1887

Abstract

infects patients with cystic fibrosis, burns, wounds and implants. Previously, our group showed that elevated Ca positively regulates the production of several virulence factors in , such as biofilm formation, production of pyocyanin and secreted proteases. We have identified a Ca-regulated β-propeller putative phytase, CarP, which is required for Ca tolerance, regulation of the intracellular Ca levels, and plays a role in Ca regulation of virulence. Here, we studied the conservation of sequence and its occurrence in diverse phylogenetic groups of bacteria. analysis revealed that and its two paralogues PA2017 and PA0319 are primarily present in and belong to the core genome of the species. We identified 155 single nucleotide alterations within , 42 of which lead to missense mutations with only three that affected the predicted 3D structure of the protein. PCR analyses with -specific primers detected specifically in 70 clinical and environmental samples. Sequence comparison demonstrated that is overall highly conserved in isolated from diverse environments. Such evolutionary preservation of illustrates its importance for adaptations to diverse environments and demonstrates its potential as a biomarker.

Funding
This study was supported by the:
  • National Institute of General Medical Sciences (Award P20GM103648)
    • Principle Award Recipient: MariannaA Patrauchan
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.001004
2020-12-09
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/167/2/micro001004.html?itemId=/content/journal/micro/10.1099/mic.0.001004&mimeType=html&fmt=ahah

References

  1. Bhagirath AY, Li Y, Somayajula D, Dadashi M, Badr S et al. Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174 [View Article][PubMed]
    [Google Scholar]
  2. Busi Rizzi E, Schininà V, Bordi E, Buontempo G, Narciso P et al. HIV-related bronchopulmonary infection by Pseudomonas aeruginosa in the HAART era: radiological findings. Acta Radiol 2006; 47:793–797 [View Article][PubMed]
    [Google Scholar]
  3. Stapleton F, Carnt N. Contact lens-related microbial keratitis: how have epidemiology and genetics helped us with pathogenesis and prophylaxis. Eye 2012; 26:185–193 [View Article][PubMed]
    [Google Scholar]
  4. Lamas Ferreiro JL, Álvarez Otero J, González González L, Novoa Lamazares L, Arca Blanco A et al. Pseudomonas aeruginosa urinary tract infections in hospitalized patients: Mortality and prognostic factors. PLoS One 2017; 12:e0178178 [View Article][PubMed]
    [Google Scholar]
  5. CDC Pseudomonas aerugionsa 2020 2017
    [Google Scholar]
  6. Meyer JM, Neely A, Stintzi A, Georges C, Holder IA. Pyoverdin is essential for virulence of Pseudomonas aeruginosa . Infect Immun 1996; 64:518–523 [View Article][PubMed]
    [Google Scholar]
  7. Laarman AJ, Bardoel BW, Ruyken M, Fernie J, Milder FJ et al. Pseudomonas aeruginosa alkaline protease blocks complement activation via the classical and lectin pathways. J Immunol 2012; 188:386–393 [View Article][PubMed]
    [Google Scholar]
  8. Kang D, Kirienko DR, Webster P, Fisher AL, Kirienko NV. Pyoverdine, a siderophore from Pseudomonas aeruginosa, translocates into C. elegans, removes iron, and activates a distinct host response. Virulence 2018; 9:804–817 [View Article][PubMed]
    [Google Scholar]
  9. Look DC, Stoll LL, Romig SA, Humlicek A, Britigan BE et al. Pyocyanin and its precursor phenazine-1-carboxylic acid increase IL-8 and intercellular adhesion molecule-1 expression in human airway epithelial cells by oxidant-dependent mechanisms. J Immunol 2005; 175:4017–4023 [View Article][PubMed]
    [Google Scholar]
  10. Mulcahy LR, Isabella VM, Lewis K. Pseudomonas aeruginosa biofilms in disease. Microb Ecol 2014; 68:1–12 [View Article][PubMed]
