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Petushkova E, Mayorova E, Tsygankov A. TCA Cycle Replenishing Pathways in Photosynthetic Purple Non-Sulfur Bacteria Growing with Acetate. Life (Basel) 2021; 11:711. [PMID: 34357087 PMCID: PMC8307300 DOI: 10.3390/life11070711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/27/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Purple non-sulfur bacteria (PNSB) are anoxygenic photosynthetic bacteria harnessing simple organic acids as electron donors. PNSB produce a-aminolevulinic acid, polyhydroxyalcanoates, bacteriochlorophylls a and b, ubiquinones, and other valuable compounds. They are highly promising producers of molecular hydrogen. PNSB can be cultivated in organic waste waters, such as wastes after fermentation. In most cases, wastes mainly contain acetic acid. Therefore, understanding the anaplerotic pathways in PNSB is crucial for their potential application as producers of biofuels. The present review addresses the recent data on presence and diversity of anaplerotic pathways in PNSB and describes different classifications of these pathways.
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Affiliation(s)
- Ekaterina Petushkova
- Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems Russian Academy of Sciences, 2, Institutskaya Str, 142290 Pushchino, Moscow Region, Russia; (E.P.); (E.M.)
| | - Ekaterina Mayorova
- Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems Russian Academy of Sciences, 2, Institutskaya Str, 142290 Pushchino, Moscow Region, Russia; (E.P.); (E.M.)
- Pushchino State Institute of Natural Science, The Federal State Budget Educational Institution of Higher Education, 3, Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Anatoly Tsygankov
- Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems Russian Academy of Sciences, 2, Institutskaya Str, 142290 Pushchino, Moscow Region, Russia; (E.P.); (E.M.)
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Yin J, Wei Y, Liu D, Hu Y, Lu Q, Ang EL, Zhao H, Zhang Y. An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine. J Biol Chem 2019; 294:15662-15671. [PMID: 31455636 DOI: 10.1074/jbc.ra119.010406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/26/2019] [Indexed: 11/06/2022] Open
Abstract
The reductive pyrimidine catabolic pathway is the most widespread pathway for pyrimidine degradation in bacteria, enabling assimilation of nitrogen for growth. This pathway, which has been studied in several bacteria including Escherichia coli B, releases only one utilizable nitrogen atom from each molecule of uracil, whereas the other nitrogen atom remains trapped in the end product β-alanine. Here, we report the biochemical characterization of a β-alanine:2-oxoglutarate aminotransferase (PydD) and an NAD(P)H-dependent malonic semialdehyde reductase (PydE) from a pyrimidine degradation gene cluster in the bacterium Lysinibacillus massiliensis Together, these two enzymes converted β-alanine into 3-hydroxypropionate (3-HP) and generated glutamate, thereby making the second nitrogen from the pyrimidine ring available for assimilation. Using bioinformatics analyses, we found that PydDE homologs are associated with reductive pyrimidine pathway genes in many Gram-positive bacteria in the classes Bacilli and Clostridia. We demonstrate that Bacillus smithii grows in a defined medium with uracil or uridine as its sole nitrogen source and detected the accumulation of 3-HP as a waste product. Our findings extend the reductive pyrimidine catabolic pathway and expand the diversity of enzymes involved in bacterial pyrimidine degradation.
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Affiliation(s)
- Jinyu Yin
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore .,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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Song CW, Kim JW, Cho IJ, Lee SY. Metabolic Engineering of Escherichia coli for the Production of 3-Hydroxypropionic Acid and Malonic Acid through β-Alanine Route. ACS Synth Biol 2016; 5:1256-1263. [PMID: 26925526 DOI: 10.1021/acssynbio.6b00007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli was metabolically engineered to produce industrially important platform chemicals, 3-hydroxypropionic acid (3-HP) and malonic acid (MA), through the β-alanine (BA) route. First, various combinations of downstream enzymes were screened and BA pyruvate transaminase (encoded by pa0132) from P. aeruginosa was selected to generate malonic semialdehyde (MSA) from BA. This platform strain was engineered by introducing E. coli MSA reductase (encoded by ydfG) to reduce MSA to 3-HP. Replacement of native promoter of the sdhC gene with the strong trc promoter in the genome increased 3-HP production to 3.69 g/L in flask culture. Introduction of E. coli semialdehyde dehydrogenase (encoded by yneI) into the platform strain resulted in the production of MA, and additional deletion of the ydfG gene increased MA production to 0.450 g/L in flask culture. Fed-batch cultures of final engineered strains resulted in the production of 31.1 g/L 3-HP or 3.60 g/L MA from glucose.
