Heat degradation of eukaryotic and bacterial DNA: an experimental model for paleomicrobiology
© Nguyen-Hieu et al.; licensee BioMed Central Ltd. 2012
Received: 29 May 2012
Accepted: 12 September 2012
Published: 25 September 2012
Theoretical models suggest that DNA degradation would sharply limit the PCR-based detection of both eukaryotic and prokaryotic DNA within ancient specimens. However, the relative extent of decay of eukaryote and prokaryote DNA over time is a matter of debate. In this study, the murine macrophage cell line J774, alone or infected with Mycobacterium smegmatis bacteria, were killed after exposure to 90°C dry heat for intervals ranging from 1 to 48 h in order to compare eukaryotic cells, extracellular bacteria and intracellular bacteria. The sizes of the resulting mycobacterial rpo B and murine rpb 2 homologous gene fragments were then determined by real-time PCR and fluorescent probing.
The cycle threshold (Ct) values of PCR-amplified DNA fragments from J774 cells and the M. smegmatis negative controls (without heat exposure) varied from 26–33 for the J774 rpb 2 gene fragments and from 24–29 for M. smegmatis rpo B fragments. After 90°C dry heat incubation for up to 48 h, the Ct values of test samples increased relative to those of the controls for each amplicon size. For each dry heat exposure time, the Ct values of the 146-149-bp fragments were lower than those of 746-747-bp fragments. During the 4- to 24-h dry heat incubation, the non-infected J774 cell DNA was degraded into 597-bp rpb 2 fragments. After 48 h, however, only 450-bp rpb 2 fragments of both non-infected and infected J774 cells could be amplified. In contrast, the 746-bp rpo B fragments of M. smegmatis DNA could be amplified after the 48-h dry heat exposure in all experiments. Infected and non-infected J774 cell DNA was degraded more rapidly than M. smegmatis DNA after dry heat exposure (ANOVA test, p < 0.05).
In this study, mycobacterial DNA was more resistant to dry-heat stress than eukaryotic DNA. Therefore, the detection of large, experimental, ancient mycobacterial DNA fragments is a suitable approach for paleomicrobiological studies.
KeywordsAncient DNA DNA degradation Bacterial DNA Eukaryotic DNA Mycobacterium Real-time PCR
The seminal demonstration that nuclear DNA could be cloned from a 2,400-year-old Egyptian mummy  founded molecular paleontology and paleomicrobiology [2, 3]. However, the cumulative experience over the past few decades indicates that the detection of ancient DNA (aDNA) could be limited by DNA degradation influenced by pH and humidity of the burial site. Heat, ultraviolet rays and oxidative agents are also proposed to contribute to the alteration of the chemical nature of nucleic acid bases and the degradation of DNA in buried human and animal remains [4–8]. Based on theoretical models of DNA degradation [4, 9, 10], some authors have questioned the long-term stability of DNA and suspected that some paleomicrobiological detections may have resulted from the contamination of samples with modern DNA [5, 11]. Studies have demonstrated aDNA to be degraded into < 150-bp nuclear and < 400-bp mitochondrial fragments [12, 13]. Experimental models of DNA degradation have used purified DNA [14–16] because few studies have assessed the degradation of DNA within cells . Moreover, these early studies used eukaryotic DNA. Indeed, the potential degradation of prokaryotic aDNA was only extrapolated from the data obtained from eukaryotic aDNA without experimental validation. Some authors have proposed, however, that in ancient, buried specimens, bacterial DNA may be more resistant to decay over time than human DNA [18, 19]. In this study, we evaluated experimental DNA decay in both eukaryotic and prokaryotic cells.
Dry heat degradation of murine macrophage cell line J774 DNA and M. smegmatis DNA
Dry heat degradation of M. smegmatis-infected J774 cell DNA
The data presented in this manuscript can be interpreted as both authentic and biologically relevant. All blank controls used in our PCR-based experiments were negative. Additionally, the control cells not exposed to dry heat yielded the expected results. Macrophages and mycobacteria were exposed to dry heat in parallel, and the rpo B gene of mycobacteria was assessed in parallel with its homolog, the rpb 2 gene of murine macrophages. Reproducible results were observed across experiments performed in triplicate.
