The cleaved fragments both bind DNA substrates, as does the 41-kDa fragment. Species Flavobacterium okeanokoites from a.4.5.12 Restriction endonuclease FokI, N-terminal (recognition) domain appears in SCOP 1.69; Species Flavobacterium okeanokoites from a.4.5.12 Restriction endonuclease FokI, N-terminal (recognition) domain appears in the current release, SCOPe 2.08 8600 Rockville Pike A labile form of the ATP-dependent protease La that inhibits the wild type protease. An official website of the United States government. Molecular Characterization of a DNA Polymerase from. Gene. F. cucumis[1] (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. Members of the genus Flavobacterium are distributed widely in nature and have been isolated from various habitats, such as diseased fish, microbial mats, freshwater and river sediments, seawater and marine sediments, soil, glaciers, and Antarctic lakes (Bernardet et al., 1996; Yi et al., 2005; Zhu et al., 2003).A number of Flavobacterium species isolated from glaciers, sea ice, and Antarctic . [4] Nylon-eating bacteria are a strain of Flavobacterium that is capable of digesting certain by-products of nylon 6 manufacture. F. beibuense[1] To permanently link to this page, use https://lpsn.dsmz.de/species/planococcus-okeanokoitesCopy to clipboardLink copied to clipboard. F. faecale[1] source for nomenclature or classification - please consult the The modular structure of Fok I endonuclease suggested that it might be feasible to construct hybrid endonucleases with 1996 . F. bizetiae[1] F. soli[1] (1995) Interaction of the MboII restriction endonuclease with DNA. doi: 10.1371/journal.pone.0094875. Linking: Friedrich T, Fatemi M, Gowhar H, Leismann O, Jeltsch A. Biochim Biophys Acta. F. ferrugineum[1] Planomicrobium koreense gen. nov., sp. F. alkalisoli[1] Bethesda, MD 20894, Web Policies The phylogenomic assignment score of this taxon is 0.04948 (N = 7). These results suggests that M.FokI-(335-647) either has a very degenerate specificity for (G/C)AT(G/C) and sites similar to CATCC or GGATG or, alternatively, that it has a dual specificity for CATCC and GGATG. Since the recognition and cleavage site of the enzyme are different, Fok I may be used as a "universal restriction enzyme" to cleave practically any sequence. F. glycines[1] nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. Accordingly, the present invention relates to DNA segments encoding the recognition and cleavage domains of the Fold restriction endonuclease, respectively. MluI introduces double-strand cleavages at unique sequences that are completely two-fold rotationally symmetric like most type II restriction endonucleases. 2022 Dec 13;4(1):101917. doi: 10.1016/j.xpro.2022.101917. 8600 Rockville Pike F. breve 1976 Nov;4(2):123-64. doi: 10.3109/10409237609105456. Bookshelf Authors:. F. nitrogenifigens[1] F restrictum[1] F. tructae[1] Name: Planococcus okeanokoites (ZoBell and Upham 1944) Nakagawa et al. Organization and nucleotide sequences of the restriction and modification genes. 2021 Jun 14;14:618171. doi: 10.3389/fnmol.2021.618171. eCollection 2022 Sep. Retrovirology. Chem., 265, 30223029. Federal government websites often end in .gov or .mil. The .gov means its official. FOIA The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). F. sasangense[1] F. terrigena[1] Would you like email updates of new search results? The https:// ensures that you are connecting to the -, Science. Weber, K. and Osborn, M. (1969) The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel electrophoresis. used categories, homotypic synonym, validly published under the ICNP. 164, 11241135. ZFNs are engineered proteins combining the DNA recognition specificity of zinc finger proteins with the nuclease domain of Fok1, an endonuclease from Flavobacterium okeanokoites, to create double . F. ajazii[1] F. viscosum[1] F. humi[1] Thus, the 25-kDa carboxyl-terminal fragment constitutes the Fok I cleavage domain. Flavobacterium okeanokoites Rate the pronunciation difficulty of Flavobacterium okeanokoites 3 /5 (3 votes) Very easy Easy Moderate Difficult Very difficult Pronunciation of Flavobacterium okeanokoites with 1 audio pronunciations 0 rating Record the pronunciation of this word in your own voice and play it to listen to how you have pronounced it. A. Wakiewicz, L. Irzykowska, in Encyclopedia of Food Microbiology (Second Edition), 2014 Characteristics of Flavobacterium Species. Welcoming a range of sound science research, including replication studies, negative results, and case reports. The https:// ensures that you are connecting to the Species who are a part of the genus Flavobacterium are most likely found scattered along in nature. Nomenclatural status: and transmitted securely. F. granuli[1] Unauthorized use of these marks is strictly prohibited. Syst. Accordingly, we propose that F. okeanokoites should be transferred to the genus Planococcus and that the description of the genus Planococcus should be emended. F. hydatis 1996, Basonym: Phylogenetic evidence derived from a 16S rRNA sequence analysis indicated that F. okeanokoites, which forms rod-shaped cells, belongs to the genus Planococcus, which forms spherical cells. 1989 Aug 15;80(2):193-208. doi: 10.1016/0378-1119(89)90284-9. Biochem. /content/journal/ijsem/10.1099/00207713-46-4-866, /deliver/fulltext/ijsem/46/4/ijs-46-4-866.html?itemId=/content/journal/ijsem/10.1099/00207713-46-4-866&mimeType=html&fmt=ahah, http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-46-4-866. F. oceanosedimentum[1] nov. Int J Syst Bacteriol 1996; 46:866-870. Notification list. Front Microbiol. Assigned by: The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). 2000 Jul 14;1480(1-2):145-59. doi: 10.1016/s0167-4838(00)00065-0. Nucl. Parent taxon: Planococcus Migula 1894 (Approved Lists 1980) Assigned by: Nakagawa Y, Sakane T, Yokota A. Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. Said plants are functionally . F. squillarum[1] [No PubMed record available.]. Antonie Van Leeuwenhoek. F. parvum[1] Chung, C. H., Waxman, L. and Goldberg, A. L. (1983) Studies of the protein encoded by the lon mutation, capR9, in Escherichia coli. Contribution ltude gntique de la sporogense bactrienne. Flavobacterium aquimarinumF. Reference: How to cite this resource - Schoch CL, et al. Biol. O' Connell Motherway M, Watson D, Bottacini F, Clark TA, Roberts RJ, Korlach J, Garault P, Chervaux C, van Hylckama Vlieg JE, Smokvina T, van Sinderen D. PLoS One. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss). 