Article Figures & Data
Figures
- 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.
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.
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
- Table 1.
ORFs on pCD1 of Y. pestis KIM5a
Geneb or ORF Function of product Orientation Beginning of ORF (bp) End of ORF (bp) No. of amino acids in product Isoelectric point of product Mass of product (kDa) repB(copB) Negative regulator of repAtranscription + 1171 1425 85 9.72 9.58 tap Required for translation ofrepA + 1667 1741 25 9.31 2.82 repA Plasmid replication + 1734 2600 289 10.96 33.55 Orf5 Unknown − 3645 3427 73 9.96 8.22 Orf7 Unknown + 4758 5186 143 4.39 15.78 ypkA (yopO) Targeted effector; Ser Thr kinase + 5204 7402 733 6.53 81.74 yopJ(yopP) Targeted effector; causes apoptosis in macrophages and interferes with cell signaling + 7798 8664 289 7.07 32.46 yopH Targeted effector; protein tyrosine kinase; interferes with cell signaling at focal adhesions + 10347 11753 469 8.68 50.87 lcrQ(yscM) Negative regulator of LCR expression − 16148 15801 116 6.34 12.41 yscL Type III secretion component − 17038 16373 222 4.57 24.65 yscK Type III secretion component − 17613 16984 210 6.75 23.99 yscJ Type III secretion component − 18347 17613 245 7.43 27.04 yscI Type III secretion component − 18701 18354 116 4.47 12.67 yscH(yopR) Secreted; unknown function − 19199 18702 166 5.14 18.35 yscG Type III secretion component − 19543 19196 116 6.60 13.07 yscF Type III secretion component − 19808 19545 88 7.13 9.49 yscE Type III secretion component − 20009 19809 67 7.31 7.61 yscD Type III secretion component − 21265 20006 420 5.85 46.93 yscC Type III secretion component − 23085 21262 608 6.49 67.35 yscB Unknown − 23504 23091 138 9.27 15.41 yscA Unknown − 23828 23730 33 9.82 3.86 lcrF (virF) Activator of LCR gene expression − 24722 23907 272 8.91 30.84 yscW (virG) YscC lipoprotein chaperone − 25241 24846 132 10.12 14.71 yscU Type III secretion component − 26881 25817 355 8.81 40.39 yscT Type III secretion component − 27666 26881 262 5.67 28.45 yscS Type III secretion component − 27929 27663 89 6.32 9.57 yscR Type III secretion component − 28584 27931 218 4.68 24.43 yscQ Type III secretion component − 29504 28581 308 5.08 34.42 yscP Type III secretion component − 30868 29501 456 5.44 50.42 yscO Type III secretion component − 31332 30868 155 7.84 19.00 yscN Type III secretion component − 32648 31329 440 6.48 47.81 lcrE(yopN) Secretion control + 32846 33727 294 5.07 32.67 tyeA Secretion and Yop targeting control + 33708 33986 93 4.21 10.75 Orf42 Unknown + 33973 34344 124 5.54 13.61 Orf43 Unknown + 34341 34709 123 6.32 13.76 Orf44 Unknown + 34706 35050 115 6.92 13.12 lcrD(yscV) Secretion + 35037 37151 705 5.04 77.81 lcrR Unknown + 37148 37588 147 10.27 16.46 lcrG Secretion control; efficient Yop targeting + 37630 37917 96 8.15 11.02 lcrV Diffusible effector; secretion and targeting control + 37919 38899 327 5.66 37.24 lcrH(sycD) YopB and YopD chaperone + 38912 39418 169 4.61 19.02 yopB Yop targeting + 39396 40601 402 7.09 41.83 yopD Yop targeting; negative regulator + 40620 41540 307 6.80 33.39 Orf54 Unknown − 42709 42386 108 9.66 12.61 yopM Targeted effector + 43481 44710 410 4.23 46.21 Orf60 Unknown − 46365 45946 140 7.79 15.81 Orf61 Unknown + 46637 47026 130 7.33 14.80 sycT YopT chaperone − 47468 47070 133 4.43 15.42 yopT Targeted effector − 48436 47468 323 9.13 36.31 yopK(yopQ) Yop targeting + 48936 49484 183 4.37 21.00 ylpA Pseudogene + 50089 50718 210 5.80 22.40 sopA Plasmid partitioning; negative regulator ofsopABtranscription + 52730 53896 389 5.82 43.41 sopB Plasmid partitioning; binds to sopCregion + 53896 54858 320 10.19 35.61 Orf73 Unknown + 56087 56362 92 6.16 10.10 Orf74 Unknown + 56355 56654 100 5.51 11.67 Orf75 Unknown − 56792 56496 99 9.88 11.19 yopE Targeted effector; causes actin depolymerization − 57453 56794 220 6.59 22.99 sycE (yerA) YopE chaperone + 57647 58039 131 4.49 14.65 sycH YopH chaperone + 60796 61221 142 4.81 15.76 Orf84 Unknown − 62897 62568 110 8.98 13.00 Orf85 Unknown − 63500 63036 155 4.97 17.71 yadA′ Pseudogene + 67532 67783 84 5.21 8.92 ′yadA Pseudogene + 67900 68835 312 6.84 32.47 ↵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 region Location (bp) % GC Entire pCD1 plasmid 0–70509 44.8 Replication region 1103–2935 48.3 sopABC 52628–55240 43.1 yadA′/′yadA 67532–68835 43.2 IS elements or regions IS100 12609–14562 51.4 IS1616 50753–51987 50.9 IS1616d 70056–782 51.1 IS1617 61336–62549 49.9 IS21p 58749–60418 55.1 Tn1000p 63528–66581 50.2 IS285/IS100 region 11939–15801 47.5 IS1617/Tn1000region 61231–67532 44.8 LCR genes or regions yscM-yopD (LCR cluster) 15801–41540 44.8 ypkA 5204–7402 48.1 yopJ 7798–8664 34.8 yopH 10347–11753 47.4 yopM 43418–44710 38.9 yopMupstream region 41540–43418 39.3 yopMdownstream region 44710–47070 37.6 yopT 48436–47468 43.1 yopK 48936–49484 33.5 ylpA 50089–50713 47.5 yopE 57453–56794 51.1 - Table 3.
IS element remnants
IS element homology Location (bp) Gene(s) presentb No. of inverted repeats present IS1616 4187–4519 ′OrfB 1 69062–69456 ′OrfA, OrfB′ 1 ISD1-likea 12265–12608 ′OrfB 0 14571–15326 OrfA, OrfB 1 49642–49942* ′OrfB′ 0 66594–66926* ′OrfB′ 0 IS1617 9218–9829 ′OrfB 1 IS1222 58073–58749 ′OrfB 1 60419–60470 None 1 IS285 11939–12249 None 1 41978–42191 Orf1′ 1 IS21 58748–60418 istA,istB′ 1 Tn1000 63528–66582 tnpR, ΔtnpA 1 IS6100-like 42247–42820 Δtnp ? 46470–46664 Δtnp ? ISRm3-like 44777–45191 Δtransposase ? IS1327-like 55656–56005 ΔtnpA ?
