Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway.

In meiosis, multiple different DNA sequence motifs help to position homologous recombination at hotspots in the genome. How do the seemingly disparate cis-acting regulatory modules each promote locally the activity of the basal recombination machinery? We defined molecular mechanisms of action for five different hotspot-activating DNA motifs (M26, CCAAT, Oligo-C, 4095, 4156) located independently at the same site within the ade6 locus of the fission yeast Schizosaccharomyces pombe Each motif promoted meiotic recombination (i.e., is active) within this context, and this activity required the respective binding proteins (transcription factors Atf1, Pcr1, Php2, Php3, Php5, Rst2). High-resolution analyses of chromatin structure by nucleosome scanning assays revealed that each motif triggers the displacement of nucleosomes surrounding the hotspot motif in meiosis. This chromatin remodeling required the respective sequence-specific binding proteins, was constitutive for two motifs, and was enhanced meiotically for three others. Hotspot activity of each motif strongly required the ATP-dependent chromatin remodeling enzyme Snf22 (Snf2/Swi2), with lesser dependence on Gcn5, Mst2, and Hrp3. These findings support a model in which most meiotic recombination hotspots are positioned by the binding of transcription factors to their respective DNA sites. The functional redundancy of multiple, sequence-specific protein-DNA complexes converges upon shared chromatin remodeling pathways that help provide the basal recombination machinery (Spo11/Rec12 complex) access to its DNA substrates within chromatin.

Sequence requirement of the ade6-4095 meiotic recombination hotspot in Schizosaccharomyces pombe.

Homologous recombination occurs at a greatly elevated frequency in meiosis compared to mitosis and is initiated by programmed double-strand DNA breaks (DSBs). DSBs do not occur at uniform frequency throughout the genome in most organisms, but occur preferentially at a limited number of sites referred to as hotspots. The location of hotspots have been determined at nucleotide-level resolution in both the budding and fission yeasts, and while several patterns have emerged regarding preferred locations for DSB hotspots, it remains unclear why particular sites experience DSBs at much higher frequency than other sites with seemingly similar properties. Short sequence motifs, which are often sites for binding of transcription factors, are known to be responsible for a number of hotspots. In this study we identified the minimum sequence required for activity of one of such motif identified in a screen of random sequences capable of producing recombination hotspots. The experimentally determined sequence, GGTCTRGACC, closely matches the previously inferred sequence. Full hotspot activity requires an effective sequence length of 9.5 bp, whereas moderate activity requires an effective sequence length of approximately 8.2 bp and shows significant association with DSB hotspots. In combination with our previous work, this result is consistent with a large number of different sequence motifs capable of producing recombination hotspots, and supports a model in which hotspots can be rapidly regenerated by mutation as they are lost through recombination.

Unique properties of multiple tandem copies of the M26 recombination hotspot in mitosis and meiosis in Schizosaccharomyces pombe.

The M26 hotspot of the fission yeast Schizosaccharomyces pombe is one of the best-characterized eukaryotic hotspots of recombination. The hotspot requires a seven bp sequence, ATGACGT, that serves as a binding site for the Atf1-Pcr1 transcription factor, which is also required for activity. The M26 hotspot is active in meiosis but not mitosis and is active in some but not all chromosomal contexts and not on a plasmid. A longer palindromic version of M26, ATGACGTCAT, shows significantly greater activity than the seven bp sequence. Here, we tested whether the properties of the seven bp sequence were also true of the longer sequence by placing one, two, or three copies of the sequence into the ade6 gene, where M26 was originally discovered. These constructs were tested for activity when located on a plasmid or on a chromosome in mitosis and meiosis. We found that two copies of the 10bp M26 motif on a chromosome were significantly more active for meiotic recombination than one, but no further increase was observed with three copies. However, three copies of M26 on a chromosome created an Atf1-dependent mitotic recombination hotspot. When located on a plasmid, M26 also appears to behave as a mitotic recombination hotspot; however, this behavior most likely results from Atf1-dependent inter-allelic complementation between the plasmid and chromosomal ade6 alleles.

Fission yeast hotspot sequence motifs are also active in budding yeast.

