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GENETICS AND MOLECULAR BIOLOGY

Distribution of Twelve Linear Extrachromosomal DNAs in Natural Isolates of Lyme Disease Spirochetes

Nanette Palmer, Claire Fraser, Sherwood Casjens
Nanette Palmer
Department of Oncological Sciences, University of Utah Medical School, Salt Lake City, Utah 84132, and
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Claire Fraser
The Institute for Genome Science, Rockville, Maryland 20850
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Sherwood Casjens
Department of Oncological Sciences, University of Utah Medical School, Salt Lake City, Utah 84132, and
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DOI: 10.1128/JB.182.9.2476-2480.2000
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Tables

  • Table 1.

    DNA probes used in this study

    Borrelia plasmid sourceDNA probeaLocationbORFs in probeb
    lp5CB63c3413–5195T05–T06
    lp17CL4763–2418D01–D04
    D11d6949–7679D11
    lp21CZ326788–869763-bp repeat region
    DF29c16772–18682U10–U12
    lp25DE2113151–14265E20–E21
    CG1819568–21587E29
    lp28-1DD605149–6980F11–F13
    EN57c24797–26510vlsEcassettes
    lp28-2DK441–442G01
    EI586700–8688G09–G10
    lp28-3CT53c3659–4392H08–H09
    CQ6812620–14584H18–H20
    lp28-4EE502526–3627I06–I07
    CV694726–6439I11–I14
    EL9517047–19017I27–I29
    lp36DK602334–4214K02–K04
    FI787569–9698K12–K15
    CQ33c12657–15072K19–K22
    GI8826201–26513K41
    EH8631975–33745K49–K50
    lp38BA19c22–1483J001
    DH083958–6033J07–J08
    CQ6313730–16123J20–J22
    DH4621666–23409J28–J30
    FA8426057–28222J34–J36
    CT79c35768–37561J48–J50
    lp54CM64427–2449A01–A04
    A24/25d∼15800–17300A24–A25 (dbpAB)
    lp56BL053022–3666Q05–Q06
    EK5842201–44134Q67–Q69
    • ↵a DNA clone numbers from genome sequencing project (8, 12).

    • ↵b Base pair location and open reading frame (ORF) nomenclature are as in Fraser et al. (12) and Casjens et al. (8).

    • ↵c Showed some weak hybridization to other plasmids when probing B31 MI DNA.

    • ↵d Uncloned PCR product made with whole B. burgdorferi B31 MI DNA as template.

  • Table 2.

    Similar sequences among linear plasmids of independent isolates of B. burgdorferia

    Strain (origin)Hybridization of strain B31 probes to independently isolated strains
    p5lp17lp21lp25lp28-1lp28-2lp28-3lp28-4lp36lp38lp54lp56
    CB63CL47D11CZ32DF29DE21CG18DD60EN57DK44EI58CT53CQ68EE50CV69EL95DK60FI78CQ33GI88EH86BA19DH08CQ63DH46FA84CT79CM64A24/25BL05EK58
    19678 (NY)—————(24)(24)(30)30, (27)(29)(29)28, (37)2829(28)(28)36—35, (31)3535383838383838—54——
    21645 (WI)——(17)——(24)——(25)29(29)28282929(29)——25—(25)——————(54)54——
    21721 (WI)—————(24)—26(21, 37)27—(28, 30)30303029——26—(26)363636363636, (28)(54)54——
    27579 (CT)—(15)———30——21(28, 29)(29)(31)3029292828—282829, (30)383838383838(54)54——
    27982 (PA)—17, (22)(17, 22)——(24)(24, 48)26(25, 29)(29)(29)(28)28, (30)29(29)29(17, 24)—25—(25, 30)—————(36)—(54)——
    27985 (CT)—————24(24, 54)2828 (37, 45, 54)29(29)28, 362828282836—29, 36363638383838—38(54)545555
    28534 (MD)——(17)————23, (28)(26)(26, 29)272828292929(25)—2525, 2925, 29——————5454——
    29592 (CT)—2222——2424(29)30, (36)292930, (24)3029293023—303030, (25)373737373737, (29)(54)54——
    29805 (CT)—33(17)——(24)(24)—33,(29)2930, (35)30292830(29)——34, (30)30383838383838, (30)(54)54——
    30757 (CT)——(17)242424(24)25, 2828, (45, 54)29(29)28, 362827272736363636, (28)36——————54545555
    CA-3-87 (CA)—————24(28)—33, (27)——(28)2828—29——383838——————5454——
    WI91-23 (WI)515(16)——2325—2727(27, 28)2727272728(29)—2929, (27)29, (28)383838(38)3838—(54)——
    N40 (NY)(5)2222——2324262929, (27)29(24, 29)—28283023—302930373737373737, (27, 28)(54)54——
    HB19 (CT)—————24242426, (37)24, 2727, 2928, (54)27282829(29)—2929, (28)303838383838385454——
    B31 (NY)5, (20)171720202424, (54)2828, (36, 54)292928, (36)28272727363628, 363636383838383838, (29)54545555
    • ↵a The United States state from which each of the strains was isolated is indicated in parentheses next to the strain name. Probes were picked from E. coli pUC18 plasmid clones used in the genone sequencing project (6, 12). Values in table are sizes in kilobase pairs for plasmids that hybridize to the indicated DNA probes (accurate to about ±0.5, ±1.5, and ±3 kbp for 5 to 10, 10 to 30, and 30 to 60 kbp ranges, respectively). —, no hybridization was seen. Values in parentheses indicate relatively weak hybridization.

  • Table 3.

