Erythrocyte bisulfite transport

The wide range of transport rates for anions of differing chemical structure by the human erythrocyte anion transport protein (Band 3 protein) suggests that this protein is highly selective for anions that chemically resemble its natural substrate bicarbonate. To test this hypothesis, the influx of bisulfite (HSO3-), a bicarbonate analog, was compared to influxes of chloride, sulfate, and bicarbonate, as measured by the technique of colloid osmotic lysis in isotonic ammonium salt solution. The lysis time induced in chloride solution (much greater than 10 min) was markedly accelerated to 0.6 min by the addition of small amounts (5 mM) of bicarbonate, an effect characteristic of colloid osmotic lysis induced by the anion transport pathway. Lysis in bicarbonate solution was extremely rapid (0.09 min), and was markedly inhibited by acetazolamide (2.9 min). Lysis in bisulfite solution occurred spontaneously (2.2 min) but was markedly accelerated to a time similar to that of chloride (0.56 min) by addition of 5 mM bicarbonate. In contrast, sulfate induced lysis was extremely slow (less than 10% lysis at 40 min in the presence of bicarbonate). Preincubation of erythrocytes with SITS, an inhibitor of anion exchange, prevented lysis by chloride, but had no effect on lysis by bicarbonate, indicating that lysis by bicarbonate was predominantly through diffusion and not anion transport. SITS treatment of erythrocytes eliminated the catalytic effect of bicarbonate during lysis by bisulfite, indicating that anion transport of bisulfite and diffusion of the conjugate acid in the form of SO2 both contribute to the total membrane flux. When the contribution of diffusion is taken into account, the rate of bisulfite influx through the anion exchange pathway is at least 100-fold faster than that for sulfate.     

Autoxidation and mutagenicity of sodium bisulfite

An inverse correlation exists between the autoxidation of bisulfite and its mutagenicity in Salmonella. Temperature, pH, and the addition of mannitol, ethanol, or Oxoid broth affect both autoxidation and mutagenicity. A decrease in autoxidation resulted in an increase in the half-life of the parent compound, bisulfite, and its availability for uptake by the cells, leading to increased mutagenesis. The autoxidation of bisulfite is known to produce both sulfur- and oxygen-centered free radicals. The lack of mutagenicity of ammonium persulfate and peroxymonosulfate, which generate the radicals SO4- and SO5-, respectively, argues against the involvement of these oxygen-centered radicals in bisulfite mutagenesis. Inhibition of mutagenesis by the radical spin-trapping agent, DMPO, is consistent with the hypothesis that the sulfur-centered radical, SO3-, plays an important role in bisulfite mutagenesis. The mechanism of bisulfite mutagenesis suggested in this study may have relevance to other known effects attributed to bisulfite, i.e., co-carcinogenesis and immune hypersensitivity.     

Degradation of DNA by bisulfite treatment

A significant level of target degradation was caused by bisulfite treatment for methylcytosine-selective hydrolysis. The depyrimidination proceeded via addition of bisulfite to pyrimidines in DNA. The quantification with real-time PCR after conventional bisulfite treatment showed a large decrease in the amount of full-length DNA.     

The reaction of bisulfite with liposomal membranes

Bisulfite has been shown to induce leakage of encapsulated substances from liposomal vesicles. The bisulfite induced leakage of either DNP-tyrosine, potassium ferricyanide, or [³H]glycine was observed to be greater with lipsomes composed of phospholipids containing unsaturated fatty acids. The leakage of encapsulated substances from liposomes was found to be concentration dependent when incubated for a constant time interval and time dependent when incubated at a constant bisulfite concentration. In addition, bisulfite caused the leakage of approximately 5 times more [³H]glycine from unilamellar liposomes than from multilamellar liposomes. These findings are consistent with the interaction of bisulfite with liposomal membranes via reaction with sites of unsaturation.     