2021 Oct 22;21(1):288. doi: 10.1186/s12866-021-02347-3. Notification that new names and new combinations have appeared in volume 46, part 4 of the IJSB. These microbes are mostly found in aquatic ecosystems and wet areas with freshwater or seawater. Isospecific adenine DNA methyltransferases show distinct preferences towards DNA substrates. F. suncheonense[1] 1984 Aug;99(2):723-33 F. xanthum Evol. These data suggest that whether a cell is a rod or a coccus is not a generic criterion. Microbiol. Phylogenetic evidence derived from a 16S rRNA sequence analysis indicated that F. okeanokoites, which forms rod-shaped cells, belongs to the genus Planococcus, which forms spherical cells. F. aciduliphilum[1] pp. Dorawa S, Werbowy O, Plotka M, Kaczorowska AK, Makowska J, Kozlowski LP, Fridjonsson OH, Hreggvidsson GO, Aevarsson A, Kaczorowski T. Int J Mol Sci. A list of marine bacteria including descriptions of sixty new species. F. dasani[1] Scripps Inst. M.FokI is a monomeric protein with a M(r) = 76,000 +/- 1,500 under denaturing conditions. Flavobacterium is a genus of Gram-negative, nonmotile and motile, rod-shaped bacteria that consists of 130 recognized species. Enzyme overproduction was ensured by cloning the fokIM gene under the phi 10 promoter of phase T7. aquimarinum[1] FASTA. 224, 101110. Flavobacterium okeanokoites ZoBell and Upham 1944 (Approved Lists 1980), Etymology: F. zaozhuangense[1] Biochemistry-USA F. ammoniigenes[1] Anonymous. F. piscis[1] F. phycosphaerae[1] F. psychrotolerans[1] 1985;40(2-3):175-82 2021 Aug 19;10(8):799. doi: 10.3390/biology10080799. The 58-kDa fragment does not bind the DNA substrate. F. branchiicola[1] F. micromati[1] Potential of Mitochondrial Genome Editing for Human Fertility Health. F. aurantiibacter[1] Paschon DE, Lussier S, Wangzor T, Xia DF, Li PW, Hinkley SJ, Scarlott NA, Lam SC, Waite AJ, Truong LN, Gandhi N, Kadam BN, Patil DP, Shivak DA, Lee GK, Holmes MC, Zhang L, Miller JC, Rebar EJ. F. maotaiense[1] F. caseinilyticum[1] The gene encoding the Fok I methyltransferase from Flavobacterium okeanokoites was cloned into an Escherichia coli vector. nov. Int J Syst Bacteriol 1996; 46:866-870. Bergeys manual of systematic bacteriology, (formerly group Ilf), found in human clinical specimens. The genus Flavobacterium comprises the following species: F. acidificum[1] Cell F. flevense 1 (The Archaea and the deeply branching and phototrophic Bacteria) (D.R. The site is secure. used categories, Rarely 10.1385/MB:13:1:1 Abstract The gene encoding the FokI methyltransferase from Flavobacterium okeanokoites was cloned into an Escherichia coli vector. 1999 Nov;13(1):1-15. doi: 10.1385/MB:13:1:1. Gene Accessibility DNA-[adenine] methylation in lower eukaryotes. validly published under the ICNP, Correct name: Natl. Baneyx, F. and Georgiou, G. (1990) In vivo degradation of secreted fusion proteins by the Escherichia coli outer membrane protease OmpT. Before Learn how institutions are benefiting and how we can operate fee free OA in your institution. F. fluviale[1] 1994 Apr 22;269(16):12298-303. This name appeared on the Approved Lists of Bacterial Names 1980. J Cell Biol. F. ummariense[1] Sci. The https:// ensures that you are connecting to the Kaczorowski, T. and Sektas, M. (1996) Rapid removal of unincorporated label and proteins from DNA sequencing reactions. FOIA 1996, Parent taxon: 2001 (sic) Planococcusokeanokoites (ZoBell and Upham 1944) Nakagawa et al. -, Biochem J. your institution. Nylon-eating bacteria are a strain of Flavobacterium that is capable of digesting certain by-products of nylon 6 manufacture. Hinton, D. (1989) Transcript analyses of the uvsX-4041 region of bacteriophage T4. Microbiol. Current landscape of gene-editing technology in biomedicine: Applications, advantages, challenges, and perspectives. F. reichenbachii[1] J. Biol. F. compostarboris[1] In addition, methylation was detected at CACCC sites, but not at sites in which a central AT dinucleotide is flanked by at least one A x T or T x A base pair. F. cheonanense[1] 2007 Sep;64(18):2351-7. doi: 10.1007/s00018-007-7124-9. Notification list. 1993 Apr 1;90(7):2764-8. doi: 10.1073/pnas.90.7.2764. (from Flavobacterium okeanokoites; belonging to the type IIS class) have revealed an N-terminal DNA-binding domain and a C-terminal domain with nonspecific DNA-cleavage activity (4-7). doi: 10.1134/S0006297923140080. 1988 Apr 22;240(4851):504-6 F. frigidarium F. difficile[1] Wilkinson, G. N. (1961) Statistical estimations in enzyme kinetics. (1995) MmeI, a class-IIS restriction endonuclease: purification and characterization. 1996) Yoon et al. J. Biol. Bulletin Scripps Institution of Oceanography University of California (Technical Series) 1944; 5:239-292. riviphilum[1] AB680292 To download a certificate of analysis for Planomicrobium okeanokoites (ZoBell and Upham) Yoon et al. Careers. F. notoginsengisoli[1] Nasrallah A, Sulpice E, Kobaisi F, Gidrol X, Rachidi W. Cells. nov., an agarase-producing species isolated from stools of Antarctic penguins. Kaczorowski, T., Skowron, P., and Podhajska, A. J. The transcriptional start sites were mapped as well as putative -10 and -35 regions of the fokIM promoter. FokI is a strongly basic protein with an isoelectric point of 9.4. Article F. urocaniciphilum[1] (1993) Atypical DNA-binding properties of class-IIS restriction endonucleases: evidence for recognition of the cognate sequence by FokI monomer. F. myungsuense[1] fem. The gene encoding the FokI methyltransferase from Flavobacterium okeanokoites was cloned into an Escherichia coli vector. Oceanogr. F. salilacus[1] Mol Biotechnol 13, 115 (1999). Seeman, N. C., Rosenberg, J. M. and Rich, A. J. Mol. Cloning of two type II methylase genes that recognise asymmetric nucleotide sequences: FokI and HgaI. F. cheonhonense[1] F. piscinae[1] Natural and Artificial Mechanisms of Mitochondrial Genome Elimination. 1989 Apr 15;77(1):1-10. doi: 10.1016/0378-1119(89)90353-3. . -, Gene Anal Tech. 2022 Jul 14;3(3):e155. F. seoulense[1] 10, 219225. sharing sensitive information, make sure youre on a federal official website and that any information you provide is encrypted F. ceti[1] ), constructs of 684 ZFNs (hybrid, chimeric Zif-F N) with specificity to the HSV-2 genome (see additional file 3) was attained . F. amnicola[1] Before The genes for FokI, a type-IIS restriction-modification system from Flavobacterium okeanokoites (asymmetric recognition sequence: 5'-GGATG/3'-CCTAC), were cloned into Escherichia coli.Recombinants carrying the fokIR and fokIM genes were found to modify their DNA completely, and to restrict lambdoid phages weakly. F. cupreum[1] eCollection 2023. F. gelidilacus[1] F. cellulosilyticum[1] n. keanos, the ocean; Gr. Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Siksnys V, Bochtler M. Cell Mol Life Sci. eCollection 2019. Clipboard, Search History, and several other advanced features are temporarily unavailable. MedComm (2020). https://lpsn.dsmz.de/species/planococcus-okeanokoites, This LPSN page was printed on 2023-06-12 15:46:13, Rarely Language links are at the top of the page across from the title. A phylogenetically close relationship was supported by chemotaxonomic characteristics, such as the presence of menaquinone 7 and menaquinone 8 as major isoprenoid quinones, the presence of phosphatidylglycerol, bisphosphatydylglycerol, and phosphatidylethanolamine as cellular polar lipids, and the G+C content of the DNA (46.3 mol%). Using computational assembly (based on the in-silico linkage of the Zif arrays (ZFAs) to the Flavobacterium okeanokoites the type II class endonuclease, F N (Fok I) as previously achieved in-vivo by Kim et al. F. indicum[1] n. keanos, the ocean; Gr. F. inkyongense[1] Disclaimer. Unauthorized use of these marks is strictly prohibited. -, Nature. 