Actinomycete integrative and conjugative elements - PubMed (original) (raw)

Fig. 1

Structural organisation of (a) previously characterised and sequenced AICEs: pMEA100 of A. mediterranei; pMEA300 of A. methanolica; pSE211 of Sac. erythraea NRRL23338; pSAM2 of S. ambofaciens; pMR2 of M. rosaria; SLP1 of S. coelicolor A3(2); pSE101 of Sac. erythraea NRRL23338 (b) newly found AICEs: pSE101 and pSE222 of Sac. erythraea NRRL23338; AICE_Sav_3728 and AICE_Sav_3708 of S. avermitilis MA-4680; AICE_Sco_3250 and AICE_Sco_5349 of S. coelicolor A3(2); AICE_Mflv_3036 of Myc. gilvum PYR-GCK; AICE_Franean_5323 and AICE_Franean_6303 of Frankia sp. strain EAN1pec; AICE_Fraal_5456 of F. alni ACN14a; AICE_Sare_1562 and AICE_Sare_1922 of Sal. arenicola CNS205; AICE_Strop_0058 of Sal. tropica CNB-440. (c) AICE-remnants: _Sare_1208 of Sal. arenicola CNS205; _Sco_3997 of S. coelicolor A3(2); insertion _Sco_3937 of S. coelicolor A3(2). All newly found elements were named after the locus tag of their integrase gene. The prefixes of locus tags of the AICEs of Sac. erythraea NRRL23338 (SACE), S. coelicolor A3(2) (SCO), S. avermitilis MA-4680 (SAV), Frankia sp. strain EAN1pec (Franean), F. alni ACN14a (FRAAL), Sal. arenicola CNS205 (Sare), Sal. tropica CNB-440 (Strop), and Myc. gilvum PYR-GCK (Mflv) were left out for clarity. The size of the elements and the tRNA gene in which the elements are inserted are indicated below the element name at the right. Colour coding: orange, genes and sites involved in excision/integration; dark yellow, genes most likely involved in replication and its control; dark yellow with vertical black lines, repAM genes; dark yellow with vertical red lines, repSA genes; red bar, pMEA-specific hairpin structure; blue, putative conjugation genes; dark blue, putative main transfer genes; lime, putative regulatory genes; dark green, Nudix hydrolase genes; white, orfs with unknown functions; arrows with diagonal black lines, orfs with G + C content <55%; pink, transposons (tn), IS-elements (IS), and pseudogenes (ps); lavender with white diagonal lines, genes encoding DNA primase/polymerase (Prim-pol) proteins; red, genes with annotated function: gltA, glycosyltransferase; hnh, HNH-endonuclease signature; aph, aminoglycoside phosphotransferase; flav, flavoprotein; re, predicted restriction endonuclease; phd, encoding prevent-host-death family protein; thio, thioesterase superfamily protein; exp, predicted RND superfamily drug exporter; pept, peptidase C14 caspase catalytic subunit p20; HAD, HAD-superfamily hydrolase subfamily IA; ich, isochorismatase hydrolase; dprA; encoding DNA-protecting protein; rni, ribonuclease inhibitor; thiC, thiamine biosynthetic gene. The following colours correspond to genes shared by two or more elements, lavender, pMEA100, pSE211, SLP1, AICE_Sco_5349, AICE_Sare_1922, AICE_Strop_0058, _Sare_1208; grey, pSE222, AICE_Sare_1562, AICE_Sare_1922, AICE_Strop_0058; bright yellow (GGDEF-domain), pSE211, pSAM2, AICE_Sco_5349, AICE_Sare_1562; light blue, pSE101, pSE102, pSE222; bright green (single-stranded binding protein), pMEA100 and pSE222; plum, pSE211, pSE222; black, AICE_Sare_1562, AICE_Sare_1922, _Sare_1208; arrows with black confetti; highly similar protein clusters on AICE_Sco_3250 and _Sco_3997. Grey band between pSE101 and pSE102 indicates a highly similar DNA region. Black arrow head indicates partial protein coding sequence and back diagonal bar indicates a frameshift. The shared att site located between AICE_Sco_3708 and AICE_Sco_3728 is highlighted in both elements. Figure 1 was taken from te Poele et al. (2008)