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Affiliation(s)
- Chan Woo Song
- Metabolic
and Biomolecular Engineering National Research Laboratory, Department
of Chemical and Biomolecular Engineering (BK21 plus program), Center
for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Je Woong Kim
- Metabolic
and Biomolecular Engineering National Research Laboratory, Department
of Chemical and Biomolecular Engineering (BK21 plus program), Center
for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - In Jin Cho
- Metabolic
and Biomolecular Engineering National Research Laboratory, Department
of Chemical and Biomolecular Engineering (BK21 plus program), Center
for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic
and Biomolecular Engineering National Research Laboratory, Department
of Chemical and Biomolecular Engineering (BK21 plus program), Center
for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- BioInformatics
Research Center and BioProcess Engineering Research Center, KAIST, Daejeon 34141, Republic of Korea
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A β-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain AAC. Appl Environ Microbiol 2016; 82:3846-3856. [PMID: 27107110 PMCID: PMC4907197 DOI: 10.1128/aem.00665-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
We previously isolated the transaminase KES23458 from Pseudomonas sp. strain AAC as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of KES23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via KES23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A (CoA)-dependent reaction to form acetyl-CoA and a significantly slower CoA-independent reaction to form acetate. These findings support the original functional assignment of KES23458 as a β-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for Pseudomonas sp. strain AAC. IMPORTANCE We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.
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Chohnan S, Takamura Y. Malonate Decarboxylase in Bacteria and Its Application for Determination of Intracellular Acyl-CoA Thioesters. Microbes Environ 2004. [DOI: 10.1264/jsme2.19.179] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shigeru Chohnan
- Department of Bioresource Science, College of Agriculture, Ibaraki University
| | - Yoshichika Takamura
- Department of Bioresource Science, College of Agriculture, Ibaraki University
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Gama-Castro S, Núñez C, Segura D, Moreno S, Guzmán J, Espín G. Azotobacter vinelandii aldehyde dehydrogenase regulated by sigma(54): role in alcohol catabolism and encystment. J Bacteriol 2001; 183:6169-74. [PMID: 11591659 PMCID: PMC100092 DOI: 10.1128/jb.183.21.6169-6174.2001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Encystment in Azotobacter vinelandii is induced by n-butanol or beta-hydroxybutyrate (BHB). We identified a gene, encoding an aldehyde dehydrogenase, that was named aldA. An aldA mutation impaired bacterial growth on n-butanol, ethanol, or hexanol as the sole carbon source. Expression of aldA increased in cells shifted from sucrose to n-butanol and was shown to be dependent on the alternative sigma(54) factor. A mutation in rpoN encoding the sigma(54) factor also impaired growth on alcohols. Encystment on n-butanol, but not on BHB, was impaired in aldA or rpoN mutants, indicating that n-butanol is not an inducer of encystment by itself but must be catabolized in order to induce encystment.
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Affiliation(s)
- S Gama-Castro
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, Mexico
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Maeda T, Yoshinaga I, Shiba T, Murakami M, Wada A, Ishida Y. Cloning and sequencing of the gene encoding an aldehyde dehydrogenase that is induced by growing Alteromonas sp. Strain KE10 in a low concentration of organic nutrients. Appl Environ Microbiol 2000; 66:1883-9. [PMID: 10788355 PMCID: PMC101428 DOI: 10.1128/aem.66.5.1883-1889.2000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The protein composition of Alteromonas sp. strain KE10 cultured at two different organic-nutrient concentrations was determined by using two-dimensional polyacrylamide gel electrophoresis. The cellular levels of three proteins, OlgA, -B, and -C, were considerably higher in cells grown in a low concentration of organic nutrient medium (LON medium; 0.2 mg of carbon per liter) than cells grown in a high concentration of organic nutrient medium (HON; 200 mg of C liter(-1)) or cells starved for organic nutrients. In the LON medium, the cellular levels of the Olg proteins were higher at the exponential growth phase than at the stationary growth phase. A sequence of the gene for OlgA revealed that the amino acid sequence had a high degree of similarity to the NAD(+)-dependent aldehyde dehydrogenases of several bacteria. OlgA, expressed in Escherichia coli, catalyzed the dehydrogenation of acetaldehyde, propionaldehyde, and butyraldehyde. The aldehyde dehydrogenase activity of KE10 was higher in cells growing exponentially in LON medium than in HON. OlgA may be involved in the growth under low-nutrient conditions. The physiological role of OlgA is discussed here.
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Affiliation(s)
- T Maeda
- Department of Food Science and Technology, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan.
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Okibe N, Amada K, Hirano S, Haruki M, Imanaka T, Morikawa M, Kanaya S. Gene cloning and characterization of aldehyde dehydrogenase from a petroleum-degrading bacterium, strain HD-1. J Biosci Bioeng 1999; 88:7-11. [PMID: 16232565 DOI: 10.1016/s1389-1723(99)80167-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/1999] [Accepted: 04/09/1999] [Indexed: 11/30/2022]
Abstract
The hd-ald gene encoding aldehyde dehydrogenase (hd-ALDH) from an mixotrophic petroleum-degrading bacterium, strain HD-1 was cloned and sequenced. hd-ALDH (506 amino acids) is a member of the NAD+-dependent aldehyde dehydrogenase group. The hd-ald gene was expressed in Escherichia coli, and the recombinant enzyme was purified and characterized biochemically and enzymatically. The molecular weight of the enzyme was estimated to be 55,000 by SDS-PAGE, and 224,000 by gel filtration chromatography, suggesting that it acts as a tetramer. The CD spectrum suggests that the helical content of the enzyme is 10%. hd-ALDH was active on various aliphatic aldehyde substrates. The K(m) values of the enzyme were 6.4 microM for acetaldehyde, 4.2 microM for hexanal, 2.8 microM for octanal, and 0.84 microM for decanal, whereas the kcat values for these substrates were nearly equal (51-64 min(-1)). These results indicate that hd-ALDH acts preferentially on long-chain aliphatic aldehydes.
