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Natural Selection in Virulence Genes of Francisella tularensis

Abstract

A fundamental tenet of evolution is that alleles that are under negative selection are often deleterious and confer no evolutionary advantage. Negatively selected alleles are removed from the gene pool and are eventually extinguished from the population. Conversely, alleles under positive selection do confer an evolutionary advantage and lead to an increase in the overall fitness of the organism. These alleles increase in frequency until they eventually become fixed in the population. Francisella tularensis is a zoonotic pathogen and a potential biothreat agent. The most virulent type of F. tularensis, Type A, is distributed across North America with Type A.I occurring mainly in the east and Type A.II appearing mainly in the west. F. tularensis is thought to be a genome in decay (losing genes) because of the relatively large number of pseudogenes present in its genome. We hypothesized that the observed frequency of gene loss/pseudogenes may be an artifact of evolution in response to a changing environment, and that genes involved in virulence should be under strong positive selection. To test this hypothesis, we sequenced and compared whole genomes of Type A.I and A.II isolates. We analyzed a subset of virulence and housekeeping genes from several F. tularensis subspecies genomes to ascertain the presence and extent of positive selection. Eleven previously identified virulence genes were screened for positive selection along with 10 housekeeping genes. Analyses of selection yielded one housekeeping gene and 7 virulence genes which showed significant evidence of positive selection at loci implicated in cell surface structures and membrane proteins, metabolism and biosynthesis, transcription, translation and cell separation, and substrate binding and transport. Our results suggest that while the loss of functional genes through disuse could be accelerated by negative selection, the genome decay in Francisella could also be the byproduct of adaptive evolution driven by complex interactions between host, pathogen, and thier environment, as evidenced by several of its virulence genes which are undergoing strong, positive selection.

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References

  1. Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L (1998) The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme. J Mol Biol 284(2):401–419. doi:10.1006/jmbi.1998.2086

    CAS  Article  PubMed  Google Scholar 

  2. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O (2008) Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. Omics-a Journal of Integrative Biology 12(2):137–141. doi:10.1089/omi.2008.0017

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. Antwerpen M, Schacht E, Kaysser P, Splettstoesser W (2013) Complete genome sequence of a Francisella tularensis subsp. holarctica strain from Germany causing lethal infection in common marmosets. Genome Announc 1(1):e00135-12

    Article  PubMed  PubMed Central  Google Scholar 

  4. Barabote RD, Xie G, Brettin TS, Hinrichs SH, Fey PD, Jay JJ, Engle JL, Godbole SD, Noronha JM, Scheuermann RH, Zhou LW, Lion C, Dempsey MP (2009) Complete genome sequence of Francisella tularensis subspecies holarctica FTNF002-00. Plos One. doi:10.1371/journal.pone.0007041

    PubMed  PubMed Central  Google Scholar 

  5. Beckstrom-Sternberg SM, Auerbach RK, Godbole S, Pearson JV, Beckstrom-Sternberg JS, Deng ZM, Munk C, Kubota K, Zhou Y, Bruce D, Noronha J, Scheuermann RH, Wang AH, Hao J, Wang JJ, Wagner DM, Brettin TS, Brown N, Gilna P, Keim PS (2007) Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. Plos One. doi:10.1371/journal.pone.0000947

    Google Scholar 

  6. Broekhuijsen M, Larsson P, Johansson A, Bystrom M, Eriksson U, Larsson E, Prior R, Sjostedt A, Titball RW, Forsman M (2003) Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis. J Clin Microbiol 41(7):2924–2931

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Brown NF, Wickham ME, Coombes BK, Finlay BB (2006) Crossing the line: selection and evolution of virulence traits. PLoS Pathog 2(5):e42. doi:10.1371/journal.ppat.0020042

    Article  PubMed  PubMed Central  Google Scholar 

  8. Casadevall A, Pirofski LA (1999) Host-pathogen interactions: redefining the basic concepts of virulence and pathogenicity. Infect Immun 67(8):3703–3713

