Ilinov A., Nishiyama A., Namba H., Fukushima Y., Takihara H., Nakajima C., Savitskaya A., Gebretsadik G., Hakamata M., Ozeki Y., Tateishi Y., Okuda S., Suzuki Y., Vinnik Y.S., Matsumoto S.
Department of Bacteriology, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata 951-9510, Japan; Department of General Surgery Named Professor M.I. Gulman, Professor V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1, P. Zheleznyaka str., Krasnoyarsk, 660022, Russian Federation; Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, 011-0020, Japan; International Collaboration Unit, Hokkaido University Research Center for Zoonosis Control, Sapporo, 011-0020, Japan; Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan; Division of Bioinformatics, Niigata University School of Medicine, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata 951-9510, Japan; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russian Federation; Department of Respiratory Medicine and Infectious Disease, Niigata Graduate School of Medical and Dental Sciences, 1-757, Asahimachi-Dori, Chuo-ku, Niigata, Niigata 951-9510, Japan; Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, 60115, Indonesia
DNA is basically an intracellular molecule that stores genetic information and carries instructions for growth and reproduction in all cellular organisms. However, in some bacteria, DNA has additional roles outside the cells as extracellular DNA (eDNA), which is an essential component of biofilm formation and hence antibiotic tolerance. Mycobacteria include life-threating human pathogens, most of which are slow growers. However, little is known about the nature of pathogenic mycobacteria’s eDNA. Here we found that eDNA is present in slow-growing mycobacterial pathogens, such as Mycobacterium tuberculosis, M. intracellulare, and M. avium at exponential growth phase. In contrast, eDNA is little in all tested rapid-growing mycobacteria. The physiological impact of disrupted eDNA on slow-growing mycobacteria include reduced pellicle formation, floating biofilm, and enhanced susceptibility to isoniazid and amikacin. Isolation and sequencing of eDNA revealed that it is identical to the genomic DNA in M. tuberculosis and M. intracellulare. In contrast, accumulation of phage DNA in eDNA of M. avium, suggests that the DNA released differs among mycobacterial species. Our data show important functions of eDNA necessary for biofilm formation and drug tolerance in slow-growing mycobacteria. © 2021, The Author(s).
Publisher: Nature Research
Volume 11, Issue 1, Art No 10953, Page – , Page Count
Journal Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85106920198&doi=10.1038%2fs41598-021-90156-z&partnerID=40&md5=03c493b12096e05067e294e6681bc550
Type: All Open Access, Gold, Green
Catlin, B.W., Extracellular deoxyribonucleic acid of bacteria and a deoxyribonuclease inhibitor (1956) Science (80-), 124, pp. 441-442. , COI: 1:CAS:528:DyaG2sXitlKh; Antonova, E.S., Hammer, B.K., Genetics of natural competence in Vibrio cholerae and other Vibrios (2015) Microbiol. Spectr., 3, pp. 1-18; Vilain, S., Pretorius, J.M., Theron, J., Brözel, V.S., DNA as an adhesin: Bacillus cereus requires extracellular DNA to form biofilms (2009) Appl. Environ. Microbiol., 75, pp. 2861-2868. , COI: 