1
|
Kelly JB, Nolan AC, Zeden MS. How can we escape the ESKAPEs: Antimicrobial resistance mechanisms and what lies ahead? PLoS Pathog 2024; 20:e1012270. [PMID: 38870133 PMCID: PMC11175505 DOI: 10.1371/journal.ppat.1012270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024] Open
Affiliation(s)
- Jessica B. Kelly
- Microbiology, Infectious Disease Section, School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Aaron C. Nolan
- Microbiology, Infectious Disease Section, School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Merve S. Zeden
- Microbiology, Infectious Disease Section, School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway, Ireland
| |
Collapse
|
2
|
Liao J, Qi Q, Kuang L, Zhou Y, Xiao Q, Liu T, Wang X, Guo L, Jiang Y. Chloramphenicol Binding Sites of Acinetobacter baumannii Chloramphenicol Acetyltransferase CatB8. ACS Infect Dis 2024; 10:870-878. [PMID: 38311919 DOI: 10.1021/acsinfecdis.3c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Acinetobacter baumannii is a multidrug-resistant pathogen that has become one of the most challenging pathogens in global healthcare. Several antibiotic-resistant genes, including catB8, have been identified in the A. baumannii genome. CatB8 protein, one of the chloramphenicol acetyltransferases (Cats), is encoded by the catB8 gene. Cats can convert chloramphenicol (chl) to 3-acetyl-chl, leading to bacterial resistance to chl. Here, we present the high-resolution cocrystal structure of CatB8 with chl. The structure that we resolved showed that each monomer of CatB8 binds to four chl molecules, while its homologous protein only binds to one chl molecule. One of the newly discovered chl binding site overlaps with the site of another substrate, acetyl-CoA. Through structure-based biochemical analyses, we identified key residues for chl recruiting and acetylation of chl in CatB8. Our work is of significant importance for understanding the drug resistance of A. baumannii and the effectiveness of antibiotic treatment.
Collapse
Affiliation(s)
- Jing Liao
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qianqian Qi
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Linghan Kuang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China
| | - Yanxia Zhou
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qingjie Xiao
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Ting Liu
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China
| | - Xiang Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Li Guo
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yongmei Jiang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China
| |
Collapse
|
3
|
Hoya M, Matsunaga R, Nagatoishi S, Tsumoto K. Experimental modification in thermal stability of oligomers by alanine substitution and site saturation mutagenesis of interfacial residues. Biochem Biophys Res Commun 2024; 691:149316. [PMID: 38039832 DOI: 10.1016/j.bbrc.2023.149316] [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: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
For certain industrial applications, the stability of protein oligomers is important. In this study, we demonstrated an efficient method to improve the thermal stability of oligomers using the trimeric protein chloramphenicol acetyltransferase (CAT) as the model. We substituted all interfacial residues of CAT with alanine to detect residues critical for oligomer stability. Mutation of six of the forty-nine interfacial residues enhanced oligomer thermal stability. Site saturation mutagenesis was performed on these six residues to optimize the side chains. About 15% of mutations enhanced thermal stability by more than 0.5 °C and most did not disrupt activity of CAT. Certain combinations of mutations further improved thermal stability and resistance against heat treatment. The quadruple mutant, H17V/N34S/F134A/D157C, retained the same activity as the wild-type after heat treatment at 9 °C higher temperature than the wild-type CAT. Furthermore, combinations with only alanine substitutions also improved thermal stability, suggesting the method we developed can be used for rapid modification of industrially important proteins.
Collapse
Affiliation(s)
- Megumi Hoya
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Sagami Chemical Research Institute, 2743-1 Hayakawa, Ayase, Kanagawa, 252-1193, Japan
| | - Ryo Matsunaga
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Project Division of Advanced Biopharmaceutical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Project Division of Advanced Biopharmaceutical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| |
Collapse
|
4
|
Edwards AN, Blue AJ, Conforti JM, Cordes MS, Trakselis MA, Gallagher ES. Gas-phase stability and thermodynamics of ligand-bound, binary complexes of chloramphenicol acetyltransferase reveal negative cooperativity. Anal Bioanal Chem 2023; 415:6201-6212. [PMID: 37542535 DOI: 10.1007/s00216-023-04891-5] [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: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
The biological role of the bacterial chloramphenicol (Chl)-resistance enzyme, chloramphenicol acetyltransferase (CAT), has seen renewed interest due to the resurgent use of Chl against multi-drug-resistant microbes. This looming threat calls for more rationally designed antibiotic derivatives that have improved antimicrobial properties and reduced toxicity in humans. Herein, we utilize native ion mobility spectrometry-mass spectrometry (IMS-MS) to investigate the gas-phase structure and thermodynamic stability of the type I variant of CAT from Escherichia coli (EcCATI) and several EcCATI:ligand-bound complexes. EcCATI readily binds multiple Chl without incurring significant changes to its gas-phase structure or stability. A non-hydrolyzable acetyl-CoA derivative (S-ethyl-CoA, S-Et-CoA) was used to kinetically trap EcCATI and Chl in a ternary, ligand-bound state (EcCATI:S-Et-CoA:Chl). Using collision-induced unfolding (CIU)-IMS-MS, we find that Chl dissociates from EcCATI:S-Et-CoA:Chl complexes at low collision energies, while S-Et-CoA remains bound to EcCATI even as protein unfolding occurs. Gas-phase binding constants further suggest that EcCATI binds S-Et-CoA more tightly than Chl. Both ligands exhibit negative cooperativity of subsequent ligand binding in their respective binary complexes. While we observe no significant change in structure or stability to EcCATI when bound to either or both ligands, we have elucidated novel gas-phase unfolding and dissociation behavior and provided a foundation for further characterization of alternative substrates and/or inhibitors of EcCATI.
Collapse
Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Anthony J Blue
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Jessica M Conforti
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
| |
Collapse
|
5
|
Cheung JW, Kinney WD, Wesalo JS, Reed M, Nicholson EM, Deiters A, Cropp TA. Genetic Encoding of a Photocaged Histidine for Light-Control of Protein Activity. Chembiochem 2023; 24:e202200721. [PMID: 36642698 PMCID: PMC10407765 DOI: 10.1002/cbic.202200721] [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: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023]
Abstract
The use of light to control protein function is a critical tool in chemical biology. Here we describe the addition of a photocaged histidine to the genetic code. This unnatural amino acid becomes histidine upon exposure to light and allows for the optical control of enzymes that utilize active-site histidine residues. We demonstrate light-induced activation of a blue fluorescent protein and a chloramphenicol transferase. Further, we genetically encoded photocaged histidine in mammalian cells. We then used this approach in live cells for optical control of firefly luciferase and, Renilla luciferase. This tool should have utility in manipulating and controlling a wide range of biological processes.
