4ghk › Citations

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC
PLoS One 8 e53851 (2013)

Cited: 78 times
EuropePMC logo PMID: 23382856

Abstract

Background

The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

Reviews - 4ghk mentioned but not cited (1)

  1. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Könning D, Kolmar H. Microb Cell Fact 17 32 (2018)

Articles - 4ghk mentioned but not cited (1)

  1. Combining functional and structural genomics to sample the essential Burkholderia structome. Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. PLoS One 8 e53851 (2013)


Reviews citing this publication (11)

  1. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product. Dailey HA, Dailey TA, Gerdes S, Jahn D, Jahn M, O'Brian MR, Warren MJ. Microbiol Mol Biol Rev 81 e00048-16 (2017)
  2. The design and analysis of transposon insertion sequencing experiments. Chao MC, Abel S, Davis BM, Waldor MK. Nat Rev Microbiol 14 119-128 (2016)
  3. Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Hove-Jensen B, Andersen KR, Kilstrup M, Martinussen J, Switzer RL, Willemoës M. Microbiol Mol Biol Rev 81 e00040-16 (2017)
  4. Wheat germ systems for cell-free protein expression. Harbers M. FEBS Lett 588 2762-2773 (2014)
  5. Essential Two-Component Systems Regulating Cell Envelope Functions: Opportunities for Novel Antibiotic Therapies. Cardona ST, Choy M, Hogan AM. J Membr Biol 251 75-89 (2018)
  6. From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases. Shi D, Allewell NM, Tuchman M. Int J Mol Sci 16 18836-18864 (2015)
  7. Recent contributions of structure-based drug design to the development of antibacterial compounds. Staker BL, Buchko GW, Myler PJ. Curr Opin Microbiol 27 133-138 (2015)
  8. Structure, Folding and Stability of Nucleoside Diphosphate Kinases. Georgescauld F, Song Y, Dautant A. Int J Mol Sci 21 E6779 (2020)
  9. Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. Ugbogu EA, Schweizer LM, Schweizer M. Cells 11 1909 (2022)
  10. Methodological tools to study species of the genus Burkholderia. Scoffone VC, Trespidi G, Barbieri G, Irudal S, Israyilova A, Buroni S. Appl Microbiol Biotechnol 105 9019-9034 (2021)
  11. A Review of Fatty Acid Biosynthesis Enzyme Inhibitors as Promising Antimicrobial Drugs. Bibens L, Becker JP, Dassonville-Klimpt A, Sonnet P. Pharmaceuticals (Basel) 16 425 (2023)

Articles citing this publication (65)

