RecBCD

Template:Short description Template:Infobox enzyme Exodeoxyribonuclease V (EC 3.1.11.5, RecBCD, Exonuclease V, Escherichia coli exonuclease V, E. coli exonuclease V, gene recBC endoenzyme, RecBC deoxyribonuclease, gene recBC DNase, gene recBCD enzymes) is an enzyme of E. coli that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host of other factors.<ref name=Smith2012>Template:Cite journal</ref><ref name="isbn1-55581-232-5">Template:Cite book</ref> The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA.<ref name="pmid15538360">Template:Cite journal</ref> It catalyses exonucleolytic cleavage (in the presence of ATP) in either 5′- to 3′- or 3′- to 5′-direction to yield 5′-phosphooligonucleotides.

Structure

The enzyme complex is composed of three different subunits called RecB, RecC, and RecD and hence the complex is named RecBCD (Figure 1). Before the discovery of the recD gene,<ref name="pmid3526335">Template:Cite journal</ref> the enzyme was known as “RecBC.” Each subunit is encoded by a separate gene:

gene	chain	protein	function
RecB	β	Template:Uniprot	3'-5' helicase, nuclease
RecC	γ	Template:Uniprot	Recognizes Chi (crossover hotspot instigator)
RecD	α	Template:Uniprot	5'-3' helicase

Function

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File:Chi Recombination Model for Wikipedia.tif

Figure 2 RecBCD pathway of homologous recombination where ATP is in excess.

Both the RecD and RecB subunits are helicases, i.e., energy-dependent molecular motors that unwind DNA (or RNA in the case of other proteins). The RecB subunit in addition has a nuclease function.<ref name="pmid9448271">Template:Cite journal</ref> Finally, RecBCD enzyme (perhaps the RecC subunit) recognizes a specific sequence in DNA, 5'-GCTGGTGG-3', known as Chi (sometimes designated with the Greek letter χ).

RecBCD is unusual amongst helicases because it has two helicases that travel with different rates<ref name="pmid12815437">Template:Cite journal</ref> and because it can recognize and be altered by the Chi DNA sequence.<ref name="pmid1535156">Template:Cite journal</ref><ref name="pmid18079176">Template:Cite journal</ref> RecBCD avidly binds an end of linear double-stranded (ds) DNA. The RecD helicase travels on the strand with a 5' end at which the enzyme initiates unwinding, and RecB on the strand with a 3' end. RecB is slower than RecD, so that a single-stranded (ss) DNA loop accumulates ahead of RecB (Figure 2). This produces DNA structures with two ss tails (a shorter 3’ ended tail and a longer 5’ ended tail) and one ss loop (on the 3' ended strand) observed by electron microscopy.<ref name="pmid6256081">Template:Cite journal</ref> The ss tails can anneal to produce a second ss loop complementary to the first one; such twin-loop structures were initially referred to as “rabbit ears.”

Mechanism of action

File:HR RecBCD RecA.svg

Figure 3 Beginning of the RecBCD pathway of homologous recombination where Mg²⁺ is in excess.

During unwinding the nuclease in RecB can act in different ways depending on the reaction conditions, notably the ratio of the concentrations of Mg²⁺ ions and ATP. (1) If ATP is in excess, the enzyme simply nicks the strand with Chi (the strand with the initial 3' end) (Figure 2).<ref>Template:Cite journal</ref><ref name="pmid3888405">Template:Cite journal</ref> Unwinding continues and produces a 3' ss tail with Chi near its terminus. This tail can be bound by RecA protein, which promotes strand exchange with an intact homologous DNA duplex.<ref name="pmid9230304">Template:Cite journal</ref> When RecBCD reaches the end of the DNA, all three subunits disassemble and the enzyme remains inactive for an hour or more;<ref name="pmid10197988">Template:Cite journal</ref> a RecBCD molecule that acted at Chi does not attack another DNA molecule. (2) If Mg²⁺ ions are in excess, RecBCD cleaves both DNA strands endonucleolytically, although the 5' tail is cleaved less often (Figure 3).<ref name="pmid8384931">Template:Cite journal</ref> When RecBCD encounters a Chi site on the 3' ended strand, unwinding pauses and digestion of the 3' tail is reduced.<ref name="pmid18022364">Template:Cite journal</ref> When RecBCD resumes unwinding, it now cleaves the opposite strand (i.e., the 5' tail)<ref name="pmid7592661">Template:Cite journal</ref><ref name="pmid9119222">Template:Cite journal</ref> and loads RecA protein onto the 3’-ended strand.<ref name="pmid9230304"/> After completing reaction on one DNA molecule, the enzyme quickly attacks a second DNA, on which the same reactions occur as on the first DNA.