In most organisms, including humans, meiotic recombination occurs preferentially at a limited number of sites in the genome known as hotspots. There has been substantial progress recently in elucidating the factors determining the location of meiotic recombination hotspots, and it is becoming clear that simple sequence motifs play a significant role. In S. pombe, there are at least five unique sequence motifs that have been shown to produce hotspots of recombination, and it is likely that there are more. In S. cerevisiae, simple sequence motifs have also been shown to produce hotspots or show significant correlations with hotspots. Some of the hotspot motifs in both yeasts are known or suspected to bind transcription factors (TFs), which are required for the activity of those hotspots. Here we show that four of the five hotspot motifs identified in S. pombe also create hotspots in the distantly related budding yeast S. cerevisiae. For one of these hotspots, M26 (also called CRE), we identify TFs, Cst6 and Sko1, that activate and inhibit the hotspot, respectively. In addition, two of the hotspot motifs show significant correlations with naturally occurring hotspots. The conservation of these hotspots between the distantly related fission and budding yeasts suggests that these sequence motifs, and others yet to be discovered, may function widely as hotspots in many diverse organisms.

Enzymatic synthesis of catechol and hydroxyl-carboxic acid functionalized chitosan microspheres for iron overload therapy.

Excess "free" iron which occurs under certain physiological conditions participates in the formation of toxic reactive oxygen species via the "fenton" chemistry. The reactive oxygen species oxidize biomolecules and have been implicated in many oxidative stress-related diseases. However, the ideal therapy for treating iron overload problems in humans has not yet been developed. In this study, the phenolic molecules catechol, caffeic acid, and 2,5-dihydroxybenzoic acid were successfully coupled to glucosamine as model substrate in a 1:1 ratio using laccase. Furthermore, coupling of these molecules onto chitosans of different sizes was demonstrated, resulting in decrease in -NH(2) groups as quantified via derivatization. A concomitant increase in iron-chelating capacity from below 3% to up to 70% upon phenolic functionalization was measured for the chitosans based on reduced ferrozine/Fe(2+) complex formation. Interesting these phenolic compounds seems to also participate as cross-linkers in producing characteristic microspheres. This work therefore opens-up new strategies aimed at developing a new generation of iron-chelating biomedical polymers.

Important characteristics of sequence-specific recombination hotspots in Schizosaccharomyces pombe.

In many organisms, meiotic recombination occurs preferentially at a limited number of sites in the genome known as hotspots. In the fission yeast Schizosaccharomyces pombe, simple sequence motifs determine the location of at least some, and possibly most or all, hotspots. Recently, we showed that a large number of different sequences can create hotspots. Among those sequences we identified some recurring motifs that fell into at least five distinct families, including the well-characterized CRE family of hotspots. Here we report the essential sequence for activity of two of the novel hotspots, the oligo-C and CCAAT hotspots, and identify associated trans-acting factors required for hotspot activity. The oligo-C hotspot requires a unique 8-bp sequence, CCCCGCAC, though hotspot activity is also significantly affected by adjacent nucleotides. The CCAAT hotspot requires a more complex and degenerate sequence, including the originally identified seven nucleotide CCAATCA sequence at its core. We identified transcription factors, the CCAAT-binding factor (CBF) and Rst2, which are required specifically for activity of the CCAAT hotspots and oligo-C hotspots, respectively. Each of these factors binds to its respective motifs in vitro. However, unlike CRE, the sequence required for hotspot activity is larger than the sequence required for binding, suggesting the involvement of additional factors.

Cellular and plasma antioxidant activity assay using tetramethoxy azobismethylene quinone.

The kinetics of the reduction of enzymatically generated tetramethoxy azobismethylene quinone (TMAMQ), a newly developed antioxidant activity assay method, by pure cellular and plasma antioxidants was studied. Further, the potential application of TMAMQ to the estimation of the antioxidant activity of clinical serum samples was investigated. The highest reduction rate (k) was obtained with ascorbic acid (1.11x10(-2)microM(-1) s(-1)) and glutathione showed the lowest (2.94x10(-5)microM(-1) s(-1)). Comparing TMAMQ and the commercially available antioxidant method Total Antioxidant Capacity clearly shows a similar trend, although the values differ. This study also shows that TMAMQ is highly sensitive (only a minute plasma sample was required) and reproducible, and the reaction proceeds until steady state (until all antioxidants have reacted). TMAMQ is very stable in acetonitrile (>3months), making it a highly flexible method because it can be easily adapted for analysis of just a single sample or for high-throughput analysis. This has direct implications on reducing costs and experimental steps. TMAMQ is therefore a highly promising antioxidant activity assay method for cellular and plasma antioxidant activity assay.

