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Kang X, Zhao X, Song X. Analysis of a novel strain Brevundimonas KX-1 capable of degrading 3-chlorocarbazole based on the whole genome sequence. Antonie Van Leeuwenhoek 2023; 116:577-593. [PMID: 37186067 DOI: 10.1007/s10482-023-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 04/13/2023] [Indexed: 05/17/2023]
Abstract
In this study, a strain was isolated from a sewage treatment plant in Jiangsu Province, China. The strain was identified as Brevundimonas sp. KX-1. After 5 days, 50.2% 3-chlorocarbazole (3-CCZ) was degraded under the optimum condition as follows: 1 g/L starch, 30 °C, pH 6.5 and 50 mg/L 3-CCZ. The degradation of 3-CCZ by KX-1 conformed to the first-order kinetic model under different initial concentrations in this experiment. The intermediate product of 3-CCZ degradation was identified as (2E,4Z)-6-(2-amino-5-chlorophenyl)-2-hydroxy-6-oxohexa-2,4-dienoic acid. The activities of the meta-cleavage enzymes for biphenyl-2,3-diol (the analogs of intermediate product 2'-amino-5'-chloro-[1,1'-biphenyl]-2,3-diol) were measured with the crude extracts of cells grown in the presence of 3-CCZ. The complete genome of KX-1 was sequenced and compared with the Brevundimonas diminuta BZC3. BZC3 and KX-1 belonged to the same species, displaying the genetic similarity of 99%. But BZC3 could efficiently degrade gentamicin for the potential microbial function analysis. Compared with BZC3, KX-1 possessed the primary function annotations about transportation and metabolism of amino acids (6.65%) and the transportation and metabolism of carbohydrates (5.96%). In addition, KX-1 was rich in sucrose and starch metabolism pathways (ko00500) compared with the genome of BZC3, indicating the high efficiency of KX-1 for starch utilization during degradation. This article reveals the difference between strain KX-1 and bacteria of the same genus in terms of the whole genome sequence, demonstrating that KX-1 is a novel strain Brevundimonas with the ability to degrade 3-CCZ.
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Affiliation(s)
- Xin Kang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Xiaoxiang Zhao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China.
- , Bldg. 4, 2999 Renmin North Road, Songjiang District, Shanghai, 201620, People's Republic of China.
| | - Xinshan Song
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
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2
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Pederick JL, Klose J, Jovcevski B, Pukala TL, Bruning JB. Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity. Biochemistry 2023; 62:899-911. [PMID: 36745518 DOI: 10.1021/acs.biochem.2c00592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polyamines and polyamine-containing metabolites are involved in many cellular processes related to bacterial cell growth and survival. In Escherichia coli, the bifunctional enzyme glutathionylspermidine synthetase/amidase (GspSA) controls the production of glutathionylspermidine, which has a protective role against oxidative stress. E. coli also encodes two enzymes with homology to the synthetase domain of GspSA, YgiC, and YjfC; however, these do not catalyze the formation of glutathionylspermidine, and their catalytic function remained unknown. Here, we detail the structural and functional characterization of YgiC and YjfC. Using X-ray crystallography, the high-resolution crystal structures of YgiC and YjfC were obtained. This revealed that YgiC and YjfC possess multiple substitutions in key residues required for binding of glutathione in GspSA. Despite this difference, these enzymes share a similar active site structure to GspSA, suggesting that they catalyze the formation of an alternate peptide─spermidine conjugate. As the physiological substrates of YgiC and YjfC are unknown, this was probed using the peptide triglycine as a model substrate. A combination of enzyme activity assays and mass spectrometry revealed that YgiC and YjfC can function as peptide-spermidine ligases, forming a triglycine-spermidine conjugate. For both enzymes, conjugate formation was only observed in the presence of spermidine, but not other common polyamines, supporting that spermidine or a spermidine derivative is the physiological substrate. Importantly, since YgiC and YjfC are widely distributed in Gram-negative bacterial species, this suggests that these enzymes function in a conserved cellular process, representing a currently unknown aspect of bacterial polyamine metabolism.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia5005, Australia
| | - Jack Klose
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia5005, Australia.,School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia5005, Australia
| | - Tara L Pukala
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia5005, Australia
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Liu SW, Ye JJ, Lu QP, Cheema MT, Abbas M, Huang DL, Sajid I, Sun CH. Motilibacter deserti sp. nov. and Motilibacter aurantiacus sp. nov., two novel actinobacteria isolated from soil of Cholistan Desert and emended description of the genus Motilibacter. Syst Appl Microbiol 2020; 43:126150. [PMID: 33099259 DOI: 10.1016/j.syapm.2020.126150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 02/03/2023]
Abstract
Two novel actinobacterial strains, designated as E257T and K478T, were isolated from hyper-arid soil samples collected in Cholistan Desert, Pakistan. Comparative analysis of 16S rRNA genes showed that strains E257T and K478T were assigned to the genus Motilibacter, being their closest relative M. rhizosphaerae RS-16T with 97.3% and 96.7% similarities, respectively. The sequence similarity between strain E257T and K478T was 98.9%. Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on multiple genes of conserved core proteins exhibited that these two strains belonged to the genus Motilibacter and formed a robust cluster separated from the two type species of the genus Motilibacter. Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), digital DNA-DNA hybridization (dDDH) values and Percentage of Conserved Proteins (POCP) calculated from the complete genome sequences indicated strains E257T and K478T were assigned into genus Motilibacter but clearly separated from each other and from the other species of the genus Motilibacter with values below the thresholds for species delineation. The two isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Motilibacter and also confirmed the differentiation from their closest species. The obtained results demonstrated that strains E257T and K478T represent two novel species of the genus Motilibacter, for which the names Motilibacter desertisp. nov. (type strain E257T = JCM 33651T = CGMCC 1.17159T) and Motilibacter aurantiacus sp. nov. (type strain K478T =JCM 33652T =CGMCC 1.17229T) are proposed.
