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Dewan A, Jain C, Das M, Tripathi A, Sharma AK, Singh H, Malhotra N, Seshasayee ASN, Chakrapani H, Singh A. Intracellular peroxynitrite perturbs redox balance, bioenergetics, and Fe-S cluster homeostasis in Mycobacterium tuberculosis. Redox Biol 2024; 75:103285. [PMID: 39128229 DOI: 10.1016/j.redox.2024.103285] [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] [Received: 06/26/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to tolerate nitric oxide (•NO) and superoxide (O2•-) produced by phagocytes contributes to its success as a human pathogen. Recombination of •NO and O2•- generates peroxynitrite (ONOO-), a potent oxidant produced inside activated macrophages causing lethality in diverse organisms. While the response of Mtb toward •NO and O2•- is well established, how Mtb responds to ONOO- remains unclear. Filling this knowledge gap is important to understand the persistence mechanisms of Mtb during infection. We synthesized a series of compounds that generate both •NO and O2•-, which should combine to produce ONOO-. From this library, we identified CJ067 that permeates Mtb to reliably enhance intracellular ONOO- levels. CJ067-exposed Mtb strains, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) clinical isolates, exhibited dose-dependent, long-lasting oxidative stress and growth inhibition. In contrast, Mycobacterium smegmatis (Msm), a fast-growing, non-pathogenic mycobacterial species, maintained redox balance and growth in response to intracellular ONOO-. RNA-sequencing with Mtb revealed that CJ067 induces antioxidant machinery, sulphur metabolism, metal homeostasis, and a 4Fe-4S cluster repair pathway (suf operon). CJ067 impaired the activity of the 4Fe-4S cluster-containing TCA cycle enzyme, aconitase, and diminished bioenergetics of Mtb. Work with Mtb strains defective in SUF and IscS involved in Fe-S cluster biogenesis pathways showed that both systems cooperatively protect Mtb from intracellular ONOO- in vitro and inducible nitric oxide synthase (iNOS)-dependent growth inhibition during macrophage infection. Thus, Mtb is uniquely sensitive to intracellular ONOO- and targeting Fe-S cluster homeostasis is expected to promote iNOS-dependent host immunity against tuberculosis (TB).
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Affiliation(s)
- Arshiya Dewan
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, 560012, India
| | - Charu Jain
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Mayashree Das
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, 560012, India
| | - Ashutosh Tripathi
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, 560012, India
| | - Ajay Kumar Sharma
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Harshit Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Nitish Malhotra
- National Center for Biological Sciences, Bengaluru, 560065, India
| | | | - Harinath Chakrapani
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, India.
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, 560012, India.
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Xian X, Li L, Ye J, Mo W, Liang D, Huang M, Chang Y, Cui Z. Betaine and I-LG may have a predictive value for ATB: A causal study in a large European population. PLoS One 2024; 19:e0306752. [PMID: 38968285 PMCID: PMC11226055 DOI: 10.1371/journal.pone.0306752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/22/2024] [Indexed: 07/07/2024] Open
Abstract
PURPOSE To analyze the causal relationship between 486 human serum metabolites and the active tuberculosis (ATB) in European population. METHODS In this study, the causal relationship between human serum metabolites and the ATB was analyzed by integrating the genome-wide association study (GWAS). The 486 human serum metabolites were used as the exposure variable, three different ATB GWAS databases in the European population were set as outcome variables, and single nucleotide polymorphisms were used as instrumental variables for Mendelian Randomization. The inverse variance weighting was estimated causality, the MR-Egger intercept to estimate horizontal pleiotropy, and the combined effects of metabolites were also considered in the meta-analysis. Furthermore, the web-based