Skip to main content
SpringerLink
Log in

TfoI produced by Tepidimonas fonticaldi PL17, a moderate thermophilic bacterium, is an isoschizomer of MseI

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

A moderately thermophilic Gram-negative bacterium isolated from the Polok hot spring, Sikkim, India, was identified as a strain (PL17) of Tepidimonas fonticaldi by 16S rDNA sequencing. T. fonticaldi PL17 produces a Type IIP restriction endonuclease; named TfoI. Restriction mapping, run-off sequencing of TfoI-digests of dsDNA fragments, and end compatibility of TfoI with NdeI confirmed that the enzyme recognizes and cleaves the sequence 5′–T^TAA–3′, and is thus an isoschizomer of MseI. The TfoI restriction–modification genes in the T. fonticaldi PL17 genome were identified, and the annotated TfoI protein encodes a protein of 181 amino acid residues that shares 47.2% sequence identity with MseI. The native enzyme was purified using a four-column chromatography protocol, and its functional homogeneity was confirmed by standard quality control tests. The ESI-MS measured molecular weight of purified TfoI (20.696 kDa) is in agreement with that of the calculated monomeric molecular weight of the predicted TfoI protein sequence (20.694 kDa). TfoI exhibits optimal activity in the temperature range of 55–70 °C with Mg+2 or Co+2 as cofactor. Similar to its isoschizomers, TfoI can be used as the frequent cutter for genome analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

References

  • Agarkova IV, Dunigan DD, Van Etten JL (2006) Virion-associated restriction endonucleases of chloroviruses. J Virol 80:8114–8123. doi:10.1128/JVI.00486-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75. doi:10.1186/1471-2164-9-75

    Article  Google Scholar 

  • Bickle TA, Kruger DH (1993) Biology of DNA restriction. Microbiol Rev 57:434–450

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chaturvedi D, Chakravorty M (2003) Restriction–modification system in bacteriophage MB78. Biochem Biophys Res Commun 303:884–890

    Article  CAS  PubMed  Google Scholar 

  • Das S, Sherpa MT, Sachdeva S, Thakur N (2012) Hot springs of Sikkim (Tatopani): a socio medical conjuncture which amalgamates religion, faith, traditional belief and tourism. Asian Acad Res J Social Sci Hum 1:80–93

    CAS  Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucl Acids Res 27:4636–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dempsey RM, Carroll D, Kong H, Higgins L, Keane CT, Coleman DC (2005) Sau42I, a BcgI-like restriction–modification system encoded by the Staphylococcus aureus quadruple-converting phage Phi42. Microbiol 151:1301–1311. doi:10.1099/mic.0.27646-0

    Article  CAS  Google Scholar 

  • Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C (2011) T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucl Acids Res 39:W13–W17. doi:10.1093/nar/gkr245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hadi SM, Bachi B, Iida S, Bickle TA (1983) DNA restriction–modification enzymes of phage P1 and plasmid p15B. Subunit functions and structural homologies. J Mol Biol 165:19–34

    Article  CAS  PubMed  Google Scholar 

  • Hu G (1993) DNA polymerase-catalyzed addition of nontemplated extra nucleotides to the 3′ end of a DNA fragment. DNA Cell Biol 12:763–770. doi:10.1089/dna.1993.12.763

    Article  CAS  PubMed  Google Scholar 

  • Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi S-H, Couloux A, Lee S-W, Yoon SH, Cattolico L (2009) Genome sequences of Escherichia coli B strains REL606 and BL21 (DE3). J Mol Biol 394:644–652

    Article  CAS  PubMed  Google Scholar 

  • Joshi A, Siddiqi JZ, Rao GR, Chakravorty M (1982) MB78, a virulent bacteriophage of Salmonella typhimurium. J Virol 41:1038–1043

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H, Park S-C, Jeon YS, Lee J-H, Yi H (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721. doi:10.1099/ijs.0.038075-0

