{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T11:55:51Z","timestamp":1792410951047,"version":"4.4.0"},"reference-count":48,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2007,3,1]],"date-time":"2007-03-01T00:00:00Z","timestamp":1172707200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2007,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The frequently occurring DNA uptake sequence (DUS), recognized as a 10-bp repeat, is required for efficient genetic transformation in the human pathogens\n            <jats:italic>Neisseria meningitidis<\/jats:italic>\n            and\n            <jats:italic>Neisseria gonorrhoeae<\/jats:italic>\n            . Genome scanning for DUS occurrences in three different species of\n            <jats:italic>Neisseria<\/jats:italic>\n            demonstrated that 76% of the nearly 2,000 neisserial DUS were found to have two semiconserved base pairs extending from the 5\u2032 end of DUS to constitute a 12-mer repeat. Plasmids containing sequential variants of the neisserial DUS were tested for their ability to transform\n            <jats:italic>N. meningitidis<\/jats:italic>\n            and\n            <jats:italic>N. gonorrhoeae<\/jats:italic>\n            , and the 12-mer was found to outperform the 10-mer DUS in transformation efficiency. Assessment of meningococcal uptake of DNA confirmed the enhanced performance of the 12-mer compared to the 10-mer DUS. An inverted repeat DUS was not more efficient in transformation than DNA species containing a single or direct repeat DUS. Genome-wide analysis revealed that half of the nearly 1,500 12-mer DUS are arranged as inverted repeats predicted to be involved in rho-independent transcriptional termination or attenuation. The distribution of the uptake signal sequence required for transformation in the\n            <jats:italic>Pasteurellaceae<\/jats:italic>\n            was also biased towards transcriptional terminators, although to a lesser extent. In addition to assessing the intergenic location of DUS, we propose that the 10-mer identity of DUS should be extended and recognized as a 12-mer DUS. The dual role of DUS in transformation and as a structural component on RNA affecting transcription makes this a relevant model system for assessing significant roles of repeat sequences in biology.\n          <\/jats:p>","DOI":"10.1128\/jb.01408-06","type":"journal-article","created":{"date-parts":[[2006,12,29]],"date-time":"2006-12-29T01:33:34Z","timestamp":1167356014000},"page":"2077-2085","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":110,"title":["New Functional Identity for the DNA Uptake Sequence in Transformation and Its Presence in Transcriptional Terminators"],"prefix":"10.1128","volume":"189","author":[{"given":"O. Herman","family":"Ambur","sequence":"first","affiliation":[{"name":"Centre for Molecular Biology and Neuroscience"},{"name":"Institute of Microbiology, University of Oslo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan A.","family":"Frye","sequence":"additional","affiliation":[{"name":"Centre for Molecular Biology and Neuroscience"},{"name":"Institute of Microbiology, University of Oslo"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tone","family":"T\u00f8njum","sequence":"additional","affiliation":[{"name":"Centre for Molecular Biology and Neuroscience"},{"name":"Institute of Microbiology, University of Oslo"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.1046\/j.1365-2958.2002.03265.x","volume":"46","year":"2002","unstructured":"Aas, F. E., C. Lovold, and M. Koomey. 2002. An inhibitor of DNA binding and uptake events dictates the proficiency of genetic transformation in Neisseria gonorrhoeae: mechanism of action and links to type IV pilus expression. Mol. Microbiol. 46 : 1441-1450.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_3_2","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1046\/j.1365-2958.2002.03193.x","volume":"46","year":"2002","unstructured":"Aas, F. E., M. Wolfgang, S. Frye, S. Dunham, C. Lovold, and M. Koomey. 2002. Competence for natural transformation in Neisseria gonorrhoeae: components of DNA binding and uptake linked to type IV pilus expression. Mol. Microbiol. 46 : 749-760.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_4_2","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/S0300-9084(97)86727-2","volume":"78","year":"1996","unstructured":"Abe, H., and H. Aiba. 1996. Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization. Biochimie 78 : 1035-1042.","journal-title":"Biochimie"},{"key":"e_1_3_2_5_2","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/nar\/gkf391","volume":"30","year":"2002","unstructured":"Achaz, G., E. P. Rocha, P. Netter, and E. Coissac. 2002. Origin and fate of repeats in bacteria. Nucleic Acids Res. 30 : 2987-2994.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.129.2.983-992.1977"},{"key":"e_1_3_2_7_2","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1084\/jem.170.5.1727","volume":"170","year":"1989","unstructured":"Blake, M. S., C. M. MacDonald, and K. P. Klugman. 1989. Colony morphology of piliated Neisseria meningitidis. J. Exp. Med. 170 : 1727-1736.","journal-title":"J. Exp. Med."},{"key":"e_1_3_2_8_2","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1111\/apm.1964.61.3.457","volume":"61","year":"1964","unstructured":"Boevre, K. 1964. Studies on transformation in Moraxella and organisms assumed to be related to Moraxella. 1. A method for quantitative transformation in Moraxella and Neisseria, with streptomycin resistance as the genetic marker. Acta Pathol. Microbiol. Scand. 61 : 457-473.","journal-title":"Acta Pathol. Microbiol. Scand."},{"key":"e_1_3_2_9_2","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1099\/13500872-142-10-2839","volume":"142","year":"1996","unstructured":"Boyle-Vavra, S., and H. S. Seifert. 1996. Uptake-sequence-independent DNA transformation exists in Neisseria gonorrhoeae. Microbiology 142 : 2839-2845.","journal-title":"Microbiology"},{"key":"e_1_3_2_10_2","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1080\/07391102.1986.10508457","volume":"3","year":"1986","unstructured":"Brendel, V., G. H. Hamm, and E. N. Trifonov. 1986. Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J. Biomol. Struct. Dyn. 3 : 705-723.","journal-title":"J. Biomol. Struct. Dyn."},{"key":"e_1_3_2_11_2","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1099\/00221287-26-2-303","volume":"26","year":"1961","unstructured":"Catlin, B. W., and L. S. Cunningham. 1961. Transforming activities and base contents of deoxyribonucleate preparations from various Neisseriae. J. Gen. Microbiol. 26 : 303-312.","journal-title":"J. Gen. Microbiol."},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.849004"},{"key":"e_1_3_2_13_2","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/0378-1119(80)90071-2","volume":"11","year":"1980","unstructured":"Danner, D. B., R. A. Deich, K. L. Sisco, and H. O. Smith. 1980. An eleven-base-pair sequence determines the specificity of DNA uptake in Haemophilus transformation. Gene 11 : 311-318.","journal-title":"Gene"},{"key":"e_1_3_2_14_2","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1093\/nar\/gkh255","volume":"32","year":"2004","unstructured":"Davidsen, T., E. A. Rodland, K. Lagesen, E. Seeberg, T. Rognes, and T. Tonjum. 2004. Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res. 32 : 1050-1058.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_15_2","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1111\/j.1574-6968.2001.tb10523.x","volume":"195","year":"2001","unstructured":"de Vries, J., P. Meier, and W. Wackernagel. 2001. The natural transformation of the soil bacteria Pseudomonas stutzeri and Acinetobacter sp. by transgenic plant DNA strictly depends on homologous sequences in the recipient cells. FEMS Microbiol. Lett. 195 : 211-215.","journal-title":"FEMS Microbiol. Lett."},{"key":"e_1_3_2_16_2","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/0006-291X(79)90386-3","volume":"86","year":"1979","unstructured":"Dougherty, T. J., A. Asmus, and A. Tomasz. 1979. Specificity of DNA uptake in genetic transformation of gonococci. Biochem. Biophys. Res. Commun. 86 : 97-104.","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"e_1_3_2_17_2","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1146\/annurev.micro.53.1.217","volume":"53","year":"1999","unstructured":"Dubnau, D. 1999. DNA uptake in bacteria. Annu. Rev. Microbiol. 53 : 217-244.","journal-title":"Annu. Rev. Microbiol."},{"key":"e_1_3_2_18_2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1086\/419073","volume":"70","year":"1995","unstructured":"Elder, J. F., Jr., and B. J. Turner. 1995. Concerted evolution of repetitive DNA sequences in eukaryotes. Q. Rev. Biol. 70 : 297-320.","journal-title":"Q. Rev. Biol."},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.173.12.3911-3913.1991"},{"key":"e_1_3_2_20_2","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/0378-1119(84)90209-9","volume":"31","year":"1984","unstructured":"Fitzmaurice, W. P., R. C. Benjamin, P. C. Huang, and J. J. Scocca. 