MetaboAnalyst 6.0 was engaged for enrichment pathway analysis, while R (version 4.3.2) software and Review Manager 5.3 were employed for statistical analysis. RESULTS A total of 21, 17, and 19 metabolites strongly associated with ATB were found in the three databases after preliminary screening (P < 0.05). The intersecting metabolites across these databases included tryptophan, betaine, 1-linoleoylglycerol (1-monolinolein) (1-LG), 1-eicosatrienoylglycerophosphocholine, and oleoylcarnitine. Among them, betaine (I2 = 24%, P = 0.27) and 1-LG (I2 = 0%, P = 0.62) showed the lowest heterogeneity among the different ATB databases. In addition, the metabolic pathways of phosphatidylethanolamine biosynthesis (P = 0.0068), methionine metabolism (P = 0.0089), betaine metabolism (P = 0.0205) and oxidation of branched-chain fatty acids (P = 0.0309) were also associated with ATB. CONCLUSION Betaine and 1-LG may be biomarkers or auxiliary diagnostic tools for ATB. They may provide new guidance for medical practice in the early diagnosis and surveillance of ATB. In addition, by interfering with phosphatidylethanolamine biosynthesis, methionine metabolism, betaine metabolism, oxidation of branched-chain fatty acids, and other pathways, it is helpful to develop new anti-tuberculosis drugs and explore the virulence or pathogenesis of ATB at a deeper level, providing an effective reference for future studies.
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Affiliation(s)
- Xiaomin Xian
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, China
| | - Li Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jing Ye
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Key Discipline Platform of Tuberculosis Control, Guangxi Centre for Disease Control and Prevention, Nanning, Guangxi, China
| | - Wenxiu Mo
- School of Public Health and Management, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Dabin Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Key Discipline Platform of Tuberculosis Control, Guangxi Centre for Disease Control and Prevention, Nanning, Guangxi, China
| | - Minying Huang
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Key Discipline Platform of Tuberculosis Control, Guangxi Centre for Disease Control and Prevention, Nanning, Guangxi, China
| | - Yue Chang
- School of Medicine and Health Management, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhezhe Cui
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, China
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Key Discipline Platform of Tuberculosis Control, Guangxi Centre for Disease Control and Prevention, Nanning, Guangxi, China
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Guida M, Tammaro C, Quaranta M, Salvucci B, Biava M, Poce G, Consalvi S. Amino Acid Biosynthesis Inhibitors in Tuberculosis Drug Discovery. Pharmaceutics 2024; 16:725. [PMID: 38931847 PMCID: PMC11206623 DOI: 10.3390/pharmaceutics16060725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
According to the latest World Health Organization (WHO) report, an estimated 10.6 million people were diagnosed with tuberculosis (TB) in 2022, and 1.30 million died. A major concern is the emergence of multi-drug-resistant (MDR) and extensively drug-resistant (XDR) strains, fueled by the length of anti-TB treatment and HIV comorbidity. Innovative anti-TB agents acting with new modes of action are the only solution to counteract the spread of resistant infections. To escape starvation and survive inside macrophages, Mtb has evolved to become independent of the host by synthesizing its own amino acids. Therefore, targeting amino acid biosynthesis could subvert the ability of the mycobacterium to evade the host immune system, providing innovative avenues for drug discovery. The aim of this review is to give an overview of the most recent progress in the discovery of amino acid biosynthesis inhibitors. Among the hits discovered over the past five years, tryptophan (Trp) inhibitors stand out as the most advanced and have significantly contributed to demonstrating the feasibility of this approach for future TB drug discovery. Future efforts should be directed at prioritizing the chemical optimization of these hits to enrich the TB drug pipeline with high-quality leads.