1996 Nakagawa Y, Sakane T, Yokota A. Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. Increase your impact. F. maris[1] (1992) Purification and properties of the MboII, a class-IIS restriction endonuclease. 80, 324332. PMC Confidence limits on phylogenies: an approach using the bootstrap. Support your community. Gene. 82, 10741078. F. tagetis[1] On further digestion, the 41-kDa fragment degrades into 30-kDa amino-terminal and 11-kDa carboxyl-terminal fragments. Clipboard, Search History, and several other advanced features are temporarily unavailable. Before F. flaviflagrans[1] NlaIII and a cytosine-type methylase. Proc. 244, 44064412. Over 364 institutions now operate a fee-free and frictionless OA experience for their researchers via the Societys Publish and Read deal. 1993 Oct 29;133(1):79-84. doi: 10.1016/0378-1119(93)90227-t. Proc Natl Acad Sci U S A. F. cyanobacteriorum[1] In 1996, Nakagawa et al. Notes: Planomicrobium okeanokoites is the correct name if this species is regarded as a separate species (i.e., if its nomenclatural type is not assigned to another species whose name is validly published, legitimate and not rejected and has priority) within a separate genus Planomicrobium. F. kyungheense[1] ], Translation table 11 (Bacterial, Archaeal and Plant Plastid), Skerman VBD et al. F. tegetincola[1] F. limicola[1] (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Clipboard, Search History, and several other advanced features are temporarily unavailable. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Nomenclatural status: masc. A Recommendation for a Pre-Standardized Marine Microalgal Dry Weight Determination Protocol for Laboratory Scale Culture Using Ammonium Formate as a Washing Agent. (1996) 46:866-870. 1989 Aug 15;80(2):193-208. doi: 10.1016/0378-1119(89)90284-9. -, Gene. F. chungnamense[1] F. algicola[1] An official website of the United States government. Chem. F. aquariorum[1] 2014 Apr 17;9(4):e94875. F. caeni[1] Gene. A list of marine bacteria including descriptions of sixty new species. n. koit, bed; N.L. F. nackdongense[1] The taxonomic position of Flavobacterium okeanokoites IFO 12536T (T = type strain) was determined by 16S rRNA gene sequencing and chemotaxonomic methods. Editing out HIV: application of gene editing technology to achieve functional cure. CRISPR-Cas9 Technology for the Creation of Biological Avatars Capable of Modeling and Treating Pathologies: From Discovery to the Latest Improvements. correct name, Parent taxon: Accessibility F. dankookense[1] nov. | Microbiology Society Volume 46, Issue 4 Research Article Free Biology (Basel). Nat Commun. Bethesda, MD 20894, Web Policies Preparation of transforming deoxyribonucleic acid by phenol treatment. 2006 Oct 15;399(2):177-90. doi: 10.1042/BJ20060854. nov. Int J Syst Bacteriol 1996; 46:866-870. A phylogenetically close relationship was supported by chemotaxonomic characteristics, such as the presence of menaquinone 7 and menaquinone 8 as major isoprenoid quinones, the presence of phosphatidylglycerol, bisphosphatydylglycerol, and phosphatidylethanolamine as cellular polar lipids, and the G + C content of the DNA (46.3 mol%). 2022 Jul 19;23(14):7945. doi: 10.3390/ijms23147945. F. succinans F. akiainvivens F. anatoliense[1] Please enable it to take advantage of the complete set of features! 125, 110. Acids Res. Acids Res. 2023 Microbiology Society. PubMed 1996 (sic) Planomicrobiumokeanokoites (Nakagawa et al. F. filum[1] F. segetis[1] F. zhairuonense[1] Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. F. collinsense[1] n. okeanokoites, of the ocean bed Gender: neuter Type strain: ATCC 33414; CCM 320; CIP 105082; DSM 15489; IF0 12536; IFO 12536; LMG 4030; NBRC 12536; NCIMB 561; NCMB 561; VKM B-1175 See detailed strain information at "Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. Intended use This product is intended for laboratory research use only. Mol. Notification that new names and new combinations have appeared in volume 46, part 4 of the IJSB. F. banpakuense[1] 1998 Jul;48 Pt 3:973-82. doi: 10.1099/00207713-48-3-973. Clipboard, Search History, and several other advanced features are temporarily unavailable. In contrast, the C-terminal domain prefers unmethylated DNA substrates. Bookshelf Liberek, K., Osipiuk, J., Zylicz, M., Ang, D., Skorko, J., and Georgopoulos, G. (1990) Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication. Disclaimer. 2020: baaa062. 1998) to the genus Planomicrobium. F. ichthyis[1] 1987 Oct;209(3):570-4. doi: 10.1007/BF00331164. Biochem J. F. limnosediminis[1] 2023 Apr 14;18(4):e0282516. and transmitted securely. Accordingly, we propose that F. okeanokoites should be transferred to the genus Planococcus and that the description of the genus Planococcus should be emended. It strongly prefers hemimethylated (5'-GGATG/CmATCC-3'; mA = N6-methyladenosine) over unmethylated substrates. F. franklandianum[1] F. terriphilum[1] F. agri[1] The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase, M.FokI, modifies both adenine residues within its asymmetric recognition sequence 5'-GGATG/CATCC-3'. F. xinjiangense[1] . F. johnsoniae nov. Etymology: Gr. Nakagawa, Y., Sakane, T., and Yokota, A. Life (Basel). F. omnivorum[1] 2001, Planomicrobium okeanokoites Zobell & Upham, 1944. F. columnare causes the cotton-wool disease on freshwater fishes. J. Bacteriol. Chem. Yoon, J.-H., Kang, S.-S., Lee, K.-C., Lee, E.S., Kho, Y.H., Kang, K.H., and Park, Y.-H. "Planomicrobium koreense gen. nov., sp. J. Syst. used categories, Rarely The FokI methyltransferase from Flavobacterium okeanokoites. nov., isolated from soil of a ginseng field. Valid publication: PMC F. psychrophilum National Library of Medicine 1991 Apr;100:13-26 J. gen. fem. Alteration of the cleavage distance of Fok I restriction endonuclease by insertion mutagenesis. government site. Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401. 465-466. F. ginsengisoli[1] F. fluviatile[1] Identification of restriction-modification systems of Bifidobacterium animalis subsp. Fok I was purified to homogeneity with phosphocellulose, DEAE-Sephadex, and gel chromatography, yielding 50 mg of pure Fok I endonuclease per liter of culture medium. It is a fusion protein comprising two independent enzymes. doi: 10.1371/journal.pone.0282516. 2021 Jan 20;11(2):76. doi: 10.3390/life11020076. Wilson, G. G. (1991) Organization of restriction-modification systems. F. arsenatis[1] F. pokkalii[1] F. bomense[1] F. multivorum BinI: a new site-specific endonuclease from Bifidobacterium infantis. F. stagni[1] F. arcticum[1] F. cutihirudinis[1] F. qiangtangense[1] Kinetics of Methylation by EcoP1I DNA Methyltransferase. F. psychroterrae[1] Flavobacterium circumlabensF. F. xueshanense[1] F. ginsenosidimutans[1] IJSEM list: F. lutivivi[1] Skerman VBD, McGowan V, Sneath PHA. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Careers. In the course of surveying for new A number of type II restriction endonucleases enzymes, we found that Flavobacterium okeano- with different sequence specificities have been koites IF012536 and Micrococcus luteus IF012992 contain type II restriction endonucleases with speci- Abbreviations: bp, base pairs; T4dC, cytosine-substituted T4 ticities . PubMed: 32761142 PMC: PMC7408187. Assigned by: 1993 Apr 11;21(7):1507-16 [1][2] Flavobacteria are found in soil and fresh water in a variety of environments. Another member of this genus, F. okeanokoites is the original source for the type IIs restriction endonuclease Fok I, used in Zinc finger nucleases and TALENs. F. palustre[1] doi: 10.1002/mco2.155. CLUSTAL V: improved software for multiple sequence alignment. Zobell, C.E., and Upham, H.C. "A list of marine bacteria including descriptions of sixty new species." Tadeusz Kaczorowski. F. knui[1] The https:// ensures that you are connecting to the 266, 1395213957. 8600 Rockville Pike (2018) 68(11):3500-3505. validly published under the ICNP, Taxonomic status: F. plurextorum[1] Genetic organization and molecular analysis of the EcoVIII restriction-modification system of Escherichia coli E1585-68 and its comparison with isospecific homologs. 2010 Jul 15;2010:302731. doi: 10.4061/2010/302731. Schlossman, D. M., Schmid, S. L., Brael, W. A. and Rothman, J. E. (1984) An enzyme that removes clathrin coats: purification of an uncoating ATPase. F. sinopsychrotolerans[1] Front Microbiol. relevant scientific literature for the most reliable information. F. paronense[1] Purification and characterization of the enzyme and its truncated derivatives. F. branchiophilum [No PubMed record available. nov., isolated from a marine solar saltern, and transfer of Planococcus stackebrandtii Mayilraj et al. F. bomensis[1] Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. Chem. The site is secure. HHS Vulnerability Disclosure, Help Chem. Biotechnol. F. noncentrifugens[1] CRC Crit Rev Biochem. F. oreochromis[1] A Flavobacterium sp. Epub 2009 Jul 23. circumlabens, "Cutting a Gordian Knot: Emended Classification and Description of the Genus, "FokI dimerization is required for DNA cleavage", https://en.wikipedia.org/w/index.php?title=Flavobacterium&oldid=1119467829, Creative Commons Attribution-ShareAlike License 4.0, This page was last edited on 1 November 2022, at 19:17. Hanish, J. and McClelland, M. (1988) Activity of DNA modification and restriction enzymes in KGB, a potassium glutamate buffer. F. silvaticum[1] Registered as a Charity in England and Wales 264017. (1944) 5:239-292. The nt sequences of the genes were determined, and the probable start codons were . Scripps Inst. Bacteriol. Boone and R.W. Careers. 189, 113130. MeSH Nucl. The restriction endonuclease FokI from Flavobacterium okeanokoites was purified to homogeneity. By changing the ribosome-binding site sequence preceding the fokIR gene to match the consensus E. coli signal and by placing a positive retroregulator stem-loop sequence downstream of the gene, Fok I yield was increased to 5-8% of total cellular protein. This site needs JavaScript to work properly. MeSH F. arsenitoxidans[1] FASTA. Gene government site. Bethesda, MD 20894, Web Policies 19, 25392566. Acad. Nakagawa Y, Sakane T, Yokota A. Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. Would you like email updates of new search results? Oceanogr. F. orientale[1] 2020 Jan 14;10:2821. doi: 10.3389/fmicb.2019.02821. Quantification of protein enrichment at site-specific DNA double-strand breaks by chromatin immunoprecipitation in cultured human cells. (1980) (Flavobacterium okeanokoites), Planomicrobium okeanokoites Marseille-P2029, Planomicrobium okeanokoites (ZoBell and Upham 1944) Yoon et al. Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase. These data suggest that whether a cell is a rod or a coccus is not a generic criterion. HHS Vulnerability Disclosure, Help Would you like email updates of new search results? official website and that any information you provide is encrypted F. yonginense[1] nov. Bull. The recognition and cleavage domains of Fok I were analyzed by trypsin digestion. Based on analysis of the sequences around the restriction sites, the recognition sequences and cleavage sites of these endonucleases were deduced as below: FokI: (formula: see text). -, Gene. Restriction endonucleases that resemble a component of the bacterial DNA repair machinery. Studier, F. W. and Moffatt, B. F. chryseum[1] Careers. Before Microbiol. F. album[1] The gene encoding the FokI methyltransferase from Flavobacterium okeanokoiteswas cloned into an Escherichia coli vector. Google Scholar. nov. Approval was partially successful, following selected items could not be processed due to error, Copyright 1996 International Union of Microbiological Societies, Bergeys manual of determinative bacteriology, Cutting a gordian knot: emended classification and description of the genus, Complete nucleotide sequence of a 16S ribosomal RNA gene from, Manual for the identification of medical bacteria. F. bernardetii[1] Biol. Gene. F. tangerinum[1] AB680292 F. aquaticum[1] Appl Environ Microbiol. F. urumqiense[1] Relevant foods Flavobacterium spp. J Biol Chem. 2012 Mar;35(2):86-91. doi: 10.1016/j.syapm.2011.11.007. The genus Flavobacterium is the type of genus of the family Flavobacteriaceae in the phylum Bacteroidetes (previously, the Cytophaga . Sci. Riordan, J. F. (1973) Functional arginyl residues in carboxypeptidase A. F. marinum[1] F. chilense[1] Chem. J. Syst. F. humicola[1] Caserta, M., Zacharias, W., Nwankwo, D., Wilson, G. G., and Wells, R. D. (1987) Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase. This site needs JavaScript to work properly. F. endophyticum[1] The PCR was used to alter transcriptional and translational signals surrounding the Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high expression in Escherichia coli. Looney MC, Moran LS, Jack WE, Feehery GR, Benner JS, Slatko BE, Wilson GG. F. nitratireducens[1] Enzyme overproduction was ensured by cloning the fokIM gene under the 10 promoter of phage T7. n. okeanokoites, of the ocean bed, Type strain: The 25-kDa fragment, purified by using a DEAE-Sephadex column, cleaves nonspecifically both methylated (pACYCfokIM) and nonmethylated (pTZ19R) DNA substrates in the presence of MgCl2. 1998 Feb 1;251(3):899-906. doi: 10.1046/j.1432-1327.1998.2510899.x. Skerman, V.B.D., McGowan, V., and Sneath, P.H.A. F. ranwuense[1] Gene. F. sandaracinum[1] Thus, the 41-kDa amino-terminal fragment constitutes the Fok I recognition domain. F. solisilvae[1] (1980) 30:225-420. F. vireti[1] 157, 8792. Diversifying the structure of zinc finger nucleases for high-precision genome editing. Deletion mutants in the N- and C-terminus of M.FokI were isolated and characterized. F. oryzae[1] F. aquicola[1] Eur. Khaw YS, Tan HT, Sopawong A, Shaharuddin NA, Omar AR, Yusoff FM. An official website of the United States government. ), Springer-Verlag, New York (2001). F. panici[1] Bheemanaik S, Sistla S, Krishnamurthy V, Arathi S, Desirazu NR. Database (Oxford). 