Collapse
Affiliation(s)
- Jenny W Cheung
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - William D Kinney
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Joshua S Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Megan Reed
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Eve M Nicholson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| |
Collapse
|
6
|
Mehlhoff JD, Ostermeier M. Genes Vary Greatly in Their Propensity for Collateral Fitness Effects of Mutations. Mol Biol Evol 2023; 40:7043719. [PMID: 36798991 PMCID: PMC9999109 DOI: 10.1093/molbev/msad038] [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: 10/24/2022] [Revised: 01/18/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mutations can have deleterious fitness effects when they decrease protein specific activity or decrease active protein abundance. Mutations will also be deleterious when they cause misfolding or misinteractions that are toxic to the cell (i.e., independent of whether the mutations affect specific activity and abundance). The extent to which protein evolution is shaped by these and other collateral fitness effects is unclear in part because little is known of their frequency and magnitude. Using deep mutational scanning (DMS), we previously found at least 42% of missense mutations in the TEM-1 β-lactamase antibiotic resistance gene cause deleterious collateral fitness effects. Here, we used DMS to comprehensively determine the collateral fitness effects of missense mutations in three genes encoding the antibiotic resistance proteins New Delhi metallo-β-lactamase (NDM-1), chloramphenicol acetyltransferase I (CAT-I), and 2″-aminoglycoside nucleotidyltransferase (AadB). AadB (20%), CAT-I (0.9%), and NDM-1 (0.2%) were less susceptible to deleterious collateral fitness effects than TEM-1 (42%) indicating that genes have different propensities for these effects. As was observed with TEM-1, all the studied deleterious aadB mutants increased aggregation. However, aggregation did not correlate with collateral fitness effects for many of the deleterious mutants of CAT-I and NDM-1. Select deleterious mutants caused unexpected phenotypes to emerge. The introduction of internal start codons in CAT-1 caused loss of the episome and a mutation in aadB made its cognate antibiotic essential for growth. Our study illustrates how the complexity of the cell provides a rich environment for collateral fitness effects and new phenotypes to emerge.
Collapse
Affiliation(s)
- Jacob D Mehlhoff
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
| |
Collapse
|
7
|
Shin J, Kim S, Park W, Jin KC, Kim SK, Kweon DH. Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose. J Microbiol Biotechnol 2022; 32:1471-1478. [PMID: 36437520 PMCID: PMC9720067 DOI: 10.4014/jmb.2209.09018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
Abstract
2'-Fucosyllactose (2'-FL), the most abundant fucosylated oligosaccharide in human milk, has multiple beneficial effects on human health. However, its biosynthesis by metabolically engineered Escherichia coli is often hampered owing to the insolubility and instability of α-1,2-fucosyltransferase (the rate-limiting enzyme). In this study, we aimed to enhance 2'-FL production by increasing the expression of soluble α-1,2-fucosyltransferase from Helicobacter pylori (FucT2). Because structural information regarding FucT2 has not been unveiled, we decided to improve the expression of soluble FucT2 in E. coli via directed evolution using a protein solubility biosensor that links protein solubility to antimicrobial resistance. For such a system to be viable, the activity of kanamycin resistance protein (KanR) should be dependent on FucT2 solubility. KanR was fused to the C-terminus of mutant libraries of FucT2, which were generated using a combination of error-prone PCR and DNA shuffling. Notably, one round of the directed evolution process, which consisted of mutant library generation and selection based on kanamycin resistance, resulted in a significant increase in the expression level of soluble FucT2. As a result, a batch fermentation with the ΔL M15 pBCGW strain, expressing the FucT2 mutant (F#1-5) isolated from the first round of the directed evolution process, resulted in the production of 0.31 g/l 2'-FL with a yield of 0.22 g 2'-FL/g lactose, showing 1.72- and 1.51-fold increase in the titer and yield, respectively, compared to those of the control strain. The simple and powerful method developed in this study could be applied to enhance the solubility of other unstable enzymes.
Collapse
Affiliation(s)
- Jonghyeok Shin
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi 16419, Republic of Korea,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Seungjoo Kim
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi 16419, Republic of Korea
| | - Wonbeom Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi 16419, Republic of Korea
| | - Kyoung Chan Jin
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea,
S.K. Kim Phone: +82-31-670-3261 Fax: +82-31-675-3108 E-mail:
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi 16419, Republic of Korea,Corresponding authors D.H. Kweon Phone: +82-31-290-7869 Fax: +82-31-290-7870 E-mail:
| |
Collapse
|
8
|
El-Khoury C, Mansour E, Yuliandra Y, Lai F, Hawkins BA, Du JJ, Sundberg EJ, Sluis-Cremer N, Hibbs DE, Groundwater PW. The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification. RSC Med Chem 2022; 13:1276-1299. [PMID: 36439977 PMCID: PMC9667779 DOI: 10.1039/d2md00263a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/16/2022] [Indexed: 02/03/2023] Open
Abstract
Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.
Collapse
Affiliation(s)
- Christy El-Khoury
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Elissar Mansour
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Yori Yuliandra
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Bryson A Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine Pittsburgh PA 15213 USA
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| |
Collapse
|
9
|
Towards crucial post-modification in biosynthesis of terpenoids and steroids: C3 oxidase and acetyltransferase. Enzyme Microb Technol 2022; 162:110148. [DOI: 10.1016/j.enzmictec.2022.110148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022]
|
10
|
Zhou K, Litfin T, Solayman M, Zhao H, Zhou Y, Zhan J. High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing. Int J Biol Macromol 2022; 203:543-552. [PMID: 35120933 DOI: 10.1016/j.ijbiomac.2022.01.173] [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: 08/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Splitting a protein at a position may lead to self- or assisted-complementary fragments depending on whether two resulting fragments can reconstitute to maintain the native function spontaneously or require assistance from two interacting molecules. Assisted complementary fragments with high contrast are an important tool for probing biological interactions. However, only a small number of assisted-complementary split-variants have been identified due to manual, labour-intensive optimization of a candidate gene. Here, we introduce a technique for high-throughput split-protein profiling (HiTS) that allows fast identification of self- and assisted complementary positions by transposon mutagenesis, a rapamycin-regulated FRB-FKBP protein interaction pair, and deep sequencing. We test this technique by profiling three antibiotic-resistant genes (fosfomycin-resistant gene, fosA3, erythromycin-resistant gene, ermB, and chloramphenicol-resistant gene, catI). Self- and assisted complementary fragments discovered by the high-throughput technique were subsequently confirmed by low-throughput testing of individual split positions. Thus, the HiTS technique provides a quicker alternative for discovering the proteins with suitable self- and assisted-complementary split positions when combining with a readout such as fluorescence, bioluminescence, cell survival, gene transcription or genome editing.