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Affiliation(s)
| | | | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
| | - Sara Consalvi
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
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Ren X, Wang X, Zheng G, Wang S, Wang Q, Yuan M, Xu T, Xu J, Huang P, Ge M. Targeting one-carbon metabolism for cancer immunotherapy. Clin Transl Med 2024; 14:e1521. [PMID: 38279895 PMCID: PMC10819114 DOI: 10.1002/ctm2.1521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/15/2023] [Accepted: 12/10/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND One-carbon (1C) metabolism is a metabolic network that plays essential roles in biological reactions. In 1C metabolism, a series of nutrients are used to fuel metabolic pathways, including nucleotide metabolism, amino acid metabolism, cellular redox defence and epigenetic maintenance. At present, 1C metabolism is considered the hallmark of cancer. The 1C units obtained from the metabolic pathways increase the proliferation rate of cancer cells. In addition, anticancer drugs, such as methotrexate, which target 1C metabolism, have long been used in the clinic. In terms of immunotherapy, 1C metabolism has been used to explore biomarkers connected with immunotherapy response and immune-related adverse events in patients. METHODS We collected numerous literatures to explain the roles of one-carbon metabolism in cancer immunotherapy. RESULTS In this review, we focus on the important pathways in 1C metabolism and the function of 1C metabolism enzymes in cancer immunotherapy. Then, we summarise the inhibitors acting on 1C metabolism and their potential application on cancer immunotherapy. Finally, we provide a viewpoint and conclusion regarding the opportunities and challenges of targeting 1C metabolism for cancer immunotherapy in clinical practicability in the future. CONCLUSION Targeting one-carbon metabolism is useful for cancer immunotherapy.
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Affiliation(s)
- Xinxin Ren
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
- Department of PathologyCancer CenterZhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiang Wang
- Department of PharmacyAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiangChina
| | - Guowan Zheng
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Shanshan Wang
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Qiyue Wang
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Mengnan Yuan
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Tong Xu
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Jiajie Xu
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
| | - Ping Huang
- Department of PharmacyCenter for Clinical PharmacyCancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Minghua Ge
- Department of Head and Neck SurgeryOtolaryngology & Head and Neck Center, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital)Hangzhou Medical CollegeHangzhouZhejiangChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouZhejiangChina
- Zhejiang Provincial Clinical Research Center for Malignant TumorHangzhouZhejiangChina
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Das M, Sreedharan S, Shee S, Malhotra N, Nandy M, Banerjee U, Kohli S, Rajmani RS, Chandra N, Seshasayee ASN, Laxman S, Singh A. Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents Mycobacterium tuberculosis hypervirulence. SCIENCE ADVANCES 2023; 9:eadh2858. [PMID: 38091389 PMCID: PMC10848736 DOI: 10.1126/sciadv.adh2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Iron-sulfur (Fe-S) biogenesis requires multiprotein assembly systems, SUF and ISC, in most prokaryotes. M. tuberculosis (Mtb) encodes a complete SUF system, the depletion of which was bactericidal. The ISC operon is truncated to a single gene iscS (cysteine desulfurase), whose function remains uncertain. Here, we show that MtbΔiscS is bioenergetically deficient and hypersensitive to oxidative stress, antibiotics, and hypoxia. MtbΔiscS resisted killing by nitric oxide (NO). RNA sequencing indicates that IscS is important for expressing regulons of DosR and Fe-S-containing transcription factors, WhiB3 and SufR. Unlike wild-type Mtb, MtbΔiscS could not enter a stable persistent state, continued replicating in mice, and showed hypervirulence. The suf operon was overexpressed in MtbΔiscS during infection in a NO-dependent manner. Suppressing suf expression in MtbΔiscS either by CRISPR interference or upon infection in inducible NO-deficient mice arrests hypervirulence. Together, Mtb redesigned the ISC system to "fine-tune" the expression of SUF machinery for establishing persistence without causing detrimental disease in the host.