The dry heat used in this study has been used previously to assess experimental degradation of purified DNA [16, 17] and is the most common environmental agent that may cause DNA damage in dead cells. Thus, our experiments utilizing dry heat exposure mimic an accelerated natural DNA degradation process. Furthermore, in this study, dry heat was applied to cellular DNA rather than purified DNA. We verified that these conditions killed mycobacteria. However, the experimental design of the study did not allow us to rule out the hypothesis that viable non-culturable mycobacteria persisted into infected macrophages , possibly interfering with macrophage DNA degradation. Additionally, all previously published experiments have used agarose gel electrophoresis to monitor DNA degradation [14–17]. This method of evaluation is imprecise, as it relies on the visual observation of smears and only provides estimates as to the extent of DNA degradation. In our study, we used real-time PCR in combination with TaqMan® fluorescent probes to accurately monitor the size of PCR-amplifiable fragments of mycobacterial and eukaryotic DNA following exposure to heat stress. M. smegmatis was chosen because it has a lipid-rich cell wall similar to that of Mycobacterium tuberculosis, a pathogen previously investigated in paleomicrobiological studies [3, 18]. Furthermore, M. smegmatis-infected J774 cells were used as an experimental model with which to assess DNA degradation of obligate intracellular bacteria. This model of particular interest because Rickettsia prowazekii and Mycobacterium leprae, which are obligate intracellular bacteria, have been detected in ancient specimens [21–24]. Our studies assessing experimental and comparative degradation of cellular DNA in both bacteria and eukaryotic cells are the first in the literature.
Field observations, along with the experimental data presented here, suggest that mycobacterial DNA is more resistant than eukaryotic DNA to taphonomic degradation. Bacterial DNA fragmentation could be offset by DNA repair activities [35, 36]. The measurement of carbon dioxide release from bacteria embedded in permafrost for 500,000 years found that bacterial metabolic activity ensured survival and DNA repair capacity . Additionally, thick cell walls, like those of mycobacteria, could protect bacterial DNA from certain degrading agents [18, 19]. The dogma that ancient bacterial DNA is fragmented to an extent where only targets shorter than 200-bp can be detected  is not supported by either the experimental data or the high-throughput pyrosequencing observations. Large bacterial DNA fragments can be detected from ancient buried specimens without enzymatic reparation .
Culture of murine macrophage cell line J774 and M. smegmatis
The murine macrophage J774 (ATCC TIB 67) cells were cultured in GIBCO® 1X DMEM culture medium (Invitrogen, Carlsbad, USA) supplemented with 10% heat-decomplemented fetal calf serum (Seromed, Strasbourg, France) and 1% glutamine (Seromed) at 37°C with 5% CO2 for 3 days. M. smegmatis mc2 (ATCC 700084) was cultured in trypticase-soy-casein broth (European Pharmacopia IV, Strasbourg, France) supplemented with 0.5% Tween 80 (European Pharmacopia IV) at 37°C for 10 days. For the co-culture experiment, 1.8 mL of a 106 mycobacteria/mL suspension were incubated with 15 mL of a 105 J774 cells/mL suspension at 37°C under 5% CO2 atmosphere for 4 h. The infected J774 cell monolayer was then washed two times with 15 mL sterile phosphate buffered saline (PBS) before 15 mL fresh culture medium supplemented with 1% streptomycin (Panpharma, Fougères, France) was added for 2 h, eliminating any extracellular mycobacteria . The infected-cell monolayer was then washed two times with 15 mL sterile PBS before 15 mL of fresh culture medium was added. The monolayer was incubated at 37°C with 5% CO2 for 24 h. Infection of the J774 cell layer was monitored by Ziehl-Neelsen staining. The viability of M. smegmatis mycobacteria and J774 cells after one-hour incubation at 90°C was assessed by subculture as described above.