Collapse
Affiliation(s)
- Kai Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Thomas Litfin
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Md Solayman
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| |
Collapse
|
11
|
Jain P, Bepari AK, Sen PK, Rafe T, Imtiaz R, Hossain M, Reza HM. High prevalence of multiple antibiotic resistance in clinical E. coli isolates from Bangladesh and prediction of molecular resistance determinants using WGS of an XDR isolate. Sci Rep 2021; 11:22859. [PMID: 34819576 PMCID: PMC8613203 DOI: 10.1038/s41598-021-02251-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 12/04/2022] Open
Abstract
Multi-drug-resistance (MDR) is a severe public health concern worldwide, and its containment is more challenging in developing countries due to poor antimicrobial resistance (AMR) surveillance and irrational use of antibiotics. The current study investigated 100 clinical E. coli isolates and revealed that 98% of them were MDR. PCR analysis using 25 selected isolates showed the predominance of metallo-β-lactamase gene blaNDM (80%) and ESBL genes blaOXA (48%) and blaCTX-M-15 (32%). The AmpC gene was detected in 68% of the isolates, while 32% was tetC positive. Notably, 34% of the isolates were resistant to carbapenem. Whole genome sequence (WGS) analysis of an extensively drug-resistant (XDR) isolate (L16) revealed the presence of the notorious sequence type 131 responsible for multi-drug-resistant infections, multiple antibiotic resistance genes (ARGs), virulence genes, and mobile genetic elements that pose risks to environmental transmission. Our results indicate that MDR is alarmingly increasing in Bangladesh that critically limits the treatment option against infections and contributes to further aggravation to the prevailing situation of MDR worldwide. The findings of this study will be valuable in designing sustainable strategies to contain MDR in the region.
Collapse
Affiliation(s)
- Preeti Jain
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Asim Kumar Bepari
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Prosengit Kumer Sen
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Tanzir Rafe
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Rashed Imtiaz
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Maqsud Hossain
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh.
| |
Collapse
|
12
|
Levin-Kravets O, Kordonsky A, Shusterman A, Biswas S, Persaud A, Elias S, Langut Y, Florentin A, Simpson-Lavy KJ, Yariv E, Avishid R, Sror M, Almog O, Marshanski T, Kadosh S, Ben David N, Manori B, Fischer Z, Lilly J, Borisova E, Ambrozkiewicz MC, Tarabykin V, Kupiec M, Thaker M, Rotin D, Prag G. Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B. J Mol Biol 2021; 433:167276. [PMID: 34599943 DOI: 10.1016/j.jmb.2021.167276] [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: 06/21/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Split reporter protein-based genetic section systems are widely used to identify and characterize protein-protein interactions (PPI). The assembly of split markers that antagonize toxins, rather than required for synthesis of missing metabolites, facilitates the seeding of high density of cells and selective growth. Here we present a newly developed split chloramphenicol acetyltransferase (split-CAT) -based genetic selection system. The N terminus fragment of CAT is fused downstream of the protein of interest and the C terminus fragment is tethered upstream to its postulated partner. We demonstrate the system's advantages for the study of PPIs. Moreover, we show that co-expression of a functional ubiquitylation cascade where the target and ubiquitin are tethered to the split-CAT fragments results in ubiquitylation-dependent selective growth. Since proteins do not have to be purified from the bacteria and due to the high sensitivity of the split-CAT reporter, detection of challenging protein cascades and post-translation modifications is enabled. In addition, we demonstrate that the split-CAT system responds to small molecule inhibitors and molecular glues (GLUTACs). The absence of ubiquitylation-dependent degradation and deubiquitylation in E. coli significantly simplify the interpretation of the results. We harnessed the developed system to demonstrate that like NEDD4, UBE3B also undergoes self-ubiquitylation-dependent inactivation. We show that self-ubiquitylation of UBE3B on K665 induces oligomerization and inactivation in yeast and mammalian cells respectively. Finally, we showcase the advantages of split-CAT in the study of human diseases by demonstrating that mutations in UBE3B that cause Kaufman oculocerebrofacial syndrome exhibit clear E. coli growth phenotypes.
Collapse
Affiliation(s)
- Olga Levin-Kravets
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Alina Kordonsky
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Anna Shusterman
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Sagnik Biswas
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Avinash Persaud
- Cell Biology Program, The Hospital for Sick Children and Biochemistry Department, University of Toronto, Toronto, ON, Canada
| | - Sivan Elias
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Yael Langut
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Amir Florentin
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Kobi J Simpson-Lavy
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Elon Yariv
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Reut Avishid
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Mor Sror
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Ofir Almog
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Tal Marshanski
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel. https://twitter.com/@TalMarsh
| | - Shira Kadosh
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Nicole Ben David
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Bar Manori
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Zohar Fischer
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Jeremiah Lilly
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Ekaterina Borisova
- Institute of Medical Genetics, Tomsk National Research Medical Center Neuroscience, Lobachevsky University of the Russian Academy of Sciences Nizhny Novgorod, pr. Gagarina 24, Nizhny Novgorod, Russia; Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Mateusz C Ambrozkiewicz
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany. https://twitter.com/@MAmbrozkiewicz
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Maulik Thaker
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Daniela Rotin
- Cell Biology Program, The Hospital for Sick Children and Biochemistry Department, University of Toronto, Toronto, ON, Canada
| | - Gali Prag
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
13
|
Magureanu M, Bilea F, Bradu C, Hong D. A review on non-thermal plasma treatment of water contaminated with antibiotics. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125481. [PMID: 33992019 DOI: 10.1016/j.jhazmat.2021.125481] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/05/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Large amounts of antibiotics are produced and consumed worldwide, while wastewater treatment is still rather inefficient, leading to considerable water contamination. Concentrations of antibiotics in the environment are often sufficiently high to exert a selective pressure on bacteria of clinical importance that increases the prevalence of resistance. Since the drastic reduction in the use of antibiotics is not envisaged, efforts to reduce their input into the environment by improving treatment of contaminated wastewater is essential to limit uncontrollable spread of antibiotic resistance. This paper reviews recent progress on the use of non-thermal plasma for the degradation of antibiotics in water. The target compounds removal, the energy efficiency and the mineralization are analyzed as a function of discharge configuration and the most important experimental parameters. Various ways to improve the plasma process efficiency are addressed. Based on the identified reaction intermediates, degradation pathways are proposed for various classes of antibiotics and the degradation mechanisms of these chemicals under plasma conditions are discussed.
Collapse
Affiliation(s)
- M Magureanu
- National Institute for Lasers, Plasma and Radiation Physics, Department of Plasma Physics and, Nuclear Fusion, Atomistilor Str. 409, P.O. Box MG-36, Magurele, 077125 Bucharest, Romania.