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Champion MD, Zeng QD, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, Young S, Koehrsen M, Engels R, Pearson M, Howarth C, Larson L, White J, Alvarado L, Forsman M, Bearden SW, Sjostedt A, Titball R, Michell SL, Birren B, Galagan J (2009) Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. Plos Pathogens. doi:10.1371/journal.ppat.1000459

    PubMed  PubMed Central  Google Scholar 

  10. Chaudhuri RR, Ren CP, Desmond L, Vincent GA, Silman NJ, Brehm JK, Elmore MJ, Hudson MJ, Forsman M, Isherwood KE, Gurycova D, Minton NP, Titball RW, Pallen MJ, Vipond R (2007) Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4. Plos One. doi:10.1371/journal.pone.0000352

    PubMed  PubMed Central  Google Scholar 

  11. Chiang SL, Mekalanos JJ, Holden DW (1999) In vivo genetic analysis of bacterial virulence. Annu Rev Microbiol 53:129–154. doi:10.1146/annurev.micro.53.1.129

    CAS  Article  PubMed  Google Scholar 

  12. Choi JS, Park NJ, Lim HK, Ko YK, Kim YS, Ryu SY, Hwang IT (2012) Plumbagin as a new natural herbicide candidate for Sicyon angulatus control agent with the target 8-amino-7-oxononanoate synthase. Pestic Biochem Physiol 103(3):166–172. doi:10.1016/j.pestbp.2012.04.007

    CAS  Article  Google Scholar 

  13. Chou PY, Fasman GD (1978) Empirical predictions of protein conformation. Annu Rev Biochem 47:251–276. doi:10.1146/annurev.bi.47.070178.001343

    CAS  Article  PubMed  Google Scholar 

  14. Crandall KA, Kelsey CR, Imamichi H, Lane HC, Salzman NP (1999) Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol 16(3):372–382

    CAS  Article  PubMed  Google Scholar 

  15. Demuth JP, Hahn MW (2009) The life and death of gene families. BioEssays 31(1):29–39. doi:10.1002/bies.080085

    Article  PubMed  Google Scholar 

  16. Dhanasekaran M, Negi S, Imanishi M, Suzuki M, Sugiura Y (2008) Effects of bulkiness and hydrophobicity of an aliphatic amino acid in the recognition helix of the GAGA zinc finger on the stability of the hydrophobic core and DNA binding affinity. Biochemistry 47(45):11717–11724. doi:10.1021/bi801306d

    CAS  Article  PubMed  Google Scholar 

  17. El-Etr SH, Margolis JJ, Monack D, Robison RA, Cohen M, Moore E, Rasley A (2009) Francisella tularensis Type A strains cause the rapid encystment of Acanthamoeba castellanii and survive in amoebal cysts for three weeks postinfection. Appl Environ Microbiol 75(23):7488–7500. doi:10.1128/aem.01829-09

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. Fay JC (2011) Weighing the evidence for adaptation at the molecular level. Trends Genet 27(9):343–349. doi:10.1016/j.tig.2011.06.003

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Feng Y, Chen Z, Liu SL (2011) Gene decay in Shigella as an incipient stage of host-adaptation. Plos One. doi:10.1371/journal.pone.0027754

    Google Scholar 

  20. Fraser ME, James MNG, Bridger WA, Wolodko WT (1999) A detailed structural description of Escherichia coli succinyl-CoA synthetase. J Mol Biol 285(4):1633–1653. doi:10.1006/jmbi.1998.2324

    CAS  Article  PubMed  Google Scholar 

  21. Gallagher LA, McKevitt M, Ramage ER, Manoil C (2008) Genetic dissection of the Francisella novicida restriction barrier. J Bacteriol 190(23):7830–7837. doi:10.1128/jb.01188-08

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. George MG (2005) In: David RB, Richard WC, George MG, Don JB, Noel RK, James TS (eds) Bergey’s Manual® of Systematic Bacteriology. Springer, Germany.

