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Molecular Genomics

DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5

Robert D. Perry, Susan C. Straley, Jacqueline D. Fetherston, Debra J. Rose, Jason Gregor, Frederick R. Blattner
Robert D. Perry
Department of Microbiology and Immunology, University of Kentucky, Lexington, Kentucky 40536-0084, and
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Susan C. Straley
Department of Microbiology and Immunology, University of Kentucky, Lexington, Kentucky 40536-0084, and
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Jacqueline D. Fetherston
Department of Microbiology and Immunology, University of Kentucky, Lexington, Kentucky 40536-0084, and
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Debra J. Rose
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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Jason Gregor
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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Frederick R. Blattner
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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DOI: 10.1128/IAI.66.10.4611-4623.1998
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Figures

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  • Fig. 1.
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    Fig. 1.

    Genetic organization of the LCR plasmid, pCD1, ofY. pestis KIM5. The map shows significant ORFs and transposable elements as well as replication and partitioning regions. For genes on the outside of the map, transcription proceeds clockwise. Genes on the inside are transcribed from the complementary strand. TheoriR and sopC regions are not transcribed. The placement of transposable elements (solid boxes) does not indicate the direction of transcription. A d indicates a defective element, while a p indicates a partial element. Most IS remnants are not denoted on this figure.

  • Fig. 2.
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    Fig. 2.

    Genetic organization of the replication and partitioning regions of pCD1. (A) The replication region contains four genes (repB, copA, tap, and repA) and an origin of replication (oriR). Black boxes indicate the promoter regions for repB and repA; the promoter region for copA is not shown. (B) Thepar region possesses two putative trans-acting genes (sopA and sopB) and a putative DNA binding site (sopC). Arrowheads within the promoter region show the locations and orientations of short, imperfect repeats. The six 45-bp direct repeats that compose sopC are shown as open boxes, with the locations of five 16-bp inverted repeat structures designated by arrowheads. RBS, ribosome binding site. For both panels, arrows indicate the directions of transcription of individual genes, while locations within pCD1 are indicated by numbers that follow the numbering system in Fig. 1.

  • Fig. 3.
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    Fig. 3.

    Diagrammatic representation of four clusters of intact, defective, and partial IS elements in pCD1. A p or −p indicates that only part of the IS element is present. Ad indicates an IS element that is likely defective. Arrows show the presence of inverted repeats within IS elements. Each type of IS element is represented by a unique design that is maintained in each of the four panels. In panel D, the yadA′/′yadA pseudogene is represented as yadA. Numbers correspond to nucleotide positions in Fig. 1.

Tables

  • Figures
  • Table 1.

    ORFs on pCD1 of Y. pestis KIM5a

    Geneb or ORFFunction of productOrientationBeginning of ORF (bp)End of ORF (bp)No. of amino acids in productIsoelectric point of productMass of product (kDa)
    repB(copB)Negative regulator of repAtranscription+11711425859.729.58
    tapRequired for translation ofrepA+16671741259.312.82
    repAPlasmid replication+1734260028910.9633.55
    Orf5Unknown−36453427739.968.22
    Orf7Unknown+475851861434.3915.78
    ypkA (yopO)Targeted effector; Ser Thr kinase+520474027336.5381.74
    yopJ(yopP)Targeted effector; causes apoptosis in macrophages and interferes with cell signaling+779886642897.0732.46
    yopHTargeted effector; protein tyrosine kinase; interferes with cell signaling at focal adhesions+10347117534698.6850.87
    lcrQ(yscM)Negative regulator of LCR expression−16148158011166.3412.41
    yscLType III secretion component−17038163732224.5724.65
    yscKType III secretion component−17613169842106.7523.99
    yscJType III secretion component−18347176132457.4327.04
    yscIType III secretion component−18701183541164.4712.67
    yscH(yopR)Secreted; unknown function−19199187021665.1418.35
    yscGType III secretion component−19543191961166.6013.07
    yscFType III secretion component−1980819545887.139.49
    yscEType III secretion component−2000919809677.317.61
    yscDType III secretion component−21265200064205.8546.93
    yscCType III secretion component−23085212626086.4967.35
    yscBUnknown−23504230911389.2715.41
    yscAUnknown−2382823730339.823.86
    lcrF (virF)Activator of LCR gene expression−24722239072728.9130.84
    yscW (virG)YscC lipoprotein chaperone−252412484613210.1214.71
    yscUType III secretion component−26881258173558.8140.39
    yscTType III secretion component−27666268812625.6728.45
    yscSType III secretion component−2792927663896.329.57
    yscRType III secretion component−28584279312184.6824.43
    yscQType III secretion component−29504285813085.0834.42
    yscPType III secretion component−30868295014565.4450.42
    yscOType III secretion component−31332308681557.8419.00
    yscNType III secretion component−32648313294406.4847.81
    lcrE(yopN)Secretion control+32846337272945.0732.67
    tyeASecretion and Yop targeting control+3370833986934.2110.75
    Orf42Unknown+33973343441245.5413.61
    Orf43Unknown+34341347091236.3213.76
    Orf44Unknown+34706350501156.9213.12
    lcrD(yscV)Secretion+35037371517055.0477.81
    lcrRUnknown+371483758814710.2716.46
    lcrGSecretion control; efficient Yop targeting+3763037917968.1511.02
    lcrVDiffusible effector; secretion and targeting control+37919388993275.6637.24
    lcrH(sycD)YopB and YopD chaperone+38912394181694.6119.02
    yopBYop targeting+39396406014027.0941.83
    yopDYop targeting; negative regulator+40620415403076.8033.39
    Orf54Unknown−42709423861089.6612.61
    yopMTargeted effector+43481447104104.2346.21
    Orf60Unknown−46365459461407.7915.81
    Orf61Unknown+46637470261307.3314.80
    sycTYopT chaperone−47468470701334.4315.42
    yopTTargeted effector−48436474683239.1336.31
    yopK(yopQ)Yop targeting+48936494841834.3721.00
    ylpAPseudogene+50089507182105.8022.40
    sopAPlasmid partitioning; negative regulator ofsopABtranscription+52730538963895.8243.41
    sopBPlasmid partitioning; binds to sopCregion+538965485832010.1935.61
    Orf73Unknown+5608756362926.1610.10
    Orf74Unknown+56355566541005.5111.67
    Orf75Unknown−5679256496999.8811.19
    yopETargeted effector; causes actin depolymerization−57453567942206.5922.99
    sycE (yerA)YopE chaperone+57647580391314.4914.65
    sycHYopH chaperone+60796612211424.8115.76
    Orf84Unknown−62897625681108.9813.00
    Orf85Unknown−63500630361554.9717.71
    yadA′Pseudogene+6753267783845.218.92
    ′yadAPseudogene+67900688353126.8432.47
    • ↵a ORFs within transposable elements, as well as disrupted or partial ORFs (except for ylpA,yadA′, and ′yadA), are not included in the table.

