The Multiple Cellular Roles of SMUG1 in Genome Maintenance and Cancer

Single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1) works to remove uracil and certain oxidized bases from DNA during base excision repair (BER). This review provides a historical characterization of SMUG1 and 5-hydroxymethyl-2′-deoxyuridine (5-hmdU) one important substrate of this enzyme. Biochemical and structural analyses provide remarkable insight into the mechanism of this glycosylase: SMUG1 has a unique helical wedge that influences damage recognition during repair. Rodent studies suggest that, while SMUG1 shares substrate specificity with another uracil glycosylase UNG2, loss of SMUG1 can have unique cellular phenotypes. This review highlights the multiple roles SMUG1 may play in preserving genome stability, and how the loss of SMUG1 activity may promote cancer. Finally, we discuss recent studies indicating SMUG1 has moonlighting functions beyond BER, playing a critical role in RNA processing including the RNA component of telomerase.     

Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation

DNA repair proteins participate in extensive protein−protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent “RPA−Spy−UNG2” complex could identify and excise uracil bases in duplex areas next to ssDNA−dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA−Spy−UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA−dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.     

Studies on the biosorption of Pb(II) ions using Pseudomonas putida

ABSTRACT

The complete removal of Pb(II) was achieved by intact Pseudomonas putida cells. The biosorption isotherm exhibited Langmuirian behaviour and followed pseudo-second-order rate kinetics. The standard Gibbs free energy change (?G°) for the biosorption of Pb(II) ions was found to be ?26.4 kJ mol^?1, attesting to a chemisorption process. Thermolysis of P. putida cells improved the Pb(II) binding capacity by around 27%. All the four components tested, namely DNA, protein, polysaccharide and lipid, were found to contribute to the uptake of Pb(II) ions. The possible mechanisms of Pb(II) binding by P. putida have been delineated.     

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.     

Statistical modeling and optimization for enhanced hyaluronic acid production by batch culture of Sreptococcus zooepidemicus via the supplement of uracil

This work is aimed to achieve the optimal hyaluronic acid (HA) production by batch culture of Streptococcus zooepidemicus via the supplement of nucleotide bases using response surface methodology (RSM). First, the influence of nucleotide bases (adenine, guanine, cytosine, thymine, and uracil) on microbial HA production was investigated using fractional factorial design (FFD). By a 2^5-2 FFD, uracil was found to be the most significant factor for cell growth and HA production, while the other nucleotide bases were shown to have no significant effects on cell growth and HA production. Also, the impact of uracil on cell growth and HA production was further investigated by RSM, where two variables were considered: uracil concentration and supplement time. The optimal uracil concentration and supplement time were found to be 0.051 g/L and 7 h, respectively, and the predicted maximal HA production reached 6.42 g/L. The maximal HA production increased from 5.0 g/L of the control without uracil supplement to 6.31 g/L at the optimal conditions in validation experiments.     

Bioactivity‐Guided Genome Mining Reveals the Lomaiviticin Biosynthetic Gene Cluster in Salinispora tropica

The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico‐chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo‐ and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB‐440 by a DNA interference bioassay to isolate DNA‐targeting enediyne polyketides. An organic extract of S. tropica showed DNA‐interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA‐interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.     

Relationship between Mutagenicity of Heterocyclic Aromatic Amines and Stability of Their DNA Adducts: A Study by Semi-empirical Molecular Orbital Method

Quantitative structure-mutagenicity correlations were investigated for heterocyclic aromatic amines (HCAs) by use of a DNA model with three-base pairs. DNA adducts of thirteen HCAs were optimized by the PM3 method and energy decrease, ΔE, of each HCA due to formation of a DNA adduct was obtained as the stability of the adduct. The calculations for the HCA-DNA adducts revealed the interaction between HCA's methyl group and DNA's phosphate, which plays an important role in the stabilization of the adducts. The ΔE values plotted against the logarithm of HCA's mutagenicity, M, provided an almost straight line with the regression coefficient (R) of ?0.89 (R ²= 0.79). This good correlation suggests that binding reaction between HCA's nitrenium ion and DNA is an important rate-determining step in the metabolic transformation of HCAs.     

