Involvement of phenylalanine 272 of DNA polymerase beta in discriminating between correct and incorrect deoxynucleoside triphosphates

DNA polymerase beta is a small monomeric polymerase that participates in base excision repair and meiosis [Sobol, R., et al. (1996) Nature 379, 183-186; Plug, A., et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 1327-1331]. A DNA polymerase beta mutator mutant, F272L, was identified by an in vivo genetic screen [Washington, S., et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 1321-1326]. Residue 272 is located within the deoxynucleoside triphosphate (dNTP) binding pocket of DNA polymerase beta according to the known DNA polymerase beta crystal structures [Pelletier, H., et al. (1994) Science 264, 1891-1893; Sawaya, M., et al. (1997) Biochemistry 36, 11205-11215]. The F272L mutant produces errors at a frequency 10-fold higher than that of wild type in vivo and in the in vitro HSV-tk gap-filling assay. F272L shows an increase in the frequency of both base substitution mutations and frameshift mutations. Single-enzyme turnover studies of misincorporation by wild type and F272L DNA polymerase beta demonstrate that there is a 4-fold decrease in fidelity of the mutant as compared to that of the wild type enzyme for a G:A mismatch. The decreased fidelity is due primarily to decreased discrimination between the correct and incorrect dNTP during ground-state binding. These results suggest that the phenylalanine 272 residue is critical for maintaining fidelity during the binding of the dNTP.     

Xenopus egg lysates repair heat-generated DNA nicks with an average patch size of 36 nucleotides.

Base excision repair (BER) is an essential DNA repair pathway since it processes spontaneous (endogenous) DNA damage such as abasic sites, oxidized and alkylated bases, as well as mismatches arising from deamination of cytosine and 5-methylcytosine. Some of these lesions are repaired by the exchange of a single deoxynucleotide [Dianov, G. et al. (1992) Mol. Cell. Biol. 12, 1605-1612; Wiebauer, K. and Jiricny, J. (1990) Proc. Natl. Acad. Sci. USA, 87, 5842-5845] or a few deoxynucleotides [Matsumoto, Y. et al. (1994) Mol. Cell. Biol., 14 6187-6197]. Here we report that DNA single strand breaks induced by hyperthermic conditions are repaired with an average patch size of approximately 36 nt in Xenopus laevis egg lysates.     

Milk, revealed "silent" chemistry: new mode of cycloretinal synthesis

Bovine milk is by far the most commonly consumed milk in the western world. The protein composition in milk consists of casein and whey proteins, of which β-lactoglobulin (BLG) is the principal constituent of the latter. Here we provide biochemical evidence that this milk protein, in purified form and in pasteurized store-bought milk, promotes the formation of cycloretinal (all-trans retinal dimer), and a variety of other cycloterpenals of biological relevance [Fishkin et al., Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 7091-7096; Fishkin et al., Chirality, 2004, 16, 637-641; Kim et al., Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 19273-19278]. Cycloretinal is an eye metabolite and among several toxic byproducts of the visual cycle firmly established to cause age-related macular degeneration. Experiments in rabbits further demonstrate that BLG/milk can survive the digestive system and promote this reaction in vivo [Caillard et al., Am. J. Physiol., 1994, 266(6), G1053-G1059]. Proteomic studies on age-related macular degeneration patients have detected BLG in the eye of these patients further suggesting that this milk protein could contribute to disease progression [Crabb et al., Proc. Natl. Acad. Sci. U. S. A., 2002, 99(23), 14682-14687].     

Differences underlying EGFR and HER2 oncogene addiction

Comment on: Faber AC, et al. Differential induction of apoptosis in HER2 and EGFR addicted cancers following PI3K inhibition. Proc Natl Acad Sci USA 2009; 106:19503-8.     