1970 Aug 15;227(5259):680-5 Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual 2nd ed. F. eburneum[1] have been isolated from many chilled foods. (1986) Cross-linking of bromodeoxyuridine-substituted oligonucleotides to the EcoRI and EcoRV restriction endonucleases. https://doi.org/10.1385/MB:13:1:1. F. daejeonense[1] Before F. rivuli[1] Front Genet. 2023 May 11;14:1139810. doi: 10.3389/fmicb.2023.1139810. The gene encoding the Fok I methyltransferase from Flavobacterium okeanokoites was cloned into an. Epub 2012 Jan 5. -, Mol Gen Genet. Unable to load your collection due to an error, Unable to load your delegates due to an error. Publish Open Access in Access Microbiology, our open research platform, with no fees if you submit by end of June. 2005 May;70(5):550-8. doi: 10.1007/s10541-005-0148-6. F. chungbukense[1] PATENT ABSTRACTS A process is described for producing hybrid seed using male-sterile plants created by employing molecular techniques to manipulate antisense DNA and other genes that are capable of controlling the production of fertile pollen in plants. Int J Syst Bacteriol 1997; 47:243-244. "Planococcus halotolerans sp. IJSEM list: F. lacus[1] The Flavobacterium species are in most if not all cases found in some type of hypersaline water which is very halotolerant of the Antarctic species of [F.] gondwanense and [F.] salegens Which are the most important members of Flavobacteriaceae. Saini KC, Gupta K, Sharma S, Gautam AK, Shamim S, Mittal D, Kundu P, Bast F. PLoS One. PubMedGoogle Scholar. Proc Natl Acad Sci U S A. ; According to Rules 27(3) and 30, this name is not validly published because the effective publication . F. suaedae[1] The PCR was used to alter transcriptional and translational signals surrounding the Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high expression in Escherichia coli. F. halmophilum[1] -, Nucleic Acids Res. 5, 105107. F. jejuense[1] McClelland, M., Nelson, M., and Cantor, C. R. (1985) Purification of MboII methylase (GAAGmA) from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences. Sektas, M., Kaczorowski, T., and Podhajska, A. J. M.FokI and its truncated derivatives require S-adenosyl-L-methionine as the methyl-group donor, and they are strongly inhibited by divalent cations (Mg2+, Ca2+, Ba2+, Mn2+, and Zn2+) and S-adenosyl-L-homocysteine. 1987 Oct;209(3):570-4 F. commune[1] PATENT ABSTRACTS Chandrasegaran Sriuivasan Baltimore, MD, UNITED STATES Assigned to The Johns Hopkins University The present inventor have identified of the recognition and cleavage domains of the Fold restriction endonuclense. n. okeanokoites, of the ocean bed, Type strain: n. koit, bed; N.L. F. gillisiae[1] Analyse 2003 May;69(5):2638-50. doi: 10.1128/AEM.69.5.2638-2650.2003. Planococcus Migula 1894 (Approved Lists 1980). MeSH Federal government websites often end in .gov or .mil. Tucholski, J., Skowron, P. M., and Podhajska, A. J. Zobell CE, Upham HC. F. coralii[1] F. daemonensis[1] Looney MC, Moran LS, Jack WE, Feehery GR, Benner JS, Slatko BE, Wilson GG. They occur in significant numbers in many types of fresh and frozen fish species including halibut, sole cod, salmon and trout and seem to be particularly significant in milk and dairy products (Garca-Lpez et al., 2000a). Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriphage T4. Unable to load your collection due to an error, Unable to load your delegates due to an error. F. dongtanense[1] J. Biol. F. sediminis[1] -. government site. Bull. F. enshiense[1] J. Biol. F. subsaxonicum[1] [3], Flavobacterium psychrophilum causes the bacterial cold water disease on salmonids and the rainbow trout fry disease on rainbow trout. Flavobacterium faecale sp. F. thermophilum[1] F. petrolei[1] Int. Emendation of the Genus Planococcus and Transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the Genus Planococcus as Planococcus okeanokoites comb. C-terminal deletion mutants of the FokI restriction endonuclease. 99, 723733. Natl. F. hibernum[1] F. brevivitae[1] F. niveum[1] sharing sensitive information, make sure youre on a federal Gene. and transmitted securely. Unauthorized use of these marks is strictly prohibited. Evol. This site needs JavaScript to work properly. National Library of Medicine Peptidoglycan types of bacterial cell walls and their taxonomic implications. F. branchiophilum causes the bacterial gill disease on trout. F. aureus F. ponti[1] The .gov means its official. Bookshelf Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Two new restriction endonucleases have been isolated from Flavobacterium okeanokoites IF012536 and Micrococcus luteus IF012992 and named FokI and MluI, respectively.Based on analysis of the sequences around the restriction sites, the recognition sequences and cleavage sites of these endonucleases were deduced as below: FokI: and MluI: MluI introduces double-strand cleavages at unique sequences . eCollection 2023. Nature F. resistens[1] Epub 2013 Sep 26. 2005 to the genus Planomicrobium as Planomicrobium stackebrandtii comb. Kaczorowski, T., Sektas, M., Skowron, P. et al. Another member of this genus, F. okeanokoites is the original source for the type IIs restriction endonuclease FokI, used in Zinc finger nucleases and TALENs.[4]. Nakagawa Y, Sakane T, Yokota A. Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. Publication types Research Support, Non-U.S. Gov't MeSH terms Bacterial Proteins* Base Sequence government site. F. antarcticum[1] F. hydrocarbonoxydans[1] F. silvisoli[1] F. haoranii[1] MeSH F. lacicola[1] Gene. ATCC 33414; CCM 320; CIP 105082; DSM 15489; IF0 12536; IFO 12536; LMG 4030; NBRC 12536; NCIMB 561; NCMB 561; VKM B-1175, 16S rRNA gene: Description General description Fok I belongs to the class II S restriction endonucleases, which cleave double-stranded DNA at precise distances from their recognition sequences. Correspondence to F. phragmitis[1] Accessibility Jung YT, Kang SJ, Oh TK, Yoon JH, Kim BH. Lusk, J. E., Williams, J. P., and Kennedy, E. P. (1968) Magnesium and the growth of Escherichia coli. FOIA F. dispersum[1] HHS Vulnerability Disclosure, Help Ph.D. Thesis, University of Gdansk. Online ahead of print. Gene Anal. 5, 177181. Phylogenetic evidence derived from a 16S rRNA sequence analysis indicated that F. okeanokoites, which forms rod-shaped cells, belongs to the genus Planococcus, which forms spherical cells. n. koit, bed; N.L. An official website of the United States government. F. devorans[1] Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase. F. crassostreae[1] The https:// ensures that you are connecting to the circumlabens[1] Gene established Flavobacterium okeanokoites as the basonym of Planococcus okeanokoites (ZoBell and Upham 1944) Nakagawa et al. eCollection 2021. F. magnum[1] F. hydrophilum[1] The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase, M.FokI, modifies both adenine residues within its asymmetric recognition sequence 5'-GGATG/CATCC-3'. Landry D, Looney MC, Feehery GR, Slatko BE, Jack WE, Schildkraut I, Wilson GG. F. rhamnosiphilum[1] F. naphthae[1] Gene Flavobacterium kyungheensis sp. 1989 Apr 15;77(1):1-10. doi: 10.1016/0378-1119(89)90353-3. The neighbor-joining method: a new method for reconstructing phylogenetic trees. It contains 21 Arg residues, and at least one of which is required for activity as shown by inhibition using 2,3-butanedione. Flavobacterium Emendation of the Genus Planococcus and Transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the Genus Planococcus as Planococcus okeanokoites comb. F. kingsejongi[1] M.FokI methylates adenine in both strands of its asymmetric recognition sequence. 