Construction and analysis of a Pseudomonas-Saccharomyces microbial consortium for mcl-PHA production from xylose and octanoate

Microbial consortia have great potential for the production of polyhydroxyalkanoates (PHAs) due to their comprehensive capability. In this study, a microbial consortium consisting of Pseudomonas putida NBRC14164 and Saccharomyces cerevisiae SyBE_Sc01020078 was constructed where xylose was converted into nutrients utilizable to P. putida by S. cerevisiae to realize the production of medium-chain-length polyhydroxyalkanoates (mcl-PHAs) from xylose and octanoate, followed by a preliminary analysis of the interaction between the two strains. The optimal inoculation ratio consisted of 1% P. putida and 10% S. cerevisiae, and both strains exhibited the highest PHA production at their mid-exponential phase. The two microorganisms were grown in a mineral salt medium with xylose and octanoate as substrates without washing and cultured at 200 rpm. The mcl-PHA titre of this consortium was 295.7 mg/L, which was 150% higher than that of P. putida in pure culture. Metabolites analysis by gas chromatography–mass spectrometry revealed metabolic communication between P. putida and S. cerevisiae, whereby the former provided histidine, methionine, and leucine for the latter, while the latter converted xylose into lactic acid, which is a more accessible carbon source for the former.     

Recognition and Excision Properties of 8‐Halogenated‐7‐Deaza‐2′‐Deoxyguanosine as 8‐Oxo‐2′‐Deoxyguanosine Analogues and Fpg and hOGG1 Inhibitors

Cellular DNA continuously suffers various types of damage, and unrepaired damage increases disease progression risk. 8‐Oxo‐2′‐deoxyguanine (8‐oxo‐dG) is excised by repair enzymes, and their analogues are of interest as inhibitors and as bioprobes for study of these enzymes. We have developed 8‐halogenated‐7‐deaza‐2′‐deoxyguanosine derivatives that resemble 8‐oxo‐dG in that they adopt the syn conformation. In this study, we investigated their effects on Fpg (formamidopyrimidine DNA glycosylase) and hOGG1 (human 8‐oxoguanine DNA N‐glycosylase 1). Relative to 8‐oxo‐dG, Cl‐ and Br‐deaza‐dG were good substrates for Fpg, whereas they were less efficient substrates for hOGG1. Kinetics and binding experiments indicated that, although hOGG1 effectively binds Cl‐ and Br‐deaza‐dG analogues with low K_m values, their lower k_cat values result in low glycosylase activities. The benefits of the high binding affinities and low reactivities of 8‐oxo‐dG analogues with hOGG1 have been successfully applied to the competitive inhibition of the excision of 8‐oxoguanine from duplex DNA by hOGG1.     

A Single‐Electrode,Dual‐Potential Ferrocene–PNA Biosensor for the Detection of DNA

A Fc–PNA biosensor (Fc: ferrocenyl, C₁₀H₉Fe) was designed by using two electrochemically distinguishable recognition elements with different molecular information at a single electrode. Two Fc–PNA capture probes were therefore synthesized by N‐terminal labeling different dodecamer PNA sequences with different ferrocene derivatives by click chemistry. Each of the two strands was thereby tethered with one specific ferrocene derivative. The two capture probes revealed quasi‐reversible redox processes of the Fc^0/+ redox couple with a significant difference in their electrochemical half‐wave potentials of ΔE_1/2=160 mV. A carefully designed biosensor interface, consisting of a ternary self‐assembled monolayer (SAM) of the two C‐terminal cysteine‐tethered Fc–PNA capture probes and 6‐mercaptohexanol, was electrochemically investigated by square wave (SWV) and cyclic voltammetry (CV). The biosensor properties of this interface were analyzed by studying the interaction with DNA sequences that were complementary to either of the two capture probes by SWV. Based on distinct changes in both peak current and potential, a parallel identification of these two DNA sequences was successful with one interface design. Moreover, the primary electrochemical response could be converted by a simple mathematical analysis into a clear‐cut electrochemical signal about the hybridization event. The discrimination of single‐nucleotide polymorphism (SNP) was proven with a chosen single‐mismatch DNA sequence. Furthermore, experiments with crude bacterial RNA confirm the principal suitability of this dual‐potential sensor under real‐life conditions.     

