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Lin N, Sha Y, Zhang G, Song C, Zhang Y, Zhao J, Huang D, Lu J, Bao Q, Pan W. APH(3')-Ie, an aminoglycoside-modifying enzyme discovered in a rabbit-derived Citrobacter gillenii isolate. Front Cell Infect Microbiol 2024; 14:1435123. [PMID: 39139766 PMCID: PMC11320999 DOI: 10.3389/fcimb.2024.1435123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Background Aminoglycoside-modifying enzymes (AMEs) play an essential role in bacterial resistance to aminoglycoside antimicrobials. With the development of sequencing techniques, more bacterial genomes have been sequenced, which has aided in the discovery of an increasing number of novel resistance mechanisms. Methods The bacterial species was identified by 16S rRNA gene homology and average nucleotide identity (ANI) analyses. The minimum inhibitory concentration (MIC) of each antimicrobial was determined by the agar dilution method. The protein was expressed with the pCold I vector in E. coli BL21, and enzyme kinetic parameters were examined. The whole-genome sequence of the bacterium was obtained via the Illumina and PacBio sequencing platforms. Reconstruction of the phylogenetic tree, identification of conserved functional residues, and gene context analysis were performed using the corresponding bioinformatic techniques. Results A novel aminoglycoside resistance gene, designated aph(3')-Ie, which confers resistance to ribostamycin, kanamycin, sisomicin and paromomycin, was identified in the chromosome of the animal bacterium Citrobacter gillenii DW61, which exhibited a multidrug resistance phenotype. APH(3')-Ie showed the highest amino acid identity of 74.90% with the functionally characterized enzyme APH(3')-Ia. Enzyme kinetics analysis demonstrated that it had phosphorylation activity toward four aminoglycoside substrates, exhibiting the highest affinity (K m, 4.22 ± 0.88 µM) and the highest catalytic efficiency [k cat/K m, (32.27 ± 8.14) × 104] for ribomycin. Similar to the other APH(3') proteins, APH(3')-Ie contained all the conserved functional sites of the APH family. The aph(3')-Ie homologous genes were present in C. gillenii isolates from different sources, including some of clinical significance. Conclusion In this work, a novel chromosomal aminoglycoside resistance gene, designated aph(3')-Ie, conferring resistance to aminoglycoside antimicrobials, was identified in a rabbit isolate C. gillenii DW61. The elucidation of the novel resistance mechanism will aid in the effective treatment of infections caused by pathogens carrying such resistance genes.
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Affiliation(s)
- Naru Lin
- Institute of Bioinformatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuning Sha
- Institute of Bioinformatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Guozhi Zhang
- Institute of Bioinformatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunhan Song
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Yuan Zhang
- Institute of Bioinformatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingxuan Zhao
- Institute of Bioinformatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dawei Huang
- Department of Laboratory Sciences, The People’s Hospital of Yuhuan, Yuhuan, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Institute of Bioinformatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Department of Laboratory Sciences, Pingyang Hospital of Wenzhou Medical University, Pingyang, China
| | - Wei Pan
- Department of Laboratory Sciences, The People’s Hospital of Yuhuan, Yuhuan, China
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Chen C, Li Y, Wu Z, Ruan Y, Long T, Wang X, Li W, Ren H, Liao X, Liu Y, Lian X, Sun J. Cat and dog feces as reservoirs of diverse novel antibiotic resistance genes. ENVIRONMENTAL RESEARCH 2024; 261:119690. [PMID: 39068967 DOI: 10.1016/j.envres.2024.119690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/21/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Companion animals have the potential to greatly enhance the physical and mental health of humans, thus leading to an increased focus on the interactions between humans and pets. Currently, the inappropriate and excessive utilization of antimicrobial agents has become prevalent in veterinary clinical practice for pets. This antibiotic contamination phenomenon has a profound impact on the enrichment of antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) in pets. However, the pet-associated resistome, especially the novel ARGs in pets, represents a relatively neglected area. In this study, we successfully constructed a total of 12 libraries using the functional metagenomics approach to assess the diversity of ARGs in pet cats and dogs from four pet hospitals. Through the integration of functional screening and high-throughput sequencing, a total of 122 antibiotic resistance determinants were identified, of which 15 were classified as putative novel ARGs originating from five classes. Functional assessment demonstrated that 6 novel ARGs including one β-lactam, two macrolides, two aminoglycosides, and one rifamycin (RIF), namely blaPF, ermPF, msrPF, aac(6')PF, aph(3')PF, and arrPF, exhibited functionally activity in conferring bacterial phenotypic resistance by increasing the minimum inhibitory concentrations (MICs) with a 4- to 128-fold. Genetic context analysis demonstrated that, with the exception of aac(6')PF and arrPF, the remaining four novel ARGs were found adjacent to mobile genetic elements (MGEs) including IS elements or transposases, which provided a prerequisite for horizontal transfer of these novel ARGs, thereby offering an explanation for their detection in diverse samples collected from various sampling sites. The current study has unveiled the significant role of cat and dog feces as one source of reservoirs of diverse novel ARGs, while also highlighting the potential adverse consequences of their further spread to medically significant pathogens and human commensal organisms.
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Affiliation(s)
- Caiping Chen
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanyuan Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihong Wu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yali Ruan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Tengfei Long
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Xiran Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Wenjie Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Ren
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoping Liao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yahong Liu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Xinlei Lian
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China.
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China.
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Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [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: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
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Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Sha Y, Lin N, Zhang G, Zhang Y, Zhao J, Lu J, Zhu T, Zhang X, Li Q, Zhang H, Lin X, Li K, Bao Q, Li D. Identification and characterization of a novel chromosomal aminoglycoside 3'- O-phosphotransferase, APH(3')-Id, from Kluyvera intermedia DW18 isolated from the sewage of an animal farm. Front Microbiol 2023; 14:1224464. [PMID: 37700861 PMCID: PMC10493288 DOI: 10.3389/fmicb.2023.1224464] [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: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023] Open
Abstract
Background Aminoglycosides, as important clinical antimicrobials, are used as second-line drugs for treating multidrug-resistant tuberculosis or combined with β-lactam drugs for treating severe infections such as sepsis. Aminoglycoside-modifying enzyme (AME) is the most important mechanism of aminoglycoside resistance and deserves more attention. Methods The bacterium Kluyvera intermedia DW18 was isolated from the sewage of an animal farm using the conventional method. The agar dilution method was used to determine the minimum inhibitory concentrations (MICs) of antimicrobials. A novel resistance gene was cloned, and the enzyme was expressed. The kinetic parameters were measured by a SpectraMax M5 multifunctional microplate reader. Bioinformatic analysis was performed to reveal the genetic context of the aph(3')-Id gene and its phylogenetic relationship with other AMEs. Results A novel aminoglycoside 3'-O-phosphotransferase gene designated aph(3')-Id was identified in K. intermedia DW18 and shared the highest amino acid identity of 77.49% with the functionally characterized aminoglycoside 3'-O-phosphotransferase APH(3')-Ia. The recombinant plasmid carrying the novel resistance gene (pMD19-aph(3')-Id/E. coli DH5α) showed 1,024-, 512-, 128- and 16-fold increased MIC levels for kanamycin, ribostamycin, paromomycin and neomycin, respectively, compared with the reference strain DH5α. APH(3')-Id showed the highest catalytic efficiency for ribostamycin [kcat/Km of (4.96 ± 1.63) × 105 M-1/s-1], followed by paromomycin [kcat/Km of (2.18 ± 0.21) × 105 M-1/s-1], neomycin [kcat/Km of (1.73 ± 0.20) × 105 M-1/s-1], and kanamycin [kcat/Km of (1.10 ± 0.18) × 105 M-1/s-1]. Three conserved functional domains of the aminoglycoside phosphotransferase family and ten amino acid residues responsible for the phosphorylation of kanamycin were found in the amino acid sequence of APH(3')-Id. No mobile genetic element (MGE) was discovered surrounding the aph(3')-Id gene. Conclusion In this work, a novel aminoglycoside 3'-O-phosphotransferase gene designated aph(3')-Id encoded in the chromosome of the environmental isolate Kluyvera intermedia DW18 was identified and characterized. These findings will help clinicians select effective antimicrobials to treat infections caused by pathogens with this kind of resistance gene.
