scholarly journals Heteroduplex Formation, Mismatch Resolution, and Genetic Sectoring During Homologous Recombination in the Hyperthermophilic Archaeon Sulfolobus Acidocaldarius

2012 ◽  
Vol 3 ◽  
Author(s):  
Dominic Mao ◽  
Dennis W. Grogan
Keyword(s):  
Homologous Recombination ◽  
Sulfolobus Acidocaldarius ◽  
Hyperthermophilic Archaeon ◽  
Heteroduplex Formation

scholarly journals Discontinuity and Limited Linkage in the Homologous Recombination System of a Hyperthermophilic Archaeon

2010 ◽  
Vol 192 (18) ◽  
pp. 4660-4668 ◽  
Author(s):  
Dennis W. Grogan ◽  
Jananie Rockwood
Keyword(s):  
High Resolution ◽  
Homologous Recombination ◽  
Genetic Transformation ◽  
Base Pair ◽  
Average Length ◽  
Sulfolobus Acidocaldarius ◽  
Hyperthermophilic Archaeon ◽  
Short Intervals ◽  
Ectopic Recombination ◽  
Recombination System

ABSTRACT Genetic transformation of Sulfolobus acidocaldarius by a multiply marked pyrE gene provided a high-resolution assay of homologous recombination in a hyperthermophilic archaeon. Analysis of 100 Pyr+ transformants revealed that this recombination system could transfer each of 23 nonselected base pair substitutions to the recipient chromosome along with the selected marker. In 30% of the recombinants, donor markers were transferred as multiple blocks. In at least 40% of the recombinants, donor markers separated by 5 or 6 bp segregated from each other, whereas similar markers separated by 2 bp did not segregate. Among intermarker intervals, the frequency of recombination tract endpoints varied 40-fold, but in contrast to other recombination systems, it did not correlate with the length of the interval. The average length of donor tracts (161 bp) and the frequent generation of multiple tracts seemed generally consistent with the genetic properties observed previously in S. acidocaldarius conjugation. The efficiency with which short intervals of diverged pyrE sequence were incorporated into the genome raises questions about the threat of ectopic recombination in Sulfolobus spp. mediated by this apparently efficient yet permissive system.

UV Stimulation of Chromosomal Marker Exchange in Sulfolobus acidocaldarius: Implications for DNA Repair, Conjugation and Homologous Recombination at Extremely High Temperatures

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1407-1415 ◽  
Author(s):  
Katherine J Schmidt ◽  
Kristen E Beck ◽  
Dennis W Grogan
Keyword(s):  
Homologous Recombination ◽  
Incubation Temperature ◽  
Uv Light ◽  
Dna Lesions ◽  
Sulfolobus Acidocaldarius ◽  
Chromosomal Marker ◽  
Marker Exchange ◽  
Chromosomal Markers ◽  
Rate Of Decay ◽  
Uv Photoproducts

Abstract The hyperthermophilic archaeon Sulfolobus acidocaldarius exchanges and recombines chromosomal markers by a conjugational mechanism, and the overall yield of recombinants is greatly increased by previous exposure to UV light. This stimulation was studied in an effort to clarify its mechanism and that of marker exchange itself. A variety of experiments failed to identify a significant effect of UV irradiation on the frequency of cell pairing, indicating that subsequent steps are primarily affected, i.e., transfer of DNA between cells or homologous recombination. The UV-induced stimulation decayed rather quickly in parental cells during preincubation at 75°, and the rate of decay depended on the incubation temperature. Preincubation at 75° decreased the yield of recombinants neither from unirradiated parental cells nor from parental suspensions subsequently irradiated. We interpret these results as evidence that marker exchange is stimulated by recombinogenic DNA lesions formed as intermediates in the process of repairing UV photoproducts in the S. acidocaldarius chromosome.

Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 Å resolution 1 1Edited by R. Huber

1999 ◽  
Vol 285 (2) ◽  
pp. 689-702 ◽  
Author(s):  
Stefan Knapp ◽  
Simone Kardinahl ◽  
Niklas Hellgren ◽  
Gudrun Tibbelin ◽  
Günter Schäfer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Superoxide Dismutase ◽  
Sulfolobus Acidocaldarius ◽  
Hyperthermophilic Archaeon

scholarly journals Molecular Characteristics of Spontaneous Deletions in the Hyperthermophilic Archaeon Sulfolobus acidocaldarius

2003 ◽  
Vol 185 (4) ◽  
pp. 1266-1272 ◽  
Author(s):  
Dennis W. Grogan ◽  
Josh E. Hansen
Keyword(s):  
Consensus Sequence ◽  
Low Frequency ◽  
Sulfolobus Acidocaldarius ◽  
Nucleotide Sequence Analysis ◽  
Molecular Characteristics ◽  
Sequence Dependence ◽  
Stem Loop ◽  
High Frequencies ◽  
Hyperthermophilic Archaeon ◽  
Basic Parameters