The dehalogenation of halocytosines by bisulfite buffers

Both 5-bromo- and 5-iodocytosine are rapidly dehalogenated in dilute bisulfite buffers to yield cytosine. With 5-bromocytosine, but not with 5-iodocytosine, extrapolation of semilogarithmic plots of extent reaction versus time indicates the bisulfite buffer concentration-dependent formation of an intermediate which subsequently reacts to control the rate of 5-bromocytosine dehalogenation. The disappearance of both halocytosines has a second-order dependence on bisulfite buffer concentration. Both imidazole and acetate buffers catalyze the reaction of 5-iodocytosine, but not that of 5-bromocytosine, with bisulfite. In the case of acetate buffer catalysis of the reaction of 5-iodocytosine with bisulfite, the dependence of the observed rate constants changes from first order to zero order as a function of increasing buffer concentration. The observed rate constants for 5-bromocytosine dehalogenation increase, reach a maximum at about 4.5, and then decrease as a function of pH. Iodometric titration of sulfite utilization coupled with spectrophotometric analysis of pyrimidine reactants and products indicates that 1 mole of sulfite is consumed per mole of halocytosine dehalogenated. The spectrophotometrically determined pK_a values for the conjugate acids of 5-bromo- and 5-iodocytosine at 25°C and ionic strength 1.0 M are 3.25 and 3.56, respectively. These results are discussed in terms of a multistep reaction pathway which is analogous to the bisulfite-catalyzed dehalogenation of the 5-halouracils.     

A polymerase engineered for bisulfite sequencing

Bisulfite sequencing is a key methodology in epigenetics. However, the standard workflow of bisulfite sequencing involves heat and strongly basic conditions to convert the intermediary product 5,6-dihydrouridine-6-sulfonate (dhU6S) (generated by reaction of bisulfite with deoxycytidine (dC)) to uracil (dU). These harsh conditions generally lead to sample loss and DNA damage while milder conditions may result in incomplete conversion of intermediates to uracil. Both can lead to poor recovery of bisulfite-treated DNA by the polymerase chain reaction (PCR) as either damaged DNA and/or intermediates of bisulfite treatment are poor substrate for standard DNA polymerases. Here we describe an engineered DNA polymerase (5D4) with an enhanced ability to replicate and PCR amplify bisulfite-treated DNA due to an ability to bypass both DNA lesions and bisulfite intermediates, allowing significantly milder conversion conditions and increased sensitivity in the PCR amplification of bisulfite-treated DNA. Incorporation of the 5D4 DNA polymerase into the bisulfite sequencing workflow thus promises significant sensitivity and efficiency gains.     

Library-free methylation sequencing with bisulfite padlock probes

Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sample-preparation cost and time and is compatible with automation, and an efficient bioinformatics pipeline to accurately obtain both methylation levels and genotypes from sequencing of bisulfite-converted DNA.     

Identification and resolution of artifacts in bisulfite sequencing

Bisulfite sequencing has become the most widely used application to detect 5-methylcytosine (5-MeC) in DNA, and provides a reliable way of detecting any methylated cytosine at single-molecule resolution in any sequence context. The process of bisulfite treatment exploits the different sensitivity of cytosine and 5-MeC to deamination by bisulfite under acidic conditions, in which cytosine undergoes conversion to uracil while 5-MeC remains unreactive. In this article, we address the more commonly encountered experimental artifacts associated with bisulfite sequencing, and provide methods for the detection and elimination of these artifacts. In particular, we focus on conditions that inhibit complete bisulfite-mediated conversion of cytosines in a target sequence, and demonstrate the necessity of complete protein removal from DNA samples prior to bisulfite treatment. We also include a brief summary of the experimental protocol for bisulfite treatment and tips for designing polymerase chain reaction (PCR) primers to amplify from bisulfite-treated DNA.     

Dissimilatory reduction of bisulfite by Desulfovibrio vulgaris.

The reduction of bisulfite by Desulfovibrio vulgaris was investigated. Crude extracts reduced bisulfite to sulfide without the formation (detection) of any intermediates such as trithionate or thiosulfate. When the particulate fractions was removed from crude extracts by high-speed centrifugation, the soluble supernatant fraction reduced bisulfite sequentially to trithionate, thiosulfate, and sulfide. Addition of particles or purified membranes to the soluble fraction restored the original activity demonstrated by crude extracts, i.e., reduction of bisulfite to sulfide without the formation of trithionate and/or thiosulfate. By using antiserum directed against bisulfite reductase, the reduction of bisulfite by crude extracts was inhibited. This finding, in addition to several recycling studies of thiosulfate reduction, provided evidence that bisulfite reduction by D. vulgaris operated through the pathway involving trithionate and thiosulfate as intermediates. The role of membranes in this process is discussed.     