Development of a novel expression, ZI MAX/K ZI, for determination of the counter-anion effect on the antimicrobial activity of tetrabutylammonium salts.

Due to the increasing number of strains of drug-resistant bacteria, the development of new antibiotics has become increasingly important. The antibacterial properties of quaternary amines and their derivatives on both Gram-positive and Gram-negative bacteria are well known. However, an encompassing study with specific emphasis on the role of the counter-anion has not been reported in the literature. By monitoring the Zone of Inhibition of various concentrations of tetrabutylammonium (TBA) salts, we observed that the counter anion plays a significant role in activity. We developed a novel method of reporting activity using zone of inhibition tests (ZI(MAX)/K(ZI)) and found it to be strongly correlated with the minimum inhibitory concentration (MIC).

Novel nucleotide sequence motifs that produce hotspots of meiotic recombination in Schizosaccharomyces pombe.

In many organisms, including yeasts and humans, meiotic recombination is initiated preferentially at a limited number of sites in the genome referred to as recombination hotspots. Predicting precisely the location of most hotspots has remained elusive. In this study, we tested the hypothesis that hotspots can result from multiple different sequence motifs. We devised a method to rapidly screen many short random oligonucleotide sequences for hotspot activity in the fission yeast Schizosaccharomyces pombe and produced a library of approximately 500 unique 15- and 30-bp sequences containing hotspots. The frequency of hotspots found suggests that there may be a relatively large number of different sequence motifs that produce hotspots. Within our sequence library, we found many shorter 6- to 10-bp motifs that occurred multiple times, many of which produced hotspots when reconstructed in vivo. On the basis of sequence similarity, we were able to group those hotspots into five different sequence families. At least one of the novel hotspots we found appears to be a target for a transcription factor, as it requires that factor for its hotspot activity. We propose that many hotspots in S. pombe, and perhaps other organisms, result from simple sequence motifs, some of which are identified here.

Antioxidant activity assay based on laccase-generated radicals.

A novel antioxidant activity assay was developed using laccase-oxidized phenolics. In a three-step approach, phenolic compounds were first oxidized by laccase. Laccase was then inhibited using 80% (v/v) methanol which also stabilized the oxidized phenolics which were then used to measure antioxidant activities of ascorbic acid and Trolox. From a number of laccase-oxidized phenolics screened for potential use in the measurement of antioxidant activities, syringaldazine emerged the best, giving results comparable to the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical, which is currently used in conventional methods. Like DPPH radicals, two moles of stoichiometric oxidized syringaldazine were reduced by one mole of either ascorbic acid or Trolox. For the first time we show that antioxidant activity can be correlated to oxygen consumption by laccase. Reduction of one molecule of oxygen corresponded to oxidation of four molecules of syringaldazine which in turn is reduced by two molecules of Trolox or ascorbic acid. This study therefore demonstrates the great potential of using laccase-oxidized syringaldazine for the measurement of antioxidant activity.

Incorporation of 2,4,6-trinitrotoluene (TNT) transforming bacteria into explosive formulations.

Pseudomonas putida GG04 and Bacillus SF have been successfully incorporated into an explosive formulation to enhance biotransformation of TNT residues and/or explosives which fail to detonate due to technical faults. The incorporation of the microorganisms into the explosive did not affect the quality of the explosive (5 years storage) in terms of detonation velocity while complete biotransformation of TNT moieties upon transfer in liquid media was observed after 5 days. The incorporated microorganisms reduced TNT sequentially leading to the formation of hydroxylaminodinitrotoluenes (HADNT), 4-amino-2,6-dinitrotoluenes; 2-amino-4,6-dinitrotoluenes, different azoxy compounds; 2,6-diaminonitrotoluenes (2,4-DAMNT) and 2,4-diaminonitrotoluenes (2,6-DAMNT). However, the accumulation of AMDNT and DAMNT (major dead-end metabolites) was effectively prevented by incorporating guaiacol and catechol during the biotransformation process.

Multiple modes of chromatin configuration at natural meiotic recombination hot spots in fission yeast.