Experimental degradation of DNA
200 μL suspensions of 2.104 J774 cells/mL, 2.105 M. smegmatis/mL or 2.104 M. smegmatis-infected J774 cells/mL were incubated in parallel at 90°C in a dry heat incubator (Techne Dri-Block®, Staffordshire, UK) for 1, 2, 4, 8, 12, 24 or 48 h. All experiments were conducted in triplicate. The cell suspensions not exposed to dry heat were included as negative controls. The DNA was extracted by adding 0.3 g of 106-μm glass beads (Sigma Aldrich, Steinheim, Germany) to 200 μL J774 cells or to M. smegmatis or M. smegmatis-infected J774 cells in 1.5 mL Eppendorf tubes. The cell suspensions were homogenized in a FastPrep-24 Instrument (MP Biomedicals Europe) 3 times for 20 s at 4 m/s and were then centrifuged at 16,045 x g for 3 min. DNA extraction was then performed using the QIAamp® DNA Mini kit (Qiagen, Hilden, Germany) following a modified protocol. Briefly, 200 μL ATL buffer and 20 μL proteinase K were added to each cell tube. The cell suspensions were vortexed for 15 s and then incubated at 56°C for 45 min. The 420-μL supernatant was transferred to a new Eppendorf tube and mixed with 200 μL absolute ethanol by vortexing for 15 s. The 620-μL mixture was transferred to a NucleoSpin column, and all following steps were conducted according to the QIAamp® DNA Mini Kit protocol. The resulting DNA was diluted with 60 μL AE buffer.
Real-time PCR measurements
The value of the negative control (Ct0) was used as baseline. For each amplicon size, the DNA degradation was calibrated by Ctx – Ct0. The ANOVA test was used to compare the means of (Ctx – Ct0) values.
This study was supported by Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes.
- Paabo S: Molecular cloning of ancient Egyptian mummy DNA. Nature. 1985, 314: 644-645. 10.1038/314644a0.PubMedView ArticleGoogle Scholar
- Drancourt M, Raoult D: Palaeomicrobiology: current issues and perspectives. Nat Rev Microbiol. 2005, 3: 23-35. 10.1038/nrmicro1063.PubMedView ArticleGoogle Scholar
- Spigelman M, Lemma E: The use of the polymerase chain reaction (PCR) to detect mycobacterium tuberculosis in ancient skeletons. Int J Osteoarchaeol. 1993, 3: 137-143. 10.1002/oa.1390030211.View ArticleGoogle Scholar
- Lindahl T: Instability and decay of the primary structure of DNA. Nature. 1993, 362: 709-715. 10.1038/362709a0.PubMedView ArticleGoogle Scholar
- Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S: Ancient DNA. Nat Rev Genet. 2001, 2: 353-359.PubMedView ArticleGoogle Scholar
- Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC: Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res. 2007, 35: 1-10.PubMedPubMed CentralView ArticleGoogle Scholar
- Hofreiter M, Jaenicke V, Serre D, Haeseler AA, Paabo S: DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001, 29: 4793-4799. 10.1093/nar/29.23.4793.PubMedPubMed CentralView ArticleGoogle Scholar
- Willerslev E, Cooper A: Ancient DNA. Proc Biol Sci. 2005, 272: 3-16. 10.1098/rspb.2004.2813.PubMedPubMed CentralView ArticleGoogle Scholar
- Poinar HN, Hoss M, Bada JL, Paabo S: Amino acid racemization and the preservation of ancient DNA. Science. 1996, 272: 864-866. 10.1126/science.272.5263.864.PubMedView ArticleGoogle Scholar
- Smith CI, Chamberlain AT, Riley MS, Cooper A, Stringer CB, Collins MJ: Neanderthal DNA. Not just old but old and cold?. Nature. 2001, 410: 771-772.PubMedView ArticleGoogle Scholar
- Cooper A, Poinar HN: Ancient DNA: do it right or not at all. Science. 2000, 289: 1139-PubMedView ArticleGoogle Scholar
- Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM: New developments in ancient genomics. Trends Ecol Evol. 2008, 23: 386-393. 10.1016/j.tree.2008.04.002.PubMedView ArticleGoogle Scholar
- Paabo S: Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA. 1989, 86: 1939-1943. 10.1073/pnas.86.6.1939.PubMedPubMed CentralView ArticleGoogle Scholar
- Cataldo F: DNA degradation with ozone. Int J Biol Macromol. 2006, 38: 248-254. 10.1016/j.ijbiomac.2006.02.029.PubMedView ArticleGoogle Scholar
- Tanaka K, Okamoto A: Degradation of DNA by bisulfite treatment. Bioorgan Med Chem Lett. 2007, 17: 1912-1915. 10.1016/j.bmcl.2007.01.040.View ArticleGoogle Scholar
- Zhang L, Wu Q: Single gene retrieval from thermally degraded DNA. J Biosci. 2005, 30: 599-604. 10.1007/BF02703559.PubMedView ArticleGoogle Scholar
- Dobberstein RC, Huppertz J, von Wurmb-Schwark N, Ritz-Timme S: Degradation of biomolecules in artificially and naturally aged teeth: implications for age estimation based on aspartic acid racemization and DNA analysis. Forensic Sci Int. 2008, 179: 181-191. 10.1016/j.forsciint.2008.05.017.PubMedView ArticleGoogle Scholar
- Donoghue HD, Spigelman M, Greenblatt CL, Lev-Maor G, Bar-Gal GK, Matheson C, Vernon K, Nerlich AG, Zink AR: Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA. Lancet Infect Dis. 2004, 4: 584-592. 10.1016/S1473-3099(04)01133-8.PubMedView ArticleGoogle Scholar
- Zink AR, Reischl U, Wolf H, Nerlich AG: Molecular analysis of ancient microbial infections. FEMS Microbiol Lett. 2002, 213: 141-147. 10.1111/j.1574-6968.2002.tb11298.x.PubMedView ArticleGoogle Scholar
- Shleeva M, Mukamolova GV, Young M, Williams HD, Kaprelyants AS: Formation of 'non-culturable' cells of mycobacterium smegmatis in stationary phase in response to growth under suboptimal conditions and their Rpf-mediated resuscitation. Microbiology. 2004, 150: 1687-1697. 10.1099/mic.0.26893-0.PubMedView ArticleGoogle Scholar
- Donoghue HD, Marcsik A, Matheson C, Vernon K, Nuorala E, Molto JE, Greenblatt CL, Spigelman M: Co-infection of mycobacterium tuberculosis and mycobacterium leprae in human archaeological samples: a possible explanation for the historical decline of leprosy. Proc Biol Sci. 2005, 272: 389-394. 10.1098/rspb.2004.2966.PubMedPubMed CentralView ArticleGoogle Scholar
- Haas CJ, Zink A, Palfi G, Szeimies U, Nerlich AG: Detection of leprosy in ancient human skeletal remains by molecular identification of mycobacterium leprae. Am J Clin Pathol. 2000, 114: 428-436.PubMedGoogle Scholar
- Nguyen-Hieu T, Aboudharam G, Signoli M, Rigeade C, Drancourt M, Raoult D: Evidence of a louse-borne outbreak involving typhus in Douai, 1710–1712 during the war of Spanish succession. PLoS One. 2010, 5: e15405-10.1371/journal.pone.0015405.PubMedPubMed CentralView ArticleGoogle Scholar
- Raoult D, Dutour O, Houhamdi L, Jankauskas R, Fournier PE, Ardagna Y, Drancourt M, Signoli M, La VD, Macia Y, Aboudharam G: Evidence for louse-transmitted diseases in soldiers of Napoleon's grand army in Vilnius. J Infect Dis. 2006, 193: 112-120. 10.1086/498534.PubMedView ArticleGoogle Scholar
- Bianucci R, Rahalison L, Massa ER, Peluso A, Ferroglio E, Signoli M: Technical note: a rapid diagnostic test detects plague in ancient human remains: an example of the interaction between archeological and biological approaches (Southeastern France, 16th-18th centuries). Am J Phys Anthropol. 2008, 136: 361-367. 10.1002/ajpa.20818.PubMedView ArticleGoogle Scholar