  1. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Luo H, Lin Y, Gao F, Zhang CT, Zhang R. Nucleic Acids Res 42 D574-80 (2014)
  2. Sequence-defined transposon mutant library of Burkholderia thailandensis. Gallagher LA, Ramage E, Patrapuvich R, Weiss E, Brittnacher M, Manoil C. mBio 4 e00604-13 (2013)
  3. DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. Luo H, Lin Y, Liu T, Lai FL, Zhang CT, Gao F, Zhang R. Nucleic Acids Res 49 D677-D686 (2021)
  4. Increasing the structural coverage of tuberculosis drug targets. Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ. Tuberculosis (Edinb) 95 142-148 (2015)
  5. Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development. Moule MG, Hemsley CM, Seet Q, Guerra-Assunção JA, Lim J, Sarkar-Tyson M, Clark TG, Tan PB, Titball RW, Cuccui J, Wren BW. mBio 5 e00926-13 (2014)
  6. Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue. Palace SG, Proulx MK, Lu S, Baker RE, Goguen JD. mBio 5 e01385-14 (2014)
  7. Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS. Wong YC, Abd El Ghany M, Naeem R, Lee KW, Tan YC, Pain A, Nathan S. Front Microbiol 7 1288 (2016)
  8. Comprehensive identification of virulence factors required for respiratory melioidosis using Tn-seq mutagenesis. Gutierrez MG, Yoder-Himes DR, Warawa JM. Front Cell Infect Microbiol 5 78 (2015)
  9. Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library. Veeranagouda Y, Husain F, Tenorio EL, Wexler HM. BMC Genomics 15 429 (2014)
  10. Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae. Perry BJ, Yost CK. BMC Microbiol 14 298 (2014)
  11. Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. Grazziotin AL, Vidal NM, Venancio TM. FEBS J 282 3395-3411 (2015)
  12. Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia. Gislason AS, Turner K, Domaratzki M, Cardona ST. Microb Genom 3 (2017)
  13. Chromids Aid Genome Expansion and Functional Diversification in the Family Burkholderiaceae. diCenzo GC, Mengoni A, Perrin E. Mol Biol Evol 36 562-574 (2019)
  14. The Essential Genome of Burkholderia cenocepacia H111. Higgins S, Sanchez-Contreras M, Gualdi S, Pinto-Carbó M, Carlier A, Eberl L. J Bacteriol 199 e00260-17 (2017)
  15. Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining. Schallmey M, Koopmeiners J, Wells E, Wardenga R, Schallmey A. Appl Environ Microbiol 80 7303-7315 (2014)
  16. Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex. Loveridge EJ, Jones C, Bull MJ, Moody SC, Kahl MW, Khan Z, Neilson L, Tomeva M, Adams SE, Wood AC, Rodriguez-Martin D, Pinel I, Parkhill J, Mahenthiralingam E, Crosby J. J Bacteriol 199 e00125-17 (2017)
  17. Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing. Rosconi F, de Vries SP, Baig A, Fabiano E, Grant AJ. Appl Environ Microbiol 82 6664-6671 (2016)
  18. Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. Xavier JC, Patil KR, Rocha I. PLoS Comput Biol 14 e1006556 (2018)
  19. Structural basis for the site-specific incorporation of lysine derivatives into proteins. Flügel V, Vrabel M, Schneider S. PLoS One 9 e96198 (2014)
  20. Comparison of histidine recognition in human and trypanosomatid histidyl-tRNA synthetases. Koh CY, Wetzel AB, de van der Schueren WJ, Hol WG. Biochimie 106 111-120 (2014)
  21. Determinants of Extreme β-Lactam Tolerance in the Burkholderia pseudomallei Complex. Held K, Gasper J, Morgan S, Siehnel R, Singh P, Manoil C. Antimicrob Agents Chemother 62 (2018)
  22. Naegleria fowleri: Protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba. Tillery L, Barrett K, Goldstein J, Lassner JW, Osterhout B, Tran NL, Xu L, Young RM, Craig J, Chun I, Dranow DM, Abendroth J, Delker SL, Davies DR, Mayclin SJ, Calhoun B, Bolejack MJ, Staker B, Subramanian S, Phan I, Lorimer DD, Myler PJ, Edwards TE, Kyle DE, Rice CA, Morris JC, Leahy JW, Manetsch R, Barrett LK, Smith CL, Van Voorhis WC. PLoS One 16 e0241738 (2021)
  23. Structural modeling and docking studies of ribose 5-phosphate isomerase from Leishmania major and Homo sapiens: a comparative analysis for Leishmaniasis treatment. Capriles PV, Baptista LP, Guedes IA, Guimarães AC, Custódio FL, Alves-Ferreira M, Dardenne LE. J Mol Graph Model 55 134-147 (2015)