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Affiliation(s)
- Shao-Wei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jing-Jing Ye
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, China
| | - Qin-Pei Lu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mohsin Tassawar Cheema
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan
| | - Muhammad Abbas
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan
| | - Da-Lin Huang
- College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, China
| | - Imran Sajid
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quid-i-Azam Campus, Lahore 54590, Pakistan.
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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4
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Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
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Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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Dunn LL, Smith DM, Critzer FJ. Transcriptomic Behavior of Salmonella enterica Newport in Response to Oxidative Sanitizers. J Food Prot 2020; 83:221-232. [PMID: 31934775 DOI: 10.4315/0362-028x.jfp-19-299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/04/2019] [Indexed: 11/11/2022]
Abstract
ABSTRACT Agricultural water is a known source of contamination to fresh produce and can contain foodborne pathogens including Salmonella enterica, pathogenic Escherichia coli, Listeria monocytogenes, and Campylobacter jejuni. To mitigate such risks, antimicrobial agents such as hypochlorites and peroxyacetic acid (PAA) can be applied to in-line irrigation systems as well as to water used in postharvest washing. Although these compounds are effective and widely used, some pathogenic bacteria adapt to survive exposure. RNA sequencing was used to analyze the Salmonella Newport transcriptome after exposure to sodium hypochlorite (NaOCl) and PAA in a simulated agricultural water system. Overall cellular adaptive response was determined quantitatively as a function of overall gene expression of the >4,000 genes in the Salmonella Newport genome. Differentially expressed genes ranged from 11 due to 10-ppm NaOCl treatment, 316 due to 20-ppm NaOCl treatment, 1,719 due to 10-ppm PAA treatment, and 2,010 due to 20-ppm PAA treatment compared with that of the controls (water only). Differentially expressed transcripts included cellular functions such as biosynthesis, degradation, energy generation, and nonmetabolically linked functions. Oxidative exposure upregulated genes associated with key virulence, attachment, and gene transfer. Amino acid biosynthesis was upregulated due to NaOCl exposure but primarily downregulated when Salmonella Newport was exposed to PAA. Slight upregulation occurred in nucleoside and nucleotide biosynthesis, a known DNA repair mechanism seen during exposure to sanitizers. Our results indicate that Salmonella Newport reacts differently when exposed to NaOCl versus PAA, despite oxidative activity being the primary modes of antimicrobial action of both compounds. HIGHLIGHTS
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Affiliation(s)
- Laurel L Dunn
- Department of Food Science and Technology, Food Science Building, University of Georgia, 100 Cedar Street, Athens, Georgia 30602 (ORCID: https://orcid.org/0000-0003-0786-5253 [L.L.D.])
| | - Dara M Smith
- Department of Food Science, University of Tennessee, 2600 River Drive, Knoxville, Tennessee 37996
| | - Faith J Critzer
- School of Food Science, Irrigated Agriculture Research and Extension Center, Washington State University, 24106 North Bunn Road, Prosser, Washington 99350, USA
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6
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Abstract
Polyamines (PAs) are indispensable polycations ubiquitous to all living cells. Among their many critical functions, PAs contribute to the oxidative balance of the cell. Beginning with studies by the Tabor laboratory in bacteria and yeast, the requirement for PAs as protectors against oxygen radical-mediated damage has been well established in many organisms, including mammals. However, PAs also serve as substrates for oxidation reactions that produce hydrogen peroxide (H2O2) both intra- and extracellularly. As intracellular concentrations of PAs can reach millimolar concentrations, the H2O2 amounts produced through their catabolism, coupled with a reduction in protective PAs, are sufficient to cause the oxidative damage associated with many pathologies, including cancer. Thus, the maintenance of intracellular polyamine homeostasis may ultimately contribute to the maintenance of oxidative homeostasis. Again, pioneering studies by Tabor and colleagues led the way in first identifying spermine oxidase in Saccharomyces cerevisiae. They also first purified the extracellular bovine serum amine oxidase and elucidated the products of its oxidation of primary amine groups of PAs when included in culture medium. These investigations formed the foundation for many polyamine-related studies and experimental procedures still performed today. This Minireview will summarize key innovative studies regarding PAs and oxidative damage, starting with those from the Tabor laboratory and including the most recent advances, with a focus on mammalian systems.
