RecA is a protein in E. coli involved in recombinational repair of damaged DNA and in SOS repair (also called error prone repair. RecA catalyzes strand pairing, or strand assimilation-the joining of two different DNAs by homologous base pairing with each other. RecA is also a genetic regulator, activating the synthesis of many proteins, including DNA repair proteins, that help a bacterium adapt to a variety of metabolic stresses. Bacteria carrying mutations in recA are defective in general recombination and DNA repair.

RecA is a multifunctional protein with Mr of about 38,000. In recombination it promotes the pairing of homologous strands, in connection with recombinational repair. Several strand-pairing reactions can be demonstrated in vitro, as summarized in Figure 25.23. For example, a circular, single-strand DNA can invade a homologous linear duplex (such as the linearized replicative form of phage X174 DNA). RecA-catalyzed strand invasion and assimilation reactions in vitro have three requirements: (1) sequence homology (at least 40-60 base pairs) between the reacting DNAs, (2) a free end on one or both of the reactants, and (3) a single-strand region on one or both of the partners.

In vitro studies of these reactions reveal five distinct steps in RecA-promoted strand assimilation (Figure 25.24). In step 1, RecA coats the single-strand DNA to form a nucleoprotein filament of regular structure, in which the DNA length is extended by about 50% relative to its length in a duplex. In step 2, known as synapsis, the coated single-strand DNA reacts with a duplex, not necessarily at a homologous sequence. In step 3, homologous alignment, the two DNAs move with respect to each other until homologous sequences come into contact. This process requires ATP, but that ATP need not be cleaved, because ATP S, a noncleavable analog of ATP, can substitute. In step 4, a joint molecule is formed by base pairing between the two reacting molecules. RecA catalyzes local denaturation of the duplex partner and strand exchange with the single-strand partner. Finally (step 5), branch migration, occurs, essentially a continuation of joint molecule formation. The incoming strand pairs with its homolog, using the energy of ATP cleavage to advance (in a 5' ---> 3' direction relative to the single-strand DNA) and displacing the other strand as it moves. In this respect, RecA acts as a helicase.

LexA is a repressor that binds to at least 15 different operators scattered about the E. coli genome. Each operator controls the transcription of one or more proteins that help the cell respond after environmental damage that might harm the genetic apparatus. These proteins include the gene products of uvrA and uvrB, involved in excision repair; umuC,D, involved in error-prone mutagenesis; sulA, involved in cell division control; recA itself; lexA itself; and several genes of unknown function, including dinA, dinB, and dinF. In a healthy cell, lexA and recA are expressed at low levels, with sufficient LexA protein to turn off the synthesis of the other SOS genes completely. LexA protein does not completely abolish either lexA transcription or that of recA. The trigger that activates the SOS system after damage is thought to be single-strand DNA. RecA binding within a gapped DNA activates a proteolytic activity of RecA (by a mechanism not yet clear) that results in cleavage of LexA. Intracellular levels of LexA thus decrease, removing the LexA barrier to recA transcription, as well as other DNA repair genes. RecA protein and DNA repair gene products accumulates in large amounts.

See also: Recombination Repair, RecA/SOS Response, SOS Regulon