    [Google Scholar]
  11. Percival SL, Suleman L, Vuotto C, Donelli G. Healthcare-associated infections, medical devices and biofilms: risk, tolerance and control. J Med Microbiol 2015; 64:323–334 [View Article][PubMed]
    [Google Scholar]
  12. Clapham DE. Calcium signaling. Cell 2007; 131:1047–1058 [View Article][PubMed]
    [Google Scholar]
  13. Ratner D, Mueller C. Immune responses in cystic fibrosis: are they intrinsically defective?. Am J Respir Cell Mol Biol 2012; 46:715–722 [View Article][PubMed]
    [Google Scholar]
  14. Sarkisova S, Patrauchan MA, Berglund D, Nivens DE, Franklin MJ. Calcium-Induced virulence factors associated with the extracellular matrix of mucoid Pseudomonas aeruginosa biofilms. J Bacteriol 2005; 187:4327–4337 [View Article][PubMed]
    [Google Scholar]
  15. Guragain M, King MM, Williamson KS, Pérez-Osorio AC, Akiyama T et al. The Pseudomonas aeruginosa PAO1 two-component regulator CarSR regulates calcium homeostasis and calcium-induced virulence factor production through its regulatory targets CarO and CarP. J Bacteriol 2016; 198:951–963 [View Article][PubMed]
    [Google Scholar]
  16. Khanam S, Guragain M, Lenaburg DL, Kubat R, Patrauchan MA. Calcium induces tobramycin resistance in Pseudomonas aeruginosa by regulating RND efflux pumps. Cell Calcium 2017; 61:32–43 [View Article][PubMed]
    [Google Scholar]
  17. Guragain M, Lenaburg DL, Moore FS, Reutlinger I, Patrauchan MA. Calcium homeostasis in Pseudomonas aeruginosa requires multiple transporters and modulates swarming motility. Cell Calcium 2013; 54:350–361 [View Article][PubMed]
    [Google Scholar]
  18. Mena A, Smith EE, Burns JL, Speert DP, Moskowitz SM et al. Genetic adaptation of Pseudomonas aeruginosa to the airways of cystic fibrosis patients is catalyzed by hypermutation. J Bacteriol 2008; 190:7910–7917 [View Article][PubMed]
    [Google Scholar]
  19. Wang Y, Gao L, Rao X, Wang J, Yu H et al. Characterization of lasR-deficient clinical isolates of Pseudomonas aeruginosa . Sci Rep 2018; 8:13344 [View Article][PubMed]
    [Google Scholar]
  20. Cornforth DM, Dees JL, Ibberson CB, Huse HK, Mathiesen IH et al. Pseudomonas aeruginosa transcriptome during human infection. Proc Natl Acad Sci U S A 2018; 115:E5125–E5134 [View Article][PubMed]
    [Google Scholar]
  21. Salma R, Dabboussi F, Kassaa I, Khudary R, Hamze M, Dabboussi F. gyrA and parC mutations in quinolone-resistant clinical isolates of Pseudomonas aeruginosa from Nini Hospital in north Lebanon. J Infect Chemother 2013; 19:77–81 [View Article][PubMed]
    [Google Scholar]
  22. De Vos D, Lim A, Pirnay JP, Struelens M, Vandenvelde C et al. Direct detection and identification of Pseudomonas aeruginosa in clinical samples such as skin biopsy specimens and expectorations by multiplex PCR based on two outer membrane lipoprotein genes, oprI and oprL. J Clin Microbiol 1997; 35:1295–1299 [View Article][PubMed]
    [Google Scholar]
  23. DA Silva Filho LVF, Levi JE, Bento CNO, DA Silva Ramos SRT, Rozov T. PCR identification of Pseudomonas aeruginosa and direct detection in clinical samples from cystic fibrosis patients. J Med Microbiol 1999; 48:357–361 [View Article][PubMed]
    [Google Scholar]
  24. Khan AA, Cerniglia CE. Detection of Pseudomonas aeruginosa from clinical and environmental samples by amplification of the exotoxin A gene using PCR. Appl Environ Microbiol 1994; 60:3739–3745 [View Article][PubMed]
    [Google Scholar]
  25. Žukovskaja O, Agafilushkina S, Sivakov V, Weber K, Cialla-May D et al. Rapid detection of the bacterial biomarker pyocyanin in artificial sputum using a SERS-active silicon nanowire matrix covered by bimetallic noble metal nanoparticles. Talanta 2019; 202:171–177 [View Article][PubMed]