  23. Gestin B, Valade E, Thibault F, Schneider D, Maurin M (2010) Phenotypic and genetic characterization of macrolide resistance in Francisella tularensis subsp. holarctica biovar I. J Antimicrob Chemother 65(11):2359–2367. doi:10.1093/jac/dkq315

    CAS  Article  PubMed  Google Scholar 

  24. Grenha R, Levdikov VM, Fogg MJ, Blagova EV, Brannigan JA, Wilkinson AJ, Wilson KS (2005) Structure of purine nucleoside phosphorylase (DeoD) from Bacillus anthracis. Acta Crystallogr Sect F 61:459–462. doi:10.1107/s174430910501095x

    CAS  Article  Google Scholar 

  25. Gunnell MK, Lovelace CD, Satterfield BA, Moore EA, O’Neill KL, Robison RA (2012) A multiplex real-time PCR assay for the detection and differentiation of Francisella tularensis subspecies. J Med Microbiol 61(11):1525–1531. doi:10.1099/jmm.0.046631-0

    CAS  Article  PubMed  Google Scholar 

  26. Hain T, Chatterjee SS, Ghaia R, Kuenne CT, Billion A, Steinweg C, Domann E, Karst U, Jansch L, Wehland J, Eisenreich W, Bacherc A, Joseph B, Schar J, Kreft J, Klumpp J, Loessner MJ, Dorscht J, Neuhaus K, Fuchs TM, Scherer S, Doumith M, Jacquet C, Martin P, Cossart P, Rusniock C, Glaser P, Buchrieser C, Goebel W, Chakraborty T (2007) Pathogenomics of Listeria spp. Int J Med Microbiol 297(7–8):541–557. doi:10.1016/j.ijmm.2007.03.016

    CAS  Article  PubMed  Google Scholar 

  27. Harris SR, Robinson C, Steward KF, Webb KS, Paillot R, Parkhill J, Holden MTG, Waller AS (2015) Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection. Genome Res 25(9):1360–1371. doi:10.1101/gr.189803.115

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. Hasegawa M, Kishino H, Yano TA (1985) Dating of the human ape splitting by a molecular clock of mitochondrial-DNA. J Mol Evol 22(2):160–174. doi:10.1007/bf02101694

    CAS  Article  PubMed  Google Scholar 

  29. Hensel M, Shea JE, Gleeson C, Jones MD, Dalton E, Holden DW (1995) Simultaneous identification of bacterial virulence genes by negative selection. Science 269(5222):400–403. doi:10.1126/science.7618105

    CAS  Article  PubMed  Google Scholar 

  30. Hormoz S (2013) Amino acid composition of proteins reduces deleterious impact of mutations. Scientific Reports. doi:10.1038/srep02919

    PubMed  PubMed Central  Google Scholar 

  31. Johansson A, Farlow J, Larsson P, Dukerich M, Chambers E, Bystrom M, Fox J, Chu M, Forsman M, Sjostedt A, Keim P (2004) Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. J Bacteriol 186(17):5808–5818

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292(2):195–202. doi:10.1006/jmbi.1999.3091

    CAS  Article  PubMed  Google Scholar 

  33. Jones CL, Napier BA, Sampson TR, Llewellyn AC, Schroeder MR, Weiss DS (2012) Subversion of host recognition and defense systems by Francisella spp. Microbiol Mol Biol Rev 76(2):383–404. doi:10.1128/mmbr.05027-11

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Kaper JB (2005) Pathogenic Escherichia coli. Int J Med Microbiol 295(6–7):355–356. doi:10.1016/j.ijmm.2005.06.008

    Article  PubMed  Google Scholar 

  35. Keim P, Johansson A, Wagner DM (2007) Molecular epidemiology, evolution, and ecology of Francisella. Francisella Tularensis: Biology, Pathogenicity, Epidemiology, and Biodefense 1105:30–66. doi:10.1196/annals.1409.011

