The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames

ABSTRACTPhage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to theMyoviridaefamily and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical ofSpounavirinaemembers, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I introns. In addition, four genes encoding tRNAs were identified in phiIPLA-RODI. Comparative DNA sequence analysis showed high similarities with two phages, GH15 and 676Z, belonging to theTwort-like virusgenus (nucleotide identities of >84%); for phiIPLA-C1C, a high similarity with phage phiIBB-SEP1 was observed (identity of 80%). Challenge assays of phages phiIPLA-RODI and phiIPLA-C1C against planktonic staphylococcal cells confirmed their lytic ability, as they were able to remove 5 log units in 8 h. Exposure of biofilms to phages phiIPLA-RODI and phiIPLA-C1C reduced the amount of adhered bacteria to about 2 log units in both monospecies and dual-species biofilms, but phiIPLA-RODI turned out to be as effective as the mixture of both phages. Moreover, the frequencies of bacteriophage-insensitive mutants (BIMs) ofStaphylococcus aureusandS. epidermidiswith resistance to phiIPLA-RODI and phiIPLA-C1C were low, at 4.05 × 10−7± 2.34 × 10−9and 1.1 × 10−7± 2.08 × 10−9, respectively. Overall, a generally reduced fitness in the absence of phages was observed for BIMs, which showed a restored phage-sensitive phenotype in a few generations. These results confirm that lytic bacteriophages can be efficient biofilm-disrupting agents, supporting their potential as antimicrobials against staphylococcal infections.

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Nucleolar introns fromPhysarum flavicomumcontain insertion elements that may explain how mobile group I introns gained their open reading frames

Nucleic Acids Research ◽

10.1093/nar/22.22.4553 ◽

1994 ◽

Vol 22 (22) ◽

pp. 4553-4559 ◽

Cited By ~ 18

Author(s):

Anna Vader ◽

Jørund Naess ◽

Kari Haugli ◽

Finn Haugli ◽

Steinar Johansen

Keyword(s):

Open Reading Frames ◽

Group I Introns ◽

Group I ◽

Insertion Elements ◽

Reading Frames

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Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽

10.1093/genetics/143.2.777 ◽

1996 ◽

Vol 143 (2) ◽

pp. 777-788 ◽

Cited By ~ 2

Author(s):

Carole H Sellem ◽

Yves d'Aubenton-Carafa ◽

Michèle Rossignol ◽

Léon Belcour

Keyword(s):

Mitochondrial Genome ◽

Open Reading Frames ◽

Nucleotide Substitutions ◽

Sequence Comparisons ◽

Modular Evolution ◽

Group I ◽

Sequence Variations ◽

Type Strains ◽

Reading Frames ◽

Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

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Mobile Self-Splicing Group I Introns from thepsbA Gene of Chlamydomonas reinhardtii: Highly Efficient Homing of an Exogenous Intron Containing Its Own Promoter

Molecular and Cellular Biology ◽

10.1128/mcb.21.10.3472-3481.2001 ◽

2001 ◽

Vol 21 (10) ◽

pp. 3472-3481 ◽

Cited By ~ 16

Author(s):

Obed W. Odom ◽

Stephen P. Holloway ◽

Nita N. Deshpande ◽

Jaesung Lee ◽

David L. Herrin

Keyword(s):

Chlamydomonas Reinhardtii ◽

Open Reading Frames ◽

Group I Introns ◽

Resistance Marker ◽

Free Standing ◽

Spectinomycin Resistance ◽

Highly Efficient ◽

Group I ◽

Short Exon ◽

Self Splicing

ABSTRACT Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 andCr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16Srrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. TheCr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/μg of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp −88 and −194 (relative to the ORF) that stimulated homing and contained a possible bacterial (−10, −35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.

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A Novel DNA Polymerase Family Found inArchaea

Journal of Bacteriology ◽

10.1128/jb.180.8.2232-2236.1998 ◽

1998 ◽

Vol 180 (8) ◽

pp. 2232-2236 ◽

Cited By ~ 69

Author(s):

Yoshizumi Ishino ◽

Kayoko Komori ◽

Isaac K. O. Cann ◽

Yosuke Koga

Keyword(s):

Escherichia Coli ◽

Dna Polymerase ◽

Pyrococcus Furiosus ◽

Dna Polymerases ◽

Open Reading Frames ◽

Gene Products ◽

Polymerase Gene ◽

Hyperthermophilic Archaeon ◽

Dna Polymerase Ii ◽

Reading Frames

ABSTRACT One of the most puzzling results from the complete genome sequence of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is because no other DNA polymerase-like open reading frames (ORFs) were found besides one ORF having the typical α-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the second DNA polymerase) from the hyperthermophilic archaeonPyrococcus furiosus, which has also at least one α-like DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino, Genes Cells 2:499–512, 1997). The genes in M. jannaschiiencoding the proteins that are homologous to the DNA polymerase II ofP. furiosus have been located and cloned. The gene products of M. jannaschii expressed in Escherichia colihad both DNA polymerizing and 3′→5′ exonuclease activities. We propose here a novel DNA polymerase family which is entirely different from other hitherto-described DNA polymerases.

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A Self-Splicing Group I Intron in DNA Polymerase Genes of T7-Like Bacteriophages

Journal of Bacteriology ◽

10.1128/jb.186.23.8153-8155.2004 ◽

2004 ◽

Vol 186 (23) ◽

pp. 8153-8155 ◽

Cited By ~ 11

Author(s):

Richard P. Bonocora ◽

David A. Shub

Keyword(s):

Dna Polymerase ◽

Group I Intron ◽

Group I Introns ◽

Homing Endonucleases ◽

Structural Element ◽

Group I ◽

Close Relatives ◽

Self Splicing

ABSTRACT Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive bacteria. However, among the phages of enteric and other gram-negative proteobacteria, introns have been encountered only in phage T4 and several of its close relatives. Here we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymerase genes of ΦI and W31, phages that are closely related to T7. The introns belong to subgroup IA2 and both contain an open reading frame, inserted into structural element P6a, encoding a protein belonging to the HNH family of homing endonucleases. The introns splice efficiently in vivo and self-splice in vitro under mild conditions of ionic strength and temperature. We conclude that there is no barrier for maintenance of group I introns in phages of proteobacteria.

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