    Article  CAS  PubMed  Google Scholar 

  • Labaer J, Qiu Q, Anumanthan A, Mar W, Zuo D, Murthy TV, Taycher H, Halleck A, Hainsworth E, Lory S, Brizuela L (2004) The Pseudomonas aeruginosa PA01 gene collection. Genome Res 14:2190–2200. doi:10.1101/gr.2482804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loenen WA, Dryden DT, Raleigh EA, Wilson GG, Murray NE (2014) Highlights of the DNA cutters: a short history of the restriction enzymes. Nucl Acids Res 42:3–19. doi:10.1093/nar/gkt990

    Article  CAS  PubMed  Google Scholar 

  • Ludena P, Sentis C, De Cabo SF, Velazquez M, Fernandez-Piqueras J (1991) Visualization of R-bands in human metaphase chromosomes by the restriction endonuclease MseI. Cytogenet Cell Genet 57:82–86. DOI:10.1159/000133119 doi

    Article  CAS  PubMed  Google Scholar 

  • Morgan RD (1988) Mse I, a unique restriction endonuclease from Micrococcus species which recognizes 5′ T/TAA 3′. Nucl Acids Res 16:3104. doi:10.1093/nar/16.7.3104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nobre MF, Truper HG, Costa. MSD (1996) Transfer of Thermus ruber (Loginova et al. 1984), Themus silvanus (Tenreiro et al. 1999, and Themus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb. nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus. Int J Syst Bacteriol 46:604–606

    Article  Google Scholar 

  • Oliveira PH, Touchon M, Rocha EP (2014) The interplay of restriction–modification systems with mobile genetic elements and their prokaryotic hosts. Nucl Acids Res 42:10618–10631. doi:10.1093/nar/gku734

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Park YJ, Nishikawa T, Matsushima K, Minami M, Nemoto K (2014) A rapid and reliable PCR-restriction fragment length polymorphism (RFLP) marker for the identification of Amaranthus cruentus species. Breed Sci 64:422–426. doi:10.1270/jsbbs.64.422

    Article  PubMed  PubMed Central  Google Scholar 

  • Pingoud A, Wilson GG, Wende W (2014) Type II restriction endonucleases—a historical perspective and more. Nucl Acids Res 42:7489–7527. doi:10.1093/nar/gku447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raleigh EA, Brooks JE (1998) Restriction modification systems: where they are and what they do. In: de Brujin FJ, Lupski JR, Weinstock GM (eds) Bacterial genomes. Chapman and Hall, New York, pp 78–92. doi:10.1007/978-1-4615-6369-3_8

    Google Scholar 

  • Rao DN, Dryden DT, Bheemanaik S (2014) Type III restriction–modification enzymes: a historical perspective. Nucl Acids Res 42:45–55. doi:10.1093/nar/gkt616

    Article  CAS  PubMed  Google Scholar 

  • Reasoner DJ, Geldreich EE (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts RJ (2005) How restriction enzymes became the workhorses of molecular biology. Proc Natl Acad Sci USA 102:5905–5908. doi:10.1073/pnas.0500923102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev S, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucl Acids Res 31:1805–1812. doi:10.1093/nar/gkg274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts RJ, Vincze T, Posfai J, Macelis D (2015) REBASE–a database for DNA restriction and modification: enzymes, genes and genomes. Nucl Acids Res 43:D298–D299. doi:10.1093/nar/gku1046

    Article  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Samuelson JC, Zhu Z, Xu SY (2004) The isolation of strand-specific nicking endonucleases from a randomized SapI expression library. Nucl Acids Res 32:3661–3671. doi:10.1093/nar/gkh674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma P, Kumar R, Capalash N (2013) Restriction enzymes from thermophiles. In: Satyanarayana T, Littlechild J, Kawarabayasi Y (eds) Thermophilic microbes in environmental and industrial biotechnology: biotechnology of thermophiles. Springer, pp 611–647. doi: 10.1007/978-94-007-5899-5_23