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Affiliation(s)
- N Okibe
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Osaka 565-0871 Japan
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Xu J, Johnson RC. aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp. J Bacteriol 1995; 177:3166-75. [PMID: 7768815 PMCID: PMC177007 DOI: 10.1128/jb.177.11.3166-3175.1995] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli aldB was identified as a gene that is negatively regulated by Fis but positively regulated by RpoS. The complete DNA sequence determined in this study indicates that aldB encodes a 56.3-kDa protein which shares a high degree of homology with an acetaldehyde dehydrogenase encoded by acoD of Alcaligenes eutrophus and an aldehyde dehydrogenase encoded by aldA of Vibrio cholerae and significant homology with a group of other aldehyde dehydrogenases from prokaryotes and eukaryotes. Expression of aldB is maximally induced during the transition from exponential phase to stationary phase. Its message levels are elevated three- to fourfold by a fis mutation and abolished by an rpoS mutation. In addition, the expression of an aldB-lacZ fusion was decreased about 20-fold in the absence of crp. DNase I footprinting analysis showed that five Fis binding sites and one Crp binding site are located within the aldB promoter region, suggesting that Fis and Crp are acting directly to control aldB transcription. AldB expression is induced by ethanol, but in contrast to that of most of the RpoS-dependent genes, the expression of aldB is not altered by an increase in medium osmolarity.
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Affiliation(s)
- J Xu
- Department of Biological Chemistry, UCLA School of Medicine 90095, USA
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Abstract
Rat brain contains substantial concentrations of free malonate (192 nmol/g wet weight) but origin and biological importance of the dicarboxylic acid are poorly understood. A dietary source has been excluded. A recently described malonyl-CoA decarboxylase deficiency is associated with malonic aciduria and clinical manifestations, including mental retardation. In an effort to study the metabolic origin of free malonate, several labeled acetyl-CoA precursors were administered by intracerebral injection. [2-14C]pyruvate or [1,5-14C]citrate produced radioactive glutamate but failed to label malonate. In contrast, [1-14C]acetate, [2-14C]acetate, and [1-14C]butyrate were converted to labeled glutamate and malonate after the same route of administration. The intracerebral injection of [1-14C]-beta-alanine as a precursor of malonic semialdehyde and possibly free malonate did not give rise to radioactivity in the dicarboxylate. The labeling pattern of malonic acid is compatible with the reaction sequence: acetyl-CoA----malonyl-CoA----malonate. The final step is thought to occur by transfer of the CoA-group from malonyl-CoA to succinate and/or acetoacetate. Labeling of malonate from acetate is most effective at the age of 7 days when the net concentration of the dicarboxylic acid in rat brain is still very low. At this age, butyrate was a better precursor of malonate than acetate. It is proposed that fatty acid oxidation provides the acetyl-CoA which functions as the precursor of free brain malonate. Compartmentation of malonate biosynthesis is likely because the acetyl-CoA precursors citrate and pyruvate are ineffective.
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Affiliation(s)
- K M Riley
- Research Service, Veterans Administration Medical Center, Albany, N.Y. 12208
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Holo H. Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO2 and acetate. Arch Microbiol 1989. [DOI: 10.1007/bf00413138] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Baldomà L, Aguilar J. Involvement of lactaldehyde dehydrogenase in several metabolic pathways of Escherichia coli K12. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47893-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Sugawara Y, Sasaki S. Purification and properties of aldehyde dehydrogenase from Proteus vulgaris. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 480:343-50. [PMID: 13839 DOI: 10.1016/0005-2744(77)90026-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
NADP-linked aldehyde dehydrogenase (aldehyde : NADP+ oxidoreductase, EC 1.2.1.4) was purified from Proteus vulgaris to the stage of homogeneity as judged by ultracentrifugation and polyacrylamide gel electrophoresis. The molecular weight of the purified enzyme was estimated to be 130000 by gel filtration. The enzyme which was crystallized from ammonium sulfate solution, lost its activity. The enzyme did not require coenzyme A, and the reaction was completely dependent on ammonium ions which could be partially replaced by Rb+ or K+. The optimum pH was about 9. Broad substrate specificity was observed and Km values for propionaldehyde, acetaldehyde and isovaleraldehyde were 1.7 - 10(-5), 4 - 10(-5) and 3 - 10(-5) M, respectively. The physiological role of the enzyme in living cells is obscure, but might account for another degradative pathway of L-leucine in P. vulgaris differing from the established pathway.
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Grossfeld RM. The metabolism of beta-alanine by lobster nervous tissue in vitro. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. C: COMPARATIVE PHARMACOLOGY 1976; 53:41-9. [PMID: 3383 DOI: 10.1016/0306-4492(76)90049-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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