1
|
Huynh TN, Stewart V. Purine catabolism by enterobacteria. Adv Microb Physiol 2023; 82:205-266. [PMID: 36948655 DOI: 10.1016/bs.ampbs.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.
Collapse
Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Food Science, University of Wisconsin, Madison, WI, United States
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA, United States.
| |
Collapse
|
2
|
Mokry RL, Schumacher ML, Hogg N, Terhune SS. Nitric Oxide Circumvents Virus-Mediated Metabolic Regulation during Human Cytomegalovirus Infection. mBio 2020; 11:e02630-20. [PMID: 33323506 PMCID: PMC7773989 DOI: 10.1128/mbio.02630-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022] Open
Abstract
Nitric oxide is a versatile and critical effector molecule that can modulate many cellular functions. Although recognized as a regulator of infections, the inhibitory mechanism of nitric oxide against human cytomegalovirus (HCMV) replication remains elusive. We demonstrate that nitric oxide attenuates viral replication by interfering with HCMV-mediated modulation of several cellular processes. Nitric oxide exposure reduced HCMV genome synthesis and infectious viral progeny with cell-type-dependent differences observed. Mitochondrial respiration was severely reduced in both uninfected and HCMV-infected cells during exposure with little impact on ATP levels indicating changes in cellular metabolism. Metabolomics identified significantly altered small molecules in multiple pathways during nitric oxide exposure including nucleotide biosynthesis, tricarboxylic acid (TCA) cycle, and glutamine metabolism. Glutathione metabolites were increased coinciding with a reduction in the glutathione precursor glutamine. This shift was accompanied by increased antioxidant enzymes. Glutamine deprivation mimicked defects in HCMV replication and mitochondrial respiration observed during nitric oxide exposure. These data suggest that nitric oxide limits glutaminolysis by shuttling glutamine to glutathione synthesis. In addition, lipid intermediates were severely altered, which likely contributes to the observed increase in defective viral particles. Nitric oxide disrupts multiple cellular processes, and we had limited success in rescuing replication defects by supplementing with metabolic intermediates. Our studies indicate that nitric oxide attenuation of HCMV is multifactorial with interference in viral manipulation of cellular metabolism playing a central role.IMPORTANCE Human cytomegalovirus is a prevalent pathogen that can cause serious disease in patients with compromised immune systems, including transplant patients and during congenital infection. HCMV lytic replication likely occurs in localized sites of infection with immune cells infiltrating and releasing nitric oxide with other effector molecules. This nonspecific immune response results in both uninfected and infected cells exposed to high levels of nitric oxide. The absence of nitric oxide synthase has been associated with lethal HCMV infection. We demonstrate that nitric oxide inhibition of HCMV replication is multifactorial and cell type dependent. Our results indicate that nitric oxide controls replication by interfering with viral modulation of cellular metabolism while also affecting proliferation and mitochondrial respiration of neighboring uninfected cells. These studies identify the mechanism and contribution of nitric oxide during immune control of HCMV infection and provide insight into its role in other viral infections.
Collapse
Affiliation(s)
- Rebekah L Mokry
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Megan L Schumacher
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Neil Hogg
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Scott S Terhune
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Marquette University and Medical College of Wisconsin Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| |
Collapse
|
3
|
Ding T, Tang F, Ni G, Liu J, Zhao H, Chen Q. The development of isoguanosine: from discovery, synthesis, and modification to supramolecular structures and potential applications. RSC Adv 2020. [DOI: 10.1039/c9ra09427j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
First systematical review of isoguanosine, an unnatural base, as an isomer of guanosine shows significant differences in diverse properties.
Collapse
Affiliation(s)
- Tingting Ding
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Fan Tang
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Guangcheng Ni
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Jiang Liu
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Hang Zhao
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Qianming Chen
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| |
Collapse
|
4
|
Gaded V, Anand R. Nucleobase deaminases: a potential enzyme system for new therapies. RSC Adv 2018; 8:23567-23577. [PMID: 35540270 PMCID: PMC9081823 DOI: 10.1039/c8ra04112a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 11/21/2022] Open
Abstract
This review presents an overview of the structure, function and mechanism of CDA deaminases and their potential as enzyme systems for development of new antimicrobial therapies.