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Affiliation(s)
- Yuning Sha
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Naru Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Guozhi Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuan Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingxuan Zhao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Tingting Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Dong Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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Nisa I, Driessen A, Nijland J, Rahman H, Mattner J, Qasim M. Novel plasmids in multidrug-resistant Shigella flexneri serotypes from Pakistan. Arch Microbiol 2023; 205:175. [PMID: 37027063 DOI: 10.1007/s00203-023-03523-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 02/25/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Abstract
Shigellosis is the main cause of food and waterborne diarrhea and is an emerging threat to human health. The current study characterized the indigenous multidrug-resistant Shigella flexneri serotypes for their plasmid profiles and genetic diversity, to characterize the plasmid evolutionary patterns and distribution. In total, 199 identified S. flexneri isolates belonging to six different serotypes were analyzed for plasmid profiling, followed by an analysis of whole genome sequencing. All isolates of S. flexneri resistant to antibiotics harbored multiple copies of plasmids with sizes ranging from 1.25 kbp to 9.4 kbp. These isolates were clustered into 22 distinct plasmid patterns, labeled as p1-p22. Among these, p1 (24%) and p10 (13%) were the predominant plasmid profiles. All S. flexneri strains were grouped into 12 clades with a 75% similarity level. Also, a significant association was observed among the plasmid patterns, p23 and p17 with the drug-resistant patterns AMC, SXT, C (19.5%) and OFX, AMC, NA, CIP (13.5%), respectively. Moreover, the most widespread plasmid patterns p4, p10, and p1 showed a significant association with the serotypes 1b (29.16%), 2b (36%), and 7a (100%), respectively. After plasmid sequence assembly and annotation analysis, a variety of small plasmids that vary in size from 973 to 6200 bp were discovered. Many of these plasmids displayed high homology and coverage with plasmids from non-S. flexneri. Several novel plasmids of small size were discovered in multidrug-resistant S. flexneri. The data also showed that plasmid profile analysis is more consistent than antibiotic susceptibility pattern analysis for identifying epidemic strains of S. flexneri isolated in Pakistan.
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Affiliation(s)
- Iqbal Nisa
- Department of Microbiology, Kohat University of Science and Technology, Kohat, 26000, Pakistan
- Department of Microbiology, Women University Swabi, Swabi, Pakistan
| | - Arnold Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jeroen Nijland
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Hazir Rahman
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
| | - Jochen Mattner
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie Und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat, 26000, Pakistan.
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Kim SK, Kim H, Woo SG, Kim TH, Rha E, Kwon KK, Lee H, Lee SG, Lee DH. CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids. Nucleic Acids Res 2022; 50:13155-13171. [PMID: 36511859 PMCID: PMC9825151 DOI: 10.1093/nar/gkac1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.
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Affiliation(s)
| | | | - Seung Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34143, Republic of Korea
| | - Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34143, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- To whom correspondence should be addressed. Tel: +82 42 860 4373; Fax: +82 42 860 4489;
| | - Dae-Hee Lee
- Correspondence may also be addressed to Dae-Hee Lee. Tel: +82 42 879 8225; Fax: +82 42 860 4489;
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Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
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8
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Lu W, Li K, Huang J, Sun Z, Li A, Liu H, Zhou D, Lin H, Zhang X, Li Q, Lu J, Lin X, Li P, Zhang H, Xu T, Bao Q. Identification and characteristics of a novel aminoglycoside phosphotransferase, APH(3')-IId, from an MDR clinical isolate of Brucella intermedia. J Antimicrob Chemother 2021; 76:2787-2794. [PMID: 34329431 DOI: 10.1093/jac/dkab272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To describe a novel chromosomal aminoglycoside phosphotransferase named APH(3')-IId identified in an MDR Brucella intermedia ZJ499 isolate from a cancer patient. METHODS Species identity was determined by PCR and MALDI-TOF MS analysis. WGS was performed to determine the genetic elements conferring antimicrobial resistance. Gene cloning, transcriptional analysis and targeted gene deletion, as well as protein purification and kinetic analysis, were performed to investigate the mechanism of resistance. RESULTS APH(3')-IId consists of 266 amino acids and shares the highest identity (48.25%) with the previously known APH(3')-IIb. Expression of aph(3')-IId in Escherichia coli decreased susceptibility to kanamycin, neomycin, paromomycin and ribostamycin. The aph(3')-IId gene in ZJ499 was transcriptionally active under laboratory conditions and the relative abundance of this transcript was unaffected by treatment with the above four antibiotics. However, deletion of aph(3')-IId in ZJ499 results in decreased MICs of these drugs. The purified APH(3')-IId showed phosphotransferase activity against kanamycin, neomycin, paromomycin and ribostamycin, with catalytic efficiencies (kcat/Km) ranging from ∼105 to 107 M-1 s-1. Genetic environment and comparative genomic analyses suggested that aph(3')-IId is probably a ubiquitous gene in Brucella, with no mobile genetic elements detected in its surrounding region. CONCLUSIONS APH(3')-IId is a novel chromosomal aminoglycoside phosphotransferase and plays an important role in the resistance of B. intermedia ZJ499 to kanamycin, neomycin, paromomycin and ribostamycin. To the best of our knowledge, APH(3')-IId represents the fourth characterized example of an APH(3')-II enzyme.
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Affiliation(s)
- Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jiansheng Huang
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, Zhejiang 323000, China
| | - Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Aifang Li
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, Zhejiang 323000, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hailong Lin
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xueya Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Qiaoling Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Peizhen Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hailin Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Teng Xu
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Translational Medicine, Baotou Central Hospital, Baotou 014040, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
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9
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Rigo GV, Tasca T. Vaginitis: Review on Drug Resistance. Curr Drug Targets 2020; 21:1672-1686. [PMID: 32753007 DOI: 10.2174/1389450121666200804112340] [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: 04/14/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/22/2022]
Abstract
Female genital tract infections have a high incidence among different age groups and represent an important impact on public health. Among them, vaginitis refers to inflammation of the vulva and/or vagina due to the presence of pathogens that cause trichomoniasis, bacterial vaginosis, and vulvovaginal candidiasis. Several discomforts are associated with these infections, as well as pregnancy complications and the facilitation of HIV transmission and acquisition. The increasing resistance of microorganisms to drugs used in therapy is remarkable, since women report the recurrence of these infections and associated comorbidities. Different resistant mechanisms already described for the drugs used in the therapy against Trichomonas vaginalis, Candida spp., and Gardnerella vaginalis, as well as aspects related to pathogenesis and treatment, are discussed in this review. This study aims to contribute to drug design, avoiding therapy ineffectiveness due to drug resistance. Effective alternative therapies to treat vaginitis will reduce the recurrence of infections and, consequently, the high costs generated in the health system, improving women's well-being.