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Affiliation(s)
- Tracy Murray Stewart
- From the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 and
| | - Tiffany T Dunston
- From the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 and
| | - Patrick M Woster
- the Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Robert A Casero
- From the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 and
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7
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Tsuji K, Yoon KS, Ogo S. Glyceraldehyde-3-phosphate dehydrogenase from Citrobacter sp. S-77 is post-translationally modified by CoA (protein CoAlation) under oxidative stress. FEBS Open Bio 2018; 9:53-73. [PMID: 30652074 PMCID: PMC6325607 DOI: 10.1002/2211-5463.12542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 12/17/2022] Open
Abstract
Protein CoAlation (S-thiolation by coenzyme A) has recently emerged as an alternative redox-regulated post-translational modification by which protein thiols are covalently modified with coenzyme A (CoA). However, little is known about the role and mechanism of this post-translational modification. In the present study, we investigated CoAlation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from a facultative anaerobic Gram-negative bacterium Citrobacter sp. S-77 (Cb GAPDH). GAPDH is a key glycolytic enzyme whose activity relies on the thiol-based redox-regulated post-translational modifications of active-site cysteine. LC-MS/MS analysis revealed that CoAlation of Cb GAPDH occurred in vivo under sodium hypochlorite (NaOCl) stress. The purified Cb GAPDH was highly sensitive to overoxidation by H2O2 and NaOCl, which resulted in irreversible enzyme inactivation. By contrast, treatment with coenzyme A disulphide (CoASSCoA) or H2O2/NaOCl in the presence of CoA led to CoAlation and inactivation of the enzyme; activity could be recovered after incubation with dithiothreitol, glutathione and CoA. CoAlation of the enzyme in vitro was confirmed by mass spectrometry. The presence of a substrate, glyceraldehyde-3-phosphate, fully protected Cb GAPDH from inactivation by CoAlation, suggesting that the inactivation is due to the formation of mixed disulphides between CoA and the active-site cysteine Cys149. A molecular docking study also supported the formation of mixed disulphide without steric constraints. These observations suggest that CoAlation is an alternative mechanism to protect the redox-sensitive thiol (Cys149) of Cb GAPDH against irreversible oxidation, thereby regulating enzyme activity under oxidative stress.
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Affiliation(s)
- Kohsei Tsuji
- Centre for Small Molecule Energy Kyushu University Fukuoka Japan.,Department of Chemistry and Biochemistry Graduate School of Engineering Kyushu University Fukuoka Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University Fukuoka Japan
| | - Ki-Seok Yoon
- Centre for Small Molecule Energy Kyushu University Fukuoka Japan.,Department of Chemistry and Biochemistry Graduate School of Engineering Kyushu University Fukuoka Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University Fukuoka Japan
| | - Seiji Ogo
- Centre for Small Molecule Energy Kyushu University Fukuoka Japan.,Department of Chemistry and Biochemistry Graduate School of Engineering Kyushu University Fukuoka Japan.,International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) Kyushu University Fukuoka Japan
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8
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Manta B, Bonilla M, Fiestas L, Sturlese M, Salinas G, Bellanda M, Comini MA. Polyamine-Based Thiols in Trypanosomatids: Evolution, Protein Structural Adaptations, and Biological Functions. Antioxid Redox Signal 2018; 28:463-486. [PMID: 29048199 DOI: 10.1089/ars.2017.7133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SIGNIFICANCE Major pathogenic enterobacteria and protozoan parasites from the phylum Euglenozoa, such as trypanosomatids, are endowed with glutathione (GSH)-spermidine (Sp) derivatives that play important roles in signaling and metal and thiol-redox homeostasis. For some Euglenozoa lineages, the GSH-Sp conjugates represent the main redox cosubstrates around which entire new redox systems have evolved. Several proteins underwent molecular adaptations to synthesize and utilize the new polyamine-based thiols. Recent Advances: The genomes of closely related organisms have recently been sequenced, which allows mining and analysis of gene sequences that belong to these peculiar redox systems. Similarly, the three-dimensional structures of several of these proteins have been solved, which allows for comparison with their counterparts in classical redox systems that rely on GSH/glutaredoxin and thioredoxin. CRITICAL ISSUES The evolutionary and structural aspects related to the emergence and use of GSH-Sp conjugates in Euglenozoa are reviewed focusing on unique structural specializations that proteins developed to use N1,N8-bisglutathionylspermidine (trypanothione) as redox cosubstrate. An updated overview on the biochemical and biological significance of the major enzymatic activities is also provided. FUTURE DIRECTIONS A thiol-redox system strictly dependent on trypanothione is a feature unique to trypanosomatids. The physicochemical properties of the polyamine-GSH conjugates were a major driving force for structural adaptation of proteins that use these thiols as ligand and redox cofactor. In fact, the structural differences of indispensable components of this system can be exploited toward selective drug development. Future research should clarify whether additional cellular processes are regulated by the trypanothione system. Antioxid. Redox Signal. 28, 463-486.