Collapse
Affiliation(s)
- Vandana Gaded
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
| | - Ruchi Anand
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
| |
Collapse
|
5
|
Gaded V, Anand R. Selective Deamination of Mutagens by a Mycobacterial Enzyme. J Am Chem Soc 2017; 139:10762-10768. [DOI: 10.1021/jacs.7b04967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Vandana Gaded
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
6
|
Hobbs ME, Williams HJ, Hillerich B, Almo SC, Raushel FM. l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota. Biochemistry 2014; 53:4661-70. [PMID: 24963813 PMCID: PMC4108180 DOI: 10.1021/bi500656m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A previously
unknown metabolic pathway for the utilization of l-galactose
was discovered in a prevalent gut bacterium, Bacteroides vulgatus. The new pathway consists of three
previously uncharacterized enzymes that were found to be responsible
for the conversion of l-galactose to d-tagaturonate.
Bvu0219 (l-galactose dehydrogenase) was determined to oxidize l-galactose to l-galactono-1,5-lactone with kcat and kcat/Km values of 21 s–1 and 2.0
× 105 M–1 s–1,
respectively. The kinetic product of Bvu0219 is rapidly converted
nonenzymatically to the thermodynamically more stable l-galactono-1,4-lactone.
Bvu0220 (l-galactono-1,5-lactonase) hydrolyzes both the kinetic
and thermodynamic products of Bvu0219 to l-galactonate. However, l-galactono-1,5-lactone is estimated to be hydrolyzed 300-fold
faster than its thermodynamically more stable counterpart, l-galactono-1,4-lactone. In the final step of this pathway, Bvu0222
(l-galactonate dehydrogenase) oxidizes l-galactonate
to d-tagaturonate with kcat and kcat/Km values of
0.6 s–1 and 1.7 × 104 M–1 s–1, respectively. In the reverse direction, d-tagaturonate is reduced to l-galactonate with values
of kcat and kcat/Km of 90 s–1 and 1.6
× 105 M–1 s–1,
respectively. d-Tagaturonate is subsequently converted to d-glyceraldehyde and pyruvate through enzymes encoded within
the degradation pathway for d-glucuronate and d-galacturonate.
Collapse
Affiliation(s)
- Merlin Eric Hobbs
- Department of Biochemistry and Biophysics, §Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | | | | | | | | |
Collapse
|
7
|
Yu Y, Liu K, Zhao H, Song D. Mechanism of the deamination reaction of isoguanine: a theoretical investigation. J Phys Chem A 2013; 117:5715-25. [PMID: 23789717 DOI: 10.1021/jp4031738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanisms of the deamination reactions of isoguanine with H2O, OH(-), and OH(-)/H2O and of protonated isoguanine (isoGH(+)) with H2O have been investigated by theoretical calculations. Eight pathways, paths A-H, have been explored and the thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs energies of activation were calculated for each reaction investigated. Compared with the deamination reaction of isoguanine or protonated isoguanine (isoGH(+)) with water, the deamination reaction of isoguanine with OH(-) shows a lower Gibbs energy of activation at the rate-determining step, indicating that the deamination reaction of isoguanine is favorably to take place for the deprotonated form isoG(-) with water. With the assistance of an extra water, the reaction of isoguanine with OH(-)/H2O, pathways F and H, are found to be the most feasible pathways in aqueous solution due to their lowest Gibbs energy of activation of 174.7 and 172.6 kJ mol(-1), respectively, at the B3LYP/6-311++G(d,p) level of theory.