- Drancourt M, Signoli M, Dang LV, Bizot B, Roux V, Tzortzis S, Raoult D: Yersinia pestis orientalis in remains of ancient plague patients. Emerg Infect Dis. 2007, 13: 332-333. 10.3201/eid1302.060197.PubMedPubMed CentralView ArticleGoogle Scholar
- Drancourt M, Aboudharam G, Signoli M, Dutour O, Raoult D: Detection of 400-year-old yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia. Proc Natl Acad Sci USA. 1998, 95: 12637-12640. 10.1073/pnas.95.21.12637.PubMedPubMed CentralView ArticleGoogle Scholar
- Drancourt M, Roux V, Dang LV, Tran-Hung L, Castex D, Chenal-Francisque V, Ogata H, Fournier PE, Crubezy E, Raoult D: Genotyping, orientalis-like yersinia pestis, and plague pandemics. Emerg Infect Dis. 2004, 10: 1585-1592. 10.3201/eid1009.030933.PubMedPubMed CentralView ArticleGoogle Scholar
- Drancourt M, Tran-Hung L, Courtin J, Lumley H, Raoult D: Bartonella quintana in a 4000-year-old human tooth. J Infect Dis. 2005, 191: 607-611. 10.1086/427041.PubMedView ArticleGoogle Scholar
- La VD, Clavel B, Lepetz S, Aboudharam G, Raoult D, Drancourt M: Molecular detection of bartonella henselae DNA in the dental pulp of 800-year-old French cats. Clin Infect Dis. 2004, 39: 1391-1394. 10.1086/424884.PubMedView ArticleGoogle Scholar
- Papagrigorakis MJ, Yapijakis C, Synodinos PN, Baziotopoulou-Valavani E: DNA examination of ancient dental pulp incriminates typhoid fever as a probable cause of the plague of Athens. Int J Infect Dis. 2006, 10: 206-214. 10.1016/j.ijid.2005.09.001.PubMedView ArticleGoogle Scholar
- Nguyen-Hieu T, Aboudharam G, Drancourt M: Mini review: dental pulp as a source for paleomicrobiology. Bull Int Assoc Paleodont. 2011, 5: 48-54.Google Scholar
- D'Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, Froese D, Zazula G, Calmels F, Debruyne R, Golding GB, Poinar HN, Wright GD: Antibiotic resistance is ancient. Nature. 2011, 477: 457-461. 10.1038/nature10388.PubMedView ArticleGoogle Scholar
- Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G, Krause J, Detter JC, Paabo S, Rubin EM: Genomic sequencing of pleistocene cave bears. Science. 2005, 309: 597-599. 10.1126/science.1113485.PubMedView ArticleGoogle Scholar
- Friedberg EC, Wagner R, Radman M: Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science. 2002, 296: 1627-1630. 10.1126/science.1070236.PubMedView ArticleGoogle Scholar
- Radman M: Fidelity and infidelity. Nature. 2001, 413: 115-10.1038/35093178.PubMedView ArticleGoogle Scholar
- Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, Brand T, Gilbert MT, Zuber MT, Bunce M, Ronn R, Gilichinsky D, Froese D, Willerslev E: Ancient bacteria show evidence of DNA repair. Proc Natl Acad Sci USA. 2007, 104: 14401-14405. 10.1073/pnas.0706787104.PubMedPubMed CentralView ArticleGoogle Scholar
- Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M: Genetic analyses from ancient DNA. Annu Rev Genet. 2004, 38: 645-679. 10.1146/annurev.genet.37.110801.143214.PubMedView ArticleGoogle Scholar
- Mitchell D, Willerslev E, Hansen A: Damage and repair of ancient DNA. Mutat Res. 2005, 571: 265-276. 10.1016/j.mrfmmm.2004.06.060.PubMedView ArticleGoogle Scholar
- Ren H, Liu J: AsnB is involved in natural resistance of mycobacterium smegmatis to multiple drugs. Antimicrob Agents Ch. 2006, 50: 250-255. 10.1128/AAC.50.1.250-255.2006.View ArticleGoogle Scholar
- Marshall OJ: PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics. 2004, 20: 2471-2472. 10.1093/bioinformatics/bth254.PubMedView ArticleGoogle Scholar