1:CAS:528:DC%2BD1MXlvFWhsrk%3D; Whitchurch, C.B., Tolker-Nielsen, T., Ragas, P.C., Mattick, J.S., Extracellular DNA required for bacterial biofilm formation (2002) Science (80-), 295, p. 1487. , COI: 1:CAS:528:DC%2BD38XhsFyqsrk%3D; Wesley Catlin, B., Interspecific transformation of neisseria by culture slime containing deoxyribonucleate (1960) Science (80-), 131, pp. 608-610; Allesen-Holm, M., A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms (2006) Mol. Microbiol., 59, pp. 1114-1128. , COI: 1:CAS:528:DC%2BD28XislWhsr4%3D; Hamilton, H.L., Domínguez, N.M., Schwartz, K.J., Hackett, K.T., Dillard, J.P., Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system (2005) Mol. Microbiol., 55, pp. 1704-1721. , COI: 1:CAS:528:DC%2BD2MXivVaks7w%3D; Toyofuku, M., Environmental factors that shape biofilm formation (2016) Biosci. Biotechnol. Biochem., 80, pp. 7-12. , COI: 1:CAS:528:DC%2BC2MXhtVygur%2FK; Flores-Valdez, M.A., Vaccines directed against microorganisms or their products present during biofilm lifestyle: Can we make a translation as a broad biological model to tuberculosis? (2016) Front. Microbiol., 7 (1-15); Bayles, K.W., The biological role of death and lysis in biofilm development (2007) Nat. Rev. Microbiol., 5, pp. 721-726. , COI: 1:CAS:528:DC%2BD2sXptFyrsrY%3D; Hall, C.W., Mah, T.F., Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria (2017) FEMS Microbiol. Rev., 41, pp. 276-301. , COI: 1:CAS:528:DC%2BC1cXhvV2nu73K; Allocati, N., Masulli, M., Di Ilio, C., De Laurenzi, V., Die for the community: An overview of programmed cell death in bacteria (2015) Cell Death Dis., 6, p. e1609. , COI: 1:CAS:528:DC%2BC2MXhsVeit7c%3D; Baskin, H., Bayrakal, V., Bahar, I.H., Effects of gentamicin, amikacin and netilmicin on the pathogenic factors and two extracellular quorum sensing systems of Pseudomonas aeruginosa strains (2012) Turkiye Klin. J. Med. Sci., 32, pp. 1319-1326. , COI: 1:CAS:528:DC%2BC38XhvFSgtLbK; Singh, S., Singh, S.K., Chowdhury, I., Singh, R., Understanding the mechanism of bacterial biofilms resistance to antimicrobial agents (2017) Open Microbiol. J., 11, pp. 53-62. , COI: 1:CAS:528:DC%2BC1cXmvVyqtb0%3D; Adelberg, E.A., Pittard, J., Chromosome transfer in bacterial conjugation (1965) Bacteriol. Rev., 29, pp. 161-172. , COI: 1:CAS:528:DyaF2MXksVSrtLk%3D; Tuberculosis, , https://www.who.int/news-room/fact-sheets/detail/tuberculosis; Xiang, X., Deng, W., Liu, M., Xie, J., Mycobacterium biofilms: Factors involved in development, dispersal, and therapeutic strategies against biofilm-relevant pathogens (2014) Crit. Rev. Eukaryot. Gene Expr., 24, pp. 269-279. , COI: 1:CAS:528:DC%2BC2cXhsFertrnK; Esteban, J., García-Coca, M., Mycobacterium biofilms (2018) Front. Microbiol., 8, p. 2651; Aung, T.T., Biofilms of pathogenic nontuberculous mycobacteria targeted by new therapeutic approaches (2016) Antimicrob. Agents Chemother., 60, pp. 24-35. , COI: 1:CAS:528:DC%2BC28XhtVCit7zN; Basaraba, R.J., Ojha, A.K., (2017) Mycobacterial biofilms: Revisiting tuberculosis bacilli in extracellular necrotizing lesions, pp. 533-539. , Tuberculosis and the Tubercle Bacillus, ASM Press; Falkinham, J.O., Nontuberculous mycobacteria in the environment (2002) Clin. Chest Med., 23, pp. 529-551; Schulze-Röbbecke, R., Janning, B., Fischeder, R., Occurrence of mycobacteria in biofilm samples (1992) Tuber. Lung