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McDermott JH, Wolf J, Hoshitsuki K, Huddart R, Caudle KE, Whirl-Carrillo M, Steyger PS, Smith RJH, Cody N, Rodriguez-Antona C, Klein TE, Newman WG. Clinical Pharmacogenetics Implementation Consortium Guideline for the Use of Aminoglycosides Based on MT-RNR1 Genotype. Clin Pharmacol Ther 2022; 111:366-372. [PMID: 34032273 PMCID: PMC8613315 DOI: 10.1002/cpt.2309] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 02/03/2023]
Abstract
Aminoglycosides are widely used antibiotics with notable side effects, such as nephrotoxicity, vestibulotoxicity, and sensorineural hearing loss (cochleotoxicity). MT-RNR1 is a gene that encodes the 12s rRNA subunit and is the mitochondrial homologue of the prokaryotic 16s rRNA. Some MT-RNR1 variants (i.e., m.1095T>C; m.1494C>T; m.1555A>G) more closely resemble the bacterial 16s rRNA subunit and result in increased risk of aminoglycoside-induced hearing loss. Use of aminoglycosides should be avoided in individuals with an MT-RNR1 variant associated with an increased risk of aminoglycoside-induced hearing loss unless the high risk of permanent hearing loss is outweighed by the severity of infection and safe or effective alternative therapies are not available. We summarize evidence from the literature supporting this association and provide therapeutic recommendations for the use of aminoglycosides based on MT-RNR1 genotype (updates at https://cpicpgx.org/guidelines/ and www.pharmgkb.org).
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Affiliation(s)
- John Henry McDermott
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Kelly E. Caudle
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Peter S. Steyger
- Translational Hearing Center, Biomedical Sciences, Creighton University, National Center for Rehabilitative Auditory Research, VA Portland Health Care System, Portland, Oregon, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Internal Medicine (Nephrology), Pediatrics and Molecular Physiology & Biophysics, University of Iowa, Iowa City, Iowa, USA
| | - Neal Cody
- Department of Genetics and Genomic Sciences, Ichan School of Medicine at Mount Sinai, New York, New York, USA,Sema4, Stamford, Connecticut, USA
| | - Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA,Department of Medicine, Stanford University, Stanford, California, USA
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK,Correspondence: William Newman ()
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Ren W, Ding Y, Gu L, Yan W, Wang C, Lyu M, Wang C, Wang S. Characterization and mechanism of the effects of Mg-Fe layered double hydroxide nanoparticles on a marine bacterium: new insights from genomic and transcriptional analyses. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:196. [PMID: 31428192 PMCID: PMC6696678 DOI: 10.1186/s13068-019-1528-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Layered double hydroxides (LDHs) have received widespread attention for their potential applications in catalysis, polymer nanocomposites, pharmaceuticals, and sensors. Here, the mechanism underlying the physiological effects of Mg-Fe layered double hydroxide nanoparticles on the marine bacterial species Arthrobacter oxidans KQ11 was investigated. RESULTS Increased yields of marine dextranase (Aodex) were obtained by exposing A. oxidans KQ11 to Mg-Fe layered double hydroxide nanoparticles (Mg-Fe-LDH NPs). Furthermore, the potential effects of Mg-Fe-LDH NPs on bacterial growth and Aodex production were preliminarily investigated. A. oxidans KQ11 growth was not affected by exposure to the Mg-Fe-LDH NPs. In contrast, a U-shaped trend of Aodex production was observed after exposure to NPs at a concentration of 10 μg/L-100 mg/L, which was due to competition between Mg-Fe-LDH NP adsorption on Aodex and the promotion of Aodex expression by the NPs. The mechanism underling the effects of Mg-Fe-LDH NPs on A. oxidans KQ11 was investigated using a combination of physiological characterization, genomics, and transcriptomics. Exposure to 100 mg/L of Mg-Fe-LDH NPs led to NP adsorption onto Aodex, increased expression of Aodex, and generation of a new Shine-Dalgarno sequence (GGGAG) and sRNAs that both influenced the expression of Aodex. Moreover, the expressions of transcripts related to ferric iron metabolic functions were significantly influenced by treatment. CONCLUSIONS These results provide valuable information for further investigation of the A. oxidans KQ11 response to Mg-Fe-LDH NPs and will aid in achieving improved marine dextranase production, and even improve such activities in other marine microorganisms.
