@article {828,
	title = {The importance of repairing stalled replication forks.},
	journal = {Nature},
	volume = {404},
	year = {2000},
	month = {2000 Mar 2},
	pages = {37-41},
	abstract = {The bacterial SOS response to unusual levels of DNA damage has been recognized and studied for several decades. Pathways for re-establishing inactivated replication forks under normal growth conditions have received far less attention. In bacteria growing aerobically in the absence of SOS-inducing conditions, many replication forks encounter DNA damage, leading to inactivation. The pathways for fork reactivation involve the homologous recombination systems, are nonmutagenic, and integrate almost every aspect of DNA metabolism. On a frequency-of-use basis, these pathways represent the main function of bacterial DNA recombination systems, as well as the main function of a number of other enzymatic systems that are associated with replication and site-specific recombination.},
	keywords = {Bacteria, Bacterial Proteins, Chromosomes, Bacterial, DNA Replication, DNA, Bacterial, Escherichia coli, Recombination, Genetic, Replication Origin, SOS Response (Genetics)},
	issn = {0028-0836},
	doi = {10.1038/35003501},
	author = {Cox, M M and Goodman, M F and Kreuzer, K N and Sherratt, D J and Sandler, S J and Marians, K J}
}
@article {832,
	title = {Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker.},
	journal = {J Bacteriol},
	volume = {181},
	year = {1999},
	month = {1999 Feb},
	pages = {907-15},
	abstract = {Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species of Crenarcheota. The two most deeply branching archaeal radA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.},
	keywords = {Amino Acid Sequence, Archaea, Archaeal Proteins, Bacteria, Bacterial Proteins, Cloning, Molecular, DNA Primers, DNA Repair, DNA-Binding Proteins, Evolution, Molecular, Humans, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Recombinant Proteins, RNA, Ribosomal, 16S, Saccharomyces cerevisiae, Sequence Alignment},
	issn = {0021-9193},
	author = {Sandler, S J and Hugenholtz, P and Schleper, C and DeLong, E F and Pace, N R and Clark, A J}
}
@article {831,
	title = {Replication fork assembly at recombination intermediates is required for bacterial growth.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {96},
	year = {1999},
	month = {1999 Mar 30},
	pages = {3552-5},
	abstract = {PriA, a 3{\textquoteright} --> 5{\textquoteright} DNA helicase, directs assembly of a primosome on some bacteriophage and plasmid DNAs. Primosomes are multienzyme replication machines that contribute both the DNA-unwinding and Okazaki fragment-priming functions at the replication fork. The role of PriA in chromosomal replication is unclear. The phenotypes of priA null mutations suggest that the protein participates in replication restart at recombination intermediates. We show here that PriA promotes replication fork assembly at a D loop, an intermediate formed during initiation of homologous recombination. We also show that DnaC810, encoded by a naturally arising intergenic suppressor allele of the priA2::kan mutation, bypasses the need for PriA during replication fork assembly at D loops in vitro. These findings underscore the essentiality of replication fork restart at recombination intermediates under normal growth conditions in bacteria.},
	keywords = {Bacteria, Bacteriophage phi X 174, Base Sequence, DNA Polymerase III, DNA Replication, DNA-Binding Proteins, Escherichia coli, Molecular Sequence Data, Oligodeoxyribonucleotides, Open Reading Frames, Recombination, Genetic, Replication Protein A, Templates, Genetic},
	issn = {0027-8424},
	author = {Liu, J and Xu, L and Sandler, S J and Marians, K J}
}
@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}
}