    CAS  Google Scholar 

  36. Kerbarh O, Campopiano DJ, Baxter RL (2006) Mechanism of alpha-oxoamine synthases: identification of the intermediate Claisen product in the 8-amino-7-oxononanoate synthase reaction. Chem Commun 1:60–62. doi:10.1039/b511837a

    Article  Google Scholar 

  37. Kone BC, Kuncewicz T, Zhang WZ, Yu ZY (2003) Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide. American Journal of Physiology-Renal Physiology 285(2):F178–F190. doi:10.1152/ajprenal.00048.2003

    CAS  Article  PubMed  Google Scholar 

  38. Lan T, Yang ZL, Yang X, Liu YJ, Wang XR, Zeng QY (2009) Extensive functional diversification of the Populus glutathione S-transferase supergene family. Plant Cell 21(12):3749–3766. doi:10.1105/tpc.109.070219

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2.0. Bioinformatics 23(21):2947–2948. doi:10.1093/bioinformatics/btm404

    CAS  Article  PubMed  Google Scholar 

  40. Larsson P, Oyston PCF, Chain P, Chu MC, Duffield M, Fuxelius HH, Garcia E, Halltorp G, Johansson D, Isherwood KE, Karp PD, Larsson E, Liu Y, Michell S, Prior J, Prior R, Malfatti S, Sjostedt A, Svensson K, Thompson N, Vergez L, Wagg JK, Wren BW, Lindler LE, Andersson SGE, Forsman M, Titball RW (2005) The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nat Genet 37(2):153–159. doi:10.1038/ng1499

    CAS  Article  PubMed  Google Scholar 

  41. Lory S, Strom MS (1997) Structure-function relationship of type-IV prepilin peptidase of Pseudomonas aeruginosa - A review. Gene 192(1):117–121. doi:10.1016/s0378-1119(96)00830-x

    CAS  Article  PubMed  Google Scholar 

  42. Luo W, Liu YP, Zhu XC, Zhao WJ, Huang L, Cai J, Xu ZN, Cen PL (2011) Cloning and characterization of purine nucleoside phosphorylase in Escherichia coli and subsequent ribavirin biosynthesis using immobilized recombinant cells. Enzyme and Microbial Technology 48(6–7):438–444. doi:10.1016/j.enzmictec.2011.03.008

    CAS  Article  PubMed  Google Scholar 

  43. Masri L, Branca A, Sheppard AE, Papkou A, Laehnemann D, Guenther PS, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels NK, Schulte RD, Kurtz J, Rosenstiel P, Telschow A, Bornberg-Bauer E, Schulenburg H (2015) Host-pathogen coevolution: the selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biol 13(6):e1002169. doi:10.1371/journal.pbio.1002169

    Article  PubMed  PubMed Central  Google Scholar 

  44. McClellan D, Ellison D (2010) Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software. Int J Bioinform Res Appl 6(2):120–133

    CAS  Article  PubMed  Google Scholar 

  45. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351(6328):652–654. doi:10.1038/351652a0

    CAS  Article  PubMed  Google Scholar 

  46. Merlin C, Gardiner G, Durand S, Masters M (2002) The Escherichia coli metD locus encodes an ABC transporter which includes Abc (MetN), YaeE (MetI), and YaeC (MetQ). J Bacteriol 184(19):5513–5517. doi:10.1128/jb.184.19.5513-5517.2002

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  47. Messer PW, Petrov DA (2013) Frequent adaptation and the McDonald–Kreitman test. Proc Natl Acad Sci USA 110(21):8615–8620. doi:10.1073/pnas.1220835110