Although neither reaction has been verified by analysis of intracellular DNA, due to the transient nature of reaction intermediates, genetic evidence indicates that the first reaction more nearly mimics that in cells.<ref name="Smith2012" /> For example, the activity of Chi is influenced by nucleotides to its 3' side, both in cells and in reactions with ATP in excess but not with Mg²⁺ in excess [PMIDs 27401752, 27330137]. RecBCD mutants lacking detectable exonuclease activity retain high Chi hotspot activity in cells and nicking at Chi outside cells.<ref name="pmid17110484">Template:Cite journal</ref> A Chi site on one DNA molecule in cells reduces or eliminates Chi activity on another DNA, perhaps reflecting the Chi-dependent disassembly of RecBCD observed in vitro under conditions of excess ATP and nicking of DNA at Chi.<ref name="pmid7541534">Template:Cite journal</ref><ref name="pmid7603978">Template:Cite journal</ref>

Under both reaction conditions, the 3' strand remains intact downstream of Chi. The RecA protein is then actively loaded onto the 3' tail by RecBCD.<ref name="pmid9230304"/> At some undetermined point RecBCD dissociates from the DNA, although RecBCD can unwind at least 60 kb of DNA without falling off. RecA initiates exchange of the DNA strand to which it is bound with the identical, or nearly identical, strand in an intact DNA duplex; this strand exchange generates a joint DNA molecule, such as a D-loop (Figure 2). The joint DNA molecule is thought to be resolved either by replication primed by the invading 3’ ended strand containing Chi or by cleavage of the D-loop and formation of a Holliday junction. The Holliday junction can be resolved into linear DNA by the RuvABC complex or dissociated by the RecG protein. Each of these events can generate intact DNA with new combinations of genetic markers by which the parental DNAs may differ. This process, homologous recombination, completes the repair of the double-stranded DNA break.

RecD1 and RecD2

RecD enzymes are divided into two groups RecD1 (known as RecD) and RecD2.<ref name = Ramos2022>Template:Cite journal</ref> Many organisms have a recD gene even though the other members of a recBCD complex, i. e. rec B and recC, are not present.<ref name = Montague2009>Template:Cite journal</ref> For instance, the bacterium Deinococcus radiodurans, that has an extraordinary DNA repair capability, is an example of an organism that does not possess a recB or recC gene, and yet does have a recD gene.<ref name = Montague2009/> In the bacterium Escherichia coli, RecD protein is part of the well studied RecBCD complex that is necessary for recombinational DNA repair (as described above). In the bacterium Bacillus subtilis, RecD2 protein has a role as a modulator of replication restart and also a modulator of the RecA recombinase.<ref name = Ramos2022/> RecD2 may inhibit unwanted recombination events when replication forks are stalled, and also may have a role in displacing RecA protein from recombination intermediates in order to permit advance of the replication fork.<ref name = Ramos2022/>

Applications

RecBCD is a model enzyme for the use of single molecule fluorescence as an experimental technique used to better understand the function of protein-DNA interactions.<ref name="pmid11201750">Template:Cite journal</ref> The enzyme is also useful in removing linear DNA, either single- or double-stranded, from preparations of circular double-stranded DNA, since it requires a DNA end for activity.

External links

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