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Wong YC, Naeem R, Abd El Ghany M, Hoh CC, Pain A, Nathan S. Genome-wide transposon mutagenesis analysis of Burkholderia pseudomallei reveals essential genes for in vitro and in vivo survival. Front Cell Infect Microbiol 2022; 12:1062682. [PMID: 36619746 PMCID: PMC9816413 DOI: 10.3389/fcimb.2022.1062682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Burkholderia pseudomallei, a soil-dwelling microbe that infects humans and animals is the cause of the fatal disease melioidosis. The molecular mechanisms that underlie B. pseudomallei's versatility to survive within a broad range of environments are still not well defined. Methods We used the genome-wide screening tool TraDIS (Transposon Directed Insertion-site Sequencing) to identify B. pseudomallei essential genes. Transposon-flanking regions were sequenced and gene essentiality was assessed based on the frequency of transposon insertions within each gene. Transposon mutants were grown in LB and M9 minimal medium to determine conditionally essential genes required for growth under laboratory conditions. The Caenorhabditis elegans infection model was used to assess genes associated with in vivo B. pseudomallei survival. Transposon mutants were fed to the worms, recovered from worm intestines, and sequenced. Two selected mutants were constructed and evaluated for the bacteria's ability to survive and proliferate in the nematode intestinal lumen. Results Approximately 500,000 transposon-insertion mutants of B. pseudomallei strain R15 were generated. A total of 848,811 unique transposon insertion sites were identified in the B. pseudomallei R15 genome and 492 genes carrying low insertion frequencies were predicted to be essential. A total of 96 genes specifically required to support growth under nutrient-depleted conditions were identified. Genes most likely to be involved in B. pseudomallei survival and adaptation in the C. elegans intestinal lumen, were identified. When compared to wild type B. pseudomallei, a Tn5 mutant of bpsl2988 exhibited reduced survival in the worm intestine, was attenuated in C. elegans killing and showed decreased colonization in the organs of infected mice. Discussion The B. pseudomallei conditional essential proteins should provide further insights into the bacteria's niche adaptation, pathogenesis, and virulence.
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Affiliation(s)
- Yee-Chin Wong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Raeece Naeem
- Bioscience program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Moataz Abd El Ghany
- Bioscience program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia,School of Public Health, The University of Sydney, Sydney, NSW, Australia,Centre for Infectious Disease and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
| | | | - Arnab Pain
- Bioscience program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia,*Correspondence: Sheila Nathan,
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Crespo R, Dang Q, Zhou NE, Guthrie LM, Snavely TC, Dong W, Loesch KA, Suzuki T, You L, Wang W, O’Malley T, Parish T, Olsen DB, Sacchettini JC. Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase. J Med Chem 2019; 62:4483-4499. [PMID: 31002508 PMCID: PMC6511943 DOI: 10.1021/acs.jmedchem.9b00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis adenosine kinase (MtbAdoK) is an essential enzyme of Mtb and forms part of the purine salvage pathway within mycobacteria. Evidence suggests that the purine salvage pathway might play a crucial role in Mtb survival and persistence during its latent phase of infection. In these studies, we adopted a structural approach to the discovery, structure-guided design, and synthesis of a series of adenosine analogues that displayed inhibition constants ranging from 5 to 120 nM against the enzyme. Two of these compounds exhibited low micromolar activity against Mtb with half maximal effective inhibitory concentrations of 1.7 and 4.0 μM. Our selectivity and preliminary pharmacokinetic studies showed that the compounds possess a higher degree of specificity against MtbAdoK when compared with the human counterpart and are well tolerated in rodents, respectively. Finally, crystallographic studies showed the molecular basis of inhibition, potency, and selectivity and revealed the presence of a potentially therapeutically relevant cavity unique to the MtbAdoK homodimer.
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Affiliation(s)
- Roberto
A. Crespo
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Qun Dang
- Merck
Sharp Dohme Corporation, West Point Pennsylvania 19486, United States
| | - Nian E. Zhou
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Liam M. Guthrie
- College
of Medicine, Texas A&M University Health
Science Center, Bryan, Texas 77807, United
States
| | - Thomas C. Snavely
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Wen Dong
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kimberly A. Loesch
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Takao Suzuki
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Lanying You
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Wei Wang
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Theresa O’Malley
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue E, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue E, Seattle, Washington 98102, United States
| | - David B. Olsen
- Merck
Sharp Dohme Corporation, West Point Pennsylvania 19486, United States,E-mail: . Phone: 215-652-5250 (D.B.O.)