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Affiliation(s)
- Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
- School of Chemical and Biotechnology, (SASTRA)-Deemed to be University, Thanjavur 613401, India
| | - Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Nitish Malhotra
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Meghna Nandy
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sakshi Kohli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
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Zamakhov IM, Anashkin VA, Moiseenko AV, Orlov VN, Vorobyeva NN, Sokolova OS, Baykov AA. The Structure and Nucleotide-Binding Characteristics of Regulated Cystathionine β-Synthase Domain-Containing Pyrophosphatase without One Catalytic Domain. Int J Mol Sci 2023; 24:17160. [PMID: 38138989 PMCID: PMC10742508 DOI: 10.3390/ijms242417160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Regulatory adenine nucleotide-binding cystathionine β-synthase (CBS) domains are widespread in proteins; however, information on the mechanism of their modulating effects on protein function is scarce. The difficulty in obtaining structural data for such proteins is ascribed to their unusual flexibility and propensity to form higher-order oligomeric structures. In this study, we deleted the most movable domain from the catalytic part of a CBS domain-containing bacterial inorganic pyrophosphatase (CBS-PPase) and characterized the deletion variant both structurally and functionally. The truncated CBS-PPase was inactive but retained the homotetrameric structure of the full-size enzyme and its ability to bind a fluorescent AMP analog (inhibitor) and diadenosine tetraphosphate (activator) with the same or greater affinity. The deletion stabilized the protein structure against thermal unfolding, suggesting that the deleted domain destabilizes the structure in the full-size protein. A "linear" 3D structure with an unusual type of domain swapping predicted for the truncated CBS-PPase by Alphafold2 was confirmed by single-particle electron microscopy. The results suggest a dual role for the CBS domains in CBS-PPase regulation: they allow for enzyme tetramerization, which impedes the motion of one catalytic domain, and bind adenine nucleotides to mitigate or aggravate this effect.
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Affiliation(s)
- Ilya M. Zamakhov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
- Department of Chemistry, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Viktor A. Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Andrey V. Moiseenko
- Department of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (O.S.S.)
| | - Victor N. Orlov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Natalia N. Vorobyeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Olga S. Sokolova
- Department of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (O.S.S.)
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Alexander A. Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
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7
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Conter C, Favretto F, Dominici P, Martinez-Cruz LA, Astegno A. Key substrate recognition residues in the active site of cystathionine beta-synthase from Toxoplasma gondii. Proteins 2023; 91:1383-1393. [PMID: 37163386 DOI: 10.1002/prot.26507] [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] [Received: 02/08/2023] [Revised: 03/28/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Abstract
Cystathionine β-synthase (CBS) catalyzes the condensation of l-serine and l-homocysteine to give l-cystathionine in the transsulfuration pathway. Recently, a few O-acetylserine (l-OAS)-dependent CBSs (OCBSs) have been found in bacteria that can exclusively function with l-OAS. CBS from Toxoplasma gondii (TgCBS) can efficiently use both l-serine and l-OAS to form l-cystathionine. In this work, a series of site-specific variants substituting S84, Y160, and Y246 with hydrophobic residues found at the same positions in OCBSs was generated to explore the roles of the hydroxyl moieties of these residues as determinants of l-serine/l-OAS preference in TgCBS. We found that the S84A/Y160F/Y246V triple mutant behaved like an OCBS in terms of both substrate requirements, showing β-replacement activity only with l-OAS, and pH optimum, which is decreased by ~1 pH unit. Formation of a stable aminoacrylate upon reaction with l-serine is prevented by the triple mutation, indicating the importance of the H-bonds between the hydroxyl groups of Y160, Y246, and S84 with l-serine in formation of the intermediate. Analysis of the independent effect of each mutation on TgCBS activity and investigation of the protein-aminoacrylate complex structure allowed for the conclusion that the hydroxyl group of Y246 has a major, but not exclusive, role in controlling the l-serine preference by efficiently stabilizing its leaving group. These studies demonstrate that differences in substrate specificity of CBSs are controlled by natural variations in as few as three residue positions. A better understanding of substrate specificity in TgCBS will facilitate the design of new antimicrobial compounds.
