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Biochemistry
Published in Ronald Fayer, Lihua Xiao, Cryptosporidium and Cryptosporidiosis, 2007
Pyruvate may be converted to acetyl-CoA by a bifunctional pyruvate, pyruvate:NADP+ oxidoreductase (PNO), which contains a pyruvate-ferredoxin oxidoreductase (PFO) domain and an NADPH-cytochrome P450 reductase domain (CPR) (Rotte et al., 2001). The architecture of PNO is unique to Cryptosporidium, as it is not present in any other apicomplexans examined so far, but found only in a distant free-living protist, Euglena gracilis (Rotte et al., 2001). Whereas Euglena PNO apparently contains a signal peptide sequence and is localized in the mitochondria, CpPNO is found in the cytosol (Ctrnacta et al., 2006). Acetyl-CoA can be converted by acetyl-CoA carboxylase (ACC) to malonyl-CoA, which serves as the building block in synthesizing fatty acids and polyketides. This parasite possesses only one cytosolic ACC, lacking the plastid ortholog found in Toxoplasma and Plasmodium (Jelenska et al., 2001, 2002; Gornicki, 2003). At least two organic end products can be formed from acetyl-CoA, including acetate by an acetate-CoA ligase (AceCL, also referred to as acetyl-CoA synthetase), in which an extra ATP molecule can be generated from AMP and PPi, and ethanol, by a bifunctional type E alcohol dehydrogenase (adhE) that first makes aldehyde and then ethanol. Ethanol may also be produced from pyruvate by pyruvate decarboxylase (PDC) coupled with a monofunctional ADH1. Pyruvate may also be converted to lactate by lactate dehydrogenase (LDH).
Systems Biology Approach and Modeling for the Design of Microbial Cell Factories
Published in Kazuyuki Shimizu, Metabolic Regulation and Metabolic Engineering for Biofuel and Biochemical Production, 2017
In E. coli, acetate is formed from AcCoA by Pta-Ack and also from pyruvate by pyruvate oxidase, Pox (Wolfe 2005). Acetate can be metabolized to AcCoA either by the reversed reactions of Pta-Ack or by acetyl CoA synthetase (ACS). Acetate formation has been known to be due to metabolic imbalance, where the rate of AcCoA formation via glycolysis surpasses the capacity of the TCA cycle in E. coli (Majewski and Domach 1990). Pox and Acs may be expressed as functions of the sigma factor (σ38) RpoS, but it may be difficult to predict the behavior of RpoS, while Acs may be expressed as a function of cAMP-Crp, where ACS is activated by cAMP-Crp during gluconeogenic phase (Matsuoka and Shimizu 2013).
Pseudomonas putida
Published in Martin Koller, The Handbook of Polyhydroxyalkanoates, 2020
Maria Tsampika Manoli, Natalia Tarazona, Aranzazu Mato, Beatriz Maestro, Jesús M. Sanz, Juan Nogales, M. Auxiliadora Prieto
A detailed β-oxidation pathway in P. putida and its connection with PHA metabolism is shown (see Figure 4.7 and Table 4.2). In short, the fatty acids are activated into acyl-CoA through the acyl-CoA synthetase (FadD). Subsequently, an acyl-CoA dehydrogenase (FadE) catalyzes the formation of a double bond yielding an enoyl-CoA. In the next step, a tetrameric complex formed by FadBA proteins carries out the hydration, oxidation, and thiolysis processes. This complex comprises five enzymatic reactions (enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, cis-Δ3-trans-Δ2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA epimerase, and 3-ketoacyl-CoA thiolase) and it is responsible for the removal of two carbon units from the acyl-chain [59]. The intermediates of the β-oxidation enoyl-CoA, (S)-3-hydroxyacyl-CoA, and 3-ketoacyl-CoA can be converted into (R)-3-HA-CoA, which are the PHA synthase substrates through a stereospecific trans-enoyl-CoA hydratase (PhaJ), an epimerase (FadB), or a specific ketoacyl-CoA reductase (FabG), respectively [20] (see Figure 4.7 and Table 4.2). Fatty acid β-oxidation pathway and its connection with PHA metabolism. Diagram with the main metabolic steps involved in the β-oxidation pathway (black lines), the proposed connection with PHA metabolism, the responsible genes involved in these metabolic pathways (bold gray letters), and the reaction exchanges (gray color) are shown. Figure abbreviations: (S)-HA-CoA: (S)-3-hydroxyacyl-CoA, (R)-HA-CoA: (R)-3-hydroxyacyl-CoA.
