A method for preparing genomic DNA that restrains branch migration of Holliday junctions

Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae

The DNA double-strand breaks that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in Saccharomyces cerevisiae contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red1 are important for double-strand break formation; double-strand break levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with double-strand break levels. How axis protein levels influence double-strand break formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased double-strand breaks and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in double-strand breaks did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote double-strand break formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, crossovers that formed at an insert locus were only modestly reduced in the absence of MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local double-strand break levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.

Effect of the natural establishment of two plant species on microbial activity, on the composition of the fungal community, and on the mitigation of potentially toxic elements in an abandoned mine tailing

In Mexico, millions of tons of mining wastes are deposited in the open pit. Their content in potentially toxic elements (PTE) represents an environmental risk. In the tailings, pioneer plant communities are established, associated with a determined diversity of fungi; plants, and fungi are fundamental in the natural rehabilitation of mining wastes. The objective was to evaluate the impact of the natural establishment of two plant species on the microbial activity, on the composition of the fungal community, and on the mitigation of the effect of PTE in a contaminated mine tailing. In a tailing, we selected three sites: one non-vegetated; one vegetated by Reseda luteola, and one vegetated by Asphodelus fistulosus. In the substrates, we conducted a physical and chemical characterization; we evaluated the enzymatic activity, the mineralization of the carbon, and the concentration of PTE. We also determined the fungal diversity in the substrates and in the interior of the roots, and estimated the accumulation of carbon, nitrogen, phosphorus and PTE in plant tissues. The tailings had a high percentage of sand; the non-vegetated site presented the highest electric conductivity, and the plant cover reduced the concentration of PTE in the substrates. Plants increased the carbon content in tailings. The enzymatic activities of β-glucosidase and dehydrogenase, and the mineralization of carbon were highest at the site vegetated with A. fistulosus. Both plant species accumulated PTE in their tissues and exhibited potential in the phytoremediation of lead (Pb), cadmium (Cd), and copper (Cu). Fungal diversity was more elevated at the vegetated sites than in the bare substrate. Ascomycota prevailed in the substrates; the substrates and the plants shared some fungal taxa, but other taxa were specific. The plant coverage and the rhizosphere promoted the natural attenuation and a rehabilitation of the extreme conditions of the mining wastes, modulated by the plant species.

Gel Electrophoresis Analysis of rDNