Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance

BMC Microbiology

Christopher J Marx¹  Katherine S Xue³  Sean Michael Carroll² 

[1] Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA, USA;Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA;Chemical and Physical Biology, Harvard College, Cambridge, MA, USA

关键词: Strain integrity;    Whole-genome sequencing;    Rifamycin;    Antibiotic resistance;    Methylobacterium extorquens AM1;    Laboratory domestication;   

Others  :  1142191
DOI  :  10.1186/1471-2180-14-2

 received in 2013-08-15, accepted in 2013-12-16,  发布年份 2014

【 摘 要 】

Background

A common assumption of microorganisms is that laboratory stocks will remain genetically and phenotypically constant over time, and across laboratories. It is becoming increasingly clear, however, that mutations can ruin strain integrity and drive the divergence or “domestication” of stocks. Since its discovery in 1960, a stock of Methylobacterium extorquens AM1 (“AM1”) has remained in the lab, propagated across numerous growth and storage conditions, researchers, and facilities. To explore the extent to which this lineage has diverged, we compared our own “Modern” stock of AM1 to a sample archived at a culture stock center shortly after the strain’s discovery. Stored as a lyophilized sample, we hypothesized that this Archival strain would better reflect the first-ever isolate of AM1 and reveal ways in which our Modern stock has changed through laboratory domestication or other means.

Results

Using whole-genome re-sequencing, we identified some 29 mutations – including single nucleotide polymorphisms, small indels, the insertion of mobile elements, and the loss of roughly 36 kb of DNA - that arose in the laboratory-maintained Modern lineage. Contrary to our expectations, Modern was both slower and less fit than Archival across a variety of growth substrates, and showed no improvement during long-term growth and storage. Modern did, however, outperform Archival during growth on nutrient broth, and in resistance to rifamycin, which was selected for by researchers in the 1980s. Recapitulating selection for rifamycin resistance in replicate Archival populations showed that mutations to RNA polymerase B (rpoB) substantially decrease growth in the absence of antibiotic, offering an explanation for slower growth in Modern stocks. Given the large number of genomic changes arising from domestication (28), it is somewhat surprising that the single other mutation attributed to purposeful laboratory selection accounts for much of the phenotypic divergence between strains.

Conclusions

These results highlight the surprising degree to which AM1 has diverged through a combination of unintended laboratory domestication and purposeful selection for rifamycin resistance. Instances of strain divergence are important, not only to ensure consistency of experimental results, but also to explore how microbes in the lab diverge from one another and from their wild counterparts.

【 授权许可】

   
2014 Carroll et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Stanley NR, Lazazzera BA: Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-gamma-dl-glutamic acid production and biofilm formation. Mol Microbiol 2005, 57:1143-1158.
• [2]Kearns DB, Losick R: Swarming motility in undomesticated Bacillus subtilis. Mol Microbiol 2003, 49:581-590.
• [3]Branda SS, González-Pastor JE, Ben-Yehuda S, Losick R, Kolter R: Fruiting body formation by Bacillus subtilis. Proc Natl Acad Sci U S A 2001, 98:11621-11626.
• [4]Eisenstark A: Genetic diversity among offspring from archived Salmonella enterica ssp. enterica Serovar Typhimurium (Demerec Collection): In search of survival strategies. Annu Rev Microbiol 2010, 64:277-292.
• [5]Liu G-R, Edwards K, Eisenstark A, Fu Y-M, Liu W-Q, Sanderson KE, Johnston RN, Liu S-L: Genomic diversification among archival strains of Salmonella enterica serovar typhimurium LT7. J Bacteriol 2003, 185:2131-2142.
• [6]Faure D, Frederick R, Wloch D, Portier P, Blot M, Adams J: Genomic changes arising in long-term stab cultures of Escherichia coli. J Bacteriol 2004, 186:6437-6442.
• [7]Naas T, Blot M, Fitch WM, Arber W: Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 1994, 136:721-730.
• [8]Naas T, Blot M, Fitch WM, Arber W: Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol Biol Evol 1995, 12:198-207.
• [9]Davidson CJ, White AP, Surette MG: Evolutionary loss of the rdar morphotype in Salmonella as a result of high mutation rates during laboratory passage. ISME J 2008, 2:293-307.
• [10]Spira B, de Almeida Toledo R, Maharjan RP, Ferenci T: The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example. BMC Microbiol 2011, 11:248. BioMed Central Full Text
• [11]Eydallin G, Ryall B, Maharjan R, Ferenci T: The nature of laboratory domestication changes in freshly isolated Escherichia coli strains. Environ Microbiol 2013. doi:10.1111/1462-2920.12208
• [12]Bachmann H, Starrenburg MJC, Molenaar D, Kleerebezem M, van Hylckama Vlieg JET: Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res 2012, 22:115-124.
• [13]Kuthan M, Devaux F, Janderová B, Slaninová I, Jacq C, Palková Z: Domestication of wild Saccharomyces cerevisiae is accompanied by changes in gene expression and colony morphology. Mol Microbiol 2003, 47:745-754.
• [14]Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M: Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One 2010, 5:e13922.
• [15]McGrath PT, Xu Y, Ailion M, Garrison JL, Butcher RA, Bargmann CI: Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes. Nature 2011, 477:321-325.
• [16]Egan CM, Sridhar S, Wigler M, Hall IM: Recurrent DNA copy number variation in the laboratory mouse. Nat Genet 2007, 39:1384-1389.
• [17]Wiltshire T: Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proc Natl Acad Sci U S A 2003, 100:3380-3385.
• [18]Peel D, Quayle JR: Microbial growth on C1 compounds. 1. Isolation and characterization of Pseudomonas AM1. Biochem J 1961, 81:465.
• [19]Salem AR, Wagner C, Hacking AJ, Quayle JR: The metabolism of lactate and pyruvate by Pseudomonas AM1. J Gen Microbiol 1973, 76:375-388.
• [20]Chistoserdova L, Chen S-W, Lapidus A, Lidstrom ME: Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol 2003, 185:2980-2987.
• [21]Vuilleumier S, Chistoserdova L, Lee M-C, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, et al.: Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One 2009, 4:e5584.
• [22]Marx CJ, Lidstrom ME: Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 2002, 33:1062-1067.
• [23]Marx CJ: Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Research Notes 2008, 1:1. BioMed Central Full Text
• [24]Marx CJ, Lidstrom ME: Development of improved versatile broad-host-range vectors for use in methylotrophs and other Gram-negative bacteria. Microbiology 2001, 147:2065-2075.
• [25]Marx CJ, Lidstrom ME: Development of an insertional expression vector system for Methylobacterium extorquens AM1 and generation of null mutants lacking mtdA and/or fch. Microbiology 2004, 150:9-19.
• [26]Chubiz LM, Purswani J, Carroll SM, Marx CJ: A novel pair of inducible expression vectors for use in Methylobacterium extorquens. BMC Res Notes 2013, 6:183. BioMed Central Full Text
• [27]Delaney NF, Kaczmarek ME, Ward LM, Swanson PK, Lee M-C, Marx CJ: Development of an optimized medium, strain and high-throughput culturing methods for Methylobacterium extorquens. PLoS One 2013, 8:e62957.
• [28]Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais J-C: Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst Biol 2011, 5:189. BioMed Central Full Text
• [29]Skovran E, Crowther GJ, Guo X, Yang S, Lidstrom ME: A systems biology approach uncovers cellular strategies used by Methylobacterium extorquens AM1 during the switch from multi- to single-carbon growth. PLoS One 2010, 5:e14091.
• [30]Lee M-C, Chou H-H, Marx CJ: Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Evolution 2009, 63:2816-2830.
• [31]Chou H-H, Chiu H-C, Delaney NF, Segrè D, Marx CJ: Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 2011, 332:1190-1192.
• [32]Lee M-C, Marx CJ: Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet 2012, 8:e1002651.
• [33]Carroll SM, Marx CJ: Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology. PLoS Genet 2013, 9:e1003427.
• [34]Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, Mering Von C, Vorholt JA: Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 2009, 106:16428-16433.
• [35]Knief C, Frances L, Vorholt JA: Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb Ecol 2010, 60:440-452.
• [36]Jourand P, Giraud E, Béna G, Sy A, Willems A, Gillis M, Dreyfus B, de Lajudie P: Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Microbiol 2004, 54:2269-2273.
• [37]Van Aken B, Peres CM, Doty SL, Yoon JM, Schnoor JL: Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34). Int J Syst Evol Microbiol 2004, 54:1191-1196.
• [38]Doronina NV, Sokolov AP, Trotsenko YA: Isolation and initial characterization of aerobic chloromethane-utilizing bacteria. FEMS Microbiol Lett 1996, 142:179-183.
• [39]Gälli R, Leisinger T: Specialized bacterial strains for the removal of dichloromethane from industrial waste. Conservation & Recycling 1985, 8:91-100.
• [40]Alber BE: Biotechnological potential of the ethylmalonyl-CoA pathway. Appl Microbiol Biotechnol 2011, 89:17-25.
• [41]Schrader J, Schilling M, Holtmann D, Sell D, Filho MV, Marx A, Vorholt JA: Methanol-based industrial biotechnology: current status and future perspectives of methylotrophic bacteria. Trends Biotechnol 2009, 27:107-115.
• [42]Quayle J, Peel D: Methanol and carbon dioxide incorporation by Pseudomonas sp. AM1. Biochem J 1960, 76:3P.
• [43]Marx CJ, Bringel F, Chistoserdova L, Moulin L, Farhan Ul Haque M, Fleischman DE, Gruffaz C, Jourand P, Knief C, Lee M-C, Muller EEL, Nadalig T, Peyraud R, Roselli S, Russ L, Goodwin LA, Ivanova N, Kyrpides N, Lajus A, Land ML, Médigue C, Mikhailova N, Nolan M, Woyke T, Stolyar S, Vorholt JA, Vuilleumier S: Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol 2012, 194:4746-4748.
• [44]Delaney NF, Rojas Echenique JI, Marx CJ: Clarity: an open-source manager for laboratory automation. J Lab Autom 2013, 18:171-177.
• [45]Fulton GL, Nunn DN, Lidstrom ME: Molecular cloning of a malyl coenzyme A lyase gene from Pseudomonas sp. strain AM1, a facultative methylotroph. J Bacteriol 1984, 160:718-723.
• [46]Andersson DI: The biological cost of mutational antibiotic resistance: any practical conclusions? Curr Opin Microbiol 2006, 9:461-465.
• [47]Floss HG, Yu T-W: Rifamycin: mode of action, resistance, and biosynthesis. Chem Rev 2005, 105:621-632.
• [48]Goodwin PM, Piercy R, Stone S: The increased sensitivity of rifamycin-resistant mutants of Methylobacterium AM1 to a variety of antimicrobial agents. Lett Appl Microbiol 1988, 7:99-101.
• [49]Schrag SJ, Perrot V, Levin BR: Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc Biol Sci 1997, 264:1287-1291.
• [50]Stieglitz B, Mateles RI: Methanol metabolism in pseudomonad C. J Bacteriol 1973, 114:390-398.
• [51]Finkel SE: Long-term survival during stationary phase: evolution and the GASP phenotype. Nat Rev Micro 2006, 4:113-120.
• [52]Chou H-H, Berthet J, Marx CJ: Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genet 2009, 5:e1000652.
• [53]Leiby N, Harcombe WR, Marx CJ: Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose. BMC Evol Biol 2012, 12:1-1. BioMed Central Full Text
• [54]O’Keefe KJ, Morales NM, Ernstberger H, Benoit G, Turner PE: Laboratory-dependent bacterial ecology: a cautionary tale. Appl Environ Microbiol 2006, 72:3032-3035.
• [55]Agashe D, Martinez-Gomez NC, Drummond DA, Marx CJ: Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Mol Biol Evol 2013, 30:549-560.
• [56]Chou H-H, Marx CJ: Optimization of gene expression through divergent mutational paths. Cell Reports 2012, 1:133-140.
• [57]Wilson K: Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol 2001. 00:2.4.1–2.4.5
• [58]Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF: Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 2009, 461:1243-1247.
• [59]Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Meth 2012, 9:357-359.
• [60]Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I: ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19:1117-1123.
• [61]Geneious version 6.1.6, created by Biomatters. http://www.geneious.com webcite
• [62]Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C: MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 2013, 41(Database issue):D636-D647.