  24. Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine. Hew K, Dahlroth SL, Veerappan S, Pan LX, Cornvik T, Nordlund P. PLoS One 10 e0143947 (2015)
  25. Crystal structure of peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Å resolution shows the closed structure of the substrate-binding cleft. Singh A, Gautam L, Sinha M, Bhushan A, Kaur P, Sharma S, Singh TP. FEBS Open Bio 4 915-922 (2014)
  26. Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. Fabian BK, Foster C, Asher AJ, Elbourne LDH, Cain AK, Hassan KA, Tetu SG, Paulsen IT. J Bacteriol 203 e00432-20 (2021)
  27. Inactivation of the Thymidylate Synthase thyA in Non-typeable Haemophilus influenzae Modulates Antibiotic Resistance and Has a Strong Impact on Its Interplay with the Host Airways. Rodríguez-Arce I, Martí S, Euba B, Fernández-Calvet A, Moleres J, López-López N, Barberán M, Ramos-Vivas J, Tubau F, Losa C, Ardanuy C, Leiva J, Yuste JE, Garmendia J. Front Cell Infect Microbiol 7 266 (2017)
  28. Mapping of the Denitrification Pathway in Burkholderia thailandensis by Genome-Wide Mutant Profiling. Vitale A, Paszti S, Takahashi K, Toyofuku M, Pessi G, Eberl L. J Bacteriol 202 e00304-20 (2020)
  29. ePath: an online database towards comprehensive essential gene annotation for prokaryotes. Kong X, Zhu B, Stone VN, Ge X, El-Rami FE, Donghai H, Xu P. Sci Rep 9 12949 (2019)
  30. Crystal structure of E. coli PRPP synthetase. Zhou W, Tsai A, Dattmore DA, Stives DP, Chitrakar I, D'alessandro AM, Patil S, Hicks KA, French JB. BMC Struct Biol 19 1 (2019)
  31. Crystal structure of Staphylococcus aureus peptidyl-tRNA hydrolase at a 2.25 Å resolution. Zhang F, Song Y, Niu L, Teng M, Li X. Acta Biochim Biophys Sin (Shanghai) 47 1005-1010 (2015)
  32. Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites. Santos ARS, Gerhardt ECM, Moure VR, Pedrosa FO, Souza EM, Diamanti R, Högbom M, Huergo LF. J Biol Chem 293 7397-7407 (2018)
  33. Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Moen SO, Edwards TE, Dranow DM, Clifton MC, Sankaran B, Van Voorhis WC, Sharma A, Manoil C, Staker BL, Myler PJ, Lorimer DD. Sci Rep 7 223 (2017)
  34. Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis. Škerlová J, Fábry M, Hubálek M, Otwinowski Z, Rezáčová P. FEBS J 281 4280-4292 (2014)
  35. Crystal structures of Mycobacterial MeaB and MMAA-like GTPases. Edwards TE, Baugh L, Bullen J, Baydo RO, Witte P, Thompkins K, Phan IQ, Abendroth J, Clifton MC, Sankaran B, Van Voorhis WC, Myler PJ, Staker BL, Grundner C, Lorimer DD. J Struct Funct Genomics 16 91-99 (2015)
  36. Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+ synthetases. Chuenchor W, Doukov TI, Chang KT, Resto M, Yun CS, Gerratana B. Nat Commun 11 16 (2020)
  37. Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase. Kaur G, Subramanian S. Cell Cycle 16 1918-1926 (2017)
  38. Human PRPS1 filaments stabilize allosteric sites to regulate activity. Hvorecny KL, Hargett K, Quispe JD, Kollman JM. Nat Struct Mol Biol 30 391-402 (2023)
  39. Identification of Chemical Compounds That Inhibit the Function of Histidyl-tRNA Synthetase from Pseudomonas aeruginosa. Hu Y, Palmer SO, Robles ST, Resto T, Dean FB, Bullard JM. SLAS Discov 23 65-75 (2018)
  40. Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1. Ferguson PP, Holloway WB, Setzer WN, McFeeters H, McFeeters RL. Antibiotics (Basel) 5 E16 (2016)
  41. Structure of the E. coli agmatinase, SPEB. Chitrakar I, Ahmed SF, Torelli AT, French JB. PLoS One 16 e0248991 (2021)
  42. Structure-Based Virtual Screening of Pseudomonas aeruginosa LpxA Inhibitors Using Pharmacophore-Based Approach. Bhaskar BV, Babu TMC, Rammohan A, Zheng GY, Zyryanov GV, Gu W. Biomolecules 10 E266 (2020)
  43. tRNAGlu increases the affinity of glutamyl-tRNA synthetase for its inhibitor glutamyl-sulfamoyl-adenosine, an analogue of the aminoacylation reaction intermediate glutamyl-AMP: mechanistic and evolutionary implications. Blais SP, Kornblatt JA, Barbeau X, Bonnaure G, Lagüe P, Chênevert R, Lapointe J. PLoS One 10 e0121043 (2015)
  44. Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity. Maturana P, Orellana MS, Herrera SM, Martínez I, Figueroa M, Martínez-Oyanedel J, Castro-Fernandez V, Uribe E. Int J Mol Sci 22 4769 (2021)