DETECTION OF POLYCYCLIC AROMATIC COMPOUNDS IN SINGLE LIVING CELLS USING OPTICAL NANOPROBES

Exposure of mammalian cells to polycyclic aromatic compounds (PACs) such as the carcinogen benzo[a]pyrene (BaP) leads to the formation of DNA adducts N²-deoxyguanosine (dG) and N⁶-deoxyadenosine (dA) with adenine and guanine nucleotides, which are integral parts of DNA, RNA, and ATP. DNA adduct formation causes alteration of the DNA (RNA) sequence since neither adenine nor guanine can normally bind to its complementary nucleotide base, thymine (uracil) and cytosine respectively. The inability to form these bonds leads to mutations in the DNA double-helix structure during DNA replication, and eventually carcinogenesis. Therefore, the capability to detect and measure PAC species such as BaP in single living cells is important for studies required to establish the limits of BaP exposure necessary for carcinogenesis. Along these lines, we have developed antibody-based optical nanoprobes capable of detecting and measuring BaP in single living cells. The results obtained in this work demonstrate the practical application of antibody-based nanoprobes for performing measurements inside single living cells with their elements and their relationships intact.     

MTHFR Knockdown Assists Cell Defense against Folate Depletion Induced Chromosome Segregation and Uracil Misincorporation in DNA

Folate depletion causes chromosomal instability by increasing DNA strand breakage, uracil misincorporation, and defective repair. Folate mediated one-carbon metabolism has been suggested to play a key role in the carcinogenesis and progression of hepatocellular carcinoma (HCC) through influencing DNA integrity. Methylenetetrahydrofolate reductase (MTHFR) is the enzyme catalyzing the irreversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate that can control folate cofactor distributions and modulate the partitioning of intracellular one-carbon moieties. The association between MTHFR polymorphisms and HCC risk is inconsistent and remains controversial in populational studies. We aimed to establish an in vitro cell model of liver origin to elucidate the interactions between MTHFR function, folate status, and chromosome stability. In the present study, we (1) examined MTHFR expression in HCC patients; (2) established cell models of liver origin with stabilized inhibition of MTHFR using small hairpin RNA delivered by a lentiviral vector, and (3) investigated the impacts of reduced MTHFR and folate status on cell cycle, methyl group homeostasis, nucleotide biosynthesis, and DNA stability, all of which are pathways involved in DNA integrity and repair and are critical in human tumorigenesis. By analyzing the TCGA/GTEx datasets available within GEPIA2, we discovered that HCC cancer patients with higher MTHFR had a worse survival rate. The shRNA of MTHFR (shMTHFR) resulted in decreased MTHFR gene expression, MTHFR protein, and enzymatic activity in human hepatoma cell HepG2. shMTHFR tended to decrease intracellular S-adenosylmethionine (SAM) contents but folate depletion similarly decreased SAM in wildtype (WT), negative control (Neg), and shMTHFR cells, indicating that in cells of liver origin, shMTHFR does not exacerbate the methyl group supply in folate depletion. shMTHFR caused cell accumulations in the G2/M, and cell population in the G2/M was inversely correlated with MTHFR gene level (r = −0.81, p < 0.0001), MTHFR protein expression (r = −0.8; p = 0.01), and MTHFR enzyme activity (r = −0.842; p = 0.005). Folate depletion resulted in G2/M cell cycle arrest in WT and Neg but not in shMTHFR cells, indicating that shMTHFR does not exacerbate folate depletion-induced G2/M cell cycle arrest. In addition, shMTHFR promoted the expression and translocation of nuclei thymidine synthetic enzyme complex SHMT1/DHFR/TYMS and assisted folate-dependent de novo nucleotide biosynthesis under folate restriction. Finally, shMTHFR promoted nuclear MLH1/p53 expression under folate deficiency and further reduced micronuclei formation and DNA uracil misincorporation under folate deficiency. In conclusion, shMTHFR in HepG2 induces cell cycle arrest in G2/M that may promote nucleotide supply and assist cell defense against folate depletion-induced chromosome segregation and uracil misincorporation in the DNA. This study provided insight into the significant impact of MTHFR function on chromosome stability of hepatic tissues. Data from the present study may shed light on the potential regulatory mechanism by which MTHFR modulates the risk for hepatic malignancies.     