ABSTRACT Prokaryotic genomes acquire and eliminate blocks of DNA sequence by lateral gene transfer and spontaneous deletion, respectively. The basic parameters of spontaneous deletion, which are expected to influence the course of genome evolution, have not been determined for any hyperthermophilic archaeon. We therefore screened a number of independent pyrimidine auxotrophs of Sulfolobus acidocaldarius for deletions and sequenced those detected. Deletions accounted for only 0.4% of spontaneous pyrE mutations, corresponding to a frequency of about 10−8 per cell. Nucleotide sequence analysis of five independent deletions showed no significant association of the endpoints with short direct repeats, despite the fact that several such repeats occur within the pyrE gene and that duplication mutations in pyrE reverted at high frequencies. Endpoints of the spontaneous deletions did not coincide with short inverted repeats or potential stem-loop structures. No consensus sequence common to all the deletions could be identified, although two deletions showed the potential of being stabilized by octanucleotide sequences elsewhere in pyrE, and another pair of deletions shared an octanucleotide at their 3′ ends. The unusually low frequency and low sequence dependence of spontaneous deletions in the S. acidocaldarius pyrE gene compared to other genetic systems could not be explained in terms of possible constraints imposed by the 5-fluoroorotate selection.

Characterization of a trehalose-degrading enzyme from the hyperthermophilic archaeon Sulfolobus acidocaldarius

2016 ◽  
Vol 122 (1) ◽  
pp. 47-51 ◽  
Author(s):  
Jeong Hyun Moon ◽  
Whiso Lee ◽  
Jihee Park ◽  
Kyoung-Hwa Choi ◽  
Jaeho Cha
Keyword(s):  
Sulfolobus Acidocaldarius ◽  
Hyperthermophilic Archaeon ◽  
Degrading Enzyme

Homologous recombination in Sulfolobus acidocaldarius: genetic assays and functional properties

2009 ◽  
Vol 37 (1) ◽  
pp. 88-91 ◽  
Author(s):  
Dennis W. Grogan
Keyword(s):  
Homologous Recombination ◽  
Functional Properties ◽  
Point Mutations ◽  
Sulfolobus Acidocaldarius ◽  
Intragenic Recombination ◽  
Chromosomal Markers ◽  
Cell To Cell Transfer ◽  
Initial Results ◽  
Pyre Gene

HR (homologous recombination) is expected to play important roles in the molecular biology and genetics of archaea, but, so far, few functional properties of archaeal HR have been measured in vivo. In the extreme thermoacidophile Sulfolobus acidocaldarius, a conjugational mechanism of DNA transfer enables quantitative analysis of HR between chromosomal markers. Early studies of this system indicated that HR occurred frequently between closely spaced mutations within the pyrE gene, and this result was later supported by various analyses involving defined point mutations and deletions. These properties of intragenic HR suggested a non-reciprocal mechanism in which donor sequences become incorporated into the recipient genome as short segments. Because fragmentation of donor DNA during cell-to-cell transfer could not be excluded from contributing to this result, subsequent analyses have focused on electroporation of selectable donor DNA directly into recipient strains. For example, S. acidocaldarius was found to incorporate synthetic ssDNA (single-stranded DNA) of more than ∼20 nt readily into its genome. With respect to various molecular properties of the ssDNA substrates, the process resembled bacteriophage λRed-mediated ‘recombineering’ in Escherichia coli. Another approach used electroporation of a multiply marked pyrE gene to measure donor sequence tracts transferred to the recipient genome in individual recombination events. Initial results indicate multiple discontinuous tracts in the majority of recombinants, representing a relatively broad distribution of tract lengths. This pattern suggests that properties of the HR process could, in principle, account for many of the apparent peculiarities of intragenic recombination initiated by S. acidocaldarius conjugation.

scholarly journals The Extent of Migration of the Holliday Junction Is a Crucial Factor for Gene Conversion in Rhizobium etli

2009 ◽  
Vol 191 (15) ◽  
pp. 4987-4995 ◽  
Author(s):  
Mildred Castellanos ◽  
David Romero
Keyword(s):  
Homologous Recombination ◽  
Gene Conversion ◽  
Holliday Junction ◽  
Relative Role ◽  
Rhizobium Etli ◽  
Wild Type ◽  
Migration Activity ◽  
Efficient System ◽  
In The Wild ◽  
Heteroduplex Formation

ABSTRACT Gene conversion, defined as the nonreciprocal transfer of DNA, is one result of homologous recombination. Three steps in recombination could give rise to gene conversion: (i) DNA synthesis for repair of the degraded segment, (ii) Holliday junction migration, leading to heteroduplex formation, and (iii) repair of mismatches in the heteroduplex. There are at least three proteins (RuvAB, RecG, and RadA) that participate in the second step. Their roles have been studied for homologous recombination, but evidence of their relative role in gene conversion is lacking. In this work, we showed the effect on gene conversion of mutations in ruvB, recG, and radA in Rhizobium etli, either alone or in combination, using a cointegration strategy previously developed in our laboratory. The results indicate that the RuvAB system is highly efficient for gene conversion, since its absence provokes smaller gene conversion segments than those in the wild type as well as a shift in the preferred position of conversion tracts. The RecG system possesses a dual role for gene conversion. Inactivation of recG leads to longer gene conversion tracts than those in the wild type, indicating that its activity may hinder heteroduplex extension. However, under circumstances where it is the only migration activity present (as in the ruvB radA double mutant), conversion segments can still be seen, indicating that RecG can also promote gene conversion. RadA is the least efficient system in R. etli but is still needed for the production of detectable gene conversion tracts.

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