| | - F Bilea
- National Institute for Lasers, Plasma and Radiation Physics, Department of Plasma Physics and, Nuclear Fusion, Atomistilor Str. 409, P.O. Box MG-36, Magurele, 077125 Bucharest, Romania; University of Bucharest, Faculty of Chemistry, Department of Analytical Chemistry, Panduri Avenue 90, 050663 Bucharest, Romania
| | - C Bradu
- University of Bucharest, Faculty of Biology, Department of Systems Ecology and Sustainability, Splaiul Independentei 91-95, 050095 Bucharest, Romania
| | - D Hong
- GREMI, UMR 7344, Université d'Orléans, CNRS, Orléans, France
| |
Collapse
|
14
|
Acyltransferase AniI, a Tailoring Enzyme with Broad Substrate Tolerance for High-Level Production of Anisomycin. Appl Environ Microbiol 2021; 87:e0017221. [PMID: 33931417 DOI: 10.1128/aem.00172-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anisomycin (compound 1), a pyrrolidine antibiotic, exhibits diverse biological and pharmacologic activities. The biosynthetic gene cluster of compound 1 has been identified previously, and the multistep assembly of the core benzylpyrrolidine scaffold was characterized. However, enzymatic modifications, such as acylation, involved in compound 1 biosynthesis are unknown. In this study, the genetic manipulation of aniI proved that it encoded an indispensable acetyltransferase for compound 1 biosynthesis. Bioinformatics analysis suggested AniI as a member of maltose (MAT) and galactoside O-acetyltransferases (GAT) with C-terminal left-handed parallel beta-helix (LbH) subdomain, which were referred to as LbH-MAT-GAT sugar O-acetyltransferases. However, the biochemical assay identified that its target site was the hydroxyl group of the pyrrolidine ring. AniI was found to be tolerant of acyl donors with different chain lengths for the biosynthesis of compound 1 and derivatives 12 and 13 with butyryl and isovaleryl groups, respectively. Meanwhile, it showed comparable activity toward biosynthetic intermediates and synthesized analogues, suggesting promiscuity to the pyrrolidine ring structure of compound 1. These data may inspire new viable synthetic routes for the construction of more complex pyrrolidine ring scaffolds in compound 1. Finally, the overexpression of aniI under the control of strong promoters contributed to the higher productivities of compound 1 and its analogues. These findings reported here not only improve the understanding of anisomycin biosynthesis but also expand the substrate scope of O-acetyltransferase working on the pyrrolidine ring and pave the way for future metabolic engineering construction of high-yield strains. IMPORTANCE Acylation is an important tailoring reaction during natural product biosynthesis. Acylation could increase the structural diversity and affect the chemical stability, volatility, biological activity, and even the cellular localization of specialized compounds. Many acetyltransferases have been reported in natural product biosynthesis. The typical example of the LbH-MAT-GAT sugar O-acetyltransferase subfamily was reported to catalyze the coenzyme A (CoA)-dependent acetylation of the 6-hydroxyl group of sugars. However, no protein of this family has been characterized to acetylate a nonsugar secondary metabolic product. Here, AniI was found to catalyze the acylation of the hydroxyl group of the pyrrolidine ring and be tolerant of diverse acyl donors and acceptors, which made the biosynthesis more efficient and exclusive for biosynthesis of compound 1 and its derivatives. Moreover, the overexpression of aniI serves as a successful example of genetic manipulation of a modification gene for the high production of final products and might set the stage for future metabolic engineering.
Collapse
|
15
|
Ghafoori SM, Robles AM, Arada AM, Shirmast P, Dranow DM, Mayclin SJ, Lorimer DD, Myler PJ, Edwards TE, Kuhn ML, Forwood JK. Structural characterization of a Type B chloramphenicol acetyltransferase from the emerging pathogen Elizabethkingia anophelis NUHP1. Sci Rep 2021; 11:9453. [PMID: 33947893 PMCID: PMC8096840 DOI: 10.1038/s41598-021-88672-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023] Open
Abstract
Elizabethkingia anophelis is an emerging multidrug resistant pathogen that has caused several global outbreaks. E. anophelis belongs to the large family of Flavobacteriaceae, which contains many bacteria that are plant, bird, fish, and human pathogens. Several antibiotic resistance genes are found within the E. anophelis genome, including a chloramphenicol acetyltransferase (CAT). CATs play important roles in antibiotic resistance and can be transferred in genetic mobile elements. They catalyse the acetylation of the antibiotic chloramphenicol, thereby reducing its effectiveness as a viable drug for therapy. Here, we determined the high-resolution crystal structure of a CAT protein from the E. anophelis NUHP1 strain that caused a Singaporean outbreak. Its structure does not resemble that of the classical Type A CATs but rather exhibits significant similarity to other previously characterized Type B (CatB) proteins from Pseudomonas aeruginosa, Vibrio cholerae and Vibrio vulnificus, which adopt a hexapeptide repeat fold. Moreover, the CAT protein from E. anophelis displayed high sequence similarity to other clinically validated chloramphenicol resistance genes, indicating it may also play a role in resistance to this antibiotic. Our work expands the very limited structural and functional coverage of proteins from Flavobacteriaceae pathogens which are becoming increasingly more problematic.
Collapse
Affiliation(s)
| | - Alyssa M Robles
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Angelika M Arada
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Paniz Shirmast
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
| |
Collapse
|
16
|
Abstract
Apramycin is an aminoglycoside antibiotic with the potential to be developed to combat multidrug-resistant pathogens. Its unique structure evades the clinically widespread mechanisms of aminoglycoside resistance that currently compromise the efficacy of other members in this drug class. Of the aminoglycoside-modifying enzymes that chemically alter these antibiotics, only AAC(3)-IVa has been demonstrated to confer resistance to apramycin through N-acetylation. Knowledge of other modification mechanisms is important to successfully develop apramycin for clinical use. Here, we show that ApmA is structurally unique among the previously described aminoglycoside-modifying enzymes and capable of conferring a high level of resistance to apramycin. In vitro experiments indicated ApmA to be an N-acetyltransferase, but in contrast to AAC(3)-IVa, ApmA has a unique regiospecificity of the acetyl transfer to the N2' position of apramycin. Crystallographic analysis of ApmA conclusively showed that this enzyme is an acetyltransferase from the left-handed β-helix protein superfamily (LβH) with a conserved active site architecture. The success of apramycin will be dependent on consideration of the impact of this potential form of clinical resistance.IMPORTANCE Apramycin is an aminoglycoside antibiotic that has been traditionally used in veterinary medicine. Recently, it has become an attractive candidate to repurpose in the fight against multidrug-resistant pathogens prioritized by the World Health Organization. Its atypical structure circumvents most of the clinically relevant mechanisms of resistance that impact this class of antibiotics. Prior to repurposing apramycin, it is important to understand the resistance mechanisms that could be a liability. Our study characterizes the most recently identified apramycin resistance element, apmA We show ApmA does not belong to the protein families typically associated with aminoglycoside resistance and is responsible for modifying a different site on the molecule. The data presented will be critical in the development of apramycin derivatives that will evade apmA in the event it becomes prevalent in the clinic.
