which may concomitantly impact macromorphology, and protein/organic acid fermentation. This identified genes predicted to encode the Golgi localized ArfA GTPase activating protein (GAP, AgeB), and ArfA guanine nucleotide exchange factors (GEFs SecG and GeaB) to be co-expressed with citric acid cycle genes. Consequently, we used CRISPR-based genome editing to place the titratable Tet-on expression system upstream of ageB, secG, and geaB in A. niger. Functional analysis revealed that ageB and geaB are essential whereas secG was dispensable for early filamentous growth. Next, gene expression was titrated during submerged cultivations under conditions for either protein or organic acid production. ArfA regulators played varied and culture-dependent roles on pellet formation. Notably, ageB or geaB expression levels had major impacts on protein secretion, whereas secG was dispensable. In contrast, reduced expression of each predicted ArfA regulator resulted in an absence of citric acid in growth media. Finally, titrated expression of either GEFs resulted in an increase in oxaloacetic acid concentrations in supernatants.ConclusionOur data suggest that the Golgi may play an underappreciated role in modulating organic acid titres during industrial applications, and that this is SecG, GeaB and AgeB dependent in A. niger. These data may lead to novel avenues for strain optimization in filamentous fungi for improved protein and organic acid titres.

Long‐Term Electrically‐Induced Muscle Exercise Duration Modulates Distinct Gene Signaling Pathways in People with Spinal Cord Injury

Exercise as a form of medicine attenuates the development of chronic non‐communicable diseases (NCDs) in people with intact nervous systems as they age. However, there is a knowledge gap regarding the influence of electrically induced skeletal muscle exercise on NCDs in people with spinal cord injury (SCI). Gene signaling pathway analysis offers an opportunity to understand the long‐term effects of electrically induced exercise on people with chronic and complete paralysis from SCI; providing a basis for interventions to be studied in future clinical trials.PurposeTo determine if long term electrically induced skeletal muscle exercise regulates complex network signaling pathways associated with improved metabolic health in people with SCI.MethodsWe analyzed 17 paired muscle samples from 11 males with complete SCI who completed at least 3 months of a unilateral exercise training program using electrical stimulation. During their exercise training, participants underwent routine physiological assessments. At the end of their exercise training, muscle samples were obtained from the exercised and non‐exercised limb. Extracted RNA was hybridized to Affymetrix Human Exon microarrays. Probe intensities were normalized using a robust multi‐array average. Gene expression values were analyzed using an a priori list of gene sets defined by the Reactome Pathways Knowledgebase and genes related to metabolic and hypertrophy pathways in skeletal muscle using the gene set enrichment algorithm and a fold‐change signature. Muscle biopsy samples were grouped together as a single cohort, and subdivided into 2 groups based on the training duration and muscle physiologic properties (<6 and >6 months of training). All participants provided written consent approved by the University of Iowa Institutional Review Board in compliance with the Declaration of Helsinki.ResultsWe analyzed over 17,000 genes and 1,900 genesets curated from the Reactome Pathways Knowledgebase. When we subdivided the muscle samples into 2 phenotypes based on training duration, we found 19 pathways associated with metabolism and mitochondrial function to be significantly up regulated (FDR < 0.25) in the trained phenotype compared to the untrained phenotype. A subset of representative genes that were up regulated included the mitochondria protein carrier genes (MPC1 and MPC2), the citric acid cycle genes (SDHA, SDHB), the oxidative phosphorylation genes (NDUFA2 and NDUFB1), and mitochondrial biogenesis genes (PGC1α).ConclusionsOverall health is dependent, in part, on skeletal muscle size and metabolic capacity. 6 months of chronic electrically induced exercise was sufficient to reverse the expression of important metabolic gene pathways needed to recreate an oxidative phenotype in chronically paralyzed skeletal muscles. Future studies are underway to ascertain if electrically induced exercise attenuates the development of NCDs in people with SCI.Support or Funding InformationResearch Support: This study was funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development: R01HD084645, R01HD082109This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Effects of gltA and arcA Mutations on Biomass and 1,3-Propanediol Production in Klebsiella pneumoniae

We have previously engineered a Klebsiella pneumoniae strain to increase the 1,3-production (1,3-PDO) yield from glycerol. Here, we describe the further engineering of this strain to improve the biomass formation, resulting in an increase in the 1,3-PDO production. The amino acid lysine at the 167th position in citrate synthase was substituted with alanine using genome editing method to reduce the binding affinity of the enzyme to nicotinamide adenine dinucleotide (NADH). In addition, the arcA gene was deleted that resulted in the inhibition of the expression of citric acid cycle genes under limited aeration conditions. As a consequence, the biomass production was enhanced by 34% and 1,3-PDO formation was elevated from 9.58 to 16.71 g/L. The production of 1,3-PDO per dry cell weight enhanced by 30% from 2.40 to 3.11 g·L−1·DCW−1. The phenotypic changes in the strains were confirmed through the analyses of redox ratio, ATP levels, and changes in the expression of genes related to citric acid cycle and 1,3-PDO pathway.

Comparison of fruit organic acids and metabolism-related gene expression between Cerasus humilis (Bge.) Sok and Cerasus glandulosa (Thunb.) Lois.

Cerasus humilis (Bge.) Sok and Cerasus glandulosa (Thunb.) Lois are economically important fruit-producing shrubs. Although these two species have similar looking fruits, their fruit organic acid contents differ drastically. In this study, we focused on comparing the organic acid content, activity of enzymes gene expression involved in organic acid metabolism in both C. humilis and C. glandulosa fruits. To investigate the differences of organic acid metabolism in fruits of these two species, a comparative transcriptome analysis was performed. Our results showed that temporal changes of two main organic acids exhibited different trends in these two species. Transcriptome sequencing of developing C. humilis and C. glandulosa fruits systematically revealed 6,594 differentially expressed genes. Compared with C. humilis, the expression levels of 3,469 and 3,125 genes were up- and down-regulated in C. glandulosa, respectively, including one PEPC gene, 12 malic acid metabolism genes, 25 citric acid cycle genes, and 194 NAD/NADP metabolism genes. The correlation analysis and principal component analysis of gene expression, enzymatic activity and organic acid content showed that differences in the expression of genes encoding the NAD-malate dehydrogenase (NAD-MDH) and NADP-malate enzyme (NADP-ME) contributed substantially to the observed differences in organic acid accumulation of two species. Our results provide a solid foundation for future elucidation of key mechanisms regulating organic acid biosynthesis in C. humilis and C. glandulosa fruits and could lead to efficient and highly targeted generation of more commercially accepted cultivars.

Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs.

The genome sequence of the obligate chemolithoautotroph Hydrogenovibrio crunogenus paradoxically predicts a complete oxidative citric acid cycle (CAC). This prediction was tested by multiple approaches including whole cell carbon assimilation to verify obligate autotrophy, phylogenetic analysis of CAC enzyme sequences and enzyme assays. Hydrogenovibrio crunogenus did not assimilate any of the organic compounds provided (acetate, succinate, glucose, yeast extract, tryptone). Enzyme activities confirmed that its CAC is mostly uncoupled from the NADH pool. 2-Oxoglutarate:ferredoxin oxidoreductase activity is absent, though pyruvate:ferredoxin oxidoreductase is present, indicating that sequence-based predictions of substrate for this oxidoreductase were incorrect, and that H. crunogenus may have an incomplete CAC. Though the H. crunogenus CAC genes encode uncommon enzymes, the taxonomic distribution of their top matches suggests that they were not horizontally acquired. Comparison of H. crunogenus CAC genes to those present in other 'Proteobacteria' reveals that H. crunogenus and other obligate autotrophs lack the functional redundancy for the steps of the CAC typical for facultative autotrophs and heterotrophs, providing another possible mechanism for obligate autotrophy.

Inverse Regulation of Inflammation and Mitochondrial Function in Adipose Tissue Defines Extreme Insulin Sensitivity in Morbidly Obese Patients

Obesity is associated with insulin resistance, a major risk factor for type 2 diabetes and cardiovascular disease. However, not all obese individuals are insulin resistant, which confounds our understanding of the mechanistic link between these conditions. We conducted transcriptome analyses on 835 obese subjects with mean BMI of 48.8, on which we have previously reported genetic associations of gene expression. Here, we selected ∼320 nondiabetic (HbA1c <7.0) subjects and further stratified the cohort into insulin-resistant versus insulin-sensitive subgroups based on homeostasis model assessment–insulin resistance. An unsupervised informatics analysis revealed that immune response and inflammation-related genes were significantly downregulated in the omental adipose tissue of obese individuals with extreme insulin sensitivity and, to a much lesser extent, in subcutaneous adipose tissue. In contrast, genes related to β-oxidation and the citric acid cycle were relatively overexpressed in adipose of insulin-sensitive patients. These observations were verified by querying an independent cohort of our published dataset of 37 subjects whose subcutaneous adipose tissue was sampled before and after treatment with thiazolidinediones. Whereas the immune response and inflammation pathway genes were downregulated by thiazolidinedione treatment, β-oxidation and citric acid cycle genes were upregulated. This work highlights the critical role that omental adipose inflammatory pathways might play in the pathophysiology of insulin resistance, independent of body weight.