Soil cations influence bryophyte susceptibility to bisulfite

The hypothesis that metal ions absorbed by bryophytes from the underlying soil may ameliorate adverse effects of SO2 was investigated in the terricolous moss species Pleurozium schreberi (Brid.) Mitt. and Rhytidiadelphus triquetrus (Hedw.) Warnst. Dilute sodium bisulfite solutions (equivalent to dissolved SO2) were applied to shoots isolated from soil or in contact with artificial substrata. Marked inhibition of net photosynthesis was observed within 2 h of treatment with 0.3 mM bisulfite in both mosses. Progressive recovery of net photosynthesis occurred 2-8 h after bisulfite treatment, although the extent of this depended on the concentration and pH of the solution. When R. triquetrus and P. schreberi were grown on artificial substrata (calcareous, acid-mineral or acid-organic) with weekly bisulfite applications, the only significant effect was poorer growth of P. schreberi receiving bisulfite on the calcareous and acid-organic substrata. In both species, growth on the calcareous substratum led to increased concentrations of exchangeable Ca2+, whereas exchangeable Fe3+ concentrations increased following growth on the acid-mineral soil. In another experiment the two mosses were pre-treated with either Ca2+ or Fe3+ before incubation with bisulfite. In P. schreberi, the depression of net photosynthetic rate caused by bisulfite was ameliorated from 33 to 64% of the control by pre-treatment with Fe3+, but it was unaffected by Ca2+ pre-treatment. In R. triquetrus, the amelioration caused by Fe3+ pre-treatment was from 16 to 60% of the control, but pre-treatment with Ca2+ gave a greater amelioration, to 75% of the control value. The responses are discussed in terms of soil preferences of the mosses and possible underlying bisulfite amelioration mechanisms.     

The interaction of bisulfite with milk xanthine oxidase

Bisulfite ion competitively inhibits xanthine oxidase activity. The ability of HSO3- to bind at the molybdenum center is controlled by pH due to a pKa of 6.91 for SO3(2-)/HSO3-. The Kd for the enzyme-bisulfite complex is 4.5 x 10(-5) M at pH 7.0 and 25 degrees C. The relative magnitude of extinction changes in the optical absorption spectra, the number of inhibitor ions reversibly bound, and the number of electrons required for complete bleaching of the visible spectrum of the milk xanthine oxidase-HSO3- complex were all dependent on the percentage of fully functional xanthine oxidase. Binding of HSO3- causes perturbations of the visible spectrum: the maximum extinction changes at 320 and 422 nm were calculated to be -4300 and -2150 M-1 cm-1, respectively. The stoichiometry of reversible binding was determined to be one molecule of HSO3-/active molybdenum center. Combined optical and EPR analyses of anaerobic dithionite titrations revealed that the relative redox potentials of the Mo6+/5+ and Mo5+/4+ couples decreased by approximately 35 and 45 mV on binding bisulfite, respectively. The finding that bisulfite has a profound effect on the redox properties of xanthine oxidase necessitates a re-evaluation of dithionite titrations previously carried out with this enzyme at neutral and low pH values since bisulfite produced as an oxidation product of dithionite binds to the enzyme during the course of titration.     

DNA methylome analysis using short bisulfite sequencing data

Bisulfite conversion of genomic DNA combined with next-generation sequencing (BS-seq) is widely used to measure the methylation state of a whole genome, the methylome, at single-base resolution. However, analysis of BS-seq data still poses a considerable challenge. Here we summarize the challenges of BS-seq mapping as they apply to both base and color-space data. We also explore the effect of sequencing errors and contaminants on inferred methylation levels and recommend the most appropriate way to analyze this type of data.     

MOABS: model based analysis of bisulfite sequencing data

Background

Human aging is associated with DNA methylation changes at specific sites in the genome. These epigenetic modifications may be used to track donor age for forensic analysis or to estimate biological age.

Results

We perform a comprehensive analysis of methylation profiles to narrow down 102 age-related CpG sites in blood. We demonstrate that most of these age-associated methylation changes are reversed in induced pluripotent stem cells (iPSCs). Methylation levels at three age-related CpGs - located in the genes ITGA2B, ASPA and PDE4C - were subsequently analyzed by bisulfite pyrosequencing of 151 blood samples. This epigenetic aging signature facilitates age predictions with a mean absolute deviation from chronological age of less than 5 years. This precision is higher than age predictions based on telomere length. Variation of age predictions correlates moderately with clinical and lifestyle parameters supporting the notion that age-associated methylation changes are associated more with biological age than with chronological age. Furthermore, patients with acquired aplastic anemia or dyskeratosis congenita - two diseases associated with progressive bone marrow failure and severe telomere attrition - are predicted to be prematurely aged.

Conclusions

Our epigenetic aging signature provides a simple biomarker to estimate the state of aging in blood. Age-associated DNA methylation changes are counteracted in iPSCs. On the other hand, over-estimation of chronological age in bone marrow failure syndromes is indicative for exhaustion of the hematopoietic cell pool. Thus, epigenetic changes upon aging seem to reflect biological aging of blood.