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Affiliation(s)
- Graziela Vargas Rigo
- Research Group on Trichomonas, Pharmaceutical Sciences Graduate Program, Faculty of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tiana Tasca
- Research Group on Trichomonas, Pharmaceutical Sciences Graduate Program, Faculty of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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10
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Takenoya M, Shimamura T, Yamanaka R, Adachi Y, Ito S, Sasaki Y, Nakamura A, Yajima S. Structural basis for the substrate recognition of aminoglycoside 7''-phosphotransferase-Ia from Streptomyces hygroscopicus. Acta Crystallogr F Struct Biol Commun 2019; 75:599-607. [PMID: 31475927 PMCID: PMC6718145 DOI: 10.1107/s2053230x19011105] [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: 07/02/2019] [Accepted: 08/09/2019] [Indexed: 10/14/2023] Open
Abstract
Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7''-phosphotransferase-Ia [APH(7'')-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7'' and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7'')-Ia and APH(4)-Ia, the crystal structure of APH(7'')-Ia complexed with HygB is reported. The overall structure of APH(7'')-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7'')-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7'')-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.
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Affiliation(s)
- Mihoko Takenoya
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryuji Yamanaka
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuya Adachi
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinsaku Ito
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
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11
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Alekseeva MG, Boyko KM, Nikolaeva AY, Mavletova DA, Rudakova NN, Zakharevich NV, Korzhenevskiy DA, Ziganshin RH, Popov VO, Danilenko VN. Identification, functional and structural characterization of novel aminoglycoside phosphotransferase APH(3″)-Id from Streptomyces rimosus subsp. rimosus ATCC 10970. Arch Biochem Biophys 2019; 671:111-122. [DOI: 10.1016/j.abb.2019.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 01/03/2023]
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12
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Schiermeyer A, Schneider K, Kirchhoff J, Schmelter T, Koch N, Jiang K, Herwartz D, Blue R, Marri P, Samuel P, Corbin DR, Webb SR, Gonzalez DO, Folkerts O, Fischer R, Schinkel H, Ainley WM, Schillberg S. Targeted insertion of large DNA sequences by homology-directed repair or non-homologous end joining in engineered tobacco BY-2 cells using designed zinc finger nucleases. PLANT DIRECT 2019; 3:e00153. [PMID: 31360827 PMCID: PMC6639735 DOI: 10.1002/pld3.153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/11/2019] [Accepted: 07/03/2019] [Indexed: 05/13/2023]
Abstract
Targeted integration of recombinant DNA fragments into plant genomes by DNA double-strand break (DSB) repair mechanisms has become a powerful tool for precision engineering of crops. However, many targeting platforms require the screening of many transgenic events to identify a low number of targeted events among many more random insertion events. We developed an engineered transgene integration platform (ETIP) that uses incomplete marker genes at the insertion site to enable rapid phenotypic screening and recovery of targeted events upon functional reconstitution of the marker genes. The two marker genes, encoding neomycin phosphotransferase II (nptII) and Discosoma sp. red fluorescent protein (DsRed) enable event selection on kanamycin-containing selective medium and subsequent screening for red fluorescent clones. The ETIP design allows targeted integration of donor DNA molecules either by homology-directed repair (HDR) or non-homologous end joining (NHEJ)-mediated mechanisms. Targeted donor DNA integration is facilitated by zinc finger nucleases (ZFN). The ETIP cassette was introduced into Nicotiana tabacum BY-2 suspension cells to generate target cell lines containing a single copy locus of the transgene construct. The utility of the ETIP platform has been demonstrated by targeting DNA constructs containing up to 25-kb payload. The success rate for clean targeted DNA integration was up to 21% for HDR and up to 41% for NHEJ based on the total number of calli analyzed by next-generation sequencing (NGS). The rapid generation of targeted events with large DNA constructs expands the utility of the nuclease-mediated gene addition platform both for academia and the commercial sector.
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Affiliation(s)
- Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Katja Schneider
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Janina Kirchhoff
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Thomas Schmelter
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Natalie Koch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Ke Jiang
- Corteva AgriscienceIndianapolisINUSA
| | - Denise Herwartz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | - Ryan Blue
- Corteva AgriscienceIndianapolisINUSA
| | | | | | | | | | | | | | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Indiana Biosciences Research InstituteIndianapolisINUSA
| | - Helga Schinkel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
| | | | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
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13
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Holbrook SYL, Gentry MS, Tsodikov OV, Garneau-Tsodikova S. Nucleoside triphosphate cosubstrates control the substrate profile and efficiency of aminoglycoside 3'- O-phosphotransferase type IIa. MEDCHEMCOMM 2018; 9:1332-1339. [PMID: 30151088 DOI: 10.1039/c8md00234g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/03/2018] [Indexed: 11/21/2022]
Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics that play an important role in the control and treatment of bacterial infections. Despite the great antibacterial potency of AGs, resistance to these antibiotics has limited their clinical applications. The AG 3'-O-phosphotransferase of type IIa (APH(3')-IIa) encoded by the neoR gene is a common bacterial AG resistance enzyme that inactivates AG antibiotics. This enzyme is used as a selection marker in molecular biology research. APH(3')-IIa catalyzes the transfer of the γ-phosphoryl group of ATP to an AG at its 3'-OH group. Although APH(3')-IIa has been reported to utilize exclusively ATP as a cosubstrate, we demonstrate that this enzyme can utilize a broad array of NTPs. By substrate profiling, TLC, and enzyme kinetics experiments, we probe AG phosphorylation by APH(3')-IIa with an extensive panel of substrates and cosubstrates (13 AGs and 10 NTPs) for the purpose of gaining a thorough understanding of this resistance enzyme. We find, for the first time, that the identity of the NTP cosubstrate dictates the set of AGs modified by APH(3')-IIa and the phosphorylation efficiency for different AGs.
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Affiliation(s)
- Selina Y L Holbrook
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Kentucky , Lexington , KY 40536-0596 , USA . ; ; ; Tel: +859 218 1686
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry , College of Medicine , University of Kentucky , Lexington , KY 40536 , USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Kentucky , Lexington , KY 40536-0596 , USA . ; ; ; Tel: +859 218 1686
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Kentucky , Lexington , KY 40536-0596 , USA . ; ; ; Tel: +859 218 1686
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14
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Khattab M, Wang F, Clayton AHA. Conformational Plasticity in Tyrosine Kinase Inhibitor-Kinase Interactions Revealed with Fluorescence Spectroscopy and Theoretical Calculations. J Phys Chem B 2018; 122:4667-4679. [PMID: 29629773 DOI: 10.1021/acs.jpcb.8b01530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To understand drug-protein dynamics, it is necessary to account for drug molecular flexibility and binding site plasticity. Herein, we exploit fluorescence from a tyrosine kinase inhibitor, AG1478, as a reporter of its conformation and binding site environment when complexed with its cognate kinase. Water-soluble kinases, aminoglycoside phosphotransferase APH(3')-Ia and mitogen-activated protein kinase 14 (MAPK14), were chosen for this study. On the basis of our prior work, the AG1478 conformation (planar or twisted) was inferred from the fluorescence excitation spectrum and the polarity of the AG1478-binding site was deduced from the fluorescence emission spectrum, while red-edge excitation shift (REES) probed the heterogeneity of the binding site (protein conformation and hydration) distributions in the protein conformational ensemble. In the AG1478-APH(3')-Ia complex, both twisted (or partially twisted) and planar AG1478 conformations were evidenced from emission wavelength-dependent excitation spectra. The binding site environment provided by APH(3')-Ia was moderately polar (λmax = 480 nm) with evidence for considerable heterogeneity (REES = 34 nm). In contrast, in the AG1478-MAPK14 complex, AG1478 was in a predominantly planar conformation with a lower degree of conformational heterogeneity. The binding site environment provided by the MAPK14 protein was of relatively low polarity (λmax = 430 nm) with a smaller degree of heterogeneity (REES = 11 nm). The results are compared with the available X-ray data and discussed in the context of our current understanding of tyrosine kinase inhibitor conformation and protein conformational ensembles.