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Affiliation(s)
- Bruno Manta
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica , Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mariana Bonilla
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay .,2 Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica , Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía Fiestas
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Mattia Sturlese
- 3 Department of Chemical Sciences, Università degli Studi di Padova , Padova, Italy
| | - Gustavo Salinas
- 4 Worm Biology Lab, Institut Pasteur de Montevideo , Montevideo, Uruguay .,5 Departamento de Biociencias, Facultad de Química, Universidad de la República , Montevideo, Uruguay
| | - Massimo Bellanda
- 3 Department of Chemical Sciences, Università degli Studi di Padova , Padova, Italy
| | - Marcelo A Comini
- 1 Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo , Montevideo, Uruguay
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Cyclic AMP Regulates Bacterial Persistence through Repression of the Oxidative Stress Response and SOS-Dependent DNA Repair in Uropathogenic Escherichia coli. mBio 2018; 9:mBio.02144-17. [PMID: 29317513 PMCID: PMC5760743 DOI: 10.1128/mbio.02144-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial persistence is a transient, nonheritable physiological state that provides tolerance to bactericidal antibiotics. The stringent response, toxin-antitoxin modules, and stochastic processes, among other mechanisms, play roles in this phenomenon. How persistence is regulated is relatively ill defined. Here we show that cyclic AMP, a global regulator of carbon catabolism and other core processes, is a negative regulator of bacterial persistence in uropathogenic Escherichia coli, as measured by survival after exposure to a β-lactam antibiotic. This phenotype is regulated by a set of genes leading to an oxidative stress response and SOS-dependent DNA repair. Thus, persister cells tolerant to cell wall-acting antibiotics must cope with oxidative stress and DNA damage and these processes are regulated by cyclic AMP in uropathogenic E. coli. Bacterial persister cells are important in relapsing infections in patients treated with antibiotics and also in the emergence of antibiotic resistance. Our results show that in uropathogenic E. coli, the second messenger cyclic AMP negatively regulates persister cell formation, since in its absence much more persister cells form that are tolerant to β-lactams antibiotics. We reveal the mechanism to be decreased levels of reactive oxygen species, specifically hydroxyl radicals, and SOS-dependent DNA repair. Our findings suggest that the oxidative stress response and DNA repair are relevant pathways to target in the design of persister-specific antibiotic compounds.
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Ulrich K, Finkenzeller C, Merker S, Rojas F, Matthews K, Ruppert T, Krauth-Siegel RL. Stress-Induced Protein S-Glutathionylation and S-Trypanothionylation in African Trypanosomes-A Quantitative Redox Proteome and Thiol Analysis. Antioxid Redox Signal 2017; 27:517-533. [PMID: 28338335 PMCID: PMC5567454 DOI: 10.1089/ars.2016.6947] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIMS Trypanosomatids have a unique trypanothione-based thiol redox metabolism. The parasite-specific dithiol is synthesized from glutathione and spermidine, with glutathionylspermidine as intermediate catalyzed by trypanothione synthetase. In this study, we address the oxidative stress response of African trypanosomes with special focus on putative protein S-thiolation. RESULTS Challenging bloodstream Trypanosoma brucei with diamide, H2O2 or hypochlorite results in distinct levels of reversible overall protein S-thiolation. Quantitative proteome analyses reveal 84 proteins oxidized in diamide-stressed parasites. Fourteen of them, including several essential thiol redox proteins and chaperones, are also enriched when glutathione/glutaredoxin serves as a reducing system indicating S-thiolation. In parasites exposed to H2O2, other sets of proteins are modified. Only three proteins are S-thiolated under all stress conditions studied in accordance with a highly specific response. H2O2 causes primarily the formation of free disulfides. In contrast, in diamide-treated cells, glutathione, glutathionylspermidine, and trypanothione are almost completely protein bound. Remarkably, the total level of trypanothione is decreased, whereas those of glutathione and glutathionylspermidine are increased, indicating partial hydrolysis of protein-bound trypanothione. Depletion of trypanothione synthetase exclusively induces protein S-glutathionylation. Total mass analyses of a recombinant peroxidase treated with T(SH)2 and either diamide or hydrogen peroxide verify protein S-trypanothionylation as stable modification. INNOVATION Our data reveal for the first time that trypanosomes employ protein S-thiolation when exposed to exogenous and endogenous oxidative stresses and trypanothione, despite its dithiol character, forms protein-mixed disulfides. CONCLUSION The stress-specific responses shown here emphasize protein S-trypanothionylation and S-glutathionylation as reversible protection mechanism in these parasites. Antioxid. Redox Signal. 27, 517-533.
