Limits...
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).

Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I - Nucleic Acids Res. (2010)

Bottom Line: Subsequently, the protein, named R.PluTI, was expressed in vivo, purified and found to be a novel type IIF restriction enzyme that recognizes 5'-GGCGC/C-3' (/ indicates position of cleavage).These results suggested that they constitute a restriction-modification system, present on the putative mobile element.Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Japan.

ABSTRACT
Genome comparison and genome context analysis were used to find a putative mobile element in the genome of Photorhabdus luminescens, an entomopathogenic bacterium. The element is composed of 16-bp direct repeats in the terminal regions, which are identical to a part of insertion sequences (ISs), a DNA methyltransferase gene homolog, two genes of unknown functions and an open reading frame (ORF) (plu0599) encoding a protein with no detectable sequence similarity to any known protein. The ORF (plu0599) product showed DNA endonuclease activity, when expressed in a cell-free expression system. Subsequently, the protein, named R.PluTI, was expressed in vivo, purified and found to be a novel type IIF restriction enzyme that recognizes 5'-GGCGC/C-3' (/ indicates position of cleavage). R.PluTI cleaves a two-site supercoiled substrate at both the sites faster than a one-site supercoiled substrate. The modification enzyme homolog encoded by plu0600, named M.PluTI, was expressed in Escherichia coli and shown to protect DNA from R.PluTI cleavage in vitro, and to suppress the lethal effects of R.PluTI expression in vivo. These results suggested that they constitute a restriction-modification system, present on the putative mobile element. Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins.

Show MeSH

Related in: MedlinePlus

Genome organization of the PluTI RM complex. pluTIR and pluTIM genes are shown in solid boxes. The flanking 16-bp direct repeats are shown below. ISPlu6 indicates nucleotide sequence similarity to the 3'-end of ISPlu6 of IS982 family, while IS indicates homology to the 3'- and 5'-ends of IS copies from another subfamily of the IS982 family.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2875022&req=5

Figure 1: Genome organization of the PluTI RM complex. pluTIR and pluTIM genes are shown in solid boxes. The flanking 16-bp direct repeats are shown below. ISPlu6 indicates nucleotide sequence similarity to the 3'-end of ISPlu6 of IS982 family, while IS indicates homology to the 3'- and 5'-ends of IS copies from another subfamily of the IS982 family.

Mentions: A bioinformatic survey of systematic genome comparisons discovered, in the genome of a Photorhabdus luminescence strain, a subgenomic, potentially mobile unit containing a DNA methyltransferase homolog (plu0600) and three other genes, lying between plu0594 (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) and plu0602 (dihydrodipicolinate reductase) (Figure 1). This rod-shaped bacterium (classification: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobactereriaceae; Photorhabdus; Photorhabdus luminescens subsp. laumondii TTO1) lives symbiotically in the gut of nematodes that attack insect larvae and eventually kill their host using various toxins (26,33).Figure 1.


A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).

Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I - Nucleic Acids Res. (2010)

Genome organization of the PluTI RM complex. pluTIR and pluTIM genes are shown in solid boxes. The flanking 16-bp direct repeats are shown below. ISPlu6 indicates nucleotide sequence similarity to the 3'-end of ISPlu6 of IS982 family, while IS indicates homology to the 3'- and 5'-ends of IS copies from another subfamily of the IS982 family.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875022&req=5

Figure 1: Genome organization of the PluTI RM complex. pluTIR and pluTIM genes are shown in solid boxes. The flanking 16-bp direct repeats are shown below. ISPlu6 indicates nucleotide sequence similarity to the 3'-end of ISPlu6 of IS982 family, while IS indicates homology to the 3'- and 5'-ends of IS copies from another subfamily of the IS982 family.
Mentions: A bioinformatic survey of systematic genome comparisons discovered, in the genome of a Photorhabdus luminescence strain, a subgenomic, potentially mobile unit containing a DNA methyltransferase homolog (plu0600) and three other genes, lying between plu0594 (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) and plu0602 (dihydrodipicolinate reductase) (Figure 1). This rod-shaped bacterium (classification: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobactereriaceae; Photorhabdus; Photorhabdus luminescens subsp. laumondii TTO1) lives symbiotically in the gut of nematodes that attack insect larvae and eventually kill their host using various toxins (26,33).Figure 1.

Bottom Line: Subsequently, the protein, named R.PluTI, was expressed in vivo, purified and found to be a novel type IIF restriction enzyme that recognizes 5'-GGCGC/C-3' (/ indicates position of cleavage).These results suggested that they constitute a restriction-modification system, present on the putative mobile element.Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Japan.

ABSTRACT
Genome comparison and genome context analysis were used to find a putative mobile element in the genome of Photorhabdus luminescens, an entomopathogenic bacterium. The element is composed of 16-bp direct repeats in the terminal regions, which are identical to a part of insertion sequences (ISs), a DNA methyltransferase gene homolog, two genes of unknown functions and an open reading frame (ORF) (plu0599) encoding a protein with no detectable sequence similarity to any known protein. The ORF (plu0599) product showed DNA endonuclease activity, when expressed in a cell-free expression system. Subsequently, the protein, named R.PluTI, was expressed in vivo, purified and found to be a novel type IIF restriction enzyme that recognizes 5'-GGCGC/C-3' (/ indicates position of cleavage). R.PluTI cleaves a two-site supercoiled substrate at both the sites faster than a one-site supercoiled substrate. The modification enzyme homolog encoded by plu0600, named M.PluTI, was expressed in Escherichia coli and shown to protect DNA from R.PluTI cleavage in vitro, and to suppress the lethal effects of R.PluTI expression in vivo. These results suggested that they constitute a restriction-modification system, present on the putative mobile element. Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins.

Show MeSH
Related in: MedlinePlus