Wheat Gene Expression is Differentially Affected by a Virulent Russian Wheat Aphid Biotype

An improved understanding of the complex interactions between plants and aphids is emerging. Recognition of aphid feeding in plant tissues involves production of several defense response signaling pathways and downstream production of defense and detoxification compounds. Feeding by Russian wheat aphid, Diuraphis noxia (Kurdjumov), a serious pest of cereal crops worldwide, induces foliar deformity and chlorophyll loss during compatible wheat-D. noxia interactions. Experiments described here revealed significant differences in level and pattern of gene expression in defense response signaling and metabolic pathways between compatible and incompatible D. noxia-wheat interactions. The jasmonate (JA)-signaling genes LOX, AOS, and AOC were significantly more upregulated (~3- to 7 fold) in incompatible interactions than in compatible interactions (~2.5 to 3.5 fold) as early as 1 h post D. noxia infestation (hpi). Cellulose synthase, responsible for strengthening plant cell walls via cellulose production, was also more upregulated in incompatible interactions (4 to 7 fold) than in compatible interactions (1 to 3.5 fold). In contrast, glycolysis and citric acid cycle genes were significantly downregulated (~1.5 to 2 fold) in incompatible interactions and upregulated or less downregulated in compatible interactions from 6 to 72 hpi. Differences in expression of JA-signaling genes between feeding site tissues and non-feeding site tissues suggest that D. noxia defense response signals in wheat are restricted primarily to aphid feeding sites in the initial 6 hpi. This is the first report of differential upregulation of plant genes at 1 hpi in incompatible interactions involving aphid herbivory. Early wheat plant defense responses in incompatible D. noxia interactions at 1, 3, and 6 hpi appear to be important aspects of D. noxia resistance in wheat.

Short-term administration of rhGH increases markers of cellular proliferation but not milk protein gene expression in normal lactating women

Growth hormone is one of few pharmacologic agents known to augment milk production in humans. We hypothesized that recombinant human GH (rhGH) increases the expression of cell proliferation and milk protein synthesis genes. Sequential milk and blood samples collected over four days were obtained from five normal lactating women. Following 24 h of baseline milk and blood sampling, rhGH (0.1 mg/kg/day) was administered subcutaneously once daily for 3 days. Gene expression changes were determined by microarray studies utilizing milk fat globule RNA isolated from each milk sample. Following rhGH administration, DNA synthesis and cell cycle genes were induced, while no significant changes were observed in the expression of milk synthesis genes. Expression of glycolysis and citric acid cycle genes were increased by day 4 compared with day 1, while lipid synthesis genes displayed a circadian-like pattern. Cell cycle gene upregulation occurred after a lag of ∼2 days, likely explaining the failure to increase milk production after only 3 days of rhGH treatment. We conclude that rhGH induces expression of cellular proliferation and metabolism genes but does not induce milk protein gene expression, as potential mechanisms for increasing milk production and could account for the known effect of rhGH to increase milk production following 7-10 days.

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in ε-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.

Transition of Escherichia coli from Aerobic to Micro-aerobic Conditions Involves Fast and Slow Reacting Regulatory Components

Understanding life at a systems level is a major aim of biology. The bacterium Escherichia coli offers one of the best opportunities to achieve this goal. It is a metabolically versatile bacterium able to respond to changes in oxygen availability. This ability is a crucial component of its lifestyle, allowing it to thrive in aerobic external environments and under the oxygen-starved conditions of a host gut. The controlled growth conditions of chemostat culture were combined with transcript profiling to investigate transcriptome dynamics during the transition from aerobic to micro-aerobic conditions. In addition to predictable changes in transcripts encoding proteins of central metabolism, the abundances of transcripts involved in homeostasis of redox-reactive metals (Cu and Fe), and cell envelope stress were significantly altered. To gain further insight into the responses of the regulatory networks, the activities of key transcription factors during the transition to micro-aerobic conditions were inferred using a probabilistic modeling approach, which revealed that the response of the direct oxygen sensor FNR was rapid and overshot, whereas the indirect oxygen sensor ArcA reacted more slowly. Similarly, the cell envelope stress sensors RpoE and CpxR reacted rapidly and more slowly, respectively. Thus, it is suggested that combining rapid and slow reacting components in regulatory networks might be a feature of systems in which a signal is perceived by two or more functionally related transcription factors controlling overlapping regulons.