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Affiliation(s)
- Kathrin Ulrich
- 1 Biochemie-Zentrum der Universität Heidelberg (BZH) , Heidelberg, Germany
| | | | - Sabine Merker
- 2 Zentrum für Molekularbiologie der Universität Heidelberg (ZMBH) , Heidelberg, Germany
| | - Federico Rojas
- 3 Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh , Edinburgh, United Kingdom
| | - Keith Matthews
- 3 Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh , Edinburgh, United Kingdom
| | - Thomas Ruppert
- 2 Zentrum für Molekularbiologie der Universität Heidelberg (ZMBH) , Heidelberg, Germany
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11
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Biosynthesis of polyamines and polyamine-containing molecules. Biochem J 2016; 473:2315-29. [DOI: 10.1042/bcj20160185] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Polyamines are evolutionarily ancient polycations derived from amino acids and are pervasive in all domains of life. They are essential for cell growth and proliferation in eukaryotes and are essential, important or dispensable for growth in bacteria. Polyamines present a useful scaffold to attach other moieties to, and are often incorporated into specialized metabolism. Life has evolved multiple pathways to synthesize polyamines, and structural variants of polyamines have evolved in bacteria, archaea and eukaryotes. Among the complex biosynthetic diversity, patterns of evolutionary reiteration can be distinguished, revealing evolutionary recycling of particular protein folds and enzyme chassis. The same enzyme activities have evolved from multiple protein folds, suggesting an inevitability of evolution of polyamine biosynthesis. This review discusses the different biosynthetic strategies used in life to produce diamines, triamines, tetra-amines and branched and long-chain polyamines. It also discusses the enzymes that incorporate polyamines into specialized metabolites and attempts to place polyamine biosynthesis in an evolutionary context.
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Peng T, Berghoff BA, Oh JI, Weber L, Schirmer J, Schwarz J, Glaeser J, Klug G. Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides. RNA Biol 2016; 13:988-999. [PMID: 27420112 DOI: 10.1080/15476286.2016.1212152] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Singlet oxygen is generated by bacteriochlorophylls when light and oxygen are simultaneously present in Rhodobacter sphaeroides. Singlet oxygen triggers a specific response that is partly regulated by the alternative sigma factor RpoHI/HII. The sRNA RSs2461 has previously been identified as an RpoHI/HII-dependent sRNA and is derived from the 3' UTR of the mRNA for an OmpR-type transcriptional regulator. Similar to the RpoHI/HII-dependent CcsR and SorY sRNAs, RSs2461 affects the resistance of R. sphaeroides against singlet oxygen and was therefore renamed here SorX. Furthermore, SorX has a strong impact on resistance against organic hydroperoxides that usually occur as secondary damages downstream of singlet oxygen. The 75-nt SorX 3' fragment, which is generated by RNase E cleavage and highly conserved among related species, represents the functional entity. A target search identified potA mRNA, which encodes a subunit of a polyamine transporter, as a direct SorX target and stress resistance via SorX could be linked to potA. The PotABCD transporter is an uptake system for spermidine in E. coli. While spermidine is generally described as beneficial during oxidative stress, we observed significantly increased sensitivity of R. sphaeroides to organic hydroperoxides in the presence of spermidine. We therefore propose that the diminished import of spermidine, due to down-regulation of potA by SorX, counteracts oxidative stress. Together with results from other studies this underlines the importance of regulated transport to bacterial stress defense.
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Affiliation(s)
- Tao Peng
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Bork A Berghoff
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jeong-Il Oh
- b Department of Microbiology , Pusan National University , Busan , Korea
| | - Lennart Weber
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jasmin Schirmer
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Johannes Schwarz
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jens Glaeser
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Gabriele Klug
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
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Ilott NE, Bollrath J, Danne C, Schiering C, Shale M, Adelmann K, Krausgruber T, Heger A, Sims D, Powrie F. Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling. ISME JOURNAL 2016; 10:2389-404. [PMID: 27003245 PMCID: PMC5030693 DOI: 10.1038/ismej.2016.40] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 02/06/2016] [Accepted: 02/10/2016] [Indexed: 12/23/2022]
Abstract
The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess modifications to both bacterial community structure and transcriptional activity in a mouse model of colitis. By using transcriptomic analysis of colonic tissue and luminal RNA derived from the host, we have also characterised how host transcription relates to the microbial transcriptional response in inflammation. In colitis, increased abundance and transcription of diverse microbial gene families involved in responses to nutrient deprivation, antimicrobial peptide production and oxidative stress support an adaptation of multiple commensal genera to withstand a diverse set of environmental stressors in the inflammatory environment. These data are supported by a transcriptional signature of activated macrophages and granulocytes in the gut lumen during colitis, a signature that includes the transcription of the key antimicrobial genes S100a8 and S100a9 (calprotectin). Genes involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase were identified as changing to a greater extent at the level of transcription than would be predicted by DNA abundance changes, implicating a role for increased oxygen tension and/or host-derived reactive oxygen species in driving transcriptional changes in commensal microbes.
