The DNA exonucleases of Escherichia coli

Abstract

DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB) and III (dnaQ/mutD), Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG) and X (exoX), the RecBCD, RecJ, and RecE exonucleases, SbcCD endo/exonuclease, the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo) and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.

RecG controls DNA amplification at double‐strand breaks and arrested replication forks

“…The products of the xseA , xonA and sbcDC genes (exonuclease VII, exonuclease I and SbcCD exo/endonuclease respectively) are the major 3′–5′ exonucleases in E. coli . They participate in several DNA repair and genome stability pathways and the reader is directed to review for a more detailed discussion of their functions. The over‐replication in the xseA xonA sbcDC mutant is very interesting and does indeed suggest the existence of a pathway of DNA amplification involving 3′ overhangs.…”

3′-Terminated Overhangs Regulate DNA Double-Strand Break Processing inEscherichia coli

“…The mutant degraded ∼10% of its DNA after 130 min of incubation ( Figure 7 ), which is close to the amount of DNA degraded in its unirradiated part ( Figure 7 ), and is greatly reduced compared to degradation in its ssExo + parental strain. On the other hand, DNA degradation in a strain lacking 5′–3′ ssExos RecJ and ExoVII ( Lovett 2011 ) was similar to that in wild-type bacteria amounting to 31 ± 4% of genomic DNA after 130 min of incubation ( Figure 7 ).…”

“…It was shown earlier that inactivation of ExoI, SbcCD, and ExoVII, ssExos that degrade 3′ overhangs, prevents “reckless” DNA degradation in a recA mutant ( Zahradka et al 2009 ; Repar et al 2013 ). We made a quadruple mutant deficient in ExoI, SbcCD, ExoVII, and Exonuclease X (ExoX), ssExos that trim 3′ overhangs ( Lovett 2011 ), and measured its DNA degradation. The mutant degraded ∼10% of its DNA after 130 min of incubation ( Figure 7 ), which is close to the amount of DNA degraded in its unirradiated part ( Figure 7 ), and is greatly reduced compared to degradation in its ssExo + parental strain.…”

“…However, we revealed two notable exceptions in the RecA-imposed control of DNA degradation, which enabled further insight into the mechanism of DSB processing regulation in E. coli . Namely, inactivation of four ssExos (ExoI, ExoVII, ExoX, and SbcCD) that degrade a 3′ tail ( Lovett 2011 ) greatly reduced DNA degradation in both RecA + and RecA − bacteria, making them an ExoV − phenocopy, even though the RecBCD enzyme is active in these cells and able to degrade DNA (as it prevented proliferation of the T4 2 phage, whose genome is blunt-ended). Since RecBCD poorly degrades fragmented chromosomes in cells lacking 3′–5′ ssExos while retaining ExoV activity, we infer that the enzyme is affected in binding to DNA, i.e.…”

A structural view of bacterial DNA replication

“…The structure of the catalytic N‐terminal domain of the ε subunit (ε‐NTD) of PolIII from E. coli was determined in 2002 by Hamdan et al The ε‐NTD adopts a five‐stranded mixed β‐sheet topology decorated by α helices. The N‐terminal domain belongs to the “ribonuclease H‐like” superfamily that includes many exonucleases . The active site is formed by residues contributed by α‐helices (α4 and α7) and strand β1 (Fig.…”