Abstract
Gluconacetobacter xylinus (formerly Acetobacter xylinum and presently Komagataeibacter medellinensis) is known to produce cellulose as a stable pellicle. However, it is also well known to lose this ability very easily. We investigated the on and off mechanisms of cellulose producibility in two independent cellulose-producing strains, R1 and R2. Both these strains were isolated through a repetitive static culture of a non-cellulose-producing K. medellinensis NBRC 3288 parental strain. Two cellulose synthase operons, types I and II, of this strain are truncated by the frameshift mutation in the bcsBI gene and transposon insertion in the bcsCII gene, respectively. The draft genome sequencing of R1 and R2 strains revealed that in both strains the bcsBI gene was restored by deletion of a nucleotide in its C-rich region. This result suggests that the mutations in the bcsBI gene are responsible for the on and off mechanism of cellulose producibility. When we looked at the genomic DNA sequences of other Komagataeibacter species, several non-cellulose-producing strains were found to contain similar defects in the type I and/or type II cellulose synthase operons. Furthermore, the phylogenetic relationship among cellulose synthase genes conserved in other bacterial species was analyzed. We observed that the cellulose genes in the Komagataeibacter shared sequence similarities with the γ-proteobacterial species but not with the α-proteobacteria and that the type I and type II operons could be diverged from a same ancestor in Komagataeibacter.
Similar content being viewed by others
References
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Andrés-Barrao C, Falquet L, Calderon-Copete SP, Descombes P, Ortega Pérez R, Barja F (2011) Genome sequences of the high-acetic acid-resistant bacteria Gluconacetobacter europaeus LMG 18890 T and G. europaeus LMG 18494 (reference strains), G. europaeus 5P3, and Gluconacetobacter oboediens 174Bp2 (isolated from vinegar). J Bacteriol 193:2670–2671
Azuma Y, Hosoyama A, Matsutani M, Furuya N, Horikawa H, Harada T, Hirakawa H, Kuhara S, Matsushita K, Fujita N, Shirai M (2009) Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res 37:5768–5783
Beppu T (1993–1994) Genetic organization of Acetobacter for acetic acid fermentation. Antonie Van Leeuwenhoek 64: 121–135
Bertalan M, Albano R, de Pádua V, Rouws L, Rojas C, Hemerly A, Teixeira K, Schwab S, Araujo J, Oliveira A, França L, Magalhães V, Alquéres S, Cardoso A, Almeida W, Loureiro MM, Nogueira E, Cidade D, Oliveira D, Simão T, Macedo J, Valadão A, Dreschsel M, Freitas F, Vidal M, Guedes H, Rodrigues E, Meneses C, Brioso P, Pozzer L, Figueiredo D, Montano H, Junior J, de Souza Filho G, Martin Quintana Flores V, Ferreira B, Branco A, Gonzalez P, Guillobel H, Lemos M, Seibel L, Macedo J, Alves-Ferreira M, Sachetto-Martins G, Coelho A, Santos E, Amaral G, Neves A, Pacheco AB, Carvalho D, Lery L, Bisch P, Rössle SC, Urményi T, Rael Pereira A, Silva R, Rondinelli E, von Krüger W, Martins O, Baldani JI, Ferreira PC (2009) Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10:450
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552
Castro C, Cleenwerck I, Trcek J, Zuluaga R, De Vos P, Caro G, Aguirre R, Putaux JL, Gañán P (2013) Gluconacetobacter medellinensis sp. nov., cellulose- and non-cellulose-producing acetic acid bacteria isolated from vinegar. Int J Syst Evol Microbiol 63:1119–1125
Chawla PR, Bajaj IB, Survase SA, Singhal RS (2009) Microbial cellulose: fermentative production and applications. Food Technol Biotechnol 47:107–124
Chouaia B, Gaiarsa S, Crotti E, Comandatore F, Degli Esposti M, Ricci I, Alma A, Favia G, Bandi C, Daffonchio D (2014) Acetic acid bacteria genomes reveal functional traits for adaptation to life in insect guts. Genome Biol Evol 6:912–920
Coucheron DH (1991) An Acetobacter xylinum insertion sequence element associated with inactivation of cellulose production. J Bacteriol 173:5723–5731
da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM, do Amaral AM, Bertolini MC, Camargo LE, Camarotte G, Cannavan F, Cardozo J, Chambergo F, Ciapina LP, Cicarelli RM, Coutinho LL, Cursino-Santos JR, El-Dorry H, Faria JB, Ferreira AJ, Ferreira RC, Ferro MI, Formighieri EF, Franco MC, Greggio CC, Gruber A, Katsuyama AM, Kishi LT, Leite RP, Lemos EG, Lemos MV, Locali EC, Machado MA, Madeira AM, Martinez-Rossi NM, Martins EC, Meidanis J, Menck CF, Miyaki CY, Moon DH, Moreira LM, Novo MT, Okura VK, Oliveira MC, Oliveira VR, Pereira HA, Rossi A, Sena JA, Silva C, de Souza RF, Spinola LA, Takita MA, Tamura RE, Teixeira EC, Tezza RI, Trindade dos Santos M, Truffi D, Tsai SM, White FF, Setubal JC, Kitajima JP (2002) Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417:459–463