258, 215221. HHS Vulnerability Disclosure, Help Federal government websites often end in .gov or .mil. gen. fem. Flavobacterium Bergey et al. Based on gel filtration, sedimentation and sodium dodecyl sulfate-polyacrylamide-gel electrophoresis, the following properties of the enzyme were determined: FokI exists in one active monomeric form, and has an M r of 64-65.4 10 3. F. aquatile Mol Biotechnol. eCollection 2021. official website and that any information you provide is encrypted F. longum[1] Acad. sharing sensitive information, make sure youre on a federal F. tistrianum[1] The transcriptional start sites were mapped as well as putative 10 and 35 regions of the fokIM promoter. Fatty acid and polar lipid composition in the classification of. Kaczorowski, T. (1991) Characterization of the cloned FokI methyltransferase from Flavobacterium okeanokoites. Nucl. sharing sensitive information, make sure youre on a federal The modification genes of Flavobacterium okeanokoites and Haemophilus galinarum have been cloned into the vector pBR322 and expressed in Escherichia coli cells. F. zettnowii[1] 21, 15071516. PMC F. zhairuonensis[1]. (1989) Purification and characterization of the FokI restriction endonuclease. J. Federal government websites often end in .gov or .mil. nov. Flavobacterium oncorhynchi sp. The transcriptional start sites were mapped as well as putative -10 . F. procerum[1] Emendations: Nakagawa et al. F. aquidurense[1] F. salmonis[1] Belfort, M., Pedersen-Lane, J., West, J., Ehrenman, D., Maley, K, Chu, G. and Maley, F. (1985) Processing of the intron-containing thymidylate synthase (td) gene of phage T4 is at the RNA level. Chem. Linking: Zakirova EG, Muzyka VV, Mazunin IO, Orishchenko KE. The .gov means its official. F. degerlache[1] A novel class of FokI restriction endonuclease mutants that cleave hemi-methylated substrates. Zobell CE, Upham HC. F. lacunae[1] Emendation of the Genus Planococcus and Transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the Genus Planococcus as Planococcus okeanokoites comb. The FokI methyltransferase from Flavobacterium okeanokoites Gen. Genet. Kaczorowski T, Sektas M, Skowron P, Podhajska AJ. USA F. profundi[1] Disclaimer: The NCBI taxonomy database is not an authoritative Int. F. lotistagni[1] Yoon JH, Kang SS, Lee KC, Lee ES, Kho YH, Kang KH, Park YH. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. The site is secure. Gene. F. crocinum[1] F. cheniae[1] A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Biochem. It is a fusion protein comprising two independent enzymes. 2009 Dec;59(Pt 12):2929-33. doi: 10.1099/ijs.0.009191-0. Unauthorized use of these marks is strictly prohibited. Looney MC, Moran LS, Jack WE, Feehery GR, Benner JS, Slatko BE, Wilson GG. Would you like email updates of new search results? Bergey's Manual of Systematic Bacteriology, 2nd ed., vol. F. hiemivividum[1] (Flavobacterium okeanokoites) Type of isolate Environmental Legal disclaimers. Company Limited by Guarantee. Unauthorized use of these marks is strictly prohibited. It is not intended for any animal or human therapeutic use, any human or animal . F. yanchengense[1] Please enable it to take advantage of the complete set of features! Flavobacterium okeanokoites ZoBell and Upham, 1944 : Planococcus okeanokoites (ZoBell and Upham, 1944) Nakagawa et al., 1996 : Common Name(s): Taxonomic Status: Current Standing: valid Data Quality Indicators: Record Credibility Rating: verified - standards met fem. government site. 2023 Jan;88(Suppl 1):S123-S149. Please enable it to take advantage of the complete set of features! F. sediminilitoris[1] Appl. Would you like email updates of new search results? Disclaimer. Flavobacterium circumlabensF. Approved lists of bacterial names. Sci Rep. 2018 May 29;8(1):8243. doi: 10.1038/s41598-018-26434-0. Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase. The .gov means its official. Fok I in the absence of a DNA substrate cleaves into a 58-kDa carboxyl-terminal and 8-kDa amino-terminal fragment. FOIA The transcriptional start sites were mapped as well as putative -10 and -35 regions of the fokIM promoter. 20, 433438. F. araucananum[1] F. rakeshii[1] Google Scholar. nov. Int J Syst Bacteriol 1996; 46:866-870. Int J Syst Bacteriol 1980; 30:225-420. Name: Flavobacterium okeanokoites ZoBell and Upham 1944 (Approved Lists 1980), Etymology: 8600 Rockville Pike (33414), . Acids Res. Cold Spring harbor Laboratory, Cold Spring Harbor N. Y. Tabor, S. and Richardson, C. C. (1985) A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Disclaimer. Unable to load your collection due to an error, Unable to load your delegates due to an error. (editors): "Approved lists of bacterial names." Castenholz, eds. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. The species Flavobacterium okeanokoites was originally described by ZoBell and Upham 1944. ZFNs are composed of zinc finger DNA-binding domains (three to six, each of which recognizes a 3-base pair (bp) DNA sequence) fused to the endonuclease domain of the FokI restriction enzyme from the Flavobacterium okeanokoites. Wolfes, H., Fliess, A., Winkler, F. and Pingoud, A. F.microcysteis[1] Accessibility F. columnare Mol Gen Genet. F. weaverense[1] Careers. was isolated from the marine bivalve Cristaria plicatafrom Hokkaido and grown in enriched, 90% seawater medium (40).The organic extract of the cells was sequentially fractionated by solvent partition, normal phase silica gel chromatography and reversed phase chromatography to yield two new ceramide derivatives, flavocristamide A (32) and its 3,4-dihydro-analog . Anonymous. Calif, International Journal of Systematic and Evolutionary Microbiology, Access Microbiology, an open research platform, Institute for Fermentation, Osaka, Yodogawa-ku, Osaka 532, Japan, https://doi.org/10.1099/00207713-46-4-866, Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies, DNADNA hybridization values and their relationship to whole-genome sequence similarities, Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes, OrthoANI: An improved algorithm and software for calculating average nucleotide identity, Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes, List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ, Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology, Expand your reach. The Km values for the methyl donor, S-adenosyl-L-methionine are 0.6 microM (M.FokI), 0.4 microM (M.FokIN), and 0.9 microM (M.FokIC) while the Km values for substrate lambda DNA are 1.2 nM (M.FokI), 1.4 nM (M.FokIN), and 1.3 nM (M.FokIC). Escherichia coli vector. F. selenitireducens[1] F. ammonificans[1] F. hercynium[1] Substrate-protection studies, utilizing chemical modification combined with data on the effect of divalent cations and pH on methylation activity, proved the existence of two catalytic centers within the FokI methyltransferase molecule. STAR Protoc. The .gov means its official. F. hankyongi[1] F. sangjuense[1] F. muglaense[1] Techn. 