  45. Crystal structures of Entamoeba histolytica lysyl-tRNA synthetase reveal conformational changes upon lysine binding and a specific helix bundle domain. Bonnefond L, Castro de Moura M, Ribas de Pouplana L, Nureki O. FEBS Lett 588 4478-4486 (2014)
  46. Dispensability of zinc and the putative zinc-binding domain in bacterial glutamyl-tRNA synthetase. Chongdar N, Dasgupta S, Datta AB, Basu G. Biosci Rep 35 e00184 (2015)
  47. Experimental and Analytical Approaches for Improving the Resolution of Randomly Barcoded Transposon Insertion Sequencing (RB-TnSeq) Studies. Borchert AJ, Bleem A, Beckham GT. ACS Synth Biol 11 2015-2021 (2022)
  48. Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS). Cho S, Im H, Lee KY, Chen J, Kang HJ, Yoon HJ, Min KH, Lee KR, Park HJ, Lee BJ. Eur J Med Chem 108 188-202 (2016)
  49. Structural characterization of β-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Patterson EI, Nanson JD, Abendroth J, Bryan C, Sankaran B, Myler PJ, Forwood JK. Proteins 88 47-56 (2020)
  50. Chromophorylation of cyanobacteriochrome Slr1393 from Synechocystis sp. PCC 6803 is regulated by protein Slr2111 through allosteric interaction. He Q, Tang QY, Sun YF, Zhou M, Gärtner W, Zhao KH. J Biol Chem 293 17705-17715 (2018)
  51. Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans. Davidson J, Nicholas K, Young J, Conrady DG, Mayclin S, Subramanian S, Staker BL, Myler PJ, Asojo OA. Acta Crystallogr F Struct Biol Commun 78 25-30 (2022)
  52. Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection. Kiran K, Rawal HC, Dubey H, Jaswal R, Bhardwaj SC, Deshmukh R, Sharma TR. J Fungi (Basel) 7 701 (2021)
  53. Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies. Kaushik S, Iqbal N, Singh N, Sikarwar JS, Singh PK, Sharma P, Kaur P, Sharma S, Owais M, Singh TP. Biochem J 475 547-560 (2018)
  54. Comparative structural insight into the unidirectional catalysis of ornithine carbamoyltransferases from Psychrobacter sp. PAMC 21119. Do H, Nguyen DL, Lee CW, Lee MJ, Oh H, Hwang J, Han SJ, Lee SG, Lee JH. PLoS One 17 e0274019 (2022)
  55. Crystal structure of a short-chain dehydrogenase/reductase from Burkholderia phymatum in complex with NAD. Alenazi J, Mayclin S, Subramanian S, Myler PJ, Asojo OA. Acta Crystallogr F Struct Biol Commun 78 52-58 (2022)
  56. Genome-wide transposon mutagenesis analysis of Burkholderia pseudomallei reveals essential genes for in vitro and in vivo survival. Wong YC, Naeem R, Abd El Ghany M, Hoh CC, Pain A, Nathan S. Front Cell Infect Microbiol 12 1062682 (2022)
  57. High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus. Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, Ito K. Proteins 87 226-235 (2019)
  58. Mutation Space of Spatially Conserved Amino Acid Sites in Proteins. Caswell BT, Summers TJ, Licup GL, Cantu DC. ACS Omega 8 24302-24310 (2023)
  59. Semisynthesis and Biological Evaluation of Platencin Thioether Derivatives: Dual FabF and FabH Inhibitors against MRSA. Li Y, Weng X, Deng Y, Pan J, Zhu S, Wen Z, Yuan Y, Li S, Shen B, Duan Y, Huang Y. ACS Med Chem Lett 12 433-442 (2021)
  60. Seven-enzyme in vitro cascade to (3R)-3-hydroxybutyryl-CoA. Valencia LE, Zhang Z, Cepeda AJ, Keatinge-Clay AT. Org Biomol Chem 17 1375-1378 (2019)
  61. Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae. Nielipinski M, Pietrzyk-Brzezinska AJ, Wlodawer A, Sekula B. Front Plant Sci 14 1297956 (2023)
  62. Structural and Biochemical Studies on Klebsiella Pneumoniae Enoyl-ACP Reductase (FabI) Suggest Flexible Substrate Binding Site. Biswas S, Patra A, Paul P, Misra N, Kushwaha GS, Suar M. Protein J (2023)
  63. Structural characterization of aspartate-semialdehyde dehydrogenase from Pseudomonas aeruginosa and Neisseria gonorrhoeae. Teakel SL, Fairman JW, Muruthi MM, Abendroth J, Dranow DM, Lorimer DD, Myler PJ, Edwards TE, Forwood JK. Sci Rep 12 14010 (2022)
  64. Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum. Ohren J, Parungao GG, Viola RE. Acta Crystallogr F Struct Biol Commun 75 290-298 (2019)
  65. The Small RNA NcS25 Regulates Biological Amine-Transporting Outer Membrane Porin BCAL3473 in Burkholderia cenocepacia. Sass AM, Coenye T. mSphere 8 e0008323 (2023)


Quick links