Escherichia coli HU protein has a role in the repair of abasic sites in DNA
Authors: Yoke W Kow
Barry Imhoff
Steven D Goodman
Bernard Weiss
David C I Hung
Antreas A Hindoyan
Randall M Story
Journal: Nucleic Acids Research (2007)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: HU protein; DNA binding; Escherichia coli; abasic site; tetrahydrofuran
Affiliations: Department of Radiation Oncology, Emory University School of Medicine, Clifton Road NE, Atlanta, GA 30322, USA. 

Abstract:  HU is one of the most abundant DNA binding proteins in Escherichia coli. We find that it binds strongly to DNA containing an abasic (AP) site or tetrahydrofuran (THF) (apparent K(d) approximately 50 nM). It also possesses an AP lyase activity that cleaves at a deoxyribose but not at a THF residue. The binding and cleavage of an AP site was observed only with the HUalphabeta heterodimer. Site-specific mutations at K3 and R61 residues led to a change in substrate binding and cleavage. Both K3A(alpha)K3A(beta) and R61A(alpha)R61A(beta) mutant HU showed significant reduction in binding to DNA containing AP site; however, only R61A(alpha)R61A(beta) mutant protein exhibited significant loss in AP lyase activity. Both K3A(alpha)K3A(beta) and R61K(alpha)R61K(beta) showed slight reduction in AP lyase activities. The function of HU protein as an AP lyase was confirmed by the ability of hupA or hupB mutations to further reduce the viability of an E. coli dut(Ts) xth mutant, which generates lethal AP sites at 37 degrees C; the hupA and hupB derivatives, respectively, had a 6-fold and a 150-fold lower survival at 37 degrees C than did the parental strain. These data suggest, therefore, that HU protein plays a significant role in the repair of AP sites in E. coli. 

Retracted: Yes

PubPeer comments:
 Figure 2. * Panel e (Group 5: DMH+hespertin - Post Initiation) appears to be a zoomed-in version of panel f (Group 6: DMH+Hesperatin - Entire period). Shown with pink boxes.  , 
 Figure 3. * Panel c (DMH+Hesperatin - Initiation) and panel d (DMH+Hespeartin - Post-Initiation) appear to show an area of overlap. Shown with red boxes. * Panel e and f also show a large area of overlap but are both labeled as  DMH+Hesperatin (Entire period) , so this might be ok, albeit confusing. Shown with blue boxes.  , 
 Tables 3 to 5 show an unexpected narrow range of standard deviations (SDs). The majority of the 46 SDs are between 7 and 10% of the mean value they belong to. Here is a histogram of the SD percentages, showing an unexpected narrow range of values, with only 2 SDs over 12.  This is a very unusual distribution of SDs in biological measurements. Could the authors please provide the raw data? Update: For comparison, here is a collage of 12 papers from other research groups to show the expected range of SDs. All of these use groups of 6 to 8 rats, and do similar measurements. I graphed their SDs in the same way as the graph above, but with the X axis up to 100%. Each of these graphs show a much wider and more even spread of SDs than the graph above.  , 
 November 2020 retraction found here: https: onlinelibrary.wiley.com doi 10.1002 ptr.6911  The above article, published online on August 17, 2012 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor in Chief, Angelo A. Izzo, and John Wiley and Sons Ltd. The retraction has been agreed to following concerns raised regarding the appearance of some images and the calculation of some standard deviations. The authors were unable to provide the original versions of Figures 2u20133, or to provide original data to support the calculation of the standard deviations presented in Tables 3u20135. I was not notified by the journal or the publisher. ,