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Affiliation(s)
| | - Julia Bollrath
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.,Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Camille Danne
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chris Schiering
- The Francis Crick Institute, Mill Hill Laboratory, London, UK
| | - Matthew Shale
- Translational Gastroenterology Unit, Experimental Medicine, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Krista Adelmann
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Heger
- Computational Genomics Analysis and Training (CGAT), MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - David Sims
- Computational Genomics Analysis and Training (CGAT), MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
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Link H, Fuhrer T, Gerosa L, Zamboni N, Sauer U. Real-time metabolome profiling of the metabolic switch between starvation and growth. Nat Methods 2015; 12:1091-7. [PMID: 26366986 DOI: 10.1038/nmeth.3584] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
Abstract
Metabolic systems are often the first networks to respond to environmental changes, and the ability to monitor metabolite dynamics is key for understanding these cellular responses. Because monitoring metabolome changes is experimentally tedious and demanding, dynamic data on time scales from seconds to hours are scarce. Here we describe real-time metabolome profiling by direct injection of living bacteria, yeast or mammalian cells into a high-resolution mass spectrometer, which enables automated monitoring of about 300 compounds in 15-30-s cycles over several hours. We observed accumulation of energetically costly biomass metabolites in Escherichia coli in carbon starvation-induced stationary phase, as well as the rapid use of these metabolites upon growth resumption. By combining real-time metabolome profiling with modeling and inhibitor experiments, we obtained evidence for switch-like feedback inhibition in amino acid biosynthesis and for control of substrate availability through the preferential use of the metabolically cheaper one-step salvaging pathway over costly ten-step de novo purine biosynthesis during growth resumption.
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Affiliation(s)
- Hannes Link
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Luca Gerosa
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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Lin JCY, Chiang BY, Chou CC, Chen TC, Chen YJ, Chen YJ, Lin CH. Glutathionylspermidine in the modification of protein SH groups: the enzymology and its application to study protein glutathionylation. Molecules 2015; 20:1452-74. [PMID: 25599150 PMCID: PMC6272389 DOI: 10.3390/molecules20011452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/15/2014] [Indexed: 11/29/2022] Open
Abstract
Cysteine is very susceptible to reactive oxygen species. In response; posttranslational thiol modifications such as reversible disulfide bond formation have arisen as protective mechanisms against undesired in vivo cysteine oxidation. In Gram-negative bacteria a major defense mechanism against cysteine overoxidation is the formation of mixed protein disulfides with low molecular weight thiols such as glutathione and glutathionylspermidine. In this review we discuss some of the mechanistic aspects of glutathionylspermidine in prokaryotes and extend its potential use to eukaryotes in proteomics and biochemical applications through an example with tissue transglutaminase and its S-glutathionylation.
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Affiliation(s)
- Jason Ching-Yao Lin
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Bing-Yu Chiang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Tzu-Chieh Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei 11529, Taiwan.
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Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. BMC Genomics 2015; 16:2. [PMID: 25555398 PMCID: PMC4320630 DOI: 10.1186/1471-2164-16-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum. RESULTS We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina. CONCLUSIONS Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.
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Chou CC, Chiang BY, Lin JCY, Pan KT, Lin CH, Khoo KH. Characteristic tandem mass spectral features under various collision chemistries for site-specific identification of protein S-glutathionylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:120-132. [PMID: 25374333 DOI: 10.1007/s13361-014-1014-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/27/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
Protein S-glutathionylation is a reversible post-translational modification widely implicated in redox regulated biological functions. Conventional biochemical methods, however, often do not allow such a mixed disulfide modification to be reliably identified on specific cysteine residues or be distinguished from other related oxidized forms. To develop more efficient mass spectrometry (MS)-based analytical strategies for this purpose, we first investigated the MS/MS fragmentation pattern of S-glutathionylated peptides under various dissociation modes, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD), using synthetic peptides derived from protein tyrosine phosphatase as models. Our results indicate that a MALDI-based high energy CID MS/MS on a TOF/TOF affords the most distinctive spectral features that would facilitate rapid and unambiguous identification of site-specific S-glutathionylation. For more complex proteomic samples best tackled by LC-MS/MS approach, we demonstrate that HCD performed on an LTQ-Orbitrap hybrid instrument fairs better than trap-based CID and ETD in allowing more protein site-specific S-glutathionylation to be confidently identified by direct database searching of the generated MS/MS dataset using Mascot. Overall, HCD afforded more peptide sequence-informative fragment ions retaining the glutathionyl modification with less neutral losses of side chains to compromise scoring. In conjunction with our recently developed chemo-enzymatic tagging strategy, our nanoLC-HCD-MS/MS approach is sufficiently sensitive to identify endogenous S-glutathionylated peptides prepared from non-stressed cells. It is anticipated that future applications to global scale analysis of protein S-glutathionylation will benefit further from current advances in both speed and mass accuracy afforded by HCD MS/MS mode on the Orbitrap series.
