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Genomics and Proteomics

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

Tim Durfee, Richard Nelson, Schuyler Baldwin, Guy Plunkett III, Valerie Burland, Bob Mau, Joseph F. Petrosino, Xiang Qin, Donna M. Muzny, Mulu Ayele, Richard A. Gibbs, Bálint Csörgő, György Pósfai, George M. Weinstock, Frederick R. Blattner
Tim Durfee
1DNAStar, Inc., Madison, Wisconsin 53705
2Department of Genetics
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  • For correspondence: durf@genome.wisc.edu
Richard Nelson
1DNAStar, Inc., Madison, Wisconsin 53705
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Schuyler Baldwin
1DNAStar, Inc., Madison, Wisconsin 53705
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Guy Plunkett III
2Department of Genetics
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Valerie Burland
2Department of Genetics
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Bob Mau
3Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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Joseph F. Petrosino
4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030
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Xiang Qin
4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030
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Donna M. Muzny
4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030
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Mulu Ayele
4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030
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Richard A. Gibbs
4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030
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Bálint Csörgő
5Institute of Biochemistry, Biological Research Center, H-6726 Szeged, Hungary
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György Pósfai
5Institute of Biochemistry, Biological Research Center, H-6726 Szeged, Hungary
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George M. Weinstock
4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030
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Frederick R. Blattner
1DNAStar, Inc., Madison, Wisconsin 53705
2Department of Genetics
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DOI: 10.1128/JB.01695-07
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  • FIG. 1.
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    FIG. 1.

    Construction of DH10B. The steps leading to the creation of MC1061 from HfrC+ are outlined, followed by the steps described by Grant et al. (17) to generate DH10B from MC1061. Genotypes of selected key strains are indicated. The DH10B tonA genotype is a composite compiled from multiple sources. Steps involving a pBR322-recA plasmid are indicated with an asterisk. The branched pathway consisting of 25 steps leading from wild-type K-12 to HfrC+ (3) has been omitted for clarity.

  • FIG. 2.
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    FIG. 2.

    Circle diagram of the DH10B genome. Protein-encoding genes are shown in the outer ring, with blue boxes representing those genes coded on the forward strand and gold boxes representing those on the complementary strand. Large deletions and insertions are indicated outside of the circle. In the next inner ring, IS elements that cause gene disruptions or are intergenic are indicated with red or aqua tick marks, respectively, with the positions above or below the line indicating which strand is transcribed. SNPs are then indicated with black tick marks. tRNAs (green tick marks) and small regulatory RNAs (purple tick marks) are shown, with those on the forward strand above the line and those on the complementary strand below it. Finally, rRNA operons are shown as red arrowheads.

  • FIG. 3.
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    FIG. 3.

    Comparison of the DH10B and MG1655 genomes. Schematic of the two genomes showing colinear blocks of sequence. The endpoints of each block are defined by an adjacent sequence that is present only in one genome. The major structural rearrangements in DH10B are indicated below the genome representation.

  • FIG. 4.
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    FIG. 4.

    Distribution of small-scale mutations in the DH10B genome. A schematic of the genome illustrated in Fig. 3 shows the distribution of SNPs and frameshifts (A) and positioning of IS elements (B). (A) Differences in the DH10B sequence affecting conserved domain sequences are indicated by asterisks, with different colors indicating the types of change. Green, silent SNP; red, missense SNP; black, nonsense SNP; yellow, frameshift. Genes in which the mutation has a known phenotypic consequence are indicated. Note that the frameshift in rph corrects the rph-1 allele present in MG1655. SNPs in intergenic regions are indicated with a caret, and at sites where more than a SNP is present, the number of changes is given. (B) IS-disrupted genes in common with MG1655 are indicated in black, while those unique to DH10B are in red. The specific IS element at each location is indicated; the disrupted gene is in parentheses. For clarity, only differences affecting gene regions are shown.

  • FIG. 5.
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    FIG. 5.

    Comparison of φ80 and φ80dlacZΔM15 prophage structures. Diagrams of the two prophages show their chromosomal contexts and more-detailed schematics of the open reading frames (boxes) and major promoters within the two elements. Open reading frames above the center horizontal lines of the diagrams are transcribed in the forward direction, while those below the lines are coded on the complementary strand. Color boxes in the prophages indicate the source of the genes: yellow, φ80; blue, E. coli chromosome; green, Tn1000 from the F plasmid. The two types of terminal sequences, attP and res, are indicated, as is the lacZΔM15 allele. In φ80dlacZΔM15, the φ80 sequences end within gene 5 (indicated as 5′).

  • FIG. 6.
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    FIG. 6.

    Comparison of the mutational spectra in DH10B and MG1655. A bar graph shows the distribution of cycA mutations obtained in MG1655 and DH10B. Rectangles within each bar represent point mutations (black), IS150 insertions (hatched), and other IS insertions (IS1, IS2, IS5, and not determined) (white). The rectangle representing deletions in MG1655 is not visible, and no deletions were detected in DH10B.

Tables

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  • TABLE 1.