    Summary of B31 counterpart linear plasmids present in natural isolates of B. burgdorferia

    Strain (origin)Hybridization of DNA probes to B. burgdorferi isolates
    lp5lp17lp21lp25lp28-1lp28-2lp28-3lp28-4lp36lp38lp54lp56
    19678 (NY)−−−−−++++++++++++−+++++++++−+−−
    21645 (WI)−−+−−+−−++++++++−−+−+−−−−−−++−−
    21721 (WI)−−−−−+−+✙−++++++−−+−+++++++++−−
    27579 (CT)−+−−−+−−+++++++++−+++++++++++−−
    27982 (PA)−++−−++++++++++++−+−+−−−−−+−+−−
    27985 (CT)−−−−−++++++++++++−+++++++−+++++
    28534 (MD)−−+−−−−++++++++++−+++−−−−−−++−−
    29592 (CT)−++−−+++++++++++✙−+++++++++++−−
    29805 (CT)−✙+−−++−+++++++++−−++++++++++−−
    30757 (CT)−−+++++++++++++++++++−−−−−−++++
    CA-3-87 (CA)−−−−−+✙−+−−++−++−−+++−−−−−−++−−
    WI91-23 (WI)+++−−++−+++++++++−+++++++++−+−−
    N40 (NY)+++−−++✙++++−+++✙−+++++++++++−−
    HB19 (CT)−−−−−++++++++++++−+++++++++++−−
    B31 MI (NY)+++++++++++++++++++++++++++++++
    • ↵a Strain names are followed by the name of the United States state (in parentheses) in which they were isolated. Each of the remaining columns represents a different DNA probe from Table 1, going from left to right across each plasmid map (orientation as in references 8 and12). −, no hybridization; +, hybridization occurred with a plasmid similar in size (<15% different) to the B31 plasmid from which the probe was derived (hybridization to other plasmids may also have occurred); + and ✙, hybridization toonly a plasmid(s) >15% different in size from the B31 plasmid from which the probe was derived; ✙, hybridization in that strain only to a plasmid(s) of a size >10% different from the plasmid(s) with which other probes from that B31 plasmid react.

  • Table 4.

    B. garinii and B. afzelii linear plasmid hybridization targetsa

    Strain [passage no.] (location)SourceResults of hybridization with strain B31 plasmid probes
    lp17 (CL47)lp25 (DE21)lp28-1 (DD60)lp28-2 (EI58)lp28-3 (CQ68)lp28-4 (CV69)lp36 (CQ33)lp38 (DH46)lp54 (CM64)lp56 (EK58)
    B. garinii
     153 [11] (FR)R. Marconi22, (34)(37)—34, 4835, (54)48—225434
     FujiP2 (JA)R. Johnson23, (28)25—28(54)29, (23)223054, (20)23, 31
     G1 (GE)T. Schwan21, (30)(30)——(54)—(21)(22)(54)(20)
     G25 [8] (SW)R. Marconi21, (30)30——(54)—21(22)5420
     IP89 (RU)R. Johnson22(30)—29ND(29)22305631
     IP90 (RU)T. Schwan23, (35, 37, 42)(36.5)—4235, 5434232354—
     IR210 (RU)I. Schwartz22, 30, (38)(30, 38)——(54)362136, 38, (22)5420, 37
     Las (AU)I. Schwartz22, (35)———(54)—21(22)5420
     NBS23a (SW)I. Schwartz23(38)——(54)(40)—2253—
     NBS23b (SW)I. Schwartz23———54(32)—22(53)—
     PBi (GE)T. Schwan22, 3130——54(25)21(22)5420
     VSBP [10] (ST)R. Marconi(21, 30)27.5——(54)36.5(21)36, (22)55(20)
    B. afzelii
     AO1 (NL)R. Marconi2656——(54)ND——(56)—
     EMC1 (SW)R. Marconi25, (34)——26, 29(54)34—(25)54, (24)(25)
     HT10 (JA)R. Marconi23, (34)30—25(54)34, (25)—(25)54, (26)(25)
     IP21 (RU)R. Marconi25, (28)——28(54)32, (25)—(25)53, (28)(25)
     PGau (GE)T. Schwan2527—29(54)(34)—(25)54, (24)—
     PKo [5] (GE)R. Marconi2627—27(54)(34)—(26)54, (24)(32)
     UM01 (SW)R. Marconi25, (30)27—30(54)(25)—(25.5)54, (24, 30)(25)
     UO1 (SW)R. Marconi23, (34, 37, 41)24 (37)—4235, 543423.52454—
    • ↵a All cultures were low passage, exact passage number is given where it is known, and country where the strain was isolated is given in parentheses (AU, Austria; FR, France; GE, Germany; JA, Japan; NL, The Netherlands; RU, Russia; SW, Sweden; ST, Switzerland). Values are sizes (in kilobase pairs) of linear plasmids that hybridized to the probes (listed in Table 1) given at the top of each column; values in parentheses indicate less intense hybridization. ND, not determined; —, no hybridization.

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Distribution of Twelve Linear Extrachromosomal DNAs in Natural Isolates of Lyme Disease Spirochetes
Nanette Palmer, Claire Fraser, Sherwood Casjens
Journal of Bacteriology May 2000, 182 (9) 2476-2480; DOI: 10.1128/JB.182.9.2476-2480.2000

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Distribution of Twelve Linear Extrachromosomal DNAs in Natural Isolates of Lyme Disease Spirochetes
Nanette Palmer, Claire Fraser, Sherwood Casjens
Journal of Bacteriology May 2000, 182 (9) 2476-2480; DOI: 10.1128/JB.182.9.2476-2480.2000
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KEYWORDS

Borrelia burgdorferi Group
DNA, Bacterial
plasmids

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