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15
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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16
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Shi-Kunne X, Faino L, van den Berg GCM, Thomma BPHJ, Seidl MF. Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ Microbiol 2018; 20:1362-1373. [PMID: 29282842 DOI: 10.1111/1462-2920.14037] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 01/09/2023]
Abstract
The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plant pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ∼11 000 genes that are shared at least between two species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than the shared genes.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
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17
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Parulekar RS, Sonawane KD. Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains. J Cell Biochem 2017; 119:2679-2695. [DOI: 10.1002/jcb.26435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 10/18/2017] [Indexed: 01/17/2023]
Affiliation(s)
| | - Kailas D. Sonawane
- Department of MicrobiologyShivaji UniversityKolhapurMaharashtra (M.S.)India
- Department of Biochemistry, Structural Bioinformatics UnitShivaji UniversityKolhapurMaharashtra (M.S.)India
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18
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Sánchez-Carrera D, Bravo-Navas S, Cabezón E, Arechaga I, Cabezas M, Yáñez L, Pipaón C. Fludarabine resistance mediated by aminoglycoside-3'-phosphotransferase-IIa and the structurally related eukaryotic cAMP-dependent protein kinase. FASEB J 2017; 31:3007-3017. [PMID: 28373209 DOI: 10.1096/fj.201601245r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/13/2017] [Indexed: 11/11/2022]
Abstract
While working with G418-resistant stably transfected cells, we realized the neomycin resistance (NeoR) gene, which encodes the aminoglycoside-3'-phosphotransferase-IIa [APH(3')-IIa], also confers resistance to the nucleoside analog fludarabine. Fludarabine is a cytostatic drug widely used in the treatment of hematologic and solid tumors, as well as in the conditioning of patients before transplantation of hematopoietic progenitors. We present evidence that NeoR-transfected cells do not incorporate fludarabine, thus avoiding DNA damage caused by the drug, evidenced by a lack of FANCD2 monoubiquitination and impaired apoptosis. A screening of other nucleoside analogs revealed that APH(3')-IIa only protects against ATP purine analogs. Moreover, APH(3')-IIa ATPase activity is inhibited by fludarabine monophosphate, suggesting that APH(3')-IIa blocks fludarabine incorporation into DNA by dephosphorylating its active fludarabine triphosphate form. Furthermore, overexpression of the catalytic subunit of the eukaryotic kinase PKA, which is structurally related to APHs, also provides resistance to fludarabine, anticipating its putative utility as a response marker to the drug. Our results preclude the use of Neo marker plasmids in the study of purine analogs and unveils a new resistance mechanism against these chemotherapeuticals.-Sánchez-Carrera, D., Bravo-Navas, S., Cabezón, E., Arechaga, I., Cabezas, M., Yáñez, L., Pipaón, C. Fludarabine resistance mediated by aminoglycoside-3'-phosphotransferase-IIa and the structurally related eukaryotic cAMP-dependent protein kinase.
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Affiliation(s)
- Dámaso Sánchez-Carrera
- Laboratorio de Hematología Molecular, Servicio de Hematología y Hemoterapia, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Sara Bravo-Navas
- Laboratorio de Hematología Molecular, Servicio de Hematología y Hemoterapia, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Elena Cabezón
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Cientificas (CSIC), Santander, Spain
| | - Ignacio Arechaga
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Cientificas (CSIC), Santander, Spain
| | - Matilde Cabezas
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Cientificas (CSIC), Santander, Spain
| | - Lucrecia Yáñez
- Laboratorio de Hematología Molecular, Servicio de Hematología y Hemoterapia, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Carlos Pipaón
- Laboratorio de Hematología Molecular, Servicio de Hematología y Hemoterapia, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain;
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19
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Elbehery AHA, Leak DJ, Siam R. Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool. Microb Biotechnol 2016; 10:189-202. [PMID: 28004885 PMCID: PMC5270753 DOI: 10.1111/1751-7915.12468] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/29/2016] [Accepted: 11/03/2016] [Indexed: 11/29/2022] Open
Abstract
The advent of metagenomics has greatly facilitated the discovery of enzymes with useful biochemical characteristics for industrial and biomedical applications, from environmental niches. In this study, we used sequence-based metagenomics to identify two antibiotic resistance enzymes from the secluded, lower convective layer of Atlantis II Deep Red Sea brine pool (68°C, ~2200 m depth and 250‰ salinity). We assembled > 4 000 000 metagenomic reads, producing 43 555 contigs. Open reading frames (ORFs) called from these contigs were aligned to polypeptides from the Comprehensive Antibiotic Resistance Database using BLASTX. Two ORFs were selected for further analysis. The ORFs putatively coded for 3'-aminoglycoside phosphotransferase [APH(3')] and a class A beta-lactamase (ABL). Both genes were cloned, expressed and characterized for activity and thermal stability. Both enzymes were active in vitro, while only APH(3') was active in vivo. Interestingly, APH(3') proved to be thermostable (Tm = 61.7°C and ~40% residual activity after 30 min of incubation at 65°C). On the other hand, ABL was not as thermostable, with a Tm = 43.3°C. In conclusion, we have discovered two novel AR enzymes with potential application as thermophilic selection markers.
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Affiliation(s)
- Ali H A Elbehery
- Graduate Program of Biotechnology, The American University in Cairo, Cairo, Egypt.,Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Rania Siam
- Graduate Program of Biotechnology, The American University in Cairo, Cairo, Egypt.,Biology Department and YJ-Science and Technology Research Center, The American University in Cairo, Cairo, Egypt
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20
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Structural characterization of the novel aminoglycoside phosphotransferase AphVIII from Streptomyces rimosus with enzymatic activity modulated by phosphorylation. Biochem Biophys Res Commun 2016; 477:595-601. [PMID: 27338640 DOI: 10.1016/j.bbrc.2016.06.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/08/2016] [Accepted: 06/19/2016] [Indexed: 01/07/2023]
Abstract
Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3'-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2.15 Å. Deep analysis of APHVIII structure and its comparison with known structures of aminoglycoside phosphotransferases of various types reveals that AphVIII has a typical two-domain fold and, however, possesses some unique characteristics that distinguish the enzyme from its known homologues. The most important difference is the presence of the activation loop with unique Ser146 residue. We demonstrate that in the apo-state of the enzyme the activation loop does not interact with other parts of the enzyme and seems to adopt catalytically competent state only after substrate binding.
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Oruganty K, Talevich EE, Neuwald AF, Kannan N. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. BMC Evol Biol 2016; 16:7. [PMID: 26738562 PMCID: PMC4702295 DOI: 10.1186/s12862-015-0576-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (ELKs) share the same overall structural fold as EPKs, but differ in their modes of regulation, substrate recognition and specificity-the sequence and structural determinants of which are poorly understood. RESULTS To better understand the basis for ELK specificity, we applied a Bayesian classification procedure designed to identify sequence determinants responsible for functional divergence. This reveals that a large and diverse family of aminoglycoside kinases, characterized members of which are involved in antibiotic resistance, fall into major sub-groups based on differences in putative substrate recognition motifs. Aminoglycoside kinase substrate specificity follows simple rules of alternating hydroxyl and amino groups that is strongly correlated with variations at the DFG + 1 position. CONCLUSIONS Substrate specificity determining features in small molecule kinases are mostly confined to the catalytic core and can be identified based on quantitative sequence and crystal structure comparisons.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Eric E Talevich
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.
| | - Andrew F Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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Abstract
Here we describe biosensors that provide readouts for protein stability in the cytosolic compartment of prokaryotes. These biosensors consist of tripartite sandwich fusions that link the in vitro stability or aggregation susceptibility of guest proteins to the in vivo resistance of host cells to the antibiotics kanamycin, spectinomycin, and nourseothricin. These selectable markers confer antibiotic resistance in a wide range of hosts and are easily quantifiable. We show that mutations within guest proteins that affect their stability alter the antibiotic resistances of the cells expressing the biosensors in a manner that is related to the in vitro stabilities of the mutant guest proteins. In addition, we find that polyglutamine tracts of increasing length are associated with an increased tendency to form amyloids in vivo and, in our sandwich fusion system, with decreased resistance to aminoglycoside antibiotics. We demonstrate that our approach allows the in vivo analysis of protein stability in the cytosolic compartment without the need for prior structural and functional knowledge.