Collapse
|
17
|
Characterization of permissive and non-permissive peptide insertion sites in chloramphenicol acetyltransferase. Microb Pathog 2020; 149:104395. [DOI: 10.1016/j.micpath.2020.104395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/02/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
|
18
|
Latimer LN, Russ ZN, Lucas J, Dueber JE. Exploration of Acetylation as a Base-Labile Protecting Group in Escherichia coli for an Indigo Precursor. ACS Synth Biol 2020; 9:2775-2783. [PMID: 32886882 DOI: 10.1021/acssynbio.0c00297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biochemical protecting groups are observed in natural metabolic pathways to control reactivity and properties of chemical intermediates; similarly, they hold promise as a tool for metabolic engineers to achieve the same goals. Protecting groups come with costs: lower yields from carbon, metabolic load to the production host, deprotection catalyst costs and kinetics limitations, and wastewater treatment of the group. Compared to glycosyl biochemical protection, such as glucosyl groups, acetylation can mitigate each of these costs. As an example application where these benefits could be valuable, we explored acetylation protection of indoxyl, the reactive precursor to the clothing dye, indigo. First, we demonstrated denim dyeing with chemically sourced indoxyl acetate by deprotection with base, showing results comparable to industry-standard denim dyeing. Second, we modified an Escherichia coli production host for improved indoxyl acetate stability by the knockout of 14 endogenous hydrolases. Cumulatively, these knockouts yielded a 67% reduction in the indoxyl acetate hydrolysis rate from 0.22 mmol/g DCW/h to 0.07 mmol/g DCW/h. To biosynthesize indoxyl acetate, we identified three promiscuous acetyltransferases which acetylate indoxyl in vivo. Indoxyl acetate titer, while low, was improved 50%, from 43 μM to 67 μM, in the hydrolase knockout strain compared to wild-type E. coli. Unfortunately, low millimolar concentrations of indoxyl acetate proved to be toxic to the E. coli production host; however, the principle of acetylation as a readily cleavable and low impact biochemical protecting group and the engineered hydrolase knockout production host should prove useful for other metabolic products.
Collapse
Affiliation(s)
- Luke N. Latimer
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Zachary N. Russ
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - James Lucas
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
19
|
Elder FCT, Feil EJ, Snape J, Gaze WH, Kasprzyk-Hordern B. The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment. ENVIRONMENT INTERNATIONAL 2020; 139:105681. [PMID: 32251898 DOI: 10.1016/j.envint.2020.105681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/28/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance (ABR) is now recognised as a serious global health and economic threat that is most efficiently managed via a 'one health' approach incorporating environmental risk assessment. Although the environmental dimension of ABR has been largely overlooked, recent studies have underlined the importance of non-clinical settings in the emergence and spread of resistant strains. Despite this, several research gaps remain in regard to the development of a robust and fit-for-purpose environmental risk assessment for ABR drivers such as antibiotics (ABs). Here we explore the role the environment plays in the dissemination of ABR within the context of stereochemistry and its particular form, enantiomerism. Taking chloramphenicol as a proof of principle, we argue that stereoisomerism of ABs impacts on biological properties and the mechanisms of resistance and we discuss more broadly the importance of stereochemistry (enantiomerism in particular) with respect to antimicrobial potency and range of action.
Collapse
Affiliation(s)
- Felicity C T Elder
- Department of Chemistry, University of Bath, BA27AY Bath, United Kingdom
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA27AY Bath, United Kingdom
| | - JasoN Snape
- AstraZeneca Global Safety, Health and Environment, Mereside, Macclesfield SK10, 4TG, United Kingdom
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall TR1 3HD, United Kingdom
| | | |
Collapse
|
20
|
Lee JW, Trinh CT. Towards renewable flavors, fragrances, and beyond. Curr Opin Biotechnol 2020; 61:168-180. [PMID: 31986468 DOI: 10.1016/j.copbio.2019.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/01/2019] [Accepted: 12/17/2019] [Indexed: 02/08/2023]
Abstract
Esters constitute a large space of unique molecules with broad range of applications as flavors, fragrances, pharmaceuticals, cosmetics, green solvents, and advanced biofuels. Global demand of natural esters in food, household cleaner, personal care, and perfume industries is increasing while the ester supply from natural sources has been limited. Development of novel microbial cell factories for ester production from renewable feedstocks can potentially provide an alternative and sustainable source of natural esters and hence help fulfill growing demand. Here, we highlight recent advances in microbial production of esters and provide perspectives for improving its economic feasibility. As the field matures, microbial ester production platforms will enable renewable and sustainable production of flavors and fragrances, and open new market opportunities beyond what nature can offer.
Collapse
Affiliation(s)
- Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Cong T Trinh
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN, USA; Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| |
Collapse
|
21
|
Patilaya P, Husori DI, Marhafanny L. Susceptibility of Klebsiella Pneumoniae Isolated from Pus Specimens of Post-Surgery Patients in Medan, Indonesia to Selected Antibiotics. Open Access Maced J Med Sci 2019; 7:3861-3864. [PMID: 32127992 PMCID: PMC7048342 DOI: 10.3889/oamjms.2019.520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/07/2022] Open
Abstract
AIM: This study was to determine the sensitivity of Klebsiella pneumonia isolated from pus specimens of post-surgery patients in Medan, Indonesia to selected antibiotics. METHODS: Samples were collected at the Laboratory of Microbiology, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia. The isolated bacteria were identified by Gram’s stain, colony characteristics, and biochemical tests. Susceptibility of K. pneumoniae isolates were tested to selected antibiotics including amikacin, meropenem, levofloxacin, ciprofloxacin, co-trimoxazole, ceftazidime, cefoperazone, cefuroxime, cefepime, cefotaxime, tetracycline, chloramphenicol, amoxicillin and ampicillin with Kirby Bauer method by measuring the inhibitory zone. RESULTS: A total of 20 K. pneumoniae isolates were obtained in this study. The results showed that K. Pneumonia isolates exhibited good sensitivity to amikacin (100%) and meropenem (80%). Sensitivity of levofloxacin (60%), ceftazidime (55%), ciprofloxacin (55%), cefoperazone (50%), and co-trimoxazole (50%) were moderate for the bacterial isolates. K. Pneumoniae isolates indicated low sensitivity to cefuroxime (45%), chloramphenicol (35%), cefepime (30%), cefotaxime (30%), tetracycline (30%), amoxicillin (5%), and ampicillin (5%). CONCLUSION: This study concludes that K. pneumoniae isolates are most sensitive to amikacin and less sensitive to ampicillin and amoxicillin.
Collapse
Affiliation(s)
- Popi Patilaya
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Dadang Irfan Husori
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Lany Marhafanny
- Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| |
Collapse
|
22
|
Fewer DP, Metsä‐Ketelä M. A pharmaceutical model for the molecular evolution of microbial natural products. FEBS J 2019; 287:1429-1449. [DOI: 10.1111/febs.15129] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/11/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022]
Affiliation(s)
- David P. Fewer
- Department of Microbiology University of Helsinki Finland
| | | |
Collapse
|
23
|
Green KD, Fosso MY, Mayhoub AS, Garneau-Tsodikova S. Investigating the promiscuity of the chloramphenicol nitroreductase from Haemophilus influenzae towards the reduction of 4-nitrobenzene derivatives. Bioorg Med Chem Lett 2019; 29:1127-1132. [PMID: 30826292 DOI: 10.1016/j.bmcl.2019.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 01/28/2023]
Abstract
Chloramphenicol nitroreductase (CNR), a drug-modifying enzyme from Haemophilus influenzae, has been shown to be responsible for the conversion of the nitro group into an amine in the antibiotic chloramphenicol (CAM). Since CAM structurally bears a 4-nitrobenzene moiety, we explored the substrate promiscuity of CNR by investigating its nitroreduction of 4-nitrobenzyl derivatives. We tested twenty compounds containing a nitrobenzene core, two nitropyridines, one compound with a vinylogous nitro group, and two aliphatic nitro compounds. In addition, we also synthesized twenty-eight 4-nitrobenzyl derivatives with ether, ester, and thioether substituents and assessed the relative activity of CNR in their presence. We found several of these compounds to be modified by CNR, with the enzyme activity ranging from 1 to 150% when compared to CAM. This data provides insights into two areas: (i) chemoenzymatic reduction of select compounds to avoid harsh chemicals and heavy metals routinely used in reductions of nitro groups and (ii) functional groups that would aid CAM in overcoming the activity of this enzyme.