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Affiliation(s)
- Carolina Conter
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luis Alfonso Martinez-Cruz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
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8
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Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A. Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife 2023; 12:e80218. [PMID: 37642294 PMCID: PMC10501769 DOI: 10.7554/elife.80218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species (ROS) but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. Integrating redoxosome with a global network of transcriptional regulators revealed a hypothetical protein (Rv0158) as a critical node managing eROS in Mtb. Disruption of rv0158 (rv0158 KO) impaired growth, redox balance, respiration, and metabolism of Mtb on glucose but not on fatty acids. Importantly, rv0158 KO exhibited enhanced growth on propionate, and the Rv0158 protein directly binds to methylmalonyl-CoA, a key intermediate in propionate catabolism. Metabolite profiling, ChIP-Seq, and gene-expression analyses indicate that Rv0158 manages metabolic neutralization of propionate toxicity by regulating the methylcitrate cycle. Disruption of rv0158 enhanced the sensitivity of Mtb to oxidative stress, nitric oxide, and anti-TB drugs. Lastly, rv0158 KO showed poor survival in macrophages and persistence defect in mice. Our results suggest that Rv0158 is a metabolic integrator for carbon metabolism and redox balance in Mtb.
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Affiliation(s)
- Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | - Karthikeyan Mohanraj
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | - Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | | | - Hussain Beig
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shalini Birua
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sathya Narayanan Nagarajan
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Vikrant Kumar Sinha
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Areejit Samal
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
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Phillips RS, Bauer O. Characterization of aminoacrylate intermediates of pyridoxal-5'-phosphate dependent enzymes. Methods Enzymol 2023; 685:199-224. [PMID: 37245902 DOI: 10.1016/bs.mie.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Pyridoxal-5'-phosphate (PLP) Schiff's bases of 2-aminoacrylate are intermediates in β-elimination and β-substitution reaction of PLP-dependent enzymes. These enzymes are found in two major families, the α-, or aminotransferase, superfamily, and the β-family. While the α-family enzymes primarily catalyze β-eliminations, the β-family enzymes catalyze both β-elimination and β-substitution reactions. Tyrosine phenol-lyase (TPL), which catalyzes the reversible elimination of phenol from l-tyrosine, is an example of an α-family enzyme. Tryptophan synthase catalyzes the irreversible formation of l-tryptophan from l-serine and indole, and is an example of a β-family enzyme. The identification and characterization of aminoacrylate intermediates in the reactions of both of these enzymes is discussed. The use of UV-visible absorption and fluorescence spectroscopy, X-ray and neutron crystallography, and NMR spectroscopy to identify aminoacrylate intermediates in these and other PLP enzymes is presented.
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Affiliation(s)
- Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA, United States; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States.
| | - Olivia Bauer
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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Liu L, Xu J, Zhang Z, Ren D, Wu Y, Wang D, Zhang Y, Zhao S, Chen Q, Wang T. Metabolic Homeostasis of Amino Acids and Diabetic Kidney Disease. Nutrients 2022; 15:nu15010184. [PMID: 36615841 PMCID: PMC9823842 DOI: 10.3390/nu15010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Diabetic kidney disease (DKD) occurs in 25-40% of patients with diabetes. Individuals with DKD are at a significant risk of progression to end-stage kidney disease morbidity and mortality. At present, although renal function-decline can be retarded by intensive glucose lowering and strict blood pressure control, these current treatments have shown no beneficial impact on preventing progression to kidney failure. Recently, in addition to control of blood sugar and pressure, a dietary approach has been recommended for management of DKD. Amino acids (AAs) are both biomarkers and causal factors of DKD progression. AA homeostasis contributes to renal hemodynamic response and glomerular hyperfiltration alteration in diabetic patients. This review discusses the links between progressive kidney dysfunction and the metabolic homeostasis of histidine, tryptophan, methionine, glutamine, tyrosine, and branched-chain AAs. In addition, we emphasize the regulation effects of special metabolites on DKD progression, with a focus on causality and potential mechanisms. This paper may offer an optimized protein diet strategy with concomitant management of AA homeostasis to reduce the risks of DKD in a setting of hyperglycemia.
