Sequence diversity among related genes for recognition of specific targets in DNA molecules

Gough, Jill; Murray, Noreen E.; Brenner, Sydney

doi:10.1016/s0022-2836(83)80047-3

Cited by 470 publications

(192 citation statements)

References 41 publications

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“…Escherichia coli strains JM109 (Yanisch-Perron et al, 1985), NM522 (Gough & Murray, 1983) (Miller, 1972) at 37 mC in a shaking incubator. Streptococcus mutans LT11 (Tao et al, 1993) Collection and grown at 37 mC in an anaerobic chamber in CDC broth [1 %, w\v, trypticase peptone and 1 %, w\v, trypticase soy broth (Difco), 1 %, w\v, yeast extract (Oxoid), 5 mg NaCl ml − ", 400 µg -cysteine ml − " (Sigma)] containing 5 µg haemin ml − " (Sigma), 2 µg menadione ml − " (Sigma) and 2% (v\v) horse serum (Commonwealth Serum Laboratories).…”

Section: Methodsmentioning

confidence: 99%

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set

et al. 2002

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The design and evaluation of a set of universal primers and probe for the amplification of 16S rDNA from the Domain Bacteria to estimate total bacterial load by real-time PCR is reported. Broad specificity of the universal detection system was confirmed by testing DNA isolated from 34 bacterial species encompassing most of the groups of bacteria outlined in Bergey's Manual of Determinative Bacteriology. However, the nature of the chromosomal DNA used as a standard was critical. A DNA standard representing those bacteria most likely to predominate in a given habitat was important for a more accurate determination of total bacterial load due to variations in 16S rDNA copy number and the effect of generation time of the bacteria on this number, since rapid growth could result in multiple replication forks and hence, in effect, more than one copy of portions of the chromosome. The validity of applying these caveats to estimating bacterial load was confirmed by enumerating the number of bacteria in an artificial sample mixed in vitro and in clinical carious dentine samples. Taking these parameters into account, the number of anaerobic bacteria estimated by the universal probe and primers set in carious dentine was 40-fold greater than the total bacterial load detected by culture methods, demonstrating the utility of real-time PCR in the analysis of this environment.

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Section: Methodsmentioning

confidence: 99%

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set

et al. 2002

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“…Recent study in Klebsiella shows the existence of another subfamily in type I R-M enzymes, type IE (10). Whereas M-and R-subunits are highly conserved within a family, S-subunits are variable in two large regions that constitute domains for recognizing the target DNA sequences (target recognition domain, TRD) (11)(12)(13). TRDs in the Ssubunit are separated by a conserved region (CR) (central CR, CCR) and an additional CR is attached to the C terminus (distal CR, DCR) (14).…”

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confidence: 99%

Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications

Kim

DeGiovanni

Jancarik

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-Å resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel ␣-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences. structural genomics ͉ gi 15669898

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“…Escherichia coli strains employed as hosts for constructing and propagating plasmids were NM522 (Gough & Murray, 1983) Yanisch-Perron et al, 1985). Luria broth was used for the culture of E. coli and supplemented with ampicillin for the selection of the transformants (Sambrook et al, 1989).…”

Section: Methodsmentioning

confidence: 99%

Thiamin auxotrophy in yeast through altered cofactor dependence of the enzyme acetohydroxyacid synthase

Byrne

Meacock

2001

Microbiology

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The THI1 gene of Saccharomyces cerevisiae has been identified and found to be allelic with the previously characterized gene ILV2 that encodes acetohydroxyacid synthase (AHAS). This enzyme catalyses the first step in the parallel biosyntheses of the branched-chain amino acids isoleucine and valine, using thiamin pyrophosphate (TPP) as a cofactor. The ilv2-thi1 allele encodes a functional AHAS enzyme with an altered dependence for the cofactor TPP resulting in the thiamin auxotrophic phenotype. Nucleotide sequence analysis and site-directed mutagenesis revealed that the thi1 mutation is a single base substitution which causes the conserved amino acid substitution D176E in the AHAS protein. This study therefore implicates aspartate 176 as another amino acid residue important either for the efficient binding of TPP by AHAS or for the functional stability of the holoenzyme.

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Sequence diversity among related genes for recognition of specific targets in DNA molecules

Cited by 470 publications

References 41 publications

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set

Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications

Thiamin auxotrophy in yeast through altered cofactor dependence of the enzyme acetohydroxyacid synthase

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