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Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS. Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes. Nucleic Acids Res 2014; 42:e112. [PMID: 24914046 PMCID: PMC4132701 DOI: 10.1093/nar/gku511] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Deep mutational scanning has emerged as a promising tool for mapping sequence-activity relationships in proteins, ribonucleic acid and deoxyribonucleic acid. In this approach, diverse variants of a sequence of interest are first ranked according to their activities in a relevant assay, and this ranking is then used to infer the shape of the fitness landscape around the wild-type sequence. Little is currently known, however, about the degree to which such fitness landscapes are dependent on the specific assay conditions from which they are inferred. To explore this issue, we performed comprehensive single-substitution mutational scanning of APH(3')II, a Tn5 transposon-derived kinase that confers resistance to aminoglycoside antibiotics, in Escherichia coli under selection with each of six structurally diverse antibiotics at a range of inhibitory concentrations. We found that the resulting local fitness landscapes showed significant dependence on both antibiotic structure and concentration, and that this dependence can be exploited to guide protein engineering. Specifically, we found that differential analysis of fitness landscapes allowed us to generate synthetic APH(3')II variants with orthogonal substrate specificities.
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Affiliation(s)
| | - Peter Rogov
- Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Broad Technology Labs, Broad Institute, Cambridge, MA 02142, USA
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Smith CA, Toth M, Bhattacharya M, Frase H, Vakulenko SB. Structure of the phosphotransferase domain of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1561-71. [PMID: 24914967 PMCID: PMC4051501 DOI: 10.1107/s1399004714005331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/07/2014] [Indexed: 01/04/2023]
Abstract
The bifunctional acetyltransferase(6')-Ie-phosphotransferase(2'')-Ia [AAC(6')-Ie-APH(2'')-Ia] is the most important aminoglycoside-resistance enzyme in Gram-positive bacteria, conferring resistance to almost all known aminoglycoside antibiotics in clinical use. Owing to its importance, this enzyme has been the focus of intensive research since its isolation in the mid-1980s but, despite much effort, structural details of AAC(6')-Ie-APH(2'')-Ia have remained elusive. The structure of the Mg2GDP complex of the APH(2'')-Ia domain of the bifunctional enzyme has now been determined at 2.3 Å resolution. The structure of APH(2'')-Ia is reminiscent of the structures of other aminoglycoside phosphotransferases, having a two-domain architecture with the nucleotide-binding site located at the junction of the two domains. Unlike the previously characterized APH(2'')-IIa and APH(2'')-IVa enzymes, which are capable of utilizing both ATP and GTP as the phosphate donors, APH(2'')-Ia uses GTP exclusively in the phosphorylation of the aminoglycoside antibiotics, and in this regard closely resembles the GTP-dependent APH(2'')-IIIa enzyme. In APH(2'')-Ia this GTP selectivity is governed by the presence of a `gatekeeper' residue, Tyr100, the side chain of which projects into the active site and effectively blocks access to the adenine-binding template. Mutation of this tyrosine residue to a less bulky phenylalanine provides better access for ATP to the NTP-binding template and converts APH(2'')-Ia into a dual-specificity enzyme.
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Affiliation(s)
- Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Monolekha Bhattacharya
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hilary Frase
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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25
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Directed Evolution for Thermostabilization of a Hygromycin B Phosphotransferase fromStreptomyces hygroscopicus. Biosci Biotechnol Biochem 2014; 77:2234-41. [DOI: 10.1271/bbb.130486] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Strategies to overcome the action of aminoglycoside-modifying enzymes for treating resistant bacterial infections. Future Med Chem 2014; 5:1285-309. [PMID: 23859208 DOI: 10.4155/fmc.13.80] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Shortly after the discovery of the first antibiotics, bacterial resistance began to emerge. Many mechanisms give rise to resistance; the most prevalent mechanism of resistance to the aminoglycoside (AG) family of antibiotics is the action of aminoglycoside-modifying enzymes (AMEs). Since the identification of these modifying enzymes, many efforts have been put forth to prevent their damaging alterations of AGs. These diverse strategies are discussed within this review, including: creating new AGs that are unaffected by AMEs; developing inhibitors of AMEs to be co-delivered with AGs; or regulating AME expression. Modern high-throughput methods as well as drug combinations and repurposing are highlighted as recent drug-discovery efforts towards fighting the increasing antibiotic resistance crisis.
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27
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Thiel IV, Volkmann G, Pietrokovski S, Mootz HD. An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Thiel IV, Volkmann G, Pietrokovski S, Mootz HD. An Atypical Naturally Split Intein Engineered for Highly Efficient Protein Labeling. Angew Chem Int Ed Engl 2014; 53:1306-10. [DOI: 10.1002/anie.201307969] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/06/2022]
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29
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Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance. Biochem J 2013; 454:191-200. [PMID: 23758273 DOI: 10.1042/bj20130317] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules. We demonstrated previously that ePK (eukaryotic protein kinase) inhibitors could inhibit APH enzymes, owing to the structural similarity between these two enzyme families. However, limited structural information of enzyme-inhibitor complexes hindered interpretation of the results. In addition, cross-reactivity of compounds between APHs and ePKs represents an obstacle to their use as aminoglycoside adjuvants to rescue aminoglycoside antibiotic activity. In the present study, we structurally and functionally characterize inhibition of APH(3')-Ia by three diverse chemical scaffolds, anthrapyrazolone, 4-anilinoquinazoline and PP (pyrazolopyrimidine), and reveal distinctions in the binding mode of anthrapyrazolone and PP compounds to APH(3')-Ia compared with ePKs. Using this observation, we identify PP derivatives that select against ePKs, attenuate APH(3')-Ia activity and rescue aminoglycoside antibiotic activity against a resistant Escherichia coli strain. The structures described in the present paper and the inhibition studies provide an important opportunity for structure-based design of compounds to target aminoglycoside phosphotransferases for inhibition, potentially overcoming this form of antibiotic resistance.
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30
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Shi K, Caldwell SJ, Fong DH, Berghuis AM. Prospects for circumventing aminoglycoside kinase mediated antibiotic resistance. Front Cell Infect Microbiol 2013; 3:22. [PMID: 23805415 PMCID: PMC3691515 DOI: 10.3389/fcimb.2013.00022] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/04/2013] [Indexed: 01/10/2023] Open
Abstract
Aminoglycosides are a class of antibiotics with a broad spectrum of antimicrobial activity. Unfortunately, resistance in clinical isolates is pervasive, rendering many aminoglycosides ineffective. The most widely disseminated means of resistance to this class of antibiotics is inactivation of the drug by aminoglycoside-modifying enzymes (AMEs). There are two principal strategies to overcoming the effects of AMEs. The first approach involves the design of novel aminoglycosides that can evade modification. Although this strategy has yielded a number of superior aminoglycoside variants, their efficacy cannot be sustained in the long term. The second approach entails the development of molecules that interfere with the mechanism of AMEs such that the activity of aminoglycosides is preserved. Although such a molecule has yet to enter clinical development, the search for AME inhibitors has been greatly facilitated by the wealth of structural information amassed in recent years. In particular, aminoglycoside phosphotransferases or kinases (APHs) have been studied extensively and crystal structures of a number of APHs with diverse regiospecificity and substrate specificity have been elucidated. In this review, we present a comprehensive overview of the available APH structures and recent progress in APH inhibitor development, with a focus on the structure-guided strategies.