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Affiliation(s)
- Chi-Chi Chou
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, 11529, Taiwan,
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Sousa AF, Gomes-Alves AG, Benítez D, Comini MA, Flohé L, Jaeger T, Passos J, Stuhlmann F, Tomás AM, Castro H. Genetic and chemical analyses reveal that trypanothione synthetase but not glutathionylspermidine synthetase is essential for Leishmania infantum. Free Radic Biol Med 2014; 73:229-38. [PMID: 24853758 DOI: 10.1016/j.freeradbiomed.2014.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 11/23/2022]
Abstract
Trypanothione is a unique and essential redox metabolite of trypanosomatid parasites, the biosynthetic pathway of which is regarded as a promising target for antiparasitic drugs. Synthesis of trypanothione occurs by the consecutive conjugation of two glutathione molecules to spermidine. Both reaction steps are catalyzed by trypanothione synthetase (TRYS), a molecule known to be essential in Trypanosoma brucei. However, other trypanosomatids (including some Leishmania species and Trypanosoma cruzi) potentially express one additional enzyme, glutathionylspermidine synthetase (GSPS), capable of driving the first step of trypanothione synthesis yielding glutathionylspermidine. Because this monothiol can substitute for trypanothione in some reactions, the possibility existed that TRYS was redundant in parasites harboring GSPS. To clarify this issue, the functional relevance of both GSPS and TRYS was investigated in Leishmania infantum (Li). Employing a gene-targeting approach, we generated a gsps(-/-) knockout line, which was viable and capable of replicating in both life cycle stages of the parasite, thus demonstrating the superfluous role of LiGSPS. In contrast, elimination of both LiTRYS alleles was not possible unless parasites were previously complemented with an episomal copy of the gene. Retention of extrachromosomal LiTRYS in the trys(-/-)/+TRYS line after several passages in culture further supported the essentiality of this gene for survival of L. infantum (including its clinically relevant stage), hence ruling out the hypothesis of functional complementation by LiGSPS. Chemical targeting of LiTRYS with a drug-like compound was shown to also lead to parasite death. Overall, this study disqualifies GSPS as a target for drug development campaigns and, by genetic and chemical evidence, validates TRYS as a chemotherapeutic target in a parasite endowed with GSPS and, thus, probably along the entire trypanosomatid lineage.
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Affiliation(s)
- André F Sousa
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
| | - Ana G Gomes-Alves
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
| | - Diego Benítez
- Laboratory of Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, CP 11400 Montevideo, Uruguay
| | - Marcelo A Comini
- Laboratory of Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, CP 11400 Montevideo, Uruguay
| | - Leopold Flohé
- Departamento de Bioquímica, Universidad de la República, CP 11800 Montevideo, Uruguay, and Department of Molecular Medicine, Università degli Studi di Padova, 35131 Padova, Italy
| | - Timo Jaeger
- German Center for Infection Research, 38124 Braunschweig, Germany
| | - Joana Passos
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal
| | | | - Ana M Tomás
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4099-003 Porto, Portugal
| | - Helena Castro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal.
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Furdui CM, Poole LB. Chemical approaches to detect and analyze protein sulfenic acids. MASS SPECTROMETRY REVIEWS 2014; 33:126-46. [PMID: 24105931 PMCID: PMC3946320 DOI: 10.1002/mas.21384] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/03/2013] [Accepted: 04/04/2013] [Indexed: 05/08/2023]
Abstract
Orchestration of many processes relying on intracellular signal transduction is recognized to require the generation of hydrogen peroxide as a second messenger, yet relatively few molecular details of how this oxidant acts to regulate protein function are currently understood. This review describes emerging chemical tools and approaches that can be applied to study protein oxidation in biological systems, with a particular emphasis on a key player in protein redox regulation, cysteine sulfenic acid. While sulfenic acids (within purified proteins or simple mixtures) are detectable by physical approaches like X-ray crystallography, nuclear magnetic resonance and mass spectrometry, the propensity of these moieties to undergo further modification in complex biological systems has necessitated the development of chemical probes, reporter groups and analytical approaches to allow for their selective detection and quantification. Provided is an overview of techniques that are currently available for the study of sulfenic acids, and some of the biologically meaningful data that have been collected using such approaches.
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Affiliation(s)
- Cristina M. Furdui
- Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
- Correspondence to: Leslie B. Poole, Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157; ; telephone: 336-716-6711
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20
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Trypanothione: A unique bis-glutathionyl derivative in trypanosomatids. Biochim Biophys Acta Gen Subj 2013; 1830:3199-216. [DOI: 10.1016/j.bbagen.2013.01.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 11/21/2022]
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21
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Kausar H, Munagala R, Bansal SS, Aqil F, Vadhanam MV, Gupta RC. Cucurbitacin B potently suppresses non-small-cell lung cancer growth: Identification of intracellular thiols as critical targets. Cancer Lett 2013; 332:35-45. [DOI: 10.1016/j.canlet.2013.01.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/24/2012] [Accepted: 01/04/2013] [Indexed: 01/06/2023]
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22
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Deponte M. Glutathione catalysis and the reaction mechanisms of glutathione-dependent enzymes. Biochim Biophys Acta Gen Subj 2013; 1830:3217-66. [DOI: 10.1016/j.bbagen.2012.09.018] [Citation(s) in RCA: 625] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/25/2012] [Indexed: 12/12/2022]
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Chattopadhyay MK, Chen W, Tabor H. Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression. FEMS Microbiol Lett 2012; 338:132-40. [PMID: 23106382 DOI: 10.1111/1574-6968.12035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 10/17/2012] [Indexed: 11/27/2022] Open
Abstract
Glutathionylspermidine synthetase/amidase (Gss) and the encoding gene (gss) have only been studied in Escherichia coli and several members of the Kinetoplastida phyla. In the present article, we have studied the phylogenetic distribution of Gss and have found that Gss sequences are largely limited to certain bacteria and Kinetoplastids and are absent in a variety of invertebrate and vertebrate species, Archea, plants, and some Eubacteria. It is striking that almost all of the 75 Enterobacteria species that have been sequenced contain sequences with very high degree of homology to the E. coli Gss protein. To find out the physiological significance of glutathionylspermidine in E. coli, we have performed global transcriptome analyses. The microarray studies comparing gss(+) and Δgss strains of E. coli show that a large number of genes are either up-regulated (76 genes more than threefold) or down-regulated (35 genes more than threefold) by the loss of the gss gene. Most significant categories of up-regulated genes include sulfur utilization, glutamine and succinate metabolism, polyamine and arginine metabolism, and purine and pyrimidine metabolism.