    [Google Scholar]
  26. Kviatkovski I, Shushan S, Oron Y, Frumin I, Amir D et al. Smelling Pseudomonas aeruginosa infections using a whole-cell biosensor - An alternative for the gold-standard culturing assay. J Biotechnol 2018; 267:45–49 [View Article][PubMed]
    [Google Scholar]
  27. van Oort PM, Brinkman P, Slingers G, Koppen G, Maas A et al. Exhaled breath metabolomics reveals a pathogen-specific response in a rat pneumonia model for two human pathogenic bacteria: a proof-of-concept study. Am J Physiol Lung Cell Mol Physiol 2019; 316:L751–L756 [View Article]
    [Google Scholar]
  28. Tian Y, Zeng T, Tan L, Wu Y, Yu J et al. Clinical significance of BPI‐ANCA detecting in COPD patients with Pseudomonas aeruginosa colonization. J Clin Lab Anal 2019e22908
    [Google Scholar]
  29. Emerson J, Rosenfeld M, McNamara S, Ramsey B, Gibson RL. Pseudomonas aeruginosa and other predictors of mortality and morbidity in young children with cystic fibrosis. Pediatr Pulmonol 2002; 34:91–100 [View Article][PubMed]
    [Google Scholar]
  30. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  31. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 2009; 6:343345 [View Article][PubMed]
    [Google Scholar]
  32. Schneider CA, Rasband WS, Eliceiri KW. Nih image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9:671–675 [View Article][PubMed]
    [Google Scholar]
  33. Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA et al. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Res 2016; 44:D646–D653 [View Article][PubMed]
    [Google Scholar]
  34. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped blast and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article][PubMed]
    [Google Scholar]
  35. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  36. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database.. J Bioinformatics 2018
    [Google Scholar]
  37. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: the United States department of energy systems biology Knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article][PubMed]
    [Google Scholar]
  38. Liu M, Li X, Xie Y, Bi D, Sun J et al. Iceberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 2019; 47:D660–D665 [View Article][PubMed]
    [Google Scholar]
  39. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  40. King E. Isolate-Search. GitHub 2018
    [Google Scholar]
  41. Okonechnikov K, Golosova O, Fursov M. UGENE team Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012; 28:1166–1167 [View Article][PubMed]
    [Google Scholar]
  42. Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics 2010; 26:680–682 [View Article][PubMed]
    [Google Scholar]
  43. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992; 8:275–282 [View Article][PubMed]
    [Google Scholar]
  44. Kumar TA. CFSSP: Chou and Fasman secondary structure prediction server. J Wide Spectrum 2013; 1:15–19
    [Google Scholar]
  45. Yang J, Zhang Y. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 2015; 43:W174–W181 [View Article][PubMed]
    [Google Scholar]
  46. DeLano WL. Pymol: an open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography 2002; 40:82–92
    [Google Scholar]
  47. Pond SLK, Muse SV. HyPhy: hypothesis testing using phylogenies. Statistical Methods in Molecular Evolution Springer; 2005 pp 125–181
    [Google Scholar]
  48. Woodman M. Direct PCR of intact bacteria (colony PCR). Curr Protoc Microbiol 2008; 9:A. 3D. 1-A. 3D. 6A.3D.6 [View Article]
    [Google Scholar]
  49. Slack FJ, Ruvkun G. A novel repeat domain that is often associated with ring finger and B-box motifs. Trends Biochem Sci 1998; 23:474–475 [View Article][PubMed]
    [Google Scholar]