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States,E-mail: . Phone: (979) 845-8548 (J.C.S.)
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A review of the design and validation of web- and computer-based 24-h dietary recall tools. Nutr Res Rev 2016; 29:268-280. [DOI: 10.1017/s0954422416000172] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
AbstractTechnology-based dietary assessment offers solutions to many of the limitations of traditional dietary assessment methodologies including cost, participation rates and the accuracy of data collected. The 24-h dietary recall (24HDR) method is currently the most utilised method for the collection of dietary intake data at a national level. Recently there have been many developments using web-based platforms to collect food intake data using the principles of the 24HDR method. This review identifies web- and computer-based 24HDR tools that have been developed for both children and adult population groups, and examines common design features and the methods used to investigate the performance and validity of these tools. Overall, there is generally good to strong agreement between web-based 24HDR and respective reference measures for intakes of macro- and micronutrients.
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Tomoike F, Tsunetou A, Kim K, Nakagawa N, Kuramitsu S, Masui R. A putative adenosine kinase family protein possesses adenosine diphosphatase activity. Biosci Biotechnol Biochem 2016; 80:2138-2143. [PMID: 27484886 DOI: 10.1080/09168451.2016.1214532] [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] [Indexed: 10/21/2022]
Abstract
Adenosine kinase is a potential target for development of new types of drugs. The COG1839 family has been defined as "adenosine-specific kinase" family based on structural analysis and the adenosine-binding ability of a family member, PAE2307. However, there has been no experimental evidence with regard to the enzymatic function of this protein family. Here we measured the enzymatic activity of TTHA1091, a COG1839 family protein from Thermus thermophilus HB8. The phosphorylation of adenosine by TTHA1091 was undetectable when ATP or ADP were used as phosphate donor. However, the degradation of ADP to AMP was detected, indicating that this protein possessed adenosine diphosphatase (ADPase) activity. The (ADPase) activity was inhibited by divalent cations and was specific to ADP and CDP. Thus, this study provides the first experimental evidence for the enzymatic function of the "adenosine-specific kinase" family and suggests a need to reexamine its functional annotation.
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Affiliation(s)
- Fumiaki Tomoike
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka , Japan.,b Research Center for Materials Science , Nagoya University , Nagoya, Aichi , Japan
| | - Akiko Tsunetou
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Kwang Kim
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Noriko Nakagawa
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Seiki Kuramitsu
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka , Japan.,c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan
| | - Ryoji Masui
- c Department of Biological Sciences , Graduate School of Science, Osaka University , Toyonaka , Osaka , Japan.,d Graduate School of Science , Osaka City University , Osaka , Japan
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Spácilová P, Naus P, Pohl R, Votruba I, Snásel J, Zábranská H, Pichová I, Ameral R, Birkus G, Cihlár T, Hocek M. CycloSal-phosphate pronucleotides of cytostatic 6-(Het)aryl-7-deazapurine ribonucleosides: Synthesis, cytostatic activity, and inhibition of adenosine kinases. ChemMedChem 2010; 5:1386-96. [PMID: 20533504 DOI: 10.1002/cmdc.201000192] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A series of cycloSal-phosphate prodrugs of a recently described new class of nucleoside cytostatics (6-hetaryl-7-deazapurine ribonucleosides) was prepared. The corresponding 2',3'-isopropylidene 6-chloro-7-deazapurine nucleosides were converted into 5-O'-cycloSal-phosphates. These underwent a series of Stille or Suzuki cross-couplings with diverse (het)arylstannanes or -boronic acids to yield the protected 6-(het)aryl-7-deazapurine pronucleotides that were subsequently deprotected to give 12 derivatives of free pronucleotides. The in vitro cytostatic effect of the pronucleotides was compared with parent nucleoside analogues. In most cases, the activity of the pronucleotide was similar to or somewhat lower than that of the corresponding parent nucleosides, with the exception of 7-fluoro pronucleotides 13 a, 13 b, and 13 d, which had exhibited GIC(50) values that were improved by one order of magnitude (to the low nanomolar range). The presence of a cycloSal-phosphate group also influenced selectivity toward various cell lines. Several pronucleotides were found which strongly inhibit human adenosine kinase but only weakly inhibit the MTB adenosine kinase.
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Affiliation(s)
- Pavla Spácilová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic
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