Structural and biochemical characterization of mitochondrial citrate synthase 4 from Arabidopsis thaliana

Citrate synthase (CS) catalyzes the conversion of oxaloacetate and acetyl coenzyme A into citrate and coenzyme A in the mitochondrial tricarboxylic acid (TCA) cycle. In plants, mitochondrial metabolism, including the TCA cycle, occurs in interaction with photosynthetic metabolism. The controlled regulation of several enzymes in the TCA cycle, such as CS, is important in plants. Here, the first crystal structure of a plant mitochondrial CS, CSY4 from Arabidopsis thaliana (AtCSY4), has been determined. Structural comparison of AtCSY4 with mitochondrial CSs revealed a high level of similarity. Inhibition analysis showed a similar manner of inhibition as in mitochondrial CSs. The effect of oxidation on one of a pair of cysteine residues in AtCSY4 was speculated upon based on the folded structure.

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A detailed biochemical characterization of phosphopantothenate synthetase, a novel enzyme involved in coenzyme A biosynthesis in the Archaea

Extremophiles ◽

10.1007/s00792-012-0477-5 ◽

2012 ◽

Vol 16 (6) ◽

pp. 819-828 ◽

Cited By ~ 14

Author(s):

Takuya Ishibashi ◽

Hiroya Tomita ◽

Yuusuke Yokooji ◽

Tatsuya Morikita ◽

Bunta Watanabe ◽

...

Keyword(s):

Coenzyme A ◽

Biochemical Characterization ◽

Coenzyme A Biosynthesis

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Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

Applied and Environmental Microbiology ◽

10.1128/aem.00218-14 ◽

2014 ◽

Vol 80 (10) ◽

pp. 3044-3052 ◽

Cited By ~ 40

Author(s):

Alexey Vorobev ◽

Sheeja Jagadevan ◽

Sunit Jain ◽

Karthik Anantharaman ◽

Gregory J. Dick ◽

...

Keyword(s):

Methane Oxidation ◽

Coenzyme A ◽

Draft Genome ◽

Carbon Assimilation ◽

Tca Cycle ◽

Content Type ◽

The Tca Cycle ◽

Conversion Of Methane ◽

Oxidative Transformations ◽

Rate Limiting

ABSTRACTA minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotrophMethylocystissp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments withMethylocystissp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses ofMethylocystissp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears thatMethylocystissp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated.

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High-level expression of the trucated alpha chain of Human high-affinity receptor for IgE as a soluble form by baculovirus-infected insect cells. Biochemical characterization of the recombinant product.

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1994.tb18660.x ◽

1994 ◽

Vol 220 (2) ◽

pp. 593-598 ◽

Cited By ~ 20

Author(s):

Shintaro YAGI ◽

Mitsuaki YANAGIDA ◽

Akira HASEGAWA ◽

Ko OKUMURA ◽

Chisei RA

Keyword(s):

Insect Cells ◽

Biochemical Characterization ◽

Soluble Form ◽

High Level Expression ◽

Recombinant Product ◽

High Affinity Receptor ◽

Infected Insect ◽

Affinity Receptor ◽

High Level

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Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana

International Journal of Molecular Sciences ◽

10.3390/ijms21197404 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7404

Author(s):

Yanqiao Zhu ◽

Oliver Berkowitz ◽

Jennifer Selinski ◽

Andreas Hartmann ◽

Reena Narsai ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Hordeum Vulgare ◽

Mitochondrial Biogenesis ◽

Expression Patterns ◽

Tca Cycle ◽

Transcript Abundance ◽

Pentatricopeptide Repeat ◽

Orthologous Genes ◽

Regulatory Processes ◽

High Level

Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.

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High-level secretion inPichia pastorisand biochemical characterization of the recombinantkringle 2 domain of tissue-type plasminogen activator

Biotechnology and Applied Biochemistry ◽

10.1111/j.1470-8744.1997.tb00415.x ◽

1997 ◽

Vol 25 (1) ◽

pp. 63-74 ◽

Cited By ~ 14

Author(s):

Stephanie L. Nilsen ◽

Melanie E. DeFord ◽

Mary Prorok ◽

Bakshy A.K. Chibber ◽

Roger K. Bretthauer ◽

...

Keyword(s):

Plasminogen Activator ◽

Biochemical Characterization ◽

Tissue Type ◽

Tissue Type Plasminogen Activator ◽

Type Plasminogen Activator ◽

High Level

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RSM–GA Based Optimization of Bacterial PHA Production and In Silico Modulation of Citrate Synthase for Enhancing PHA Production

Biomolecules ◽

10.3390/biom9120872 ◽

2019 ◽

Vol 9 (12) ◽

pp. 872 ◽

Cited By ~ 1

Author(s):

Apoorva Rao ◽

Shafiul Haque ◽

Hesham A. El-Enshasy ◽

Vineeta Singh ◽

Bhartendu Nath Mishra

Keyword(s):

Molecular Docking ◽

Nitrogen Source ◽

In Silico ◽

Citrate Synthase ◽

Tca Cycle ◽

Management Approach ◽

Carbon And Nitrogen ◽

The Tca Cycle ◽

Different Types ◽

Pha Production

The inexhaustible nature and biodegradability of bioplastics like polyhydroxyalkanoates (PHAs) make them suitable assets to replace synthetic plastics. The eventual fate of these eco-friendly and non-toxic bioplastics relies upon the endeavors towards satisfying cost and, in addition, execution necessity. In this study, we utilized and statistically optimized different food (kitchen-/agro-) waste as a sole carbon/nitrogen source for the production of PHA at a reduced cost, indicating a proficient waste administration procedure. Seven different types of kitchen-/agro-waste were used as unique carbon source and four different types of nitrogen source were used to study their impact on PHA production by Bacillus subtilis MTCC 144. Among four different studied production media, mineral salt medium (MSM) (biomass: 37.7 g/L; cell dry weight: 1.8 g/L; and PHA: 1.54 g/L) was found most suitable for PHA production. Further, carbon and nitrogen components of MSM were optimized using one-factor-at-a-time experiments, and found that watermelon rind (PHA = 12.97 g/L) and pulse peel (PHA = 13.5 g/L) were the most suitable carbon and nitrogen sources, respectively, in terms of PHA (78.60%) recovery. The concentrations of these factors (sources) were statistically optimized using response surface methodology coupled with the genetic algorithm approach. Additionally, in order to enhance microbial PHA production, the interaction of citrate synthase, a key enzyme in the TCA cycle, with different known inhibitors was studied using in silico molecular docking approach. The inhibition of citrate synthase induces the blockage of the tricarboxylic cycle (TCA), thereby increasing the concentration of acetyl-CoA that helps in enhanced PHA production. Molecular docking of citrate synthase with different inhibitors of PubChem database revealed that hesperidin (PubChem compound CID ID 10621), generally present in citrus fruits, is the most efficient inhibitor of the TCA cycle with the binding score of –11.4 and warrants experimental validation. Overall, this study provides an efficient food waste management approach by reducing the production cost and enhancing the production of PHA, thereby lessening our reliance on petroleum-based plastics.

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