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Affiliation(s)
- Kun Shi
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill UniversityMontreal, QC, Canada
| | - Shane J. Caldwell
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill UniversityMontreal, QC, Canada
| | - Desiree H. Fong
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill UniversityMontreal, QC, Canada
| | - Albert M. Berghuis
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill UniversityMontreal, QC, Canada
- Department of Microbiology and Immunology, McGill UniversityMontreal, QC, Canada
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31
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Cheriyan M, Pedamallu CS, Tori K, Perler F. Faster protein splicing with the Nostoc punctiforme DnaE intein using non-native extein residues. J Biol Chem 2013; 288:6202-11. [PMID: 23306197 PMCID: PMC3585056 DOI: 10.1074/jbc.m112.433094] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inteins are naturally occurring intervening sequences that catalyze a protein splicing reaction resulting in intein excision and concatenation of the flanking polypeptides (exteins) with a native peptide bond. Inteins display a diversity of catalytic mechanisms within a highly conserved fold that is shared with hedgehog autoprocessing proteins. The unusual chemistry of inteins has afforded powerful biotechnology tools for controlling enzyme function upon splicing and allowing peptides of different origins to be coupled in a specific, time-defined manner. The extein sequences immediately flanking the intein affect splicing and can be defined as the intein substrate. Because of the enormous potential complexity of all possible flanking sequences, studying intein substrate specificity has been difficult. Therefore, we developed a genetic selection for splicing-dependent kanamycin resistance with no significant bias when six amino acids that immediately flanked the intein insertion site were randomized. We applied this selection to examine the sequence space of residues flanking the Nostoc punctiforme Npu DnaE intein and found that this intein efficiently splices a much wider range of sequences than previously thought, with little N-extein specificity and only two important C-extein positions. The novel selected extein sequences were sufficient to promote splicing in three unrelated proteins, confirming the generalizable nature of the specificity data and defining new potential insertion sites for any target. Kinetic analysis showed splicing rates with the selected exteins that were as fast or faster than the native extein, refuting past assumptions that the naturally selected flanking extein sequences are optimal for splicing.
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Affiliation(s)
- Manoj Cheriyan
- New England Biolabs, Inc, Ipswich, Massachusetts 01938, USA
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32
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Zhang W, Chen Y, Liang Q, Li H, Jin H, Zhang L, Meng X, Li Z. Design, Synthesis, and Antibacterial Activities of Conformationally Constrained Kanamycin A Derivatives. J Org Chem 2012; 78:400-9. [DOI: 10.1021/jo302247x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wenxuan Zhang
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Ying Chen
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Qingzhao Liang
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Hui Li
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Hongwei Jin
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Liangren Zhang
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Xiangbao Meng
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Zhongjun Li
- Department of Chemical Biology and ‡Department of
Medicinal Chemistry, School of Pharmaceutical Sciences,
The State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
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Elizarov SM, Alekseeva MG, Novikov FN, Chilov GG, Maslov DA, Shtil AA, Danilenko VN. Identification of phosphorylation sites in aminoglycoside phosphotransferase VIII from Streptomyces rimosus. BIOCHEMISTRY (MOSCOW) 2012; 77:1258-65. [DOI: 10.1134/s0006297912110041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Serpersu EH, Norris AL. Effect of protein dynamics and solvent in ligand recognition by promiscuous aminoglycoside-modifying enzymes. Adv Carbohydr Chem Biochem 2012; 67:221-48. [PMID: 22794185 DOI: 10.1016/b978-0-12-396527-1.00005-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Engin H Serpersu
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
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35
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Romanowska J, Reuter N, Trylska J. Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. Proteins 2012; 81:63-80. [PMID: 22907688 DOI: 10.1002/prot.24163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/02/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022]
Abstract
Aminoglycoside antibiotics are used against severe bacterial infections. They bind to the bacterial ribosomal RNA and interfere with the translation process. However, bacteria produce aminoglycoside modifying enzymes (AME) to resist aminoglycoside actions. AMEs form a variable group and yet they specifically recognize and efficiently bind aminoglycosides, which are also diverse in terms of total net charge and the number of pseudo-sugar rings. Here, we present the results of 25 molecular dynamics simulations of three AME representatives and aminoglycoside ribosomal RNA binding site, unliganded and complexed with an aminoglycoside, kanamycin A. A comparison of the aminoglycoside binding sites in these different receptors revealed that the enzymes efficiently mimic the nucleic acid environment of the ribosomal RNA binding cleft. Although internal dynamics of AMEs and their interaction patterns with aminoglycosides differ, the energetical analysis showed that the most favorable sites are virtually the same in the enzymes and RNA. The most copied interactions were of electrostatic nature, but stacking was also replicated in one AME:kanamycin complex. In addition, we found that some water-mediated interactions were very stable in the simulations of the complexes. We show that our simulations reproduce well findings from NMR or X-ray structural studies, as well as results from directed mutagenesis. The outcomes of our analyses provide new insight into aminoglycoside resistance mechanism that is related to the enzymatic modification of these drugs.
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Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland.
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36
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Swarts DC, Mosterd C, van Passel MWJ, Brouns SJJ. CRISPR interference directs strand specific spacer acquisition. PLoS One 2012; 7:e35888. [PMID: 22558257 PMCID: PMC3338789 DOI: 10.1371/journal.pone.0035888] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/28/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND CRISPR/Cas is a widespread adaptive immune system in prokaryotes. This system integrates short stretches of DNA derived from invading nucleic acids into genomic CRISPR loci, which function as memory of previously encountered invaders. In Escherichia coli, transcripts of these loci are cleaved into small RNAs and utilized by the Cascade complex to bind invader DNA, which is then likely degraded by Cas3 during CRISPR interference. RESULTS We describe how a CRISPR-activated E. coli K12 is cured from a high copy number plasmid under non-selective conditions in a CRISPR-mediated way. Cured clones integrated at least one up to five anti-plasmid spacers in genomic CRISPR loci. New spacers are integrated directly downstream of the leader sequence. The spacers are non-randomly selected to target protospacers with an AAG protospacer adjacent motif, which is located directly upstream of the protospacer. A co-occurrence of PAM deviations and CRISPR repeat mutations was observed, indicating that one nucleotide from the PAM is incorporated as the last nucleotide of the repeat during integration of a new spacer. When multiple spacers were integrated in a single clone, all spacer targeted the same strand of the plasmid, implying that CRISPR interference caused by the first integrated spacer directs subsequent spacer acquisition events in a strand specific manner. CONCLUSIONS The E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster--in our case the first acquired spacer--and spacers acquired thereafter, possibly through the use of specific DNA degradation products of the CRISPR interference machinery by the CRISPR adaptation machinery. This loop enables a rapid expansion of the spacer repertoire against an actively present DNA element that is already targeted, amplifying the CRISPR interference effect.