Dis., 73, pp. 141-144; Yamazaki, Y., Danelishvili, L., Wu, M., MacNab, M., Bermudez, L.E., Mycobacterium avium genes associated with the ability to form a biofilm (2006) Appl. Environ. Microbiol., 72, pp. 819-825. , COI: 1:CAS:528:DC%2BD28XmtFegug%3D%3D; Rose, S.J., Babrak, L.M., Bermudez, L.E., Mycobacterium avium possesses extracellular DNA that contributes to biofilm formation, structural integrity, and tolerance to antibiotics (2006) PLoS ONE., 10, pp. 1-17; Totani, T., Effects of nutritional and ambient oxygen condition on biofilm formation in Mycobacterium avium subsp. Hominissuis via altered glycolipid expression (2017) Sci. Rep., 7, pp. 1-12; Zambrano, M.M., Kolter, R., Mycobacterial biofilms: A greasy way to hold it together (2005) Cell, 123, pp. 762-764. , COI: 1:CAS:528:DC%2BD2MXhtlWntLjM; Ojha, A.K., Growth of Mycobacterium tuberculosis biofilms containing free mycolic acids and harbouring drug-tolerant bacteria (2008) Mol. Microbiol., 69, pp. 164-174. , COI: 1:CAS:528:DC%2BD1cXotF2iu7w%3D; Recht, J., Kolter, R., Glycopeptidolipid acetylation affects sliding motility and biofilm formation in Mycobacterium smegmatis (2001) J. Bacteriol., 183, pp. 5718-5724. , COI: 1:CAS:528:DC%2BD3MXmvF2msLg%3D; Nishiuchi, Y., The recovery of Mycobacterium avium-intracellulare complex (MAC) from the residential bathrooms of patients with pulmonary MAC (2007) Clin. Infect. Dis., 45, pp. 347-351. , COI: 1:CAS:528:DC%2BD2sXptVKqsbo%3D; Barnes, A.M.T., Ballering, K.S., Leibman, R.S., Wells, C.L., Dunnya, G.M., Enterococcus faecalis produces abundant extracellular structures containing DNA in the absence of cell lysis during early biofilm formation (2012) MBio, 3, pp. 1-9; Rose, S.J., Bermudez, L.E., Identification of bicarbonate as a trigger and genes involved with extracellular DNA export in mycobacterial biofilms (2016) MBio, 7, pp. 11-19; SYTOX® Green Nucleic Acid Stain (2006); (2010) Calcein Violet, AM, pp. 1-4; Hendon-Dunn, C.L., A flow cytometry method for rapidly assessing Mycobacterium tuberculosis responses to antibiotics with different modes of action (2016) Antimicrob. Agents Chemother., 60, pp. 3869-3883. , COI: 1:CAS:528:DC%2BC28XhvFSjtb7P; Fan, X., Xie, L., Li, W., Xie, J., Prophage-like elements present in Mycobacterium genomes (2014) BMC Genomics., 15, pp. 1-11; Lahiri, A., Sanchini, A., Semmler, T., Schäfer, H., Lewin, A., Identification and comparative analysis of a genomic island in Mycobacterium avium subsp. hominissuis (2014) FEBS Lett., 588 (21), pp. 3906-3911. , COI: 1:CAS:528:DC%2BC2cXhsFCitrvJ; Howe, K.L., Ensembl Genomes 2020-enabling non-vertebrate genomic research (2020) Nucleic Acids Res., 48, pp. D689-D695. , COI: 1:CAS:528:DC%2BB3cXhslWltrvP; Ghatak, S., Muthukumaran, R.B., Nachimuthu, S.K., A simple method of genomic DNA extraction from human samples for PCR-RFLP analysis (2013) J. Biomol. Tech., 24, pp. 224-231. , PID: 24294115; Li, H., The Sequence Alignment/Map format and SAMtools (2009) Bioinformatics, 25, pp. 2078-2079; Li, H., Durbin, R., Fast and accurate long-read alignment with Burrows–Wheeler transform (2010) Bioinformatics, 26, pp. 589-595; Liao, Y., Smyth, G.K., Shi, W., FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features (2014) Bioinformatics, 30, pp. 923-930. , COI: 1:CAS:528:DC%2BC2cXltFGqu7c%3D
Indexed by Scopus