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  48. Modise T, Ryder C, Mane SP, Bandara AB, Jensen RV, Inzana TJ (2012) Genomic comparison between a virulent type A1 strain of Francisella tularensis and its attenuated O-antigen mutant. J Bacteriol 194(10):2775-2776. doi:10.1128/JB.00152-12

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11(5):715–724

    CAS  PubMed  Google Scholar 

  50. Nalbantoglu U, Sayood K, Dempsey MP, Iwen PC, Francesconi SC, Barbote RD, Xie G, Brettin TS, Hinrichs SH, Fey PD (2010) Large direct repeats flank genomic rearrangements between a new clinical isolate of Francisella tularensis subsp. tularensis A1 and Schu S4. PLoS One 5(2):e9007. doi:10.1371/journal.pone.0009007

    Article  Google Scholar 

  51. Nandi T, Ong C, Singh AP, Boddey J, Atkins T, Sarkar-Tyson M, Essex-Lopresti AE, Chua HH, Pearson T, Kreisberg JF, Nilsson C, Ariyaratne P, Ronning C, Losada L, Ruan Y, Sung WK, Woods D, Titball RW, Beacham I, Peak I, Keim P, Nierman WC, Tan P (2010) A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog 6(4):e1000845. doi:10.1371/journal.ppat.1000845

    Article  PubMed  PubMed Central  Google Scholar 

  52. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York

    Google Scholar 

  53. Nudelman A, Marcovici-Mizrahi D, Nudelman A, Flint D, Wittenbach V (2004) Inhibitors of biotin biosynthesis as potential herbicides. Tetrahedron 60(8):1731–1748. doi:10.1016/j.tet.2003.12.047

    CAS  Article  Google Scholar 

  54. Owen CR, Lackman DB, Jellison WL, Buker EO, Bell JF (1964) Comparative studies of Francisella tularensis + Francisella novicida. J Bacteriol 87(3):000–676

    CAS  Google Scholar 

  55. Oyston PCF (2008) Francisella tularensis: unravelling the secrets of an intracellular pathogen. J Med Microbiol 57(8):921–930. doi:10.1099/jmm.0.2008/000653-0

    Article  PubMed  Google Scholar 

  56. Petrosino JF, Xiang Q, Karpathy SE, Jiang HY, Yerrapragada S, Liu YM, Gioia J, Hemphill L, Gonzalez A, Raghavan TM, Uzman A, Fox GE, Highlander S, Reichard M, Morton RJ, Clinkenbeard KD, Weinstock GM (2006) Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J Bacteriol 188(19):6977–6985. doi:10.1128/jb.00506-06

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  57. Pond SLK, Frost SDW (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22(5):1208–1222. doi:10.1093/molbev/msi105

    CAS  Article  Google Scholar 

  58. Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5):676–679. doi:10.1093/bioinformatics/bti079

    CAS  Article  PubMed  Google Scholar 

  59. Ponnuswamy PK, Prabhakaran M, Manavalan P (1980) Hydrophobic packing and spatial arrangement of amino-acid-residues in globular-proteins. Biochim Biophys Acta 623(2):301–316. doi:10.1016/0005-2795(80)90258-5

    CAS  Article  PubMed  Google Scholar 

  60. Prahhakaran M, Ponnuswamy PK (1979) The spatial distribution of physical, chemical, energetic and conformational properties of amino acid residues in globular proteins. J Theor Biol 80(4):485–504. doi:10.1016/0022-5193(79)90090-0

    Article  Google Scholar 

  61. Qu P-H, Chen S-Y, Scholz HC, Busse H-J, Gu Q, Kaempfer P, Foster JT, Glaeser SP, Chen C, Yang Z-C (2013) Francisella guangzhouensis sp nov., isolated from air-conditioning systems. Int J Syst Evol Microbiol 63:3628–3635. doi:10.1099/ijs.0.049916-0