The ade6-M26 meiotic recombination hot spot of fission yeast is defined by a cyclic AMP-responsive element (CRE)-like heptanucleotide sequence, 5'-ATGACGT-3', which acts as a binding site for the Atf1/Pcr1 heterodimeric transcription factor required for hot spot activation. We previously demonstrated that the local chromatin around the M26 sequence motif alters to exhibit higher sensitivity to micrococcal nuclease before the initiation of meiotic recombination. In this study, we have examined whether or not such alterations in chromatin occur at natural meiotic DNA double-strand break (DSB) sites in Schizosaccharomyces pombe. At one of the most prominent DSB sites, mbs1 (meiotic break site 1), the chromatin structure has a constitutively accessible configuration at or near the DSB sites. The establishment of the open chromatin state and DSB formation are independent of the CRE-binding transcription factor, Atf1. Analysis of the chromatin configuration at CRE-dependent DSB sites revealed both differences from and similarities to mbs1. For example, the tdh1+ locus, which harbors a CRE consensus sequence near the DSB site, shows a meiotically induced open chromatin configuration, similar to ade6-M26. In contrast, the cds1+ locus is similar to mbs1 in that it exhibits a constitutive open configuration. Importantly, Atf1 is required for the open chromatin formation in both tdh1+ and cds1+. These results suggest that CRE-dependent meiotic chromatin changes are intrinsic processes related to DSB formation in fission yeast meiosis. In addition, the results suggest that the chromatin configuration in natural meiotic recombination hot spots can be classified into at least three distinct categories: (i) an Atf1-CRE-independent constitutively open chromatin configuration, (ii) an Atf1-CRE-dependent meiotically induced open chromatin configuration, and (iii) an Atf1-CRE-dependent constitutively open chromatin configuration.

Natural meiotic recombination hot spots in the Schizosaccharomyces pombe genome successfully predicted from the simple sequence motif M26.

The M26 hot spot of meiotic recombination in Schizosaccharomyces pombe is the eukaryotic hot spot most thoroughly investigated at the nucleotide level. The minimum sequence required for M26 activity was previously determined to be 5'-ATGACGT-3'. Originally identified by a mutant allele, ade6-M26, the M26 heptamer sequence occurs in the wild-type S. pombe genome approximately 300 times, but it has been unclear whether any of these are active hot spots. Recently, we showed that the M26 heptamer forms part of a larger consensus sequence, which is significantly more active than the heptamer alone. We used this expanded sequence as a guide to identify a smaller number of sites most likely to be active hot spots. Ten of the 15 sites tested showed meiotic DNA breaks, a hallmark of recombination hot spots, within 1 kb of the M26 sequence. Among those 10 sites, one occurred within a gene, cds1(+), and hot spot activity of this site was confirmed genetically. These results are, to our knowledge, the first demonstration in any organism of a simple, defined nucleotide sequence accurately predicting the locations of natural meiotic recombination hot spots. M26 may be the first example among a diverse group of simple sequences that determine the distribution, and hence predictability, of meiotic recombination hot spots in eukaryotic genomes.

Activation of an alternative, rec12 (spo11)-independent pathway of fission yeast meiotic recombination in the absence of a DNA flap endonuclease.

Spo11 or a homologous protein appears to be essential for meiotic DNA double-strand break (DSB) formation and recombination in all organisms tested. We report here the first example of an alternative, mutationally activated pathway for meiotic recombination in the absence of Rec12, the Spo11 homolog of Schizosaccharomyces pombe. Rad2, a FEN-1 flap endonuclease homolog, is involved in processing Okazaki fragments. In its absence, meiotic recombination and proper segregation of chromosomes were restored in rec12Delta mutants to nearly wild-type levels. Although readily detectable in wild-type strains, meiosis-specific DSBs were undetectable in recombination-proficient rad2Delta rec12Delta strains. On the basis of the biochemical properties of Rad2, we propose that meiotic recombination by this alternative (Rec*) pathway can be initiated by non-DSB lesions, such as nicks and gaps, which accumulate during premeiotic DNA replication in the absence of Okazaki fragment processing. We compare the Rec* pathway to alternative pathways of homologous recombination in other organisms.

Fast determination of operational stability of the soluble acetylacetone-cleaving enzyme Dke1 in an enzyme membrane reactor.