Deeraksa A, Moonmangmee S, Toyama H, Yamada M, Adachi O, Matsushita K (2005) Characterization and spontaneous mutation of a novel gene, polE, involved in pellicle formation in Acetobacter tropicalis SKU1100. Microbiology 151:4111–4120
Deeraksa A, Moonmangmee S, Toyama H, Adachi O, Matsushita K (2006) Conversion of capsular polysaccharide, involved in pellicle formation, to extracellular polysaccharide by galE deletion in Acetobacter tropicalis. Biosci Biotechnol Biochem 70:2536–2539
Deng Y, Nagachar N, Xiao C, Tien M, Kao TH (2013) Identification and characterization of non-cellulose-producing mutants of Gluconacetobacter hansenii generated by Tn5 transposon mutagenesis. J Bacteriol 195:5072–5083
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498
Du XJ, Jia SR, Yang Y, Wang S (2011) Genome sequence of Gluconacetobacter sp. strain SXCC-1, isolated from Chinese vinegar fermentation starter. J Bacteriol 193:3395–3396
Dubois M, Gilles KA, Hamilton JK, Robers PA, Smith F (1956) Colorimetric method for determination of sugars and related substances. Anal Chem 28:350–356
Dulley JR, Grieve PA (1975) A simple technique for eliminating interference by detergents in the Lowry’s method of protein determination. Anal Biochem 64:136–141
Edgar RC (2004a) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Edgar RC (2004b) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma 5:113
Hu SQ, Gao YG, Tajima K, Sunagawa N, Zhou Y, Kawano S, Fujiwara T, Yoda T, Shimura D, Satoh Y, Munekata M, Tanaka I, Yao M (2010) Structure of bacterial cellulose synthase subunit D octamer with four inner passageways. Proc Natl Acad Sci U S A 107:17957–17961
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma 11:119
Iguchi M, Yamanaka S, Budhiono A (2000) Bacterial cellulose—a masterpiece of nature’s arts. J Mat Sci 35:261–270
Iyer PR, Geib SM, Catchmark J, Kao TH, Tien M (2010) Genome sequence of a cellulose-producing bacterium, Gluconacetobacter hansenii ATCC 23769. J Bacteriol 192:4256–4257
Kawai S, Goda-Tsutsumi M, Yakushi T, Kano K, Matsushita K (2013) Heterologous overexpression and characterization of a flavoprotein-cytochrome c complex fructose dehydrogenase of Gluconobacter japonicus NBRC3260. Appl Environ Microbiol 79:1654–1660
Kubiak K, Kurzawa M, Jędrzejczak-Krzepkowska M, Ludwicka K, Krawczyk M, Migdalski A, Kacprzak MM, Loska D, Krystynowicz A, Bielecki S (2014) Complete genome sequence of Gluconacetobacter xylinus E25 strain—valuable and effective producer of bacterial nanocellulose. J Biotechnol 176:18–19
Kumagai A, Mizuno M, Kato N, Nozaki K, Togawa E, Yamanaka S, Okuda K, Saxena IM, Amano Y (2011) Ultrafine cellulose fibers produced by Asaia bogorensis, an acetic acid bacterium. Biomacromolecules 12:2815–2821
Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760
Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) 1000 genome project data processing subgroup. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Matsutani M, Nishikura M, Saichana N, Hatano T, Masud-Tippayasak U, Theergool G, Yakushi T, Matsushita K (2013) Adaptive mutation of Acetobacter pasteurianus SKU1108 enhances acetic acid fermentation ability at high temperature. J Biotechnol 165:109–119
Matsutani M, Fukushima K, Kayama C, Arimitsu M, Hirakawa H, Toyama H, Adachi O, Yakushi T, Matsushita K (2014) Replacement of a terminal cytochrome c oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria. Biochim Biophys Acta 1837:1810–1820
Mayer R, Ross P, Weinhouse H, Amikam D, Volman G, Ohana P, Calhoon RD, Wong HC, Emerick AW, Benziman M (1991) Polypeptide composition of bacterial cyclic diguanylic acid-dependent cellulose synthase and the occurrence of immunologically crossreacting proteins in higher plants. Proc Natl Acad Sci U S A 88:5472–5476
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
Nair D, Memmi G, Hernandez D, Bard J, Beaume M, Gill S, Francois P, Cheung AL (2011) Whole-genome sequencing of Staphylococcus aureus strain RN4220, a key laboratory strain used in virulence research, identifies mutations that affect not only virulence factors but also the fitness of the strain. J Bacteriol 193:2332–2335