    CAS  Article  PubMed  Google Scholar 

  62. Read AF (1994) The evolution of virulence. Trends Microbiol 2(3):73–76

    CAS  Article  PubMed  Google Scholar 

  63. Rohmer L, Fong C, Abmayr S, Wasnick M, Freeman TJL, Radey M, Guina T, Svensson K, Hayden HS, Jacobs M, Gallagher LA, Manoil C, Ernst RK, Drees B, Buckley D, Haugen E, Bovee D, Zhou Y, Chang J, Levy R, Lim R, Gillett W, Guenthener D, Kang A, Shaffer SA, Taylor G, Chen JZ, Gallis B, D’Argenio DA, Forsman M, Olson MV, Goodlett DR, Kaul R, Miller SI, Brittnacher MJ (2007) Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains. Genome Biology. doi:10.1186/gb-2007-8-6-r102

    PubMed  PubMed Central  Google Scholar 

  64. Santic M, Abu Kwaik Y (2013) Nutritional virulence of Francisella tularensis. Frontiers in Cellular and Infection Microbiology. doi:10.3389/fcimb.2013.00112

    PubMed  PubMed Central  Google Scholar 

  65. Santic M, Al-Khodor S, Abu Kwaik Y (2010) Cell biology and molecular ecology of Francisella tularensis. Cell Microbiol 12(2):129–139. doi:10.1111/j.1462-5822.2009.01400.x

    CAS  Article  PubMed  Google Scholar 

  66. Schunder E, Rydzewski K, Grunow R, Heuner K (2013) First indication for a functional CRISPR/Cas system in Francisella tularensis. Int J Med Microbiol 303(2):51–60. doi:10.1016/j.ijmm.2012.11.004

    CAS  Article  PubMed  Google Scholar 

  67. Sengupta D, Kundu S (2012) Do topological parameters of amino acids within protein contact networks depend on their physico-chemical properties? Physica A 391(17):4266–4278. doi:10.1016/j.physa.2012.03.034

    CAS  Article  Google Scholar 

  68. Sharp PM (1997) In search of molecular darwinism. Nature 385(6612):111–112. doi:10.1038/385111a0

    Article  PubMed  Google Scholar 

  69. Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR (2012) Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources. Bmc Genomics. doi:10.1186/1471-2164-13-422

    Google Scholar 

  70. Sjostedt A (2007) Tularemia: history, epidemiology, pathogen physiology, and clinical manifestations. Francisella Tularensis: Biology, Pathogenicity, Epidemiology, and Biodefense 1105:1–29. doi:10.1196/annals.1409.009

    Google Scholar 

  71. Sridhar S, Sharma A, Kongshaug H, Nilsen F, Jonassen I (2012) Whole genome sequencing of the fish pathogen Francisella noatunensis subsp orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity. Bmc Genomics. doi:10.1186/1471-2164-13-598

    PubMed  PubMed Central  Google Scholar 

  72. Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL (2002) pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J Bacteriol 184(15):4246–4258. doi:10.1128/jb.184.15.4246-4258.2002

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  73. Staples JE, Kubota KA, Chalcraft LG, Mead PS, Petersen JM (2006) Epidemiologic and molecular analysis of human tularemia, United States, 1964–2004. Emerg Infect Dis 12(7):1113–1118

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  74. Steele S, Brunton J, Ziehr B, Taft-Benz S, Moorman N, Kawula T (2013) Francisella tularensis harvests nutrients derived via ATG5-independent autophagy to support intracellular growth. Plos Pathogens. doi:10.1371/journal.ppat.1003562

    Google Scholar 

  75. Strom MS, Lory S (1993) Structure-function and biogenesis of the type-IV pili. Annu Rev Microbiol 47:565–596. doi:10.1146/annurev.micro.47.1.565

    CAS  Article  PubMed  Google Scholar 

  76. Strom MS, Nunn DN, Lory S (1993) A single bifunctional enzyme, PilD, catalyzes cleavage and N-methylation of proteins belonging to the type-IV pilin family. Proc Natl Acad Sci USA 90(6):2404–2408. doi:10.1073/pnas.90.6.2404