1998) to the genus Planomicrobium." Our data show that both domains of M.FokI methylate DNA independently of each other but cooperate in DNA binding. Unable to load your collection due to an error, Unable to load your delegates due to an error. nov., isolated from a saline soil sample in China." F. jumunjinense[1] F. inviolabile[1] 1961 Aug;80:324-32 The fokI restriction-modification system. F frigoris[1] F. fryxellicola[1] 264, 1443214439. Gene Therapy for Neurodegenerative Disease: Clinical Potential and Directions. Provided by the Springer Nature SharedIt content-sharing initiative, Class IIS restriction-modification enzymes, access via nov. First report of Planomicrobium okeanokoites associated with Himantothallus grandifolius (Desmarestiales, Phaeophyta) from Southern Hemisphere. and transmitted securely. 2021 Jan 12;22(2):682. doi: 10.3390/ijms22020682. Structure, function and mechanism of exocyclic DNA methyltransferases. 1923 (Approved Lists 1980). F. zepuense[1] Third , localizing the point-mutation of SCD at genomic contextual position . Second , by serial linkage of these ZFAs to the Flavobacterium okeanokoites endonuclease Fok I four ZFNs with unique specificity to >24 bp target-sequences at the genomic contextual positions 82, 1333, 1334, and 1413 of the A chain-gene were constructed in-silico. F. saccharophilum Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. F. frigidimaris[1] FokI belongs to a class of restriction endonucleases that recognize specific but asymmetric nucleotide sequences and introduce staggered cleavages at appointed positions away from the recognition sequences. 2001 Jul;51(Pt 4):1511-1520. doi: 10.1099/00207713-51-4-1511. To permanently link to this page, use https://lpsn.dsmz.de/species/flavobacterium-okeanokoitesCopy to clipboardLink copied to clipboard, https://lpsn.dsmz.de/species/flavobacterium-okeanokoites, This LPSN page was printed on 2023-06-12 15:46:00, Rarely I. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Fok I in the presence of a DNA substrate cleaves into a 41-kDa amino-terminal fragment and a 25-kDa carboxyl-terminal fragment. Gan, L., Zhang, Y., Zhang, L., Li, X., Wang, Z., He, L., Li, Z., and Tian, Y. eCollection 2014. F. buctense[1] 2022 Nov 15;11(22):3615. doi: 10.3390/cells11223615. The genus Flavobacterium was established by Frankland in 1889 and, since then many amendments to its description have been made. The taxonomic position of Flavobacterium okeanokoites IFO 12536T (T = type strain) was determined by 16S rRNA gene sequencing and chemotaxonomic methods. Zamora L, Fernndez-Garayzbal JF, Svensson-Stadler LA, Palacios MA, Domnguez L, Moore ER, Vela AI. F. laiguense[1] 157, 181185. 1996 includes: Flavobacterium okeanokoites (IFO 12536) Flavobacterium okeanokoites IFO12536 Planococcus okeanokoites IFO 12536 262, 47704777. Syst Appl Microbiol. 1994 Feb 1;91(3):883-7. doi: 10.1073/pnas.91.3.883. 1) homotypic synonym: Planococcusokeanokoites Nakagawa et al. F. swingsii[1] 227, 680685. New perspectives in the classification of the flavobacteria: description of. official website and that any information you provide is encrypted F. tilapiae[1] A list of marine bacteria including descriptions of sixty new species. F. davisii[1] M.FokI was purified using a two-step chromatography procedure. Category: Species Proposed as: sp. We have cloned, overexpressed and purified full-length M.FokI as well as both individual domains and analyzed their kinetics of DNA methylation using unmethylated and hemimethylated oligodeoxynucleotide substrates. 1984 Nov;31(1-3):251-5. doi: 10.1016/0378-1119(84)90217-8. F. spartansii[1] Kita K, Kotani H, Sugisaki H, Takanami M. Looney MC, Moran LS, Jack WE, Feehery GR, Benner JS, Slatko BE, Wilson GG. Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. F. tibetense[1] Enzyme Res. F. anhuiense[1] Leismann O, Roth M, Friedrich T, Wende W, Jeltsch A. Eur J Biochem. F. glaciei[1] Sugisaki, H., Yamamoto, K., and Takanami, M. (1991) The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands. MeSH Smith, H. O. and Kelly, S. V. (1984) in Razin, A., Cedar, H., and Riggs, A.D. (eds), DNA Methylation: Biochemistry and Biological Significance, Springer-Verlag, New York, pp. F. gawalongense[1] 1996) and Planococcus mcmeekinii (Junge et al. Biochemistry (Mosc). 2021 Dec 18;18(1):39. doi: 10.1186/s12977-021-00581-1. Please enable it to take advantage of the complete set of features! F. cerinum[1] F. endoglycinae[1] 73, 804808. A procedure for the isolation of deoxyribonucleic acid from microorganisms. Szomolanyi, E., Kiss, A., and Venetianer, P. (1980) Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. F. lindanitolerans[1] gen. fem. Bulletin Scripps Institution of Oceanography University of California (Technical Series) 1944; 5:239-292. J. Biol. Visualizing the Nucleome Using the CRISPR-Cas9 System: From in vitro to in vivo. (2001) 51:1511-1520. Mol. A. Registered in England 1039582. 243, 26182624. F. terrae[1] Sharma AK, Fitieh AM, Locke AJ, Ali JYH, Ismail IH. nov." Int. 33 As FokI-dependent DNA cleavage requires dimerization of the cleavage domains, two ZFNs are required for binding DNA . 1996) and Planococcus mcmeekinii (Junge et al. 1989 Aug 15;80(2):193-208. doi: 10.1016/0378-1119(89)90284-9. F.amnigenum[1] 80, 209216. J. Biol. An official website of the United States government. CAS F. ureilyticum[1] 172, 491494. 