Defective carbohydrate metabolism in mice homozygous for the tubby mutation

Tub is a member of a small gene family, the tubby-like proteins (TULPs), with predominant expression in neurons. Mice carrying a mutation in Tub develop retinal and cochlear degeneration as well as late-onset obesity with insulin resistance. During behavioral and metabolic testing, we found that homozygous C57BL/6J-Tub(tub) mice have a lower respiratory quotient than C57BL/6J controls before the onset of obesity, indicating that tubby homozygotes fail to activate carbohydrate metabolism and instead rely on fat metabolism for energy needs. In concordance with this, tubby mice show higher excretion of ketone bodies and accumulation of glycogen in the liver. Quantitation of liver mRNA levels shows that, during the transition from light to dark period, tubby mice fail to induce glucose-6-phosphate dehydrogenase (G6pdh), the rate-limiting enzyme in the pentose phosphate pathway that normally supplies NADPH for de novo fatty acid synthesis and glutathione reduction. Reduced G6PDH protein levels and enzymatic activity in tubby mice lead accordingly to lower levels of NADPH and reduced glutathione (GSH), respectively. mRNA levels for the lipolytic enzymes acetyl-CoA synthetase and carnitine palmitoyltransferase are increased during the dark cycle and decreased during the light period, and several citric acid cycle genes are dysregulated in tubby mice. Examination of hypothalamic gene expression showed high levels of preproorexin mRNA leading to accumulation of orexin peptide in the lateral hypothalamus. We hypothesize that abnormal hypothalamic orexin expression leads to changes in liver carbohydrate metabolism and may contribute to the moderate obesity observed in tubby mice.

Two genetically-distinct and differentially-regulated aconitases (AcnA and AcnB) in Escherichia coli.

An acnA mutant of Escherichia coli was constructed by replacing the chromosomal acnA gene by an internally deleted derivative containing a kanR cassette. Southern and Western blotting confirmed that the acnA gene had been replaced by the disrupted gene and that the aconitase A protein was no longer expressed. However, the mutant failed to exhibit the anticipated glutamate auxotrophy and it retained a residual aconitase activity. This activity was due to an analogous unstable enzyme(s) designated aconitase B. Studies on the regulation of aconitase A synthesis using an acnA-lacZ translational fusion showed that the acnA gene resembles other citric acid cycle genes in being subject to CRP-mediated catabolite repression and ArcA-mediated anaerobic repression. In addition to being activated by the SoxRS oxidative stress regulatory system, the acnA gene appeared to be activated by the ferric uptake regulator (Fur). It was concluded that the acnA gene belongs to at least four global regulatory networks, crp, arcA, fur and soxRS. In contrast, the aconitase B activity decreased after exposure to oxidative stress and was less affected by anaerobiosis. Comparable studies with the fumarase genes (fumA, B and C) indicated that fumA (encoding the unstable aerobic iron-sulphur-containing fumarase) is activated by the ferric uptake regulator (Fur) and fumC (encoding the stable fumarase) is activated by the SoxRS oxidative stress regulatory system.

Cloning and expression of the succinyl-CoA synthetase genes of Escherichia coli K12.

The genes encoding both subunits of the succinyl-CoA synthetase of Escherichia coli have been identified as distal genes of the suc operon, which also encodes the dehydrogenase (Elo; sucA) and succinyltransferase (E2o; sucB) components of the 2-oxoglutarate dehydrogenase complex. The newly defined genes express polypeptides of 41 kDa (sucC) and 31 kDa (sucD), corresponding to the beta and alpha subunits of succinyl-CoA synthetase, respectively. The genes are thus located at 16.8 min in the E. coli linkage map, together with the citrate synthase (gltA) and succinate dehydrogenase (sdh) genes, in a cluster of nine citric acid cycle genes: gltA-sdhCDAB-sucABCD. Four deletion strains lacking all of these citric acid cycle enzymes were characterized. The succinyl-CoA synthetase activities of strains harbouring plasmids containing the sucC and sucD genes were amplified some fourfold. Further enzymological studies indicated that expression of succinyl-CoA synthetase is coordinately regulated with 2-oxoglutarate dehydrogenase.