    Select genetic alterations in DH10B

    AlleleAlteration typeaGene(s) affectedDH10B sequencebAmino acid change(s)c
    Δ(ara leu)7697 Deletion(b0059) b0060-b0079 (b0080)After 62378 (ΔMG 62379-88274)HepA Δ1-295; FruR Δ1-82, L83K
    araD139 Deletionb0061Part of Δ(ara leu)7697 Null
    tonA Wild type and missenseb0150G142348RW254W or W254STOP
    ΔlacX74 Deletion(b0321) b0322-b0352After 313972 (ΔMG 338422-3746342)YahG Δ292-472
    DH10BdupDuplicationb0553-b0655Tandem duplication of 514341-627601Wild type
    galK16 IS2 disruptionb0757IS2 insertion from 728375-729703Δ57-383
    galE15 Missenseb0759G844839AS122F
    deoR Wild typeb0840No changeWild type
    e14 Excision(b1136) b1137-b1159After 1250887 (ΔMG 1195443-1210646)Icd restored to wild type
    mcrA Deletionb1159Deleted by e14 excisionNull
    galU Wild typeb1236No changeWild type
    φ80dlacZΔM15 Insertionb0340-b0349Insert from 1349613-1396987LacZ (b0344) Δ11-42
    recA1 Missenseb2699G2913852AG160D
    relA1 IS2 disruptionb2784IS2 insertion from 3003960-3005291Δ87-744
    endA1 Missenseb2945G3184059AE208K
    Tn10.10 d Inversion(b2964) b2965-b2972 (b4466)3200798-3211928NupG Δ222-418; YghJ Δ1-541
    nupG IS10 disruptionb2964IS10R insertion at 3199443Δ222-418
    rpsL Missenseb3342T3570191CK43R
    rph Frameshiftb3643G inserted at 3911483Corrects rph-1
    spoT1 Insertionb3650ATCAGG insertion from 3918250-3918255; C3918768TQD insertion after D84; H255Ye
    Δ(mrr-hsdRMS-mcrBC)Deletionb4312-b4358 (b4359)Partial Tn10 from 4640587-4641916 (ΔMG 4538777-4595456)MdoB Δ668-750
    • ↵ a Relative to MG1655.

    • ↵ b Numbers are genomic coordinates. Base changes all refer to the forward strand. MG represents MG1655.

    • ↵ c Changes relative to the MG1655 sequence. Protein names and deleted amino acids refer to affected genes on the flanks of large deletions, except for LacZ, which is an internal deletion.

    • ↵ d Coordinates refer to the internal segment of the transposon that is inverted relative to MG1655.

    • ↵ e Residue 257 of SpoT1 due to two-amino-acid insertion after position 84.

  • TABLE 2.

    Comparison of DH10B, MG1655, and W3110 sequences

    Region affectedaTypebPolymorphism inc: DH10B correspondenced
    MG1655W3110
    alsK InsertionwtIS5 MG1655
    dcuC InsertionwtIS5 MG1655
    gatA InsertionwtIS5 MG1655
    rcsC InsertionwtIS2 MG1655
    tdcD InsertionwtIS5 MG1655
    tnaB InsertionwtIS5 MG1655
    flhD promoterInsertionIS1 IS5 W3110
    csgC-IG-ymdA InsertionwtIS2 MG1655
    lrhA-IG-yfhQ InsertionwtIS1 MG1655
    tnaC-IG-tnaA InsertionwtIS5 MG1655
    ychE-IG-oppA InsertionwtIS2 IS1A.2
    yieE-IG-yidZ InsertionwtIS2 MG1655
    eutA-IG-eutB InsertionCPZ-55wtMG1655
    acnA MissenseA (A522)G (G522)MG1655
    crp MissenseC (T29)A (K29)MG1655
    intQ MissenseT (F274)C (L274)IS2
    ycdT MissenseC (A130)T (V130)IS2
    rpoS NonsenseC (Q33)T (STOP33)MG1655
    yedJ SilentC (V219)T (V219)MG1655
    rrlE SNPA2256G2256MG1655
    dcuA FrameshiftwtTT after nt 182MG1655
    • ↵ a Mutations within genes are indicated by the gene name only. Mutations in intergenic (IG) regions are indicated along with flanking gene names.

    • ↵ b Type of mutation in W3110 relative to MG1655.

    • ↵ c SNPs in conserved domain sequences are indicated by the base present and the corresponding amino acid in parentheses. For rrlE, the base change and position within the gene are given. For dcuA, TT is inserted after nucleotide 182 in the gene. CPZ-55 is a prophage. wt, wild type.

    • ↵ d DH10B correspondence with MG1655 or W3110 is indicated. Where DH10B differs from both, the associated change is noted.

Additional Files

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  • Supplemental material

    Files in this Data Supplement:

    • Supplemental file 1 - Table S1, deleted genes in DH10B relative to MG1655
      Zipped MS Word document, 15 KB.
    • Supplemental file 2 - Table S2, genes with SNPs in DH10B relative to MG1655
      Zipped MS Word document, 14 KB.
    • Supplemental file 3 - Table S3, location of IS elements in DH10B
      Zipped MS Word document, 12 KB.
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The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse
Tim Durfee, Richard Nelson, Schuyler Baldwin, Guy Plunkett III, Valerie Burland, Bob Mau, Joseph F. Petrosino, Xiang Qin, Donna M. Muzny, Mulu Ayele, Richard A. Gibbs, Bálint Csörgő, György Pósfai, George M. Weinstock, Frederick R. Blattner
Journal of Bacteriology Mar 2008, 190 (7) 2597-2606; DOI: 10.1128/JB.01695-07

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The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse
Tim Durfee, Richard Nelson, Schuyler Baldwin, Guy Plunkett III, Valerie Burland, Bob Mau, Joseph F. Petrosino, Xiang Qin, Donna M. Muzny, Mulu Ayele, Richard A. Gibbs, Bálint Csörgő, György Pósfai, George M. Weinstock, Frederick R. Blattner
Journal of Bacteriology Mar 2008, 190 (7) 2597-2606; DOI: 10.1128/JB.01695-07
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KEYWORDS

Escherichia coli
Genome, Bacterial

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