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Affiliation(s)
- Daan C. Swarts
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Cas Mosterd
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mark W. J. van Passel
- Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Stan J. J. Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
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37
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Shi K, Berghuis AM. Structural basis for dual nucleotide selectivity of aminoglycoside 2''-phosphotransferase IVa provides insight on determinants of nucleotide specificity of aminoglycoside kinases. J Biol Chem 2012; 287:13094-102. [PMID: 22371504 DOI: 10.1074/jbc.m112.349670] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymatic phosphorylation through a family of enzymes called aminoglycoside O-phosphotransferases (APHs) is a major mechanism by which bacteria confer resistance to aminoglycoside antibiotics. Members of the APH(2″) subfamily are of particular clinical interest because of their prevalence in pathogenic strains and their broad substrate spectra. APH(2″) enzymes display differential preferences between ATP or GTP as the phosphate donor, with aminoglycoside 2″-phosphotransferase IVa (APH(2″)-IVa) being a member that utilizes both nucleotides at comparable efficiencies. We report here four crystal structures of APH(2″)-IVa, two of the wild type enzyme and two of single amino acid mutants, each in complex with either adenosine or guanosine. Together, these structures afford a detailed look at the nucleoside-binding site architecture for this enzyme and reveal key elements that confer dual nucleotide specificity, including a solvent network in the interior of the nucleoside-binding pocket and the conformation of an interdomain linker loop. Steady state kinetic studies, as well as sequence and structural comparisons with members of the APH(2″) subfamily and other aminoglycoside kinases, rationalize the different substrate preferences for these enzymes. Finally, despite poor overall sequence similarity and structural homology, analysis of the nucleoside-binding pocket of APH(2″)-IVa shows a striking resemblance to that of eukaryotic casein kinase 2 (CK2), which also exhibits dual nucleotide specificity. These results, in complement with the multitude of existing inhibitors against CK2, can serve as a structural basis for the design of nucleotide-competitive inhibitors against clinically relevant APH enzymes.
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Affiliation(s)
- Kun Shi
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada
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38
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Smith CA, Toth M, Frase H, Byrnes LJ, Vakulenko SB. Aminoglycoside 2''-phosphotransferase IIIa (APH(2'')-IIIa) prefers GTP over ATP: structural templates for nucleotide recognition in the bacterial aminoglycoside-2'' kinases. J Biol Chem 2012; 287:12893-903. [PMID: 22367198 DOI: 10.1074/jbc.m112.341206] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Contrary to the accepted dogma that ATP is the canonical phosphate donor in aminoglycoside kinases and protein kinases, it was recently demonstrated that all members of the bacterial aminoglycoside 2''-phosphotransferase IIIa (APH(2'')) aminoglycoside kinase family are unique in their ability to utilize GTP as a cofactor for antibiotic modification. Here we describe the structural determinants for GTP recognition in these enzymes. The crystal structure of the GTP-dependent APH(2'')-IIIa shows that although this enzyme has templates for both ATP and GTP binding superimposed on a single nucleotide specificity motif, access to the ATP-binding template is blocked by a bulky tyrosine residue. Substitution of this tyrosine by a smaller amino acid opens access to the ATP template. Similar GTP binding templates are conserved in other bacterial aminoglycoside kinases, whereas in the structurally related eukaryotic protein kinases this template is less conserved. The aminoglycoside kinases are important antibiotic resistance enzymes in bacteria, whose wide dissemination severely limits available therapeutic options, and the GTP binding templates could be exploited as new, previously unexplored targets for inhibitors of these clinically important enzymes.
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Affiliation(s)
- Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California 94025, USA.
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39
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Nessar R, Cambau E, Reyrat JM, Murray A, Gicquel B. Mycobacterium abscessus: a new antibiotic nightmare. J Antimicrob Chemother 2012; 67:810-8. [DOI: 10.1093/jac/dkr578] [Citation(s) in RCA: 482] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Abstract
Antibiotics remain one of our most important pharmacological tools for the control of infectious disease. However, unlike most other drugs, the use of antibiotics selects for resistant organisms and erodes their clinical utility. Resistance can emerge within populations of bacteria by mutation and be retained by subsequent selection or by the acquisition of resistance elements laterally from other organisms. The source of these resistance genes is only now being understood. The evidence supports a large bacterial resistome-the collection of all resistance genes and their precursors in both pathogenic and nonpathogenic bacteria. These genes have arisen by various means including self-protection in the case of antibiotic producers, transport of small molecules for various reasons including nutrition and detoxification of noxious chemicals, and to accomplish other goals, such as metabolism, and demonstrate serendipitous selectivity for antibiotics. Regardless of their origins, resistance genes can rapidly move through bacterial populations and emerge in pathogenic bacteria. Understanding the processes that contribute to the evolution and selection of resistance is essential to mange current stocks of antibiotics and develop new ones.
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Affiliation(s)
- Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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41
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A Small Molecule Discrimination Map of the Antibiotic Resistance Kinome. ACTA ACUST UNITED AC 2011; 18:1591-601. [DOI: 10.1016/j.chembiol.2011.10.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 12/21/2022]
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42
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Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl Environ Microbiol 2011; 77:7804-14. [PMID: 21908640 DOI: 10.1128/aem.06059-11] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Members of candidate division OP11 are widely distributed in terrestrial and marine ecosystems, yet little information regarding their metabolic capabilities and ecological role within such habitats is currently available. Here, we report on the microfluidic isolation, multiple-displacement-amplification, pyrosequencing, and genomic analysis of a single cell (ZG1) belonging to candidate division OP11. Genome analysis of the ∼270-kb partial genome assembly obtained showed that it had no particular similarity to a specific phylum. Four hundred twenty-three open reading frames were identified, 46% of which had no function prediction. In-depth analysis revealed a heterotrophic lifestyle, with genes encoding endoglucanase, amylopullulanase, and laccase enzymes, suggesting a capacity for utilization of cellulose, starch, and, potentially, lignin, respectively. Genes encoding several glycolysis enzymes as well as formate utilization were identified, but no evidence for an electron transport chain was found. The presence of genes encoding various components of lipopolysaccharide biosynthesis indicates a Gram-negative bacterial cell wall. The partial genome also provides evidence for antibiotic resistance (β-lactamase, aminoglycoside phosphotransferase), as well as antibiotic production (bacteriocin) and extracellular bactericidal peptidases. Multiple mechanisms for stress response were identified, as were elements of type I and type IV secretion systems. Finally, housekeeping genes identified within the partial genome were used to demonstrate the OP11 affiliation of multiple hitherto unclassified genomic fragments from multiple database-deposited metagenomic data sets. These results provide the first glimpse into the lifestyle of a member of a ubiquitous, yet poorly understood bacterial candidate division.
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43
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Kim S, Nguyen CMT, Kim EJ, Kim KJ. Crystal structure of Mycobacterium tuberculosis Rv3168: a putative aminoglycoside antibiotics resistance enzyme. Proteins 2011; 79:2983-7. [PMID: 21905120 DOI: 10.1002/prot.23119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/16/2011] [Accepted: 05/04/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Sangwoo Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea
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44
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Appleby-Tagoe JH, Thiel IV, Wang Y, Wang Y, Mootz HD, Liu XQ. Highly efficient and more general cis- and trans-splicing inteins through sequential directed evolution. J Biol Chem 2011; 286:34440-7. [PMID: 21832069 DOI: 10.1074/jbc.m111.277350] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inteins are internal protein sequences that post-translationally self-excise and splice together the flanking sequences, the so-called exteins. Natural and engineered inteins have been used in many practical applications. However, inteins are often inefficient or inactive when placed in a non-native host protein and may require the presence of several amino acid residues of the native exteins, which will then remain as a potential scar in the spliced protein. Thus, more general inteins that overcome these limitations are highly desirable. Here we report sequential directed evolution as a new approach to produce inteins with such properties. Random mutants of the Ssp (Synechocystis sp. PCC 6803) DnaB mini-intein were inserted into the protein conferring kanamycin resistance at a site where the parent intein was inactive for splicing. The mutants selected for splicing activity were further improved by iterating the procedure for two more cycles at different positions in the same protein. The resulting improved inteins showed high activity in the positions of the first rounds of selection, in multiple new insertion sites, and in different proteins. One of these inteins, the M86 mutant, which accumulated 8 amino acid substitutions, was also biochemically characterized in an artificially split form with a chemically synthesized N-terminal intein fragment consisting of 11 amino acids. When compared with the unevolved split intein, it exhibited an ∼60-fold increased rate in the protein trans-splicing reaction and a K(d) value for the interaction of the split intein fragments improved by an order of magnitude. Implications on the intein structure-function, practical application, and evolution are discussed.