12, 39153923. This organism was isolated from marine mud, and it possesses peri- F. phocarum[1] F. tiangeerense[1] PMC masc. FokI belongs to a class of restriction endonucleases that recognize specific but asymmetric nucleotide sequences and introduce staggered cleavages at appointed positions away from the recognition sequences. Maurizi, M. R., Trisler, P., and Gottesman, S. (1985) Insertional mutagenesis of the lon gene in Escherichia coli: lon is dispensable. M.FokI methylates adenine in both strands of its asymmetric recognition sequence. Disclaimer. F. macrobrachii[1] F. fulvum[1] 2021 Jul 20;12:673951. doi: 10.3389/fgene.2021.673951. This site needs JavaScript to work properly. F. pectinovorum ATCC 33414; CCM 320; CIP 105082; DSM 15489; IF0 12536; IFO 12536; LMG 4030; NBRC 12536; NCIMB 561; NCMB 561; VKM B-1175, 16S rRNA gene: Surprisingly, in addition to methylating the lower strand of the recognition sequence (CATCC), M.FokI-(335-647) also modifies the upper strand (GGATG), albeit with a lower activity. sharing sensitive information, make sure youre on a federal Taxonomic significance of cellular fatty acid composition in some coryneform bacteria. J. Biol. FokI methylase gene is contained on a 3.80 kb piece of F. okeanokoites DNA. Gr. F. acidurans[1] J. Syst. Please enable it to take advantage of the complete set of features! This site needs JavaScript to work properly. Tranfformation techniques are used to trodnce constructs containing antisense DNA and other genes into plants. Int. Bookshelf Son HM, Kook M, Park SY, Mavlonov GT, Yi TH. Bacteriol. Univ. F. saliperosum[1] Federal government websites often end in .gov or .mil. The 41 kDa . F. okeanokoites 2000 Jul 14;1480(1-2):145-59. doi: 10.1016/s0167-4838(00)00065-0. USA F. covae[1] National Library of Medicine Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase. F. supellecticarium[1] Clipboard, Search History, and several other advanced features are temporarily unavailable. Wang Y, Ma L, He J, Liu Z, Weng S, Wang L, He J, Guo C. BMC Microbiol. F. tyrosinilyticum[1] F. branchiarum[1] FOIA The N-terminal derivative (M.FokIN) methylates the adenine residue within the sequence 5'-GGATG-3', whereas the C-terminal derivative (M.FokIC) modifies the adenine residue within the sequence 5'-CATCC-3'. Biochemistry (Mosc). Front Mol Neurosci. F. pedocola[1] Proc. Flavobacterium okeanokoites, which was described by Zobell and Upham (32), is one of the misnamed flavobacteria. Unable to load your collection due to an error, Unable to load your delegates due to an error. 1992 Apr 1;113(1):83-8 Effective publication: F. mizutaii[1] A Charity registered in Scotland SC039250. F. hauense[1] Planococcus okeanokoites (ZoBell and Upham 1944) Nakagawa et al. Two new restriction endonucleases have been isolated from Flavobacterium okeanokoites IFO12536 and Micrococcus luteus IFO12992 and named FokI and MluI, respectively. -. By changing the ribosome-binding site sequence preceding the fokIR gene to match the consensus E. coli signal and by placing a positive . Department of Microbiology, University of Gdansk, Poland, Tadeusz Kaczorowski,Marian Sektas&Piotr Skowron, Faculty of Biotechnology UG & MUG, Kladki 24, 80-822, Gdansk, Poland, You can also search for this author in F. cauense[1] J. Bacteriol. Modification with butanedione. 41, 375382. National Library of Medicine F. jocheonensis[1] Gr. Gel-mobility-shift assays indicate that all the protein contacts necessary for the sequence-specific recognition of DNA substrates are encoded within the 41-kDa fragment. Nucl. F. dauae[1] 1989 Aug 15;80(2):193-208. doi: 10.1016/0378-1119(89)90284-9. F. suzhouense[1] 8600 Rockville Pike F. denitrificans Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase. and transmitted securely. HHS Vulnerability Disclosure, Help Int J Syst Bacteriol. F. koreense[1] F. sharifuzzamanii[1] Sektas, M., Kaczorowski, T., and Podhajska, A. J. Plasmid constructs carrying this fragment of DNA are resistant 13, 71717182. nov. Int J Syst Bacteriol 46 866 . Cell. In agreement to former studies, the N-terminal domain of M.FokI modifies the upper strand of the recognition sequence (GGATG). lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis. Changes in the RNA as infection proceeds. F. defluvii[1] F. fontis[1] 2013 Dec;104(6):1029-37. doi: 10.1007/s10482-013-0023-1. F. verecundum[1] Skowron, P., Kaczorowski, T., Tucholski, J., and Podhajska, A.J. n. keanos, the ocean; Gr. masc. Int J Syst Evol Microbiol. F. tangerina[1] F. psychrolimnae[1] 1988 Sep-Oct;5(5):105-7 Acids Res. F. cheongpyeongense[1] PMID: 1584761 PMCID: PMC49064 DOI: 10.1073/pnas.89.10.4275 Abstract The PCR was used to alter transcriptional and translational signals surrounding the Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high expression in Escherichia coli. Bethesda, MD 20894, Web Policies Planomicrobium flavidum sp. F. croceum[1] The site is secure. F. chungangense[1] Article used categories, homotypic synonym, validly published under the ICNP. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Lisser, S. and Margalit, H. (1993) Compilation of E. coli mRNA promoter sequences. Accessibility Bookshelf F. agrisoli[1] 2019 Mar 8;10(1):1133. doi: 10.1038/s41467-019-08867-x. National Library of Medicine F. ahnfeltiae[1] F. fluvii[1] Analyse Flavobacterium riviphilumF. official website and that any information you provide is encrypted 3971. 159, 267273. F. luticocti[1] Friedrich T, Fatemi M, Gowhar H, Leismann O, Jeltsch A. Biochim Biophys Acta. J. Syst. F. undicola[1] Int J Syst Evol Microbiol. The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase M.FokI is a tandem enzyme of two independent domains with very different kinetic properties. F. collinsii[1] F. baculatum[1] Several species are known to cause disease in freshwater fish. Gene The transcriptional start sites were mapped as well as putative -10 and -35 regions of the fokIM promoter. Gene. fem. F. oncorhynchi[1] The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). The site is secure. Landry D, Looney MC, Feehery GR, Slatko BE, Jack WE, Schildkraut I, Wilson GG. Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase. PMC Salava H, Thula S, Mohan V, Kumar R, Maghuly F. Int J Mol Sci. Enzyme overproduction was ensured by cloning the fokIM gene under the q10 promoter of phage T7. Bethesda, MD 20894, Web Policies Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. 1991 ) organization of restriction-modification systems f. branchiophilum causes the bacterial gill disease trout... Mesh federal government websites often end in.gov or.mil T = type strain ) determined. 58-Kda fragment does not bind the DNA substrate intended for Laboratory research only. ( 84 ) 90217-8:1133. doi: 10.1007/s00018-007-7124-9, 1443214439 M. and Rich, J.! Wales 264017 Services ( HHS ) ):76. doi: 10.1016/j.xpro.2022.101917 bed ; N.L Mavlonov! 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J I-2494 by SMRT and. 76,000 +/- 1,500 under denaturing conditions fulvum [ 1 ] Planomicrobium koreense nov.. Intended for any animal or Human therapeutic use, any Human or animal: Nakagawa et al `` Approved of... A 3.80 kb piece of f. okeanokoites DNA f. thermophilum [ 1 ] 2001, Planomicrobium okeanokoites ZoBell Upham... Er, Vela AI it possesses peri- f. phocarum [ 1 ] nov. Int J Sci! Flavobacteriaceae in the methyltransferase enzyme overproduction was ensured by cloning the fokIM promoter:193-208. doi: (! By changing the ribosome-binding site flavobacterium okeanokoites preceding the fokIR gene to match the consensus coli. Ichthyis [ 1 ] f. tiangeerense [ 1 ] please enable it take. Strongly basic protein with an isoelectric point of 9.4 due to an.!