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Affiliation(s)
- Luokun Liu
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Jingge Xu
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Zhiyu Zhang
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Dongwen Ren
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Yuzheng Wu
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Dan Wang
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Yi Zhang
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Shuwu Zhao
- School of Intergrative Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Qian Chen
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Correspondence: (Q.C.); (T.W.); Tel.: +86-22-59596164 (Q.C.); +86-22-59596185 (T.W.)
| | - Tao Wang
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Correspondence: (Q.C.); (T.W.); Tel.: +86-22-59596164 (Q.C.); +86-22-59596185 (T.W.)
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11
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Chang W, Zhang M, Jin X, Zhang H, Zheng H, Zheng S, Qiao Y, Yu H, Sun B, Hou X, Lou H. Inhibition of fungal pathogenicity by targeting the H 2S-synthesizing enzyme cystathionine β-synthase. SCIENCE ADVANCES 2022; 8:eadd5366. [PMID: 36525499 PMCID: PMC9757746 DOI: 10.1126/sciadv.add5366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The global emergence of antifungal resistance threatens the limited arsenal of available treatments and emphasizes the urgent need for alternative antifungal agents. Targeting fungal pathogenic functions is an appealing alternative therapeutic strategy. Here, we show that cystathionine β-synthase (CBS), compared with cystathionine γ-lyase, is the major enzyme that synthesizes hydrogen sulfide in the pathogenic fungus Candida albicans. Deletion of CBS leads to deficiencies in resistance to oxidative stress, retarded cell growth, defective hyphal growth, and increased β-glucan exposure, which, together, reduce the pathogenicity of C. albicans. By high-throughput screening, we identified protolichesterinic acid, a natural molecule obtained from a lichen, as an inhibitor of CBS that neutralizes the virulence of C. albicans and exhibits therapeutic efficacy in a murine candidiasis model. These findings support the application of CBS as a potential therapeutic target to fight fungal infections.
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Affiliation(s)
- Wenqiang Chang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Ming Zhang
- Institute of Medical Science, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Xueyang Jin
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Haijuan Zhang
- School of Pharmacy, Linyi University, Linyi, Shandong Province, China
| | - Hongbo Zheng
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Sha Zheng
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
| | - Yanan Qiao
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Haina Yu
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Bin Sun
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong Province, China
| | - Xuben Hou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Hongxiang Lou
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
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12
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Sao Emani C, Richter A, Singh A, Bhatt A, Av-Gay Y. The ΔCysK 2 mutant of Mycobacterium tuberculosis is sensitive to vancomycin associated with changes in cell wall phospholipid profile. Biochem Biophys Res Commun 2022; 624:120-126. [PMID: 35940124 DOI: 10.1016/j.bbrc.2022.07.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
Cysteine plays a versatile role in cellular physiology and has previously been shown to be instrumental to Mycobacterium tuberculosis (M.tb) pathophysiology. In this study, we have generated mutants deficient in CysK2 and CysH, the key Cysteine, biosynthetic enzymes. In contrast to the ΔcysH mutant, the ΔcysK2 mutant is not an auxotroph and as such not essential for cysteine biosynthesis. Interestingly, the ΔcysK2 mutant shows increased sensitivity to cumene hydroperoxide, vitamin C, diamide, rifampicin and Vancomycin and shows alterations in phospholipid profile of Mtb cell wall. Our findings suggest that alteration in phospholipids content of M.tb cell wall by CysK2 may form a mode of defence against selected antibiotics and oxidative stress.
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Affiliation(s)
- Carine Sao Emani
- Division of Infectious Diseases, Department of Medicine/Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Adrian Richter
- Martin-Luther-University of Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120, Halle, Germany
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Yossef Av-Gay
- Division of Infectious Diseases, Department of Medicine/Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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