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Homing Endonucleases and Horizontal Gene Transfer in Bacteria and Bacteriophages
Stockholm University, Faculty of Science, Department of Molecular Biology and Functional Genomics.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Homing endonuclease genes (HEGs) are selfish genetic elements that mediate their own super-Mendelian inheritance. This is mediated by the homing endonuclease cleavage of a HEG- allele followed by recombination-repair with a HEG+ allele.

The majority of the HEGs are encoded in intervening sequences (IVSs). The insertion of the IVS interrupts the endonuclease recognition site, making the genome with the IVS resistant to further cleavage by homing endonucleases with specificity for that particular sequence, but susceptible for homing endonucleases with a target not affected by the IVS insert. In 39 studied strains of the Bacillus cereus group, 28 IVSs were found in the nrdIEF operon. Phylogenetic studies of these sequences showed a scattered distribution of the IVSs, indicating a frequent horizontal gene transfer and that there might be competition between the different IVSs in the nrdIEF operon in the Bacillaceae family. One novel group I intron was shown to encode a functional homing endonuclease with a GIY-(X)8-YIG motif, expanding the family motif to GIY-(X)8-11-YIG. Interestingly, by studying the known insertion sites for IVSs in the ribonuclotide reductase genes, we show that the majority of the insertions are at conserved motifs, indicating that conservation is important for IVS survival.

Most freestanding HEGs in bacteriophage T4 cleave both HEG+ and HEG- alleles, possibly providing a competitive advantage for the host organism when two phages infect the same bacterium. Two novel freestanding HEGs replace two putative HEGs in T4 in some T-even-like phages. The characterisation of these HEGs showed that both cleave double stranded DNA. SegH was shown to promote homing of its gene. Hef showed no homing, possibly due to general exclusion of other phages. The mobE putative HEG was shown to be homing proficient and showed strong general DNA degradation when expressed in Escherichia coli.

Place, publisher, year, edition, pages
Stockholm: Institutionen för molekylärbiologi och funktionsgenomik , 2007. , 70 p.
Keyword [en]
dsDNA cleavage, ribonucleotide reductase, GIY-YIG motif
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-7042ISBN: 978-91-7155-477-2 (print)OAI: oai:DiVA.org:su-7042DiVA: diva2:197528
Public defence
2007-09-21, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 8 C, Stockholm, 10:00
Opponent
Supervisors
Available from: 2007-08-30 Created: 2007-08-30Bibliographically approved
List of papers
1. A functional homing endonuclease in the Bacillus anthracis nrdE group I intron
Open this publication in new window or tab >>A functional homing endonuclease in the Bacillus anthracis nrdE group I intron
2007 (English)In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 189, no 14, 5293-5301 p.Article in journal (Refereed) Published
Abstract [en]

The essential Bacillus anthracis nrdE gene carries a self-splicing group I intron with a putative homing endonuclease belonging to the GIY-YIG family. Here, we show that the nrdE pre-mRNA is spliced and that the homing endonuclease cleaves an intronless nrdE gene 5 nucleotides (nt) upstream of the intron insertion site, producing 2-nt 3' extensions. We also show that the sequence required for efficient cleavage spans at least 4 bp upstream and 31 bp downstream of the cleaved coding strand. The position of the recognition sequence in relation to the cleavage position is as expected for a GIY-YIG homing endonuclease. Interestingly, nrdE genes from several other Bacillaceae were also susceptible to cleavage, with those of Bacillus cereus, Staphylococcus epidermidis (nrdE1), B. anthracis, and Bacillus thuringiensis serovar konkukian being better substrates than those of Bacillus subtilis, Bacillus lichenformis, and S. epidermidis (nrdE2). On the other hand, nrdE genes from Lactococcus lactis, Escherichia coli, Salmonella enterica serovar Typhimurium, and Corynebacterium ammoniagenes were not cleaved. Intervening sequences (IVSs) residing in protein-coding genes are often found in enzymes involved in DNA metabolism, and the ribonucleotide reductase nrdE gene is a frequent target for self-splicing IVSs. A comparison of nrdE genes from seven gram-positive low-G + C bacteria, two bacteriophages, and Nocardia farcinica showed five different insertion sites for self-splicing IVSs within the coding region of the nrdE gene.

National Category
Natural Sciences
Identifiers
urn:nbn:se:su:diva-24433 (URN)10.1128/JB.00234-07 (DOI)000248019700034 ()
Available from: 2007-08-30 Created: 2007-08-30 Last updated: 2011-09-09Bibliographically approved
2. Characterisation of a novel homing endonuclease and screening of intervening sequences in closely related Bacillus thuringiensis nrdIEF genes
Open this publication in new window or tab >>Characterisation of a novel homing endonuclease and screening of intervening sequences in closely related Bacillus thuringiensis nrdIEF genes
Article in journal (Refereed) Submitted
Identifiers
urn:nbn:se:su:diva-24434 (URN)
Note
Part of urn:nbn:se:su:diva-7042Available from: 2007-08-30 Created: 2007-08-30Bibliographically approved
3. SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages
Open this publication in new window or tab >>SegH and Hef: two novel homing endonucleases whose genes replace the mobC and mobE genes in several T4-related phages
2005 In: Nucleic Acids Research, ISSN 0305-1048, Vol. 33, no 19, 6203-6213 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24435 (URN)
Note
Part of urn:nbn:se:su:diva-7042Available from: 2007-08-30 Created: 2007-08-30Bibliographically approved
4. Ribonucleotide reductase genes as havens for self-splicing elements
Open this publication in new window or tab >>Ribonucleotide reductase genes as havens for self-splicing elements
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-24436 (URN)
Note
Part of urn:nbn:se:su:diva-7042Available from: 2007-08-30 Created: 2007-08-30 Last updated: 2010-01-13Bibliographically approved

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