    • ↵b Except for copB, yopN,yscV, and yerA, all alternate gene designations (in parentheses) are Y. enterocolitica terminology.copB, plasmid R100 terminology; yopN, Y. enterocolitica and Y. pseudotuberculosis terminology;yscV, proposed terminology change; yerA, Y. pseudotuberculosis terminology.

  • Table 2.

    GC compositions of selected genes and regions of pCD1

    Gene or regionLocation (bp)% GC
    Entire pCD1 plasmid0–7050944.8
    Replication region1103–293548.3
    sopABC52628–5524043.1
    yadA′/′yadA67532–6883543.2
    IS elements or regions
     IS10012609–1456251.4
     IS161650753–5198750.9
     IS1616d70056–78251.1
     IS161761336–6254949.9
     IS21p58749–6041855.1
     Tn1000p63528–6658150.2
     IS285/IS100 region11939–1580147.5
     IS1617/Tn1000region61231–6753244.8
    LCR genes or regions
     yscM-yopD (LCR cluster)15801–4154044.8
     ypkA5204–740248.1
     yopJ7798–866434.8
     yopH10347–1175347.4
     yopM43418–4471038.9
     yopMupstream region41540–4341839.3
     yopMdownstream region44710–4707037.6
     yopT48436–4746843.1
     yopK48936–4948433.5
     ylpA50089–5071347.5
     yopE57453–5679451.1
  • Table 3.

    IS element remnants

    IS element homologyLocation (bp)Gene(s) presentbNo. of inverted repeats present
    IS16164187–4519′OrfB1
    69062–69456′OrfA, OrfB′1
    ISD1-likea12265–12608′OrfB0
    14571–15326OrfA, OrfB1
    49642–49942*′OrfB′0
    66594–66926*′OrfB′0
    IS16179218–9829′OrfB1
    IS122258073–58749′OrfB1
    60419–60470None1
    IS28511939–12249None1
    41978–42191Orf1′1
    IS2158748–60418istA,istB′1
    Tn100063528–66582tnpR, ΔtnpA1
    IS6100-like42247–42820Δtnp?
    46470–46664Δtnp?
    ISRm3-like44777–45191Δtransposase?
    IS1327-like55656–56005ΔtnpA?
    • ↵a Members of this group have amino acid homology. Only those indicated by an asterisk show similarities at the nucleotide sequence level.

    • ↵b OrfA = lcrS; OrfB =lcrT.

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DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5
Robert D. Perry, Susan C. Straley, Jacqueline D. Fetherston, Debra J. Rose, Jason Gregor, Frederick R. Blattner
Infection and Immunity Oct 1998, 66 (10) 4611-4623; DOI: 10.1128/IAI.66.10.4611-4623.1998

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DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5
Robert D. Perry, Susan C. Straley, Jacqueline D. Fetherston, Debra J. Rose, Jason Gregor, Frederick R. Blattner
Infection and Immunity Oct 1998, 66 (10) 4611-4623; DOI: 10.1128/IAI.66.10.4611-4623.1998
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KEYWORDS

calcium
plasmids
Yersinia pestis

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