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Affiliation(s)
- Julia H Appleby-Tagoe
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
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45
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Shi K, Houston DR, Berghuis AM. Crystal structures of antibiotic-bound complexes of aminoglycoside 2''-phosphotransferase IVa highlight the diversity in substrate binding modes among aminoglycoside kinases. Biochemistry 2011; 50:6237-44. [PMID: 21678960 DOI: 10.1021/bi200747f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aminoglycoside 2''-phosphotransferase IVa [APH(2'')-IVa] is a member of a family of bacterial enzymes responsible for medically relevant resistance to antibiotics. APH(2'')-IVa confers high-level resistance against several clinically used aminoglycoside antibiotics in various pathogenic Enterococcus species by phosphorylating the drug, thereby preventing it from binding to its ribosomal target and producing a bactericidal effect. We describe here three crystal structures of APH(2'')-IVa, one in its apo form and two in complex with a bound antibiotic, tobramycin and kanamycin A. The apo structure was refined to a resolution of 2.05 Å, and the APH(2'')-IVa structures with tobramycin and kanamycin A bound were refined to resolutions of 1.80 and 2.15 Å, respectively. Comparison among the structures provides insight concerning the substrate selectivity of this enzyme. In particular, conformational changes upon substrate binding, involving rotational shifts of two distinct segments of the enzyme, are observed. These substrate-induced shifts may also rationalize the altered substrate preference of APH(2'')-IVa in comparison to those of other members of the APH(2'') subfamily, which are structurally closely related. Finally, analysis of the interactions between the enzyme and aminoglycoside reveals a distinct binding mode as compared to the intended ribosomal target. The differences in the pattern of interactions can be utilized as a structural basis for the development of improved aminoglycosides that are not susceptible to these resistance factors.
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Affiliation(s)
- Kun Shi
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada.
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46
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Ramsden R, Arms L, Davis TN, Muller EGD. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP. BMC Biotechnol 2011; 11:71. [PMID: 21708017 PMCID: PMC3141402 DOI: 10.1186/1472-6750-11-71] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/27/2011] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein. RESULTS The Pch PRP8 mini-intein of Penicillium chrysogenum was modified to include: 1) aminoglycoside phosphotransferase; 2) imidazoleglycerol-phosphate dehydratase, His5 from S. pombe ; 3) hygromycin B phosphotransferase; and 4) the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in E. coli, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in S. cerevisiae. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene CMD1. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker. CONCLUSIONS Inteins continue to show their flexibility as tools in molecular biology. The Pch PRP8 intein can successfully tolerate a variety of genetic markers and still retain high splicing efficiency. We have shown that a genetically marked intein can be used to insert GFP in one-step within a target protein in vivo.
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Affiliation(s)
- Richard Ramsden
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Luther Arms
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Eric GD Muller
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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47
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Fong DH, Xiong B, Hwang J, Berghuis AM. Crystal structures of two aminoglycoside kinases bound with a eukaryotic protein kinase inhibitor. PLoS One 2011; 6:e19589. [PMID: 21573013 PMCID: PMC3090406 DOI: 10.1371/journal.pone.0019589] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 04/01/2011] [Indexed: 11/30/2022] Open
Abstract
Antibiotic resistance is recognized as a growing healthcare problem. To address this issue, one strategy is to thwart the causal mechanism using an adjuvant in partner with the antibiotic. Aminoglycosides are a class of clinically important antibiotics used for the treatment of serious infections. Their usefulness has been compromised predominantly due to drug inactivation by aminoglycoside-modifying enzymes, such as aminoglycoside phosphotransferases or kinases. These kinases are structurally homologous to eukaryotic Ser/Thr and Tyr protein kinases and it has been shown that some can be inhibited by select protein kinase inhibitors. The aminoglycoside kinase, APH(3′)-IIIa, can be inhibited by CKI-7, an ATP-competitive inhibitor for the casein kinase 1. We have determined that CKI-7 is also a moderate inhibitor for the atypical APH(9)-Ia. Here we present the crystal structures of CKI-7-bound APH(3′)-IIIa and APH(9)-Ia, the first structures of a eukaryotic protein kinase inhibitor in complex with bacterial kinases. CKI-7 binds to the nucleotide-binding pocket of the enzymes and its binding alters the conformation of the nucleotide-binding loop, the segment homologous to the glycine-rich loop in eurkaryotic protein kinases. Comparison of these structures with the CKI-7-bound casein kinase 1 reveals features in the binding pockets that are distinct in the bacterial kinases and could be exploited for the design of a bacterial kinase specific inhibitor. Our results provide evidence that an inhibitor for a subset of APHs can be developed in order to curtail resistance to aminoglycosides.
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Affiliation(s)
- Desiree H. Fong
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Groupe de Recherche GRASP, McGill University, Montreal, Quebec, Canada
| | - Bing Xiong
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jiyoung Hwang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Groupe de Recherche GRASP, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- * E-mail:
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48
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Effects of altering aminoglycoside structures on bacterial resistance enzyme activities. Antimicrob Agents Chemother 2011; 55:3207-13. [PMID: 21537023 DOI: 10.1128/aac.00312-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aminoglycoside-modifying enzymes (AMEs) constitute the most prevalent mechanism of resistance to aminoglycosides by bacteria. We show that aminoglycosides can be doubly modified by the sequential actions of AMEs, with the activity of the second AME in most cases unaffected, decreased, or completely abolished. We demonstrate that the bifunctional enzyme AAC(3)-Ib/AAC(6')-Ib' can diacetylate gentamicin. Since single acetylation does not always inactivate the parent drugs completely, two modifications likely provide more-robust inactivation in vivo.
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49
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Affiliation(s)
- Mariya Morar
- M.G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada;
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada;
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50
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Toth M, Frase H, Antunes NT, Smith CA, Vakulenko SB. Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2''-IVa. Protein Sci 2010; 19:1565-76. [PMID: 20556826 DOI: 10.1002/pro.437] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Acquired resistance to aminoglycoside antibiotics primarily results from deactivation by three families of aminoglycoside-modifying enzymes. Here, we report the kinetic mechanism and structure of the aminoglycoside phosphotransferase 2''-IVa (APH(2'')-IVa), an enzyme responsible for resistance to aminoglycoside antibiotics in clinical enterococcal and staphylococcal isolates. The enzyme operates via a Bi-Bi sequential mechanism in which the two substrates (ATP or GTP and an aminoglycoside) bind in a random manner. The APH(2'')-IVa enzyme phosphorylates various 4,6-disubstituted aminoglycoside antibiotics with catalytic efficiencies (k(cat)/K(m)) of 1.5 x 10(3) to 1.2 x 10(6) (M(-1) s(-1)). The enzyme uses both ATP and GTP as the phosphate source, an extremely rare occurrence in the phosphotransferase and protein kinase enzymes. Based on an analysis of the APH(2'')-IVa structure, two overlapping binding templates specifically tuned for hydrogen bonding to either ATP or GTP have been identified and described. A detailed understanding of the structure and mechanism of the GTP-utilizing phosphotransferases is crucial for the development of either novel aminoglycosides or, more importantly, GTP-based enzyme inhibitors which would not be expected to interfere with crucial ATP-dependent enzymes.
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Affiliation(s)
- Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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