1984. Characterization of recognition sites on bacteriophage HP1c1 DNA which interact with the DNA uptake system of Haemophilus influenzae Rd. Gene 31 : 187-196.","journal-title":"Gene"},{"key":"e_1_3_2_21_2","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0378-1119(00)00200-6","volume":"251","year":"2000","unstructured":"Francis, F., S. Ramirez-Arcos, H. Salimnia, C. Victor, and J. R. Dillon. 2000. Organization and transcription of the division cell wall (dcw) cluster in Neisseria gonorrhoeae. Gene 251 : 141-151.","journal-title":"Gene"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.5.1.98-102.1972"},{"key":"e_1_3_2_23_2","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1111\/j.1365-2958.1995.tb02420.x","volume":"16","year":"1995","unstructured":"Freitag, N. E., H. S. Seifert, and M. Koomey. 1995. Characterization of the pilF-pilD pilus-assembly locus of Neisseria gonorrhoeae. Mol. Microbiol. 16 : 575-586.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_24_2","doi-asserted-by":"crossref","first-page":"6982","DOI":"10.1073\/pnas.85.18.6982","volume":"85","year":"1988","unstructured":"Goodman, S. D., and J. J. Scocca. 1988. Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. Proc. Natl. Acad. Sci. USA 85 : 6982-6986.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.173.18.5921-5923.1991"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.152.3.1071-1077.1982"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.10.3463-3469.2006"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.9.2.186-188.1979"},{"key":"e_1_3_2_29_2","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/BF02789105","volume":"3","year":"1995","unstructured":"Horton, R. M. 1995. PCR-mediated recombination and mutagenesis. SOEing together tailor-made genes. Mol. Biotechnol. 3 : 93-99.","journal-title":"Mol. Biotechnol."},{"key":"e_1_3_2_30_2","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1111\/apm.1965.63.2.306","volume":"63","year":"1965","unstructured":"Jyssum, K., and S. Lie. 1965. Genetic factors determining competence of transformation of Neisseria meningitidis. 1. A permanent loss of competence. Acta Pathol. Microbiol. Scand. 63 : 306-316.","journal-title":"Acta Pathol. Microbiol. Scand."},{"key":"e_1_3_2_31_2","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/S0021-9258(19)57417-8","volume":"263","year":"1988","unstructured":"Lynn, S. P., L. M. Kasper, and J. F. Gardner. 1988. Contributions of RNA secondary structure and length of the thymidine tract to transcription termination at the thr operon attenuator. J Biol. Chem. 263 : 472-479.","journal-title":"J Biol. Chem."},{"key":"e_1_3_2_32_2","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1016\/0140-6736(91)91297-8","volume":"337","year":"1991","unstructured":"McGuinness, B. T., I. N. Clarke, P. R. Lambden, A. K. Barlow, J. T. Poolman, D. M. Jones, and J. E. Heckels. 1991. Point mutation in meningococcal porA gene associated with increased endemic disease. Lancet 337 : 514-517.","journal-title":"Lancet"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1038\/35006655"},{"key":"e_1_3_2_34_2","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1471-2148-6-82","volume":"6","year":"2006","unstructured":"Redfield, R. J., W. A. Findlay, J. Bosse, J. S. Kroll, A. D. Cameron, and J. H. Nash. 2006. Evolution of competence and DNA uptake specificity in the Pasteurellaceae. BMC Evol. Biol. 6 : 82.","journal-title":"BMC Evol. Biol."},{"key":"e_1_3_2_35_2","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/S0378-1119(96)00810-4","volume":"188","year":"1997","unstructured":"Seifert, H. S. 1997. Insertionally inactivated and inducible recA alleles for use in Neisseria. Gene 188 : 215-220.","journal-title":"Gene"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.60.3.1232-1236.1992"},{"key":"e_1_3_2_37_2","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/S0923-2508(99)00130-8","volume":"150","year":"1999","unstructured":"Smith, H. O., M. L. Gwinn, and S. L. Salzberg. 1999. DNA uptake signal sequences in naturally transformable bacteria. Res. Microbiol. 150 : 603-616.","journal-title":"Res. Microbiol."},{"key":"e_1_3_2_38_2","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1046\/j.1365-2958.2003.03204.x","volume":"47","year":"2003","unstructured":"Snyder, L. A., W. M. Shafer, and N. J. Saunders. 2003. Divergence and transcriptional analysis of the division cell wall (dcw) gene cluster in Neisseria spp. Mol. Microbiol. 