Photocaged Hoechst Enables Subnuclear Visualization and Cell Selective Staining of DNA in vivo

Selective targeting of DNA by means of fluorescent labeling has become a mainstay in the life sciences. While genetic engineering serves as a powerful technique and allows the visualization of nucleic acid by using DNA-targeting fluorescent fusion proteins in a cell-type- and subcellular-specific manner, it relies on the introduction of foreign genes. On the other hand, DNA-binding small fluorescent molecules can be used without genetic engineering, but they are not spatially restricted. Herein, we report a photocaged version of the DNA dye Hoechst33342 (pcHoechst), which can be uncaged by using UV to blue light for the selective staining of chromosomal DNA in subnuclear regions of live cells. Expanding its application to a vertebrate model organism, we demonstrate uncaging in epithelial cells and short-term cell tracking in vivo in zebrafish. We envision pcHoechst as a valuable tool for targeting and interrogating DNA with precise spatiotemporal resolution in living cells and wild-type organisms.     

Identification of Camphor Oxidation and Reduction Products in <Emphasis Type="Italic">Pseudomonas putida</Emphasis>: New Activity of the Cytochrome P450<Subscript>cam</Subscript> System

P450 enzymes are known for catalyzing hydroxylation reactions of non-activated C-H bonds. For example, P450_cam from Pseudomonas putida oxidizes (1R)-(+)-camphor to 5-exo-hydroxy camphor and further to 5-ketocamphor. This hydroxylation reaction proceeds via a catalytic cycle in which the reduction of dioxygen (O₂) is coupled to the oxidation of the substrate. We have observed that under conditions of low oxygen, P. putida and isolated P450_cam reduce camphor to borneol. We characterized the formation of borneol under conditions of low oxygen or when the catalytic cycle is shunted by artificial oxidants like m-chloro perbenzoic acid, cumene hydroperoxide, etc. We also tested the toxicity of camphor and borneol with P. putida and Escherichia coli. We have found that in P. putida borneol is less toxic than camphor, whereas in E. coli borneol is more toxic than camphor. We discuss a potental ecological advantage of the camphor reduction reaction for P. putida.     

Detection of Genomic Uracil Patterns

The appearance of uracil in the deoxyuridine moiety of DNA is among the most frequently occurring genomic modifications. Three different routes can result in genomic uracil, two of which do not require specific enzymes: spontaneous cytosine deamination due to the inherent chemical reactivity of living cells, and thymine-replacing incorporation upon nucleotide pool imbalances. There is also an enzymatic pathway of cytosine deamination with multiple DNA (cytosine) deaminases involved in this process. In order to describe potential roles of genomic uracil, it is of key importance to utilize efficient uracil-DNA detection methods. In this review, we provide a comprehensive and critical assessment of currently available uracil detection methods with special focus on genome-wide mapping solutions. Recent developments in PCR-based and in situ detection as well as the quantitation of genomic uracil are also discussed.     

Bioregeneration involving a coal-based adsorbent used for removing nitrophenol from water

Char produced from low rank coal briquettes is potentially a cheap adsorbent suitable for the removal of trace levels of soluble organic compounds from water. In this study, briquette char produced from Victorian low rank coal was used to adsorb the organic compound p-nitrophenol (PNP) from aqueous solution, where nitrophenol is representative of low molecular weight adsorbates. Once concentrated on the adsorbent, attempts were made to remove the PNP by desorption and biodegradation. Desorbed PNP was degraded to some degree by three bacteria (Pseudomonas putida, Arthrobacter sp., and Moraxella sp.). The rates of PNP biodegradation by the three bacteria were followed, together with the corresponding rates of formation of the nitrite ion degradation product. Evidence is presented to indicate large microbial floc particle formation for both Pseudomonas putida and Arthrobacter leads to loss of nitrite ion by denitrification. Removal of PNP from the adsorbent by desorption/biodegradation was shown to be much faster than by desorption alone, but not all nitrophenol was removed from the adsorbent by the desorption/biodegradation process. © 1998 Society of Chemical Industry     