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Affiliation(s)
- Manas K Chattopadhyay
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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Chiang BY, Chou CC, Hsieh FT, Gao S, Lin JCY, Lin SH, Chen TC, Khoo KH, Lin CH. In vivo tagging and characterization of S-glutathionylated proteins by a chemoenzymatic method. Angew Chem Int Ed Engl 2012; 51:5871-5. [PMID: 22555962 PMCID: PMC3505901 DOI: 10.1002/anie.201200321] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/13/2012] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Kay-Hooi Khoo
- Institute of Biological ChemistryAcademia Sinica No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529 (Taiwan) and Institute of Biochemical Sciences National Taiwan University (Taiwan)
| | - Chun-Hung Lin
- Institute of Biological ChemistryAcademia Sinica No. 128, Academia Road Section 2, Nan-Kang, Taipei, 11529 (Taiwan) and Institute of Biochemical Sciences National Taiwan University (Taiwan)
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25
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Chiang BY, Chou CC, Hsieh FT, Gao S, Lin JCY, Lin SH, Chen TC, Khoo KH, Lin CH. In Vivo Tagging and Characterization of S-Glutathionylated Proteins by a Chemoenzymatic Method. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Lo YC, Su WC, Ko TP, Wang NC, Wang AHJ. Terpyridine Platinum(II) Complexes Inhibit Cysteine Proteases by Binding to Active-site Cysteine. J Biomol Struct Dyn 2011; 29:267-82. [DOI: 10.1080/073911011010524993] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Chong CM, Gao S, Chiang BY, Hsu WH, Lin TC, Chen TC, Lin CH. An Acyloxymethyl Ketone-Based Probe to Monitor the Activity of Glutathionylspermidine Amidase in Escherichia coli. Chembiochem 2011; 12:2306-9. [DOI: 10.1002/cbic.201100417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Indexed: 11/10/2022]
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28
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Beisel CL, Storz G. The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol Cell 2011; 41:286-97. [PMID: 21292161 DOI: 10.1016/j.molcel.2010.12.027] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/29/2010] [Accepted: 12/01/2010] [Indexed: 01/27/2023]
Abstract
Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base-pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse nonpreferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multioutput feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base-pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression.
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Affiliation(s)
- Chase L Beisel
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA.
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Pai CH, Wu HJ, Lin CH, Wang AHJ. Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases. Protein Sci 2011; 20:557-66. [PMID: 21226054 DOI: 10.1002/pro.589] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 12/21/2010] [Accepted: 12/30/2010] [Indexed: 01/23/2023]
Abstract
The bifunctional Escherichia coli glutathionylspermidine synthetase/amidase (GspSA) catalyzes both the synthesis and hydrolysis of Gsp. Its amidase domain (GspA), which catalyzes the hydrolysis of Gsp into glutathione and spermidine, plays an important role in redox sensing and protein S-thiolation. To gain insight of the regulation and catalytic mechanism of and further understand the recycling of the Gsp dimer and Gsp-S-protein adducts, we solved two crystal structures of GspA and GspSA both with the C59A mutation and bound with the substrate, Gsp. In both structures, Cys59, His131, and Glu147 form the catalytic triad, which is similar to other cysteine proteases. Comparison of the GspA_Gsp complex and apo GspSA structures indicates that on binding with Gsp, the side chains of Asn149 and Gln58 of the amidase domain are induced to move closer to the carbonyl oxygen of the cleaved amide bond of Gsp, thereby participating in catalysis. In addition, the helix-loop region of GspA, corresponding to the sequence (30)YSSLDPQEYEDDA(42), involves in regulating the substrate binding. Our previous study indicated that the thiol of Cys59 of GspA is only oxidized to sulfenic acid by H(2)O(2). When comparing the active site of GspA with those of other cysteine proteases, we found that limited space and hydrophobicity of the environment around Cys59 play an important role to inhibit its further oxidation. The structural results presented here not only elucidate the catalytic mechanism and regulation of GspA but also help us to design small molecules to inhibit or probe for the activity of GspA.
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Affiliation(s)
- Chien-Hua Pai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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