@article {826,
	title = {Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {98},
	year = {2001},
	month = {2001 Jul 17},
	pages = {8203-10},
	abstract = {Recombinational repair of replication forks can occur either to a crossover (XO) or noncrossover (non-XO) depending on Holliday junction resolution. Once the fork is repaired by recombination, PriA is important for restarting these forks in Escherichia coli. PriA mutants are Rec(-) and UV sensitive and have poor viability and 10-fold elevated basal levels of SOS expression. PriA sulB mutant cells and their nucleoids were studied by differential interference contrast and fluorescence microscopy of 4{\textquoteright},6-diamidino-2-phenylindole-stained log phase cells. Two populations of cells were seen. Eighty four percent appeared like wild type, and 16\% of the cells were filamented and had poorly partitioned chromosomes (Par(-)). To probe potential mechanisms leading to the two populations of cells, mutations were added to the priA sulB mutant. Mutating sulA or introducing lexA3 decreased, but did not eliminate filamentation or defects in partitioning. Mutating either recA or recB virtually eliminated the Par(-) phenotype. Filamentation in the recB mutant decreased to 3\%, but increased to 28\% in the recA mutant. The ability to resolve and/or branch migrate Holliday junctions also appeared crucial in the priA mutant because removing either recG or ruvC was lethal. Lastly, it was tested whether the ability to resolve chromosome dimers caused by XOs was important in a priA mutant by mutating dif and the C-terminal portion of ftsK. Mutation of dif showed no change in phenotype whereas ftsK1cat was lethal with priA2kan. A model is proposed where the PriA-independent pathway of replication restart functions at forks that have been repaired to non-XOs.},
	keywords = {Adenosine Triphosphatases, Bacterial Proteins, Cell Division, Chromosomes, Bacterial, Dimerization, DNA Helicases, Endodeoxyribonucleases, Escherichia coli, Escherichia coli Proteins, Exodeoxyribonuclease V, Exodeoxyribonucleases, Gene Expression, Membrane Proteins, Mutagenesis, Rec A Recombinases, Recombination, Genetic, SOS Response (Genetics)},
	issn = {0027-8424},
	doi = {10.1073/pnas.121007698},
	author = {McCool, J D and Sandler, S J}
}
@article {833,
	title = {RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange.},
	journal = {Genes Dev},
	volume = {12},
	year = {1998},
	month = {1998 May 1},
	pages = {1248-53},
	abstract = {With the discovery that the Saccharomyces cerevisiae Rad51 protein is both structurally and functionally similar to the Escherichia coli RecA protein, the RecA paradigm for homologous recombination was extended to the Eucarya. The ubiquitous presence of RecA and Rad51 protein homologs raises the question of whether this archetypal protein exists within the third domain of life, the Archaea. Here we present the isolation of a Rad51/RecA protein homolog from the archaeon Sulfolobus solfataricus, and show that this protein, RadA, possesses the characteristics of a DNA strand exchange protein: The RadA protein is a DNA-dependent ATPase, forms a nucleoprotein filament on DNA, and catalyzes DNA pairing and strand exchange.},
	keywords = {Adenosine Triphosphatases, Archaeal Proteins, Bacterial Proteins, DNA Helicases, DNA, Archaeal, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Genes, Archaeal, Nucleoproteins, Rad51 Recombinase, Rec A Recombinases, Recombinant Proteins, Recombination, Genetic, Sulfolobus},
	issn = {0890-9369},
	author = {Seitz, E M and Brockman, J P and Sandler, S J and Clark, A J and Kowalczykowski, S C}
}
@article {834,
	title = {Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms.},
	journal = {J Mol Evol},
	volume = {44},
	year = {1997},
	month = {1997 May},
	pages = {528-41},
	abstract = {Protein sequences with similarities to Escherichia coli RecA were compared across the major kingdoms of eubacteria, archaebacteria, and eukaryotes. The archaeal sequences branch monophyletically and are most closely related to the eukaryotic paralogous Rad51 and Dmc1 groups. A multiple alignment of the sequences suggests a modular structure of RecA-like proteins consisting of distinct segments, some of which are conserved only within subgroups of sequences. The eukaryotic and archaeal sequences share an N-terminal domain which may play a role in interactions with other factors and nucleic acids. Several positions in the alignment blocks are highly conserved within the eubacteria as one group and within the eukaryotes and archaebacteria as a second group, but compared between the groups these positions display nonconservative amino acid substitutions. Conservation within the RecA-like core domain identifies possible key residues involved in ATP-induced conformational changes. We propose that RecA-like proteins derive evolutionarily from an assortment of independent domains and that the functional homologs of RecA in noneubacteria comprise an array of RecA-like proteins acting in series or cooperatively.},