Protein Interactions in the T7 DNA Replisome Facilitate DNA Damage Bypass

The DNA replisome inevitably encounters DNA damage during DNA replication. The T7 DNA replisome contains a DNA polymerase (gp5), the processivity factor thioredoxin (trx), a helicase‐primase (gp4), and a ssDNA‐binding protein (gp2.5). T7 protein interactions mediate this DNA replication. However, whether the protein interactions could promote DNA damage bypass is still little addressed. In this study, we investigated strand‐displacement DNA synthesis past 8‐oxoG or O⁶‐MeG lesions at the synthetic DNA fork by the T7 DNA replisome. DNA damage does not obviously affect the binding affinities between helicase, polymerase, and DNA fork. Relative to unmodified G, both 8‐oxoG and O⁶‐MeG—as well as GC‐rich template sequence clusters—inhibit strand‐displacement DNA synthesis and produce partial extension products. Relative to the gp4 ΔC‐tail, gp4 promotes DNA damage bypass. The presence of gp2.5 also promotes it. Thus, the interactions of polymerase with helicase and ssDNA‐binding protein facilitate DNA damage bypass. Accessory proteins in other complicated DNA replisomes also facilitate bypassing DNA damage in similar manner. This work provides new mechanistic information relating to DNA damage bypass by the DNA replisome.     

Gels of syndiotacticity-rich poly(vinyl alcohol)–water/dimethyl sulfoxide or – water/ethylene glycol solutions

Gels of syndiotacticity-rich poly(vinyl alcohol) (s-PVA) in mixed solvents of water/dimethyl sulfoxide (DMSO) or water/ethylene glycol (EG) were made by chilling at the temperatures of 0–70°C from those solutions with the polymer concentrations below 10g/dL. The melting points of the gels were measured warming the gel from the gelling temperature (T_gel) at a constant heating rate. The apparent enthalpy of fusion of a junction of gel, ΔH was estimated from the relation between the apparent melting temperature and the polymer concentration. The s-PVA gels made from the mixtures of the water/lower contents of DMSO or EG had a minimum at lower T_gel and a maximum ΔH at a higher T_gel. On the other hand, the s-PVA gels made from the mixtures of the water/higher contents of them had nearly a maximum ΔH at a higher T_gel. From those results, it was considered that the former gels received a high thermal history while the latter gels received only slight thermal history.     

Biosynthetic Gene Cluster of Cetoniacytone A,an Unusual Aminocyclitol from the Endosymbiotic Bacterium Actinomyces sp. Lu 9419

A gene cluster responsible for the biosynthesis of the antitumor agent cetoniacytone A was identified in Actinomyces sp. strain Lu 9419, an endosymbiotic bacterium isolated from the intestines of the rose chafer beetle (Cetonia aurata). The nucleotide sequence analysis of the 46 kb DNA region revealed the presence of 31 complete ORFs, including genes predicted to encode a 2‐epi‐5‐epi‐valiolone synthase (CetA), a glyoxalase/bleomycin resistance protein (CetB), an acyltransferase (CetD), an FAD‐dependent dehydrogenase (CetF2), two oxidoreductases (CetF1 and CetG), two aminotransferases (CetH and CetM), and a pyranose oxidase (CetL). CetA has previously been demonstrated to catalyze the cyclization of sedoheptulose 7‐phosphate to the cyclic intermediate, 2‐epi‐5‐epi‐valiolone. In this report, the glyoxalase/bleomycin resistance protein homolog CetB was identified as a 2‐epi‐5‐epi‐valiolone epimerase (EVE), a new member of the vicinal oxygen chelate (VOC) superfamily. The 24 kDa recombinant histidine‐tagged CetB was found to form a homodimer; each monomer contains two βαβββ scaffolds that form a metal binding site with two histidine and two glutamic acid residues. A BLAST search using the newly isolated cet biosynthetic genes revealed an analogous suite of genes in the genome of Frankia alni ACN14a, suggesting that this plant symbiotic nitrogen‐fixing bacterium is capable of producing a secondary metabolite related to the cetoniacytones.