Using intracellular metabolic profiling to identify novel biomarkers of cisplatin-induced acute kidney injury in NRK-52E cells
Published in Journal of Toxicology and Environmental Health, Part A, 2022
Hae Ri Kim, Jae Hyeon Park, Song Hee Lee, Seung Jun Kwack, Jaewon Lee, Suhkmann Kim, Sungpil Yoon, Kyu-Bong Kim, Byung Mu Lee, Sam Kacew, Hyung Sik Kim
Acetyl-CoA synthetase (AceCS), a critical enzyme in acetate metabolism, appears to be important for both acetate uptake and acetate-dependent lipid synthesis during growth of cancer cells with a low-glycolytic phenotype. Hallows, Lee, and Denu (2006) determined that SIRT1 deacetylates and activates mammalian AceCS1 and in this study. AceCS1 expression was decreased in NRK-52E cells treated with CDDP. Consequently, acetate was not used for acetyl CoA synthesis and transported from NRK-52E cells into the media as AceCS1 induction was reduced following dysfunction of SIRT1 in response to CDDP presence. SIRT1 was shown to play an important role in both cellular senescence and cell death pathways (Michan and Sinclair 2007; Olivares et al. 2018; Rahman and Islam 2011). In particular, several investigators reported that SIRT1 protects cells from apoptosis or senescence in response to DNA damage by deacetylating p53 (Lee and Gu 2013; Ong and Ramasamy 2018). Qin et al. (2016) demonstrated that CDDP induced downregulation of SIRT1 and upregulation of acetylated p53 and Bax in NRK-52E cells. SIRT1 is also associated with acetate metabolism and may be a critical factor in nephrotoxicity.
Syntrophy of bacteria and archaea in the anaerobic catabolism of hydrocarbon contaminants
Published in Critical Reviews in Environmental Science and Technology, 2023
Jean Damascene Harindintwali, Leilei Xiang, Fang Wang, Scott X. Chang, Zhiliang Zhao, Zhi Mei, Zhongjun Jia, Xin Jiang, Yong-guan Zhu, James M. Tiedje
Firstly, benzoate is converted into benzoyl-CoA by benzoate-CoA ligase or a CoA-transferase (Ghattas et al., 2017). The formed benzoyl-CoA may afterward go through ring cleavage, directed toward the central metabolism through β-oxidation to acetyl-CoA (Ghattas et al., 2017). Some of the reactions and enzymes involved in the conversion of benzoyl-CoA to acetyl-CoA are shown in Figure 3. The resulting acetyl-CoA can be metabolized to acetate with ATP synthesis in archaea, a process catalyzed by an ADP-forming acetyl-CoA synthetase (ACD) (Bräsen & Schönheit, 2004), according to reaction 2, ΔG°′ = − 4.0 kJ per mole.
Determination of bacterial intracellular and extracellular biotransformation compounds and biodegradation of kerosene based industrial rolling oils via gas chromatography-mass spectrometry
Published in Bioremediation Journal, 2019
Nyashadzashe P. Masvingwe, Sumaiya F. Jamal-Ally
To date, most research on the degradation of n-alkanes by bacteria has focused on the initial step of oxidation. In most of the documented cases, the n-alkane is oxidized into the corresponding primary alcohol by terminal monooxygenases/hydroxylases (Das & Chandran 2011). However, subterminal oxidation has also been reported for both short and long chain n-alkanes. From studies done on alkane hydroxylases involved in bacterial aerobic catabolism of n-alkanes, two classes of enzymes are deemed to be responsible for the biodegradation these are (1) the cytochrome P-450 enzymes in bacteria and yeast and (2) the class of bacteria particulate alkane hydroxylases (pAHs) (Shao & Wang 2013). Within the second class are Alk-B type none heme diiron monooxygenases (Karigar & Rao 2011). These enzymes facilitate the degradation of long chain alkanes from C5 to C16 by Actinomycetales and Proteobacteria (Karigar & Rao 2011). Alk-B type enzymes work in conjunction with two proteins that serve in electron transfer, a mononuclear iron rubredoxin reductase and a dinuclear iron rubredoxin (Ratledge 2012). These transfer electrons from NADH to the active site of the alkane hydroxylase (Olajire & Essien 2014). Alcohol dehydrogenase and aldehyde dehydrogenase convert the resultant primary alcohols to the corresponding aldehyde and carboxylic acid respectively (Ratledge 2012). Thereafter acetyl-Coenzyme A (acyl-CoA) synthetase converts the carboxylic acid to acyl-CoA which enters the β-oxidation pathway (Abbasian et al. 2015). Pseudomonas putida GPo1 is the most widely studied species that employs this pathway (Rojo 2010). Several n-alkane degraders possess both pAHs and cytochrome P-450 enzymes. An example of this is seen in Rhodococcus erythropolis which contains 2 cytochrome P-450 enzymes (CYP-153). It also contains up to 5 pAHs (Rojo 2010). Acitenobacter borkumensis showed further enzyme systems that are involved in the degradation of long chain n-alkanes up to C32, putative monooxygenases and oxidoreductases (Singh, Kumari, & Mishra 2012). Other bacterial strains have also shown degrading capabilities of up to C18 long chains using different enzyme systems. For example, Acitenobacter spp. M1 has a target substrate range of C10 to C30 using a Flavin-containing n-alkane dioxygenase (Singh, Kumari, & Mishra 2012). P. fluorescens has been reported to also grow on n-alkanes of length ranging from C18 to C28 (Xia et al. 2014).