	keywords = {Amino Acid Sequence, Animals, Archaeal Proteins, Bacteria, Bacterial Proteins, Cell Cycle Proteins, Consensus Sequence, Conserved Sequence, DNA-Binding Proteins, Escherichia coli Proteins, Evolution, Molecular, Humans, Molecular Sequence Data, Phylogeny, Rad51 Recombinase, Rec A Recombinases, Sequence Alignment},
	issn = {0022-2844},
	author = {Brendel, V and Brocchieri, L and Sandler, S J and Clark, A J and Karlin, S}
}
@article {835,
	title = {recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae.},
	journal = {Nucleic Acids Res},
	volume = {24},
	year = {1996},
	month = {1996 Jun 1},
	pages = {2125-32},
	abstract = {The process of homologous recombination has been documented in bacterial and eucaryotic organisms. The Escherichia coli RecA and Saccharomyces cerevisiae Rad51 proteins are the archetypal members of two related families of proteins that play a central role in this process. Using the PCR process primed by degenerate oligonucleotides designed to encode regions of the proteins showing the greatest degree of identity, we examined DNA from three organisms of a third phylogenetically divergent group, Archaea, for sequences encoding proteins similar to RecA and Rad51. The archaeans examined were a hyperthermophilic acidophile, Sulfolobus sofataricus (Sso); a halophile, Haloferax volcanii (Hvo); and a hyperthermophilic piezophilic methanogen, Methanococcus jannaschii (Mja). The PCR generated DNA was used to clone a larger genomic DNA fragment containing an open reading frame (orf), that we refer to as the radA gene, for each of the three archaeans. As shown by amino acid sequence alignments, percent amino acid identities and phylogenetic analysis, the putative proteins encoded by all three are related to each other and to both the RecA and Rad51 families of proteins. The putative RadA proteins are more similar to the Rad51 family (approximately 40\% identity at the amino acid level) than to the RecA family (approximately 20\%). Conserved sequence motifs, putative tertiary structures and phylogenetic analysis implied by the alignment are discussed. The 5{\textquoteright} ends of mRNA transcripts to the Sso radA were mapped. The levels of radA mRNA do not increase after treatment with UV irradiation as do recA and RAD51 transcripts in E.coli and S.cerevisiae. Hence it is likely that radA in this organism is a constitutively expressed gene and we discuss possible implications of the lack of UV-inducibility.},
	keywords = {Amino Acid Sequence, Archaea, Base Sequence, Cell Cycle Proteins, DNA-Binding Proteins, Escherichia coli, Halobacteriaceae, Methanococcus, Models, Molecular, Molecular Sequence Data, Phylogeny, Rad51 Recombinase, Rec A Recombinases, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Sequence Alignment, Sulfolobus},
	issn = {0305-1048},
	author = {Sandler, S J and Satin, L H and Samra, H S and Clark, A J}
}
@article {842,
	title = {Homologous genetic recombination: the pieces begin to fall into place.},
	journal = {Crit Rev Microbiol},
	volume = {20},
	year = {1994},
	month = {1994},
	pages = {125-42},
	abstract = {One of the authors (AJC) acknowledges with gratitude the important role Fernando Bastarrachea played in the author{\textquoteright}s discovery that E. coli could carry out homologous genetic recombination by multiple pathways. This in turn led to the discovery of several genes, including recF, recO, and recR, whose role in recombination would not otherwise have been detected. Subsequent genetic and biochemical studies have led to a general formulation in which there are multiple nucleolytic ways to achieve a presynaptic intermediate bound to RecA protein. Postsynaptic events in the general formulation occur by means of multiple branch migration enzymes to form Holliday DNA structures and a specific nuclease to cleave them. The general formulation is built on synapsis catalyzed by RecA protein. A second RecA-independent synapsis catalyzed by RecT (and RecE?) protein is now under study and a third type independent of both RecA and RecT has apparently been discovered. How these will affect the general formulation remains to be seen. Some proteins, most prominently RecF, RecO, and RecR, have no role in the general formulation. The hypothesis is presented that these proteins act as a switch between replication and recombination by helping to convert replication to recombination intermediates. Universality of the general formulation is supported by the widespread occurrence of recA, recB, recC, and recD genes among bacteria. Recent discovery of recA-like genes in several eukaryotes further supports its universality. We have contributed additional support by sequencing a recA-like gene from an archaeal species, thus making it plausible that the mechanism of synapsis worked out for E. coli RecA protein will hold for all three organismal domains. The boundaries of the puzzle of homologous genetic recombination therefore seem complete and the pieces to the complex picture they encompass are falling into place.},
	keywords = {DNA Replication, Escherichia coli, Genes, Bacterial, Rec A Recombinases, Recombination, Genetic},
	issn = {1040-841X},
	doi = {10.3109/10408419409113552},
	author = {Clark, A J and Sandler, S J}
}