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Affiliation(s)
- Wei Ren
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People’s Republic of China
| | - Yanshuai Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
| | - Lide Gu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
| | - Wanli Yan
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
| | - Cang Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, 230039 Anhui People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
| | - Changhai Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
- Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, 230039 Anhui People’s Republic of China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005 Jiangsu People’s Republic of China
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Ahmed N, Sormanni P, Ciryam P, Vendruscolo M, Dobson CM, O'Brien EP. Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming. Sci Rep 2019; 9:6256. [PMID: 31000737 PMCID: PMC6472398 DOI: 10.1038/s41598-019-42348-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/29/2019] [Indexed: 01/21/2023] Open
Abstract
Identifying the A- and P-site locations on ribosome-protected mRNA fragments from Ribo-Seq experiments is a fundamental step in the quantitative analysis of transcriptome-wide translation properties at the codon level. Many analyses of Ribo-Seq data have utilized heuristic approaches applied to a narrow range of fragment sizes to identify the A-site. In this study, we use Integer Programming to identify the A-site by maximizing an objective function that reflects the fact that the ribosome's A-site on ribosome-protected fragments must reside between the second and stop codons of an mRNA. This identifies the A-site location as a function of the fragment's size and its 5' end reading frame in Ribo-Seq data generated from S. cerevisiae and mouse embryonic stem cells. The correctness of the identified A-site locations is demonstrated by showing that this method, as compared to others, yields the largest ribosome density at established stalling sites. By providing greater accuracy and utilization of a wider range of fragment sizes, our approach increases the signal-to-noise ratio of underlying biological signals associated with translation elongation at the codon length scale.
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Affiliation(s)
- Nabeel Ahmed
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Prajwal Ciryam
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | | | | | - Edward P O'Brien
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
- Institute of Cyber Science, Pennsylvania State University, University Park, PA, USA.
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
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The plasmid vectors, pBS2ndd and pBS3ndd, for versatile cloning with low background in Escherichia coli. World J Microbiol Biotechnol 2018; 34:85. [PMID: 29876748 DOI: 10.1007/s11274-018-2466-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/25/2018] [Indexed: 12/21/2022]
Abstract
For decades, diverse plasmid vectors have been continuously developed for molecular cloning of DNA fragment in the bacterial host cell Escherichia coli. Even with deliberate performances in vector preparation, the cloning approaches still face inevitable background colonies, or false positive clones, that may be arisen from intact or self-ligated plasmid molecules. To assist in such problem, two plasmids, pBS2ndd and pBS3ndd, which resistant to ampicillin and kanamycin respectively, were developed in this study as more advantageous cloning vector. The plasmids carry ndd, a lethal gene from bacteriophage T4 coding for nucleoid disruption protein that binds to the host chromosome and progressively kill the cell. The deadly toxicity of Ndd inhibits host cells that obtain intact or ndd-religated vector from growing, which results in low background and dramatically reduces the effort for selection of recombinants. Moreover, their identical multiple cloning site was designed to support various cloning strategies. Digestion of plasmids with XcmI allows for in vitro T/A ligation, while with EcoRV permits blunt-end ligation, with capability of blue-white colony screening. In vivo homologous recombination cloning is also utilizable by amplification of insert fragments using primers containing homology arms and transformation into capable E. coli strains. To demonstrate their advantages, the plasmids were used to clone PCR product samples for DNA sequencing with low-background and versatile cloning strategies. Such rapid and cost-effective cloning procedures are also proposed here. Finally, the cloning for protein expression with blue-white selection was also possible using egfp as a model regulated by lac and T7 promoters on the plasmid or other build-in promoters with the insert.
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Tong H, Schliekelman P, Mrázek J. Unsupervised statistical discovery of spaced motifs in prokaryotic genomes. BMC Genomics 2017; 18:27. [PMID: 28056763 PMCID: PMC5217627 DOI: 10.1186/s12864-016-3400-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/09/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA sequences contain repetitive motifs which have various functions in the physiology of the organism. A number of methods have been developed for discovery of such sequence motifs with a primary focus on detection of regulatory motifs and particularly transcription factor binding sites. Most motif-finding methods apply probabilistic models to detect motifs characterized by unusually high number of copies of the motif in the analyzed sequences. RESULTS We present a novel method for detection of pairs of motifs separated by spacers of variable nucleotide sequence but conserved length. Unlike existing methods for motif discovery, the motifs themselves are not required to occur at unusually high frequency but only to exhibit a significant preference to occur at a specific distance from each other. In the present implementation of the method, motifs are represented by pentamers and all pairs of pentamers are evaluated for statistically significant preference for a specific distance. An important step of the algorithm eliminates motif pairs where the spacers separating the two motifs exhibit a high degree of sequence similarity; such motif pairs likely arise from duplications of the whole segment including the motifs and the spacer rather than due to selective constraints indicative of a functional importance of the motif pair. The method was used to scan 569 complete prokaryotic genomes for novel sequence motifs. Some motifs detected were previously known but other motifs found in the search appear to be novel. Selected motif pairs were subjected to further investigation and in some cases their possible biological functions were proposed. CONCLUSIONS We present a new motif-finding technique that is applicable to scanning complete genomes for sequence motifs. The results from analysis of 569 genomes suggest that the method detects previously known motifs that are expected to be found as well as new motifs that are unlikely to be discovered by traditional motif-finding methods. We conclude that our approach to detection of significant motif pairs can complement existing motif-finding techniques in discovery of novel functional sequence motifs in complete genomes.
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Affiliation(s)
- Hao Tong
- Department of Statistics, University of Georgia, Athens, GA, 30602, USA
| | - Paul Schliekelman
- Department of Statistics, University of Georgia, Athens, GA, 30602, USA
| | - Jan Mrázek
- Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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