Collapse
Affiliation(s)
- Keith D Green
- University of Kentucky, College of Pharmacy, Department of Pharmaceutical Sciences, Lexington, KY 40536-0596, USA
| | - Marina Y Fosso
- University of Kentucky, College of Pharmacy, Department of Pharmaceutical Sciences, Lexington, KY 40536-0596, USA
| | - Abdelrahman S Mayhoub
- Department of Medicinal Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, College of Pharmacy, Department of Pharmaceutical Sciences, Lexington, KY 40536-0596, USA.
| |
Collapse
|
24
|
Seo H, Lee JW, Garcia S, Trinh CT. Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:245. [PMID: 31636704 PMCID: PMC6792240 DOI: 10.1186/s13068-019-1583-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/01/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Esters are versatile chemicals and potential drop-in biofuels. To develop a sustainable production platform, microbial ester biosynthesis using alcohol acetyltransferases (AATs) has been studied for decades. Volatility of esters endows high-temperature fermentation with advantageous downstream product separation. However, due to the limited thermostability of AATs known, the ester biosynthesis has largely relied on use of mesophilic microbes. Therefore, developing thermostable AATs is important for ester production directly from lignocellulosic biomass by the thermophilic consolidated bioprocessing (CBP) microbes, e.g., Clostridium thermocellum. RESULTS In this study, we engineered a thermostable chloramphenicol acetyltransferase from Staphylococcus aureus (CATSa) for enhanced isobutyl acetate production at elevated temperatures. We first analyzed the broad alcohol substrate range of CATSa. Then, we targeted a highly conserved region in the binding pocket of CATSa for mutagenesis. The mutagenesis revealed that F97W significantly increased conversion of isobutanol to isobutyl acetate. Using CATSa F97W, we demonstrated direct conversion of cellulose into isobutyl acetate by an engineered C. thermocellum at elevated temperatures. CONCLUSIONS This study highlights that CAT is a potential thermostable AAT that can be harnessed to develop the thermophilic CBP microbial platform for biosynthesis of designer bioesters directly from lignocellulosic biomass.
Collapse
Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jong-Won Lee
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Sergio Garcia
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee, Knoxville, TN USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN USA
| |
Collapse
|
25
|
Shin B, Park C, Imlay JA, Park W. 4-Hydroxybenzaldehyde sensitizes Acinetobacter baumannii to amphenicols. Appl Microbiol Biotechnol 2018; 102:2323-2335. [PMID: 29387955 DOI: 10.1007/s00253-018-8791-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 01/02/2018] [Accepted: 01/16/2018] [Indexed: 12/21/2022]
Abstract
Bacterial metabolism modulated by environmental chemicals could alter antibiotic susceptibility. 4-Hydroxybenzaldehyde (4-HBA), which cannot support the growth of Acinetobacter baumannii, exhibited synergism only with amphenicol antibiotics including chloramphenicol (CAM) and thiamphenicol. Interestingly, this synergistic effect was not observed with other growth-supporting, structurally similar compounds such as 4-hydroxybenzoate. Transcriptomic analysis demonstrated that genes involved in protocatechuate metabolism (pca genes) and osmotic stress (bet genes) were significantly upregulated by 4-HBA and CAM treatment. The 14C-labeled CAM influx was lower in a pcaK1 (encoding a transporter of protocatechuate) deletion mutant and was higher in the pcaK1 overexpressing cells relative to that in the wild type upon 4-HBA treatment. Our kinetic data using 14C-labeled CAM clearly showed that CAM uptake is possibly through facilitated diffusion. Deletion of pcaK1 did not result in the elimination of CAM influx, indicating that CAM does not enter only through PcaK1. The amount of 4-HBA in the culture supernatant was, however, unaffected during the test conditions, validating that it was not metabolized by the bacteria. CAM resistant A. baumannii cells derived by serial passages through CAM-amended media exhibited lower level of pcaK1 gene expression. These results led us to conclude that the activation of PcaK1 transporter is probably linked to cellular CAM susceptibility. This is the first report showing a relationship between CAM influx and aromatic compound metabolism in A. baumannii.
Collapse
Affiliation(s)
- Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
| |
Collapse
|
26
|
Patel S. Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures. GENE REPORTS 2017; 7:127-141. [PMID: 32363241 PMCID: PMC7185390 DOI: 10.1016/j.genrep.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/15/2022]
Abstract
Proteins have highly conserved domains that determine their functionality. Out of the thousands of domains discovered so far across all living forms, some of the predominant clinically-relevant domains include IENR1, HNHc, HELICc, Pro-kuma_activ, Tryp_SPc, Lactamase_B, PbH1, ChtBD3, CBM49, acidPPc, G3P_acyltransf, RPOL8c, KbaA, HAMP, HisKA, Hr1, Dak2, APC2, Citrate_ly_lig, DALR, VKc, YARHG, WR1, PWI, ZnF_BED, TUDOR, MHC_II_beta, Integrin_B_tail, Excalibur, DISIN, Cadherin, ACTIN, PROF, Robl_LC7, MIT, Kelch, GAS2, B41, Cyclin_C, Connexin_CCC, OmpH, Bac_rhodopsin, AAA, Knot1, NH, Galanin, IB, Elicitin, ACTH, Cache_2, CHASE, AgrB, PRP, IGR, and Antimicrobial21. These domains are distributed in nucleases/helicases, proteases, esterases, lipases, glycosylase, GTPases, phosphatases, methyltransferases, acyltransferase, acetyltransferase, polymerase, kinase, ligase, synthetase, oxidoreductase, protease inhibitors, nucleic acid binding proteins, adhesion and immunity-related proteins, cytoskeletal component-manipulating proteins, lipid biosynthesis and metabolism proteins, membrane-associated proteins, hormone-like and signaling proteins, etc. These domains are ubiquitous stretches or folds of the proteins in pathogens and allergens. Pathogenesis alleviation efforts can benefit enormously if the characteristics of these domains are known. Hence, this review catalogs and discusses the role of such pivotal domains, suggesting hypotheses for better understanding of pathogenesis at molecular level. Proteins have highly conserved regions or domains across pathogens and allergens. Knowledge on these critical domains can facilitate our understanding of pathogenesis mechanisms. Such immune manipulation-related domains include IENR1, HNHc, HELICc, ACTIN, PROF, Robl_LC7, OmpH etc. These domains are presnt in enzyme, transcription regulators, adhesion proteins, and hormones. This review discusses and hypothesizes on these domains.
