Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes

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dc.contributor.authorF W Studier-
dc.contributor.authorP Daegelen-
dc.contributor.authorR E Lenski-
dc.contributor.authorS Maslov-
dc.contributor.authorJihyun Kim-
dc.date.accessioned2017-04-19T09:16:17Z-
dc.date.available2017-04-19T09:16:17Z-
dc.date.issued2009-
dc.identifier.issn00222836-
dc.identifier.uri10.1016/j.jmb.2009.09.021ko
dc.identifier.urihttps://oak.kribb.re.kr/handle/201005/9301-
dc.description.abstractEach difference between the genome sequences of Escherichia coli B strains REL606 and BL21(DE3) can be interpreted in light of known laboratory manipulations plus a gene conversion between ribosomal RNA operons. Two treatments with 1-methyl-3-nitro-1-nitrosoguanidine in the REL606 lineage produced at least 93 single-base-pair mutations (∼ 90% GC-to-AT transitions) and 3 single-base-pair GC deletions. Two UV treatments in the BL21(DE3) lineage produced only 4 single-base-pair mutations but 16 large deletions. P1 transductions from K-12 into the two B lineages produced 317 single-base-pair differences and 9 insertions or deletions, reflecting differences between B DNA in BL21(DE3) and integrated restriction fragments of K-12 DNA inherited by REL606. Two sites showed selective enrichment of spontaneous mutations. No unselected spontaneous single-base-pair mutations were evident. The genome sequences revealed that a progenitor of REL606 had been misidentified, explaining initially perplexing differences. Limited sequencing of other B strains defined characteristic properties of B and allowed assembly of the inferred genome of the ancestral B of Delbruck and Luria. Comparison of the B and K-12 genomes shows that more than half of the 3793 proteins of their basic genomes are predicted to be identical, although ∼ 310 appear to be functional in either B or K-12 but not in both. The ancestral basic genome appears to have had ∼ 4039 coding sequences occupying ∼ 4.0 Mbp. Repeated horizontal transfer from diverged Escherichia coli genomes and homologous recombination may explain the observed variable distribution of single-base-pair differences. Fifteen sites are occupied by phage-related elements, but only six by comparable elements at the same site. More than 50 sites are occupied by IS elements in both B and K, 16 in common, and likely founding IS elements are identified. A signature of widespread cryptic phage P4-type mobile elements was identified. Complex deletions (dense clusters of small deletions and substitutions) apparently removed nonessential genes from ∼ 30 sites in the basic genomes.-
dc.publisherElsevier-
dc.titleUnderstanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes-
dc.title.alternativeUnderstanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes-
dc.typeArticle-
dc.citation.titleJournal of Molecular Biology-
dc.citation.number4-
dc.citation.endPage680-
dc.citation.startPage653-
dc.citation.volume394-
dc.contributor.alternativeNameStudier-
dc.contributor.alternativeNameDaegelen-
dc.contributor.alternativeNameLenski-
dc.contributor.alternativeNameMaslov-
dc.contributor.alternativeName김지현-
dc.identifier.bibliographicCitationJournal of Molecular Biology, vol. 394, no. 4, pp. 653-680-
dc.identifier.doi10.1016/j.jmb.2009.09.021-
dc.subject.keywordcomplex deletions-
dc.subject.keywordCP4-type mobile elements-
dc.subject.keywordE. coli B genome-
dc.subject.keywordSNP distribution-
dc.subject.keywordUV deletions-
dc.subject.localcomplex deletions-
dc.subject.localCP4-type mobile elements-
dc.subject.localE. coli B genome-
dc.subject.localSNP distribution-
dc.subject.localUV deletions-
dc.description.journalClassY-
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