Navarro RR, Komagata K (1999) Differentiation of Gluconacetobacter liquefaciens and Gluconacetobacter xylinus on the basis of DNA base composition, DNA relatedness, and oxidation products from glucose. J Gen Appl Microbiol 45:7–15
Ogino H, Azuma Y, Hosoyama A, Nakazawa H, Matsutani M, Hasegawa A, Otsuyama K, Matsushita K, Fujita N, Shirai M (2011) Complete genome sequence of NBRC 3288, a unique cellulose-nonproducing strain of Gluconacetobacter xylinus isolated from vinegar. J Bacteriol 193:6997–6998
Salichos L, Rokas A (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327–331
Saxena IM, Brown RM Jr (1995) Identification of a second cellulose synthase gene (acsAII) in Acetobacter xylinum. J Bacteriol 177:5276–5283
Saxena IM, Kudlicka K, Okuda K, Brown RM Jr (1994) Characterization of genes in the cellulose-synthesizing operon (acs operon) of Acetobacter xylinum: implications for cellulose crystallization. J Bacteriol 176:5735–5752
Shoda M, Sugano Y (2005) Recent advances in bacterial cellulose production. Biotech Biopro Eng 10:1–8
Sievers M, Sellmer S, Teuber M (1992) Acetobacter europaeus sp, nov, a main component of industrial vinegar fermenters in Central Europe. Syst Appl Microbiol 15:386–392
Sokollek SJ, Hertel C, Hammes WP (1998) Description of Acetobacter oboediens sp. nov. and Acetobacter pomorum sp. nov., two new species isolated from industrial vinegar fermentations. Int J Syst Bacteriol 48:935–940
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
Steiner P, Sauer U (2001) Proteins induced during adaptation of Acetobacter aceti to high acetate concentrations. Appl Environ Microbiol 67:5474–5481
Sukumaran J, Holder MT (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics 26:1569–1571
Suzuki H, Lefébure T, Bitar PP, Stanhope MJ (2012) Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. BMC Genomics 13:38
Takemura H, Horinouchi S, Beppu T (1991) Novel insertion sequence IS1380 from Acetobacter pasteurianus is involved in loss of ethanol-oxidizing ability. J Bacteriol 173:7070–7076
Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
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 28:2731–2739
Trcek J, Raspor P, Teuber M (2000) Molecular identification of Acetobacter isolates from submerged vinegar production, sequence analysis of plasmid pJK2-1 and application in the development of a cloning vector. Appl Microbiol Biotechnol 53:289–295
Umeda Y, Hirano A, Ishibashi M, Akiyama H, Onizuka T, Ikeuchi M, Inoue Y (1999) Cloning of cellulose synthase genes from Acetobacter xylinum JCM 7664: implication of a novel set of cellulose synthase genes. DNA Res 6:109–115
Yamada Y (2014) Transfer of Gluconacetobacter kakiaceti, Gluconacetobacter medellinensis and Gluconacetobacter maltaceti to the genus Komagataeibacter as Komagataeibacter kakiaceti comb. nov., Komagataeibacter medellinensis comb. nov. and Komagataeibacter maltaceti comb. nov. Int J Syst Evol Microbiol 64:1670–1672
Yamada Y, Nakazawa E, Nozaki A, Kondô K (1969) Characterization of Acetobacter xylinum by ubiquinone system. Agr Biol Chem 33:1659–1661
Yamada Y, Yukphan P, Lan Vu HT, Muramatsu Y, Ochaikul D, Tanasupawat S, Nakagawa Y (2012) Description of Komagataeibacter gen. nov., with proposals of new combinations (Acetobacteraceae). J Gen Appl Microbiol 58:397–404
Yu X, Atalla RH (1996) Production of cellulose II by Acetobacter xylinum in the presence of 2,6-dichlorobenzonitrile. Int J Biol Macromol 19:145–146
Zogaj X, Nimtz M, Rohde M, Bokranz W, Römling U (2001) The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Mol Microbiol 39:1452–1463
Acknowledgments
We thank Haruo Suzuki (Yamaguchi University) for his skillful technical assistance in phylogenetic analyses. This work was financially supported by the Advanced Low Carbon Technology Research and Development Program (ALCA).
Author information
Authors and Affiliations
Corresponding author
Additional information
Minenosuke Matsutani and Kohei Ito contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
ESM 1
(PDF 199 kb)
Rights and permissions
About this article
Cite this article
Matsutani, M., Ito, K., Azuma, Y. et al. Adaptive mutation related to cellulose producibility in Komagataeibacter medellinensis (Gluconacetobacter xylinus) NBRC 3288. Appl Microbiol Biotechnol 99, 7229–7240 (2015). https://doi.org/10.1007/s00253-015-6598-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-015-6598-x