Collapse
Key Words
- CARDs, caspase activation and recruitment domains
- CBM, carbohydrate binding module
- CTD, C-terminal domain
- ChtBD, chitin-binding domain
- Diversification
- HNHc, homing endonucleases
- HTH, helix-turn-helix
- IENR1, intron-encoded endonuclease repeat
- Immune manipulation
- PAMPs, pathogen associated molecular patterns
- Pathogenesis
- Phylogenetic conservation
- Protein domains
- SMART, Simple Modular Architecture Research Tool
- Shuffling
- UDG, uracil DNA glycosylase
Collapse
Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA
| |
Collapse
|
27
|
Vincent AT, Emond-Rheault JG, Barbeau X, Attéré SA, Frenette M, Lagüe P, Charette SJ. Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida. Microbiology (Reading) 2016; 162:942-953. [DOI: 10.1099/mic.0.000286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Antony T. Vincent
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Jean-Guillaume Emond-Rheault
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Xavier Barbeau
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de Chimie, Université Laval, Québec, Canada
| | - Sabrina A. Attéré
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6
| | - Patrick Lagüe
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Steve J. Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| |
Collapse
|
28
|
Brewitz HH, Goradia N, Schubert E, Galler K, Kühl T, Syllwasschy B, Popp J, Neugebauer U, Hagelueken G, Schiemann O, Ohlenschläger O, Imhof D. Heme interacts with histidine- and tyrosine-based protein motifs and inhibits enzymatic activity of chloramphenicol acetyltransferase from Escherichia coli. Biochim Biophys Acta Gen Subj 2016; 1860:1343-53. [PMID: 27015758 DOI: 10.1016/j.bbagen.2016.03.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/10/2016] [Accepted: 03/20/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND The occurrence of free organismal heme can either contribute to serious diseases or beneficially regulate important physiological processes. Research on transient binding to heme-regulatory motifs (HRMs) in proteins resulted in the discovery of numerous Cys-based, especially Cys-Pro (CP)-based motifs. However, the number of His- and Tyr-based protein representatives is comparatively low so far, which is in part caused by a lack of information regarding recognition and binding requirements. METHODS To understand transient heme association with such motifs on the molecular level, we analyzed a set of 44 His- and Tyr-based peptides using UV-vis, resonance Raman, cw-EPR and 2D NMR spectroscopy. RESULTS We observed similarities with Cys-based sequences with respect to their spectral behavior and complex geometries. However, significant differences regarding heme-binding affinities and sequence requirements were also found. Compared to Cys-based peptides and proteins all sequences investigated structurally display increased flexibility already in the free-state, which is also maintained upon heme association. The acquired knowledge allowed for identification and prediction of a His-based HRM in chloramphenicol acetyltransferase from Escherichia coli as potential heme-regulated protein. The enzyme's heme-interacting capability was studied, and revealed an inhibitory effect of heme on the protein activity with an IC50 value of 57.69±4.37 μM. CONCLUSIONS It was found that heme inhibits a bacterial protein carrying a potential His-based HRM. This finding brings microbial proteins more into focus of regulation by free heme. GENERAL SIGNIFICANCE Understanding transient binding and regulatory action of heme with bacterial proteins, being crucial for survival, might promote new strategies for the treatment of bacterial infections.
Collapse
Affiliation(s)
- Hans Henning Brewitz
- Pharmaceutical Chemistry I, Institute of Pharmacy, University of Bonn, 53119 Bonn, Germany
| | - Nishit Goradia
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Erik Schubert
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany
| | - Kerstin Galler
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany; Leibniz Institute of Photonic Technology, 07745 Jena, Germany
| | - Toni Kühl
- Centre National de la Recherche Scientifique (CNRS), Bioénergetique et Ingenierie des Protéines, UMR 7281, 13009 Marseille, France
| | - Benjamin Syllwasschy
- Pharmaceutical Chemistry I, Institute of Pharmacy, University of Bonn, 53119 Bonn, Germany
| | - Jürgen Popp
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany; Leibniz Institute of Photonic Technology, 07745 Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ute Neugebauer
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany; Leibniz Institute of Photonic Technology, 07745 Jena, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany
| | | | - Diana Imhof
- Pharmaceutical Chemistry I, Institute of Pharmacy, University of Bonn, 53119 Bonn, Germany.
| |
Collapse
|
29
|
Mosa A, Hutter MC, Zapp J, Bernhardt R, Hannemann F. Regioselective Acetylation of C21 Hydroxysteroids by the Bacterial Chloramphenicol Acetyltransferase I. Chembiochem 2015; 16:1670-9. [DOI: 10.1002/cbic.201500125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 11/11/2022]
|
30
|
Green KD, Pricer RE, Stewart MN, Garneau-Tsodikova S. Comparative Study of Eis-like Enzymes from Pathogenic and Nonpathogenic Bacteria. ACS Infect Dis 2015; 1:272-83. [PMID: 27622743 DOI: 10.1021/acsinfecdis.5b00036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Antibiotic resistance is a growing problem worldwide. Of particular importance is the resistance of Mycobacterium tuberculosis (Mtb) to currently available antibiotics used in the treatment of infected patients. Up-regulation of an aminoglycoside (AG) acetyltransferase, the enhanced intracellular survival (Eis) protein of Mtb (Eis_Mtb), is responsible for resistance to the second-line injectable drug kanamycin A in a number of Mtb clinical isolates. This acetyltransferase is known to modify AGs, not at a single position, as usual for this type of enzyme, but at multiple amine sites. We identified, using in silico techniques, 22 homologues from a wide variety of bacteria, that we then cloned, purified, and biochemically studied. From the selected Eis homologues, 7 showed the ability to modify AGs to various degrees and displayed both similarities and differences when compared to Eis_Mtb. In addition, an inhibitor proved to be active against all homologues tested. Our findings show that this family of acetyltransferase enzymes exists in both mycobacteria and non-mycobacteria and in both pathogenic and nonpathogenic species. The bacterial strains described herein should be monitored for rising resistance rates to AGs.
Collapse
Affiliation(s)
- Keith D. Green
- College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | | | | | | |
Collapse
|
31
|
Kobayashi J, Furukawa M, Ohshiro T, Suzuki H. Thermoadaptation-directed evolution of chloramphenicol acetyltransferase in an error-prone thermophile using improved procedures. Appl Microbiol Biotechnol 2015; 99:5563-72. [PMID: 25783628 DOI: 10.1007/s00253-015-6522-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Enhancing the thermostability of thermolabile enzymes extends their practical utility. We previously demonstrated that an error-prone thermophile derived from Geobacillus kaustophilus HTA426 can generate mutant genes encoding enzyme variants that are more thermostable than the parent enzyme. Here, we used this approach, termed as thermoadaptation-directed enzyme evolution, to increase the thermostability of the chloramphenicol acetyltransferase (CAT) of Staphylococcus aureus and successfully generated a CAT variant with an A138T replacement (CAT(A138T)). This variant was heterologously produced, and its enzymatic properties were compared with those of the wild type. We found that CAT(A138T) had substantially higher thermostability than CAT but had comparable activities, showing that the A138T replacement enhanced protein thermostability without affecting the catalytic activity. Because variants CAT(A138S) and CAT(A138V), which were generated via in vitro site-directed mutagenesis, were more thermostable than CAT, the thermostability enhancement resulting from the A138T replacement can be attributed to both the presence of a hydroxyl group and the bulk of the threonine side chain. CAT(A138T) conferred chloramphenicol resistance to G. kaustophilus cells at high temperature more efficiently than CAT. Therefore, the gene encoding CAT(A138T) may be useful as a genetic marker in Geobacillus spp. Notably, CAT(A138T) generation was achieved only by implementing improved procedures (plasmid-based mutations on solid media); previous procedures (chromosome-based mutations in liquid media) were unsuccessful. This result suggests that this improved procedure is crucial for successful thermoadaptation-directed evolution in certain cases and increases the opportunities for generating thermostable enzymes.