  50. Kawalek A, Kotecka K, Modrzejewska M, Gawor J, Jagura-Burdzy G et al. Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element. BMC Genomics 2020; 21:14 [View Article][PubMed]
    [Google Scholar]
  51. Lotlikar SR, Hnatusko S, Dickenson NE, Choudhari SP, Picking WL et al. Three functional β-carbonic anhydrases in Pseudomonas aeruginosa PAO1: role in survival in ambient air. Microbiology 2013; 159:1748–1759 [View Article][PubMed]
    [Google Scholar]
  52. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF et al. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res 2013; 41:D991–D995 [View Article][PubMed]
    [Google Scholar]
  53. Chen CK-M, Chan N-L, Wang AH-J. The many blades of the β-propeller proteins: conserved but versatile. Trends Biochem Sci 2011; 36:553–561 [View Article][PubMed]
    [Google Scholar]
  54. Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E et al. Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain. Hum Mol Genet 2016; 25:927–935 [View Article][PubMed]
    [Google Scholar]
  55. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 2000; 406:959–964 [View Article][PubMed]
    [Google Scholar]
  56. He J, Baldini RL, Déziel E, Saucier M, Zhang Q et al. The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc Natl Acad Sci U S A 2004; 101:2530–2535 [View Article][PubMed]
    [Google Scholar]
  57. Silo-Suh LA, Suh S-J, Ohman DE, Wozniak DJ, Pridgeon JW. Complete genome sequence of Pseudomonas aeruginosa mucoid strain FRD1, Isolated from a cystic fibrosis patient. Genome Announc 2015; 3:e00153–00115 [View Article][PubMed]
    [Google Scholar]
  58. Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA et al. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2005; 23:873–878 [View Article][PubMed]
    [Google Scholar]
  59. Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK et al. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 2012; 8:e1002784 [View Article][PubMed]
    [Google Scholar]
  60. Biessy A, Novinscak A, Blom J, Léger G, Thomashow LS et al. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environ Microbiol 2019; 21:437–455 [View Article][PubMed]
    [Google Scholar]
  61. Wang X, Mavrodi DV, Ke L, Mavrodi OV, Yang M et al. Biocontrol and plant growth-promoting activity of rhizobacteria from Chinese fields with contaminated soils. Microb Biotechnol 2015; 8:404–418 [View Article][PubMed]
    [Google Scholar]
  62. Mavrodi DV, Ksenzenko VN, Bonsall RF, Cook RJ, Boronin AM et al. A seven-gene locus for synthesis of phenazine-1-carboxylic acid by Pseudomonas fluorescens 2-79. J Bacteriol 1998; 180:2541–2548 [View Article][PubMed]
    [Google Scholar]
  63. Lotlikar SR, Gallaway E, Grant T, Popis S, Whited M et al. Polymeric composites with silver (I) Cyanoximates inhibit biofilm formation of gram-positive and gram-negative bacteria. Polymers 2019; 11:1018 09 Jun 2019 [View Article][PubMed]
    [Google Scholar]
  64. Relman DA, Schmidt TM, MacDermott RP, Falkow S. Identification of the uncultured bacillus of Whipple's disease. N Engl J Med 1992; 327:293–301 [View Article][PubMed]
    [Google Scholar]
  65. Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 1999; 46:327–338 [View Article][PubMed]
    [Google Scholar]
  66. Sievers F, Higgins DG. Clustal omega, accurate alignment of very large numbers of sequences. Methods Mol Biol 2014; 1079:105–116 [View Article][PubMed]
    [Google Scholar]
  67. Yang J, Yan R, Roy A, Xu D, Poisson J et al. The I-TASSER suite: protein structure and function prediction. Nat Methods 2015; 12:78 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.001004
Loading
/content/journal/micro/10.1099/mic.0.001004
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error