Collapse
Affiliation(s)
- Youqing Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | | | | | | |
Collapse
|
8
|
Bitra A, Hussain B, Tanwar AS, Anand R. Identification of Function and Mechanistic Insights of Guanine Deaminase from Nitrosomonas europaea: Role of the C-Terminal Loop in Catalysis. Biochemistry 2013; 52:3512-22. [DOI: 10.1021/bi400068g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Aruna Bitra
- Department of Chemistry, IIT Bombay, Mumbai, India 400076
| | - Bhukya Hussain
- Department of Chemistry, IIT Bombay, Mumbai, India 400076
| | | | - Ruchi Anand
- Department of Chemistry, IIT Bombay, Mumbai, India 400076
| |
Collapse
|
9
|
Kim J, Copley SD. The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family. Biochemistry 2013; 52:2905-13. [PMID: 23560638 DOI: 10.1021/bi4003343] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Facile DNA sequencing became possible decades after many enzymes had been purified and characterized. Consequently, there are still "orphan" enyzmes for which activities are known but for which encoding genes have not been identified. Identification of the genes encoding orphan enzymes is important because it allows correct annotation of genes of unknown function or with misassigned function. Bis-γ-glutamylcystine reductase (GCR) is an orphan protein that was purified in 1988. This enzyme catalyzes the reduction of bis-γ-glutamylcystine. γ-Glutamylcysteine is the major low-molecular weight thiol in halobacteria. We purified GCR from Halobacterium sp. NRC-1 and identified the sequence of 23 tryptic peptides by nano-liquid chromatography electrospray ionization tandem mass spectrometry. These peptides cover 62% of the protein predicted to be encoded by a gene in Halobacterium sp. NRC-1 that is annotated as mercuric reductase. GCR and mercuric reductase activities were assayed using enzyme that was expressed in Escherichia coli and refolded from inclusion bodies. The enzyme had robust GCR activity but no mercuric reductase activity. The genomes of most, but not all, halobacteria for which whole genome sequences are available have close homologues of GCR, suggesting that there is more to be learned about the low-molecular weight thiols used in halobacteria.
Collapse
Affiliation(s)
- Juhan Kim
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, USA
| | | |
Collapse
|
10
|
Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry 2012; 51:1762-73. [PMID: 22313111 PMCID: PMC3298459 DOI: 10.1021/bi201838b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two enzymes of unknown function from the cog1735 subset of the amidohydrolase superfamily (AHS), LMOf2365_2620 (Lmo2620) from Listeria monocytogenes str. 4b F2365 and Bh0225 from Bacillus halodurans C-125, were cloned, expressed, and purified to homogeneity. The catalytic functions of these two enzymes were interrogated by an integrated strategy encompassing bioinformatics, computational docking to three-dimensional crystal structures, and library screening. The three-dimensional structure of Lmo2620 was determined at a resolution of 1.6 Å with two phosphates and a binuclear zinc center in the active site. The proximal phosphate bridges the binuclear metal center and is 7.1 Å from the distal phosphate. The distal phosphate hydrogen bonds with Lys-242, Lys-244, Arg-275, and Tyr-278. Enzymes within cog1735 of the AHS have previously been shown to catalyze the hydrolysis of substituted lactones. Computational docking of the high-energy intermediate form of the KEGG database to the three-dimensional structure of Lmo2620 highly enriched anionic lactones versus other candidate substrates. The active site structure and the computational docking results suggested that probable substrates would likely include phosphorylated sugar lactones. A small library of diacid sugar lactones and phosphorylated sugar lactones was synthesized and tested for substrate activity with Lmo2620 and Bh0225. Two substrates were identified for these enzymes, D-lyxono-1,4-lactone-5-phosphate and l-ribono-1,4-lactone-5-phosphate. The k(cat)/K(m) values for the cobalt-substituted enzymes with these substrates are ~10(5) M(-1) s(-1).
Collapse
Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330
| | - Alexander A. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Chengfu Xu
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Elena V. Fedorov
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Tamari Narindoshivili
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Howard J. Williams
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158-2330,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Steven C. Almo
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| | - Frank M. Raushel
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012,To whom correspondence may be addressed: (FMR) telephone: (979) 845-3373; fax: (979)-845-9452; , (SCA) telephone: (718) 430-2746; fax: (718)-430-8565; , (BKS) telephone: (415)-514-4126; fax: (415)-514-4260;
| |
Collapse
|