Chiroptical properties of diamino carboxylic acids

Diamino carboxylic acids have recently come to the attention of scientists working in the field of early life and its development. These are the monomers of a hypothetic early form of genetic material, the so-called Peptide Nucleic Acid (PNA) (Nielson et al., Proc Natl Acad Sci USA 2000;97:3868-3871). Since all biopolymers rely on a specific handedness of their building blocks, the question of symmetry breaking occurs in diamino acids and PNA in the same way as in amino acids and proteins. One possible mechanism for triggering this, is asymmetric photochemistry in interstellar/circumstellar matter by means of circularly polarized light (Bailey et al., Science 2005;281:672-674; Bailey, Orig Life Evol Biosphere 2001;21:167-183; Buscherm?hle, Astrophys J 2005;624:821-826; Meierhenrich, Angew Chem Int Ed Engl 2005;44:5630-5634). Here we have measured the CD-spectra of four chiral diamino carboxylic acids, three of which were found in the Murchison meteorite (Meierhenrich, Proc Natl Acad Sci USA 2004;101:9182-9186). The spectra show a uniform peak at 200 nm. These results and additional quantum mechanical calculations of the involved molecular orbitals support the assumption that the process of symmetry breaking in diamino acids does not depend significantly on the length of the side chain. This means that one process alone could suffice to lead to symmetry breaking in all four measured diamino carboxylic acids and might even to some extent be transferable to monoamino acids, the monomers of proteins.     

A two way street: The telomere and the DNA damage response

Comment on: Tanaka H, Mendonca MS, Bradshaw PS, Hoelz DJ, Malkas LH, Meyn MS, et al. DNA damage-induced phosphorylation of the human telomere-associated protein TRF2. Proc Natl Acad Sci USA 2005; 102:15539-15544.     

A novel role for Activation-induced cytidinedeaminase: Central B-cell tolerance

Comment on: Kuraoka M, et al. Proc Natl Acad Sci USA 2011; 108:11560-5     

Horizontal gene transfer in microbial genome evolution

Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to inter-organismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes, however, have shown that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. (Doolittle et al., 1990, J. Mol. Evol. 31, 383-388; Karlin et al., 1997, J. Bacteriol. 179, 3899-3913; Karlin et al., 1998, Annu. Rev. Genet. 32, 185-225; Lawrence and Ochman, 1998, Proc. Natl. Acad. Sci. USA 95, 9413-9417; Rivera et al., 1998, Proc. Natl. Acad. Sci. USA 95, 6239-6244; Campbell, 2000, Theor. Popul. Biol. 57 71-77; Doolittle, 2000, Sci. Am. 282, 90-95; Ochman and Jones, 2000, Embo. J. 19, 6637-6643; Boucher et al. 2001, Curr. Opin., Microbiol. 4, 285-289; Wang et al., 2001, Mol. Biol. Evol. 18, 792-800). Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the lateral movement of genes across vast phylogenetic distances. (Lane et al., 1988, Methods Enzymol. 167, 138-144; Lake and Rivera, 1996, Proc. Natl. Acad. Sci. USA 91, 2880-2881; Lake et al., 1999, Science 283, 2027-2028).     

The role of eIF5A in protein synthesis

Comment on: Henderson A, et al. Proc Natl Acad Sci USA 2011; 108:6415-9.     

You’d better catch that Wnt: Primitive hematopoiesis requires canonical Wnt signaling

Comment on: Tran HT, et al. Proc Natl Acad Sci USA 2010; 107:16160-5.     

A self-propelled biological process

Comment on : Park JE, et al. Proc Natl Acad Sci USA 2011; 108:8200-05.     

AGTR1 as a therapeutic target in ER-positive and ERBB-negative breast cancer cases

Comment on: Rhodes DR, et al. Proc Natl Acad Sci USA 2009; 106:10284-9.     

PARP-3, a DNA-dependent PARP with emerging roles in double-strand break repair and mitotic progression

Comment on: Boehler C, et al. Proc Natl Acad Sci USA 2011; 108:2783-8.     

Changing pace: Viral mimicry of an anaphase promoting complex subunit

Comment on: Mo M, et al. Proc Natl Acad Sci USA 2009; 106:19527-32.     

A general requirement for FcγRIIB co-engagement of agonistic anti-TNFR antibodies

Comment on: Li F, et al. Proc Natl Acad Sci USA 2012; 109:10966-71.     

Manipulation of single polymerase-DNA complexes: A mechanical view of DNA unwinding during replication

Comment on: Morin JA, et al. Proc Natl Acad Sci USA 2012; 109:8115-20.     

Recognizing the cooperative and independent mitochondrial functions of Parkin and PINK1

Comment on: Johnson BN, et al. Proc Natl Acad Sci USA 2012; 109:6283-8.     

Do transcription factories and TOP2B provide a recipe for chromosome translocations in therapy-related leukemia?

Comment on: Cowell IG, et al. Proc Natl Acad Sci USA 2012; 109:8989-94.     

Finding time: A daily clock in yeast

Comment on: Eelderink-Chen Z, et al. Proc Natl Acad Sci USA 2010; 107:2043-7.