47 : 431-442.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.92.5.1364-1371.1966"},{"key":"e_1_3_2_40_2","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1139\/m91-056","volume":"37","year":"1991","unstructured":"Stein, D. C. 1991. Transformation of Neisseria gonorrhoeae: physical requirements of the transforming DNA. Can. J. Microbiol. 37 : 345-349.","journal-title":"Can. J. Microbiol."},{"key":"e_1_3_2_41_2","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1084\/jem.171.6.2131","volume":"171","year":"1990","unstructured":"Swanson, J., S. Morrison, O. Barrera, and S. Hill. 1990. Piliation changes in transformation-defective gonococci. J. Exp. Med. 171 : 2131-2139.","journal-title":"J. Exp. Med."},{"key":"e_1_3_2_42_2","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0378-1119(96)00842-6","volume":"189","year":"1997","unstructured":"Tauschek, M., C. W. Hamilton, L. A. Hall, C. Chomvarin, J. A. Fyfe, and J. K. Davies. 1997. Transcriptional analysis of the groESL operon of Neisseria gonorrhoeae. Gene 189 : 107-112.","journal-title":"Gene"},{"key":"e_1_3_2_43_2","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1126\/science.287.5459.1809","volume":"287","year":"2000","unstructured":"Tettelin, H., N. J. Saunders, J. Heidelberg, A. C. Jeffries, K. E. Nelson, J. A. Eisen, K. A. Ketchum, D. W. Hood, J. F. Peden, R. J. Dodson, W. C. Nelson, M. L. Gwinn, R. DeBoy, J. D. Peterson, E. K. Hickey, D. H. Haft, S. L. Salzberg, O. White, R. D. Fleischmann, B. A. Dougherty, T. Mason, A. Ciecko, D. S. Parksey, E. Blair, H. Cittone, E. B. Clark, M. D. Cotton, T. R. Utterback, H. Khouri, H. Qin, J. Vamathevan, J. Gill, V. Scarlato, V. Masignani, M. Pizza, G. Grandi, L. Sun, H. O. Smith, C. M. Fraser, E. R. Moxon, R. Rappuoli, and J. C. Venter. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287 : 1809-1815.","journal-title":"Science"},{"key":"e_1_3_2_44_2","first-page":"777","volume":"2","year":"2005","unstructured":"Tonjum, T. 2005. Genus Neisseria, p. 777-798. In G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, vol. 2, 2nd ed. Springer-Verlag, New York, N.Y.","journal-title":"Bergey's manual of systematic bacteriology"},{"key":"e_1_3_2_45_2","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1046\/j.1365-2958.1998.00910.x","volume":"29","year":"1998","unstructured":"Tonjum, T., D. A. Caugant, S. A. Dunham, and M. Koomey. 1998. Structure and function of repetitive sequence elements associated with a highly polymorphic domain of the Neisseria meningitidis PilQ protein. Mol. Microbiol. 29 : 111-124.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_46_2","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1111\/j.1365-2958.1995.tb02410.x","volume":"16","year":"1995","unstructured":"Tonjum, T., N. E. Freitag, E. Namork, and M. Koomey. 1995. Identification and characterization of pilG, a highly conserved pilus-assembly gene in pathogenic Neisseria. Mol. Microbiol. 16 : 451-464.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_47_2","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1093\/nar\/30.3.675","volume":"30","year":"2002","unstructured":"Unniraman, S., R. Prakash, and V. Nagaraja. 2002. Conserved economics of transcription termination in eubacteria. Nucleic Acids Res. 30 : 675-684.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_48_2","doi-asserted-by":"crossref","first-page":"41850","DOI":"10.1074\/jbc.M106252200","volume":"276","year":"2001","unstructured":"Unniraman, S., R. Prakash, and V. Nagaraja. 2001. Alternate paradigm for intrinsic transcription termination in eubacteria. J. Biol. Chem. 276 : 41850-41855.","journal-title":"J. Biol. Chem."},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.13.3442-3449.2002"}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.01408-06","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.01408-06","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T17:38:31Z","timestamp":1627580311000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JB.01408-06"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3]]},"references-count":48,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2007,3]]}},"alternative-id":["10.1128\/JB.01408-06"],"URL":"https:\/\/doi.org\/10.1128\/jb.01408-06","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,3]]},"assertion":[{"value":"2006-09-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2006-12-15","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-12-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}