  • Szekeres M, Szmidt AE, Torok I (1983) Evidence for a restriction/modification-like system in Anacystis nidulans infected by cyanophage AS-1. Eur J Biochem 131:137–141

    Article  CAS  PubMed  Google Scholar 

  • Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucl Acids Res 44:6614–6624. doi:10.1093/nar/gkw569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thakur N, Das S, Sherpa MN, Ranjan R (2013) GPS mapping and physical description of Polok, Borong and Reshi Tatopani—hot springs of Sikkim. JIARM 10:367–647

    Google Scholar 

  • Vaquero-Sedas MI, Vega-Palas MA (2012) The restriction endonuclease Tru9I is a useful tool to analyze telomere sequences separately from interstitial telomeric sequences in Arabidopsis thaliana. AJMB 2:242–244. doi:10.4236/ajmb.2012.23025

    Article  Google Scholar 

  • Vasu K, Nagaraja V (2013) Diverse functions of restriction–modification systems in addition to cellular defense. Microbiol Mol Biol Revs 77:53–72. doi:10.1128/MMBR.00044-12

    Article  CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vuylsteke M, Peleman JD, van Eijk MJ (2007) AFLP technology for DNA fingerprinting. Nat Protoc 2:1387–1398. doi:10.1038/nprot.2007.175

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Qian PY (2009) Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PloS One 4:e7401. doi:10.1371/journal.pone.0007401

    Article  PubMed  PubMed Central  Google Scholar 

  • Wei H, Therrien C, Blanchard A, Guan S, Zhu Z (2008) The fidelity index provides a systematic quantitation of star activity of DNA restriction endonucleases. Nucleic Acids Res 36:e50. doi:10.1093/nar/gkn182

    Article  PubMed  PubMed Central  Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia YN, Van Etten JL (1986) DNA methyltransferase induced by PBCV-1 virus infection of a Chlorella-like green alga. Mol Cell Biol 6:1440–1445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia YN, Burbank DE, Uher L, Rabussay D, Van Etten JL (1986) Restriction endonuclease activity induced by PBCV-1 virus infection of a Chlorella-like green alga. Mol Cell Biol 6:1430–1439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao H, Bughrara SS, Oliveira JA (2006) Genetic diversity in colonial bentgrass (Agrostis capillaris L.) revealed by EcoRI-MseI and PstI-MseI AFLP markers. Genome 49:328–335. doi:10.1139/g05-113

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the financial assistance from CSIR-IMTECH (BSC0402, BSC0120 to AKP; OLP0091 to BK) and Department of Biotechnology-India (BT/PR7368/INF/22/177/2012 to AKP and GAP0096 to BK) funding to BK. The authors are thankful to Dr. Rakshak Kumar for sample collection, and acknowledge the support from the Sikkim State Council of Science and Technology and the Department of Forest, Govt. of Sikkim, in sample collection. RK is supported by the research fellowship scheme of University Grants Commission, India. BK is a recipient of the Department of Biotechnology-Ramalingaswami re-entry fellowship.

Author information

Authors and Affiliations

  1. Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, India

    Ravinder Kumar & Anil Kumar Pinnaka

  2. G.N. Ramachandran Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, India

    Beena Krishnan

Authors
  1. Ravinder Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anil Kumar Pinnaka
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Beena Krishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Beena Krishnan.

Additional information

Communicated by L. Huang.

The GenBank accession number for the 16S rRNA gene sequence and the whole genome shotgun sequencing data of the strain Tepidimonas fonticaldi PL17 is KF206381 and LZDH00000000, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 886 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kumar, R., Pinnaka, A.K. & Krishnan, B. TfoI produced by Tepidimonas fonticaldi PL17, a moderate thermophilic bacterium, is an isoschizomer of MseI. Extremophiles 21, 523–535 (2017). https://doi.org/10.1007/s00792-017-0922-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-017-0922-6

Keywords

Search

Navigation