Path: utzoo!utgpu!watserv1!watmath!uunet!bionet!daemon From: GenBank-Updates@genbank.bio.net Newsgroups: bionet.molbio.genbank.updates Subject: Database Update Message-ID: <9004091814.AA11355@life.lanl.gov.LANL.GOV> Date: 9 Apr 90 18:14:56 GMT Sender: daemon@genbank.BIO.NET Distribution: bionet Lines: 112 Approved: lear@genbank.bio.net Checksum: 56339 7 LOCUS CEC38P 1455 bp ds-DNA BCT 31-AUG-1987 DEFINITION Plasmid ColE3-CA38 colicinogenic region containing colicin E3 (colE3), immunity (immE3), and putative hic and immE8 genes. ACCESSION J01574 J01575 M14038 KEYWORDS colicin; colicin release protein; immune response gene; lysis protein; unidentified reading frame. SOURCE Plasmid ColE3-CA38 (from E.coli) DNA. ORGANISM Plasmid Colicin E3-CA38 Prokaryota; Bacteria. REFERENCE 1 (bases 52 to 651) AUTHORS Masaki,H. and Ohta,T. TITLE A plasmid region encoding the active fragment and the inhibitor protein of colicin E3-CA38 JOURNAL FEBS Lett. 149, 129-132 (1982) STANDARD full staff_review REFERENCE 2 (bases 1 to 651) AUTHORS Mock,M., Miyada,C.G. and Gunsalus,R.P. TITLE Nucleotide sequence for the catalytic domain of colicin E3 and its immunity protein. Evidence for a third gene overlapping colicin JOURNAL Nucleic Acids Res. 11, 3547-3557 (1983) STANDARD full staff_review REFERENCE 3 (bases 640 to 1455) AUTHORS Watson,R.J., Lau,P.C.K., Vernet,T. and Visentin,L.P. TITLE Characterization and nucleotide sequence of a colicin-release gene in the hic region of plasmid ColE3-CA38 JOURNAL Gene 29, 175-184 (1984) STANDARD full staff_review REFERENCE 4 (bases 640 to 1455) AUTHORS Watson,R.J., Lau,P.C.K., Vernet,T. and Visentin,L.P. TITLE Corrigenda: Characterization and nucleotide sequence of a colicin-release gene in the hic region of plasmid ColE3-CA38 JOURNAL Gene 42, 351-355 (1986) STANDARD full staff_review COMMENT There are three ORFs distal to the immunity gene (immE3) in plasmid ColE3-CA38. ORF1 (bases 803 to 1066) is homologous to the E2-immunity gene in plasmid ColE2-P9. [3] has tentatively assigned ORF1 as the immE8 gene, but points out that a gene product has not yet been identified. Through deletion mutation studies this region was shown to be non-essential for colicin release. There are two overlapping reading frames further downstream of ORF1 (bases 1070 to 1246 and 1128 to 1421), which are homologous to the H' and H genes in plasmid CloDF13. In CloDF13 the H gene has been shown to be the lysis gene. Because of gene homology and in vitro studies which show that the ORF3 region is necessary for cell lysis, [3] has identified ORF3 as the hic gene. However, the in vitro studies do not exclude the possibility that ORF2 functions in colicin release or that it contributes to the Hic phenotype. There is also the possibility that the hic gene initiates at bp 1095 rather than 1128. The hic gene product also has not been identified. The immE8 and hic genes have been experimentally localized to the regions annotated in the Features Table. Their coding regions were deduced by finding the open reading frames and comparing them with sequences of genes in plasmids with like phenotypes [3]. There are six inverted repeats in the hic region. IR-2, IR-3, and IR-5 (positions 762-792, 964-984, 1131-1157) are "a" + "t" rich and show resemblance to SOS boxes. IR-1 an IR-4 (673-708 and 1072-1107) show attenuator-like structure. They may attenuate transcription of the hic gene after SOS induction to a level more optimal for colicin release. IR-6 (1287-1332) has a terminator-like structure. A Shine-Delgarno sequence is present at positions 376-379 between the colE3 and immE3 genes. The putative ribosome binding site for the hic gene can be found at 1117-1122. [1] refers to colicin E3 as protein A and the immunity protein as protein B. [2] refers to the colE3 gene as the ceaC gene and the immE3 gene as the ceaC gene. Draft entry and clean copy sequence kindly provide by R.J.Watson, May 1985 [3]. FEATURES from to/span description pept < 1 375 colicin E3 (AA at 1) pept 385 642 immunity protein-E3 pept 803 1066 immE8 protein (putative; gtg start codon) pept 1128 1271 lysis protein (putative) revision 755 756 gc in [4]; cg in [3] revision 1265 1267 gca in [4]; ga in [3] revision 1348 1349 tt in [4]; ttt in [3] BASE COUNT 473 a 214 c 352 g 416 t ORIGIN 150 bp upstream of Sau3A site. 1 gctatggaaa gcaggaagaa gaaagaagat aagaaaagga gtgctgaaaa taatttaaac 61 gatgaaaaga ataagcccag aaaaggtttt aaagattacg ggcatgatta tcatccagct 121 ccgaaaactg agaatattaa agggcttggt gatcttaagc ctgggatacc aaaaacacca 181 aagcagaatg gtggtggaaa acgcaagcgc tggactggag ataaagggcg taagatttat 241 gagtgggatt ctcagcatgg tgagcttgag gggtatcgtg ccagtgatgg tcagcatctt 301 ggctcatttg accctaaaac aggcaatcag ttgaaaggtc cagatccgaa acgaaatatc 361 aagaaatatc tttgagagga agttatggga cttaaattgg atttaacttg gtttgataaa 421 agtacagaag attttaaggg tgaggagtat tcaaaagatt ttggagatga cggttcagtt 481 atggaaagtc taggtgtgcc ttttaaggat aatgttaata acggttgctt tgatgttata 541 gctgaatggg tacctttgct acaaccatac tttaatcatc aaattgatat ttccgataat 601 gagtattttg tttcgtttga ttatcgtgat ggtgattggt gatcaaatat tatcagggat 661 gagttgatat acgggcttct agtgttcatg gatgaacgct ggagcctcca aatgtagaaa 721 tgttatattt tttattgagt tcttggttat aattgctccg caatgattta aataagcatt 781 atttaaaaca ttctcaggag aggtgaaggt ggagctaaaa aaaagtattg gtgattacac 841 tgaaaccgaa ttcaaaaaat ttattgaaga catcatcaat tgtgaaggtg atgaaaaaaa 901 acaggatgat aacctcgagt attttataaa tgttactgag catcctagtg gttctgatct 961 gatttattac ccagaaggta ataatgatgg tagccctgaa ggtgttatta aagagattaa 1021 agaatggcga gccgctaacg gtaagtcagg atttaaacag ggctgaaata tgaatgccgg 1081 ttgtttatgg atgaatggct ggcattcttt cacaacaagg agtcgttatg aaaaaaataa 1141 cagggattat tttattgctt cttgcagtca ttattctgtc tgcatgtcag gcaaactata 1201 tccgggatgt tcagggcggg accgtatctc cgtcatcaac agctgaagtg accggattag 1261 caacgcagta acccgaaatc ctctttgaca aaaacaaagc gtgtcaggct gattctgatg 1321 cgcttttttt ttgaaatgtc acaaaaattc catgtgggag atgggatcta aaatcctcgt 1381 gcagaacttt ccatccaggg ggagaaaact tgtcgttttg agccgttcgg tgttcagaac 1441 gcacgaaacc gatcg //