The main aim of this study was the determination of the operational stability of soluble Dke1 (EC 1.13.11.50) in an enzyme membrane reactor. In order to calculate the half-life of soluble Dke1, the K (M) of oxygen must be known. The determination of this constant was done using progress curve analysis (K (M) = 260 micromol l(-1)). In a next step, the reactor system was studied by building a mathematical model for calculation of the reactor system, using Berkeley Madonna ver. 8.0.1 software. After that, the determination of the half-life of Dke1 under operational conditions at different temperatures (5, 10, 15, 25, 30, 35 degrees C) was performed. The quantitative criterion for stability was the value of the first-order rate constant of monomolecular inactivation. The experiments showed that soluble Dke1 is poorly stable. The half-life ranged from 308 min at 5 degrees C to 9 min at 35 degrees C. This method for determining the half-life is quite applicable for enzymes which are poorly stable. In addition, both the storage stability and the operational stability can be determined.

Optimizing the nucleotide sequence of a meiotic recombination hotspot in Schizosaccharomyces pombe.

The ade6-M26 mutation of Schizosaccharomyces pombe created a meiotic recombination hotspot. Previous analyses indicated that the heptamer 5'-ATGACGT-3' was necessary and sufficient for hotspot activity; the Atf1-Pcr1 transcription factor binds to this sequence and activates M26. After finding cases in which the M26 heptamer in ade6 was, surprisingly, not active as a hotspot, we used an in vitro selection method (SELEX) that revealed an 18-bp consensus sequence for Atf1-Pcr1 binding, 5'-GNVTATGACGTCATNBNC-3', containing the M26 heptamer at its core. Using this consensus sequence as a guide, we made mutations on each side of the heptamer at two separate sites in ade6. These mutations increased the intracellular hotspot activity of the heptamer, in some cases by >15-fold. These results show that M26, the eukaryotic recombination hotspot with the most precisely defined nucleotide sequence, is larger than previously thought, and they provide valuable information for clarifying the role of M26, and perhaps other hotspots, in meiotic recombination.

A novel recombination pathway initiated by the Mre11/Rad50/Nbs1 complex eliminates palindromes during meiosis in Schizosaccharomyces pombe.

DNA palindromes are rare in humans but are associated with meiosis-specific translocations. The conserved Mre11/Rad50/Nbs1 (MRN) complex is likely directly involved in processing palindromes through the homologous recombination pathway of DNA repair. Using the fission yeast Schizosaccharomyces pombe as a model system, we show that a 160-bp palindrome (M-pal) is a meiotic recombination hotspot and is preferentially eliminated by gene conversion. Importantly, this hotspot depends on the MRN complex for full activity and reveals a new pathway for generating meiotic DNA double-strand breaks (DSBs), separately from the Rec12 (ortholog of Spo11) pathway. We show that MRN-dependent DSBs are formed at or near the M-pal in vivo, and in contrast to the Rec12-dependent breaks, they appear early, during premeiotic replication. Analysis of mrn mutants indicates that the early DSBs are generated by the MRN nuclease activity, demonstrating the previously hypothesized MRN-dependent breakage of hairpins during replication. Our studies provide a genetic and physical basis for frequent translocations between palindromes in human meiosis and identify a conserved meiotic process that constantly selects against palindromes in eukaryotic genomes.

Electronic substituent effects on the cleavage specificity of a non-heme Fe(2+)-dependent beta-diketone dioxygenase and their mechanistic implications.

Acinetobacter johnsonii acetylacetone dioxygenase (Dke1) is a non-heme Fe(II)-dependent dioxygenase that cleaves C-C bonds in various beta-dicarbonyl compounds capable of undergoing enolization to a cis-beta-keto enol structure. Results from 18O labeling experiments and quantitative structure-reactivity relationship analysis of electronic substituent effects on the substrate cleavage specificity of Dke1 are used to distinguish between two principle chemical mechanisms of reaction: one involving a 1,2-dioxetane intermediate and another proceeding via Criegee rearrangement. Oxygenative cleavage of asymmetrically substituted beta-dicarbonyl substrates occurs at the bond adjacent to the most electron-deficient carbonyl carbon. Replacement of the acetyl group in 1-phenyl-1,3-butanedione by a trifluoro-acetyl group leads to a complete reversal of cleavage frequency from 83% to only 8% fission of the bond next to the benzoyl moiety. The structure-activity correlation for Dke1 strongly suggests that enzymatic bond cleavage takes place via nucleophilic attack to generate a dioxetane, which then decomposes into the carboxylate and alpha-keto-aldehyde products.