Collapse
Affiliation(s)
- Jyumpei Kobayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | | | | | | |
Collapse
|
32
|
Jobichen C, Swaminathan K. Molecular replacement with a large number of molecules in the asymmetric unit. Acta Crystallogr F Struct Biol Commun 2014; 70:1296-302. [PMID: 25195913 PMCID: PMC4157440 DOI: 10.1107/s2053230x14014381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 06/18/2014] [Indexed: 11/11/2022] Open
Abstract
The exponential increase in protein structures deposited in the Protein Data Bank (PDB) has resulted in the elucidation of most, if not all, protein folds, thus making molecular replacement (MR) the most frequently used method for structure determination. A survey of the PDB shows that most of the structures determined by molecular replacement contain less than ten molecules in the asymmetric unit and that it is predominantly virus and ribosome structures that contain more than 20 molecules in the asymmetric unit. While the success of the MR method depends on several factors, such as the homology and the size of an input model, it is also a well known fact that this method can become significantly difficult in cases with a large number of molecules in the asymmetric unit, higher crystallographic symmetry and tight packing. In this paper, five representative structures containing 16-18 homomeric molecules in the asymmetric unit and the strategies that have been used to solve these structures are described. The difficulties faced and the lessons learned from these structure-determination efforts will be useful for selected and similar future situations with a large number of molecules in the asymmetric unit.
Collapse
Affiliation(s)
- Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | | |
Collapse
|
33
|
Yuan M, Li Z, Zhao X, Chen ZG, Cheng L. Analysis of drug resistance of food-borne Escherichia coli in Nanyang region of Henan Province. Shijie Huaren Xiaohua Zazhi 2014; 22:3459-3463. [DOI: 10.11569/wcjd.v22.i23.3459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To explore the drug resistance of food-borne Escherichia coli (E. coli).
METHODS: The sensitivity of 288 E. colistrains isolated from 122 chicken, ready-to-eat food and other meat samples to ciprofloxacin (Cip), nalidixic acid (Nal), gentamicin (Gen), kanamycin (Kan), amikacin (Amk), streptomycin (Str), ampicillin (Amp), amoxicillin (Amx), cefoperazone (Cfp), cefoxitin (Cfx), chloramphenicol (Chl), and tetracycline (Tet) was determined. The drug resistance and drug-resistant multiplicity for E. coli strains from different sources were compared.
RESULTS: The rate of resistance to Tet was the highest (95.83%), and the most sensitive drug was Amk (8.68%). The rates of resistance to Tet were the highest for the bacteria from chicken, ready-to-eat food and other meat samples (99.34%, 96.30%, 89.02%), while the most sensitive drug was Cfx for the bacteria from chicken samples (15.13%) and Amk for the bacteria from ready-to-eat food and other meat samples (0.00%, 0.00%). Except for Tet, the rates of resistance to other 11 drugs for the bacteria from chicken samples were higher than those for the bacteria from ready-to-eat food and other meat samples (74.34% vs 25.93%, 77.63% vs 38.89%, 15.13% vs 11.11%, 40.13% vs 1.85%, 47.37% vs 7.41%, 53.95% vs 1.85%, 16.45% vs 0.00%, 65.13% vs 1.85%, 87.50% vs 14.81%, 67.11% vs 3.70%, 79.61% vs 48.15%, 74.34% vs 31.71%, 77.63% vs 37.80%, 15.13% vs 7.32%, 40.13% vs 3.66%, 47.37% vs 12.20%, 53.95% vs 15.85%, 16.45% vs 0.00%, 65.13% vs 7.32%, 87.50% vs 23.17%, 67.11% vs 4.88%, 79.61% vs 42.68%, P < 0.05). The bacteria isolated from chicken and ready-to-eat food samples were resistant to at least one agent. The bacteria isolated from other meat samples were sensitive to all of the 12 kinds of antibiotics. TheE. coli strains separated from chicken samples were mainly resistant to 9 (28 strains), 10 (23 strains) and 8 (20 strains) agents; those separated from ready-to-eat food samples were mainly resistant to 1 agent (15 strains), 2 (24 strains) and 3 agents (9 strains); those separated from other meat samples were mainly resistant to 1 agent (32 strains), 2 (15 strains) and 6 (11 strains) agents. The results showed that the drug resistance of E. coli strains separated from chicken were higher than that of E. coli strains separated from ready-to-eat food and other meat samples.
CONCLUSION: E. coli contamination occurred in the meat and ready-to-eat food samples tested. The rate of resistance of food-borne E. coli to Tet is the highest, and the most sensitive drug is Amk. The condition of multidrug resistance of E. coli strains from food samples, especially chicken, is serious.
Collapse
|
34
|
Berkov-Zrihen Y, Green KD, Labby KJ, Feldman M, Garneau-Tsodikova S, Fridman M. Synthesis and evaluation of hetero- and homodimers of ribosome-targeting antibiotics: antimicrobial activity, in vitro inhibition of translation, and drug resistance. J Med Chem 2013; 56:5613-25. [PMID: 23786357 PMCID: PMC3823688 DOI: 10.1021/jm400707f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we describe the synthesis of a full set of homo- and heterodimers of three intact structures of different ribosome-targeting antibiotics: tobramycin, clindamycin, and chloramphenicol. Several aspects of the biological activity of the dimeric structures were evaluated including antimicrobial activity, inhibition of in vitro bacterial protein translation, and the effect of dimerization on the action of several bacterial resistance mechanisms that deactivate tobramycin and chloramphenicol. This study demonstrates that covalently linking two identical or different ribosome-targeting antibiotics may lead to (i) a broader spectrum of antimicrobial activity, (ii) improved inhibition of bacterial translation properties compared to that of the parent antibiotics, and (iii) reduction in the efficacy of some drug-modifying enzymes that confer high levels of resistance to the parent antibiotics from which the dimers were derived.
Collapse
Affiliation(s)
| | - Keith D. Green
- Department of Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Kristin J. Labby
- Department of Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Mark Feldman
- School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Sylvie Garneau-Tsodikova
- Department of Medicinal Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Micha Fridman
- School of Chemistry, Tel Aviv University, Tel Aviv, 6997801, Israel
| |
Collapse
|