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  77. Su J, Yang J, Zhao D, Kawula TH, Banas JA, Zhang J-R (2007) Genome-wide identification of Francisella tularensis virulence determinants. Infect Immun 75(6):3089–3101. doi:10.1128/iai.01865-06

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  78. Sutera V, Levert M, Burmeister WP, Schneider D, Maurin M (2014) Evolution toward high-level fluoroquinolone resistance in Francisella species. J Antimicrob Chemother 69(1):101–110. doi:10.1093/jac/dkt321

    CAS  Article  PubMed  Google Scholar 

  79. Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16(10):1315–1328

    CAS  Article  PubMed  Google Scholar 

  80. Svensson K, Larsson P, Johansson D, Bystrom M, Forsman M, Johansson A (2005) Evolution of subspecies of Francisella tularensis. J Bacteriol 187(11):3903–3908

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  81. Svensson K, Sjodin A, Bystrom M, Granberg M, Brittnacher MJ, Rohmer L, Jacobs MA, Sims-Day EH, Levy R, Zhou Y, Hayden HS, Lim R, Chang J, Guenthener D, Kang A, Haugen E, Gillett W, Kaul R, Forsman M, Larsson P, Johansson A (2012) Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia. J Bacteriol 194(24):6965–6966. doi:10.1128/jb.01040-12

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  82. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. doi:10.1093/molbev/msr121

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  83. Taylor SD, de la Cruz KD, Porter ML, Whiting MF (2005) Characterization of the long-wavelength opsin from Mecoptera and Siphonaptera: does a flea see? Mol Biol Evol 22(5):1165–1174. doi:10.1093/molbev/msi110

    CAS  Article  PubMed  Google Scholar 

  84. Walshaw DL, Wilkinson A, Mundy M, Smith M, Poole PS (1997) Regulation of the TCA cycle and the general amino acid permease by overflow metabolism in Rhizobium leguminosarum. Microbiology-Uk 143:2209–2221

    CAS  Article  Google Scholar 

  85. Ward PN, Holden MTG, Leigh JA, Lennard N, Bignell A, Barron A, Clark L, Quail MA, Woodward J, Barrell BG, Egan SA, Field TR, Maskell D, Kehoe M, Dowson CG, Chanter N, Whatmore AM, Bentley SD, Parkhill J (2009) Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis. Bmc Genomics. doi:10.1186/1471-2164-10-54

    Google Scholar 

  86. Weiss DS, Brotcke A, Henry T, Margolis JJ, Chan K, Monack DM (2007) In vivo negative selection screen identifies genes required for Francisella virulence. Proc Natl Acad Sci USA 104(14):6037–6042. doi:10.1073/pnas.0609675104

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  87. Wolodko WT, Fraser ME, James MNG, Bridger WA (1994) The crystal-structure of cussinyl-CoA synthetase from Escherichia coli at 2.5 angstrom resolution. J Biol Chem 269(14):10883–10890

    CAS  PubMed  Google Scholar 

  88. Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA (2003) TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics 19(5):671–672. doi:10.1093/bioinformatics/btg043

    CAS  Article  PubMed  Google Scholar 

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Acknowledgments

We thank the Utah Department of Health and the New Mexico Department of Health for help in obtaining the isolates used in this study, and for the thoughtful and constructive criticisms of the anonymous reviewers. Dr. Angelo Madonna of Dugway Proving Ground provided expert guidance and assistance in completing this work.

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Correspondence to Mark K. Gunnell.

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Gunnell, M.K., Robison, R.A. & Adams, B.J. Natural Selection in Virulence Genes of Francisella tularensis . J Mol Evol 82, 264–278 (2016). https://doi.org/10.1007/s00239-016-9743-y

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Keywords

  • Francisella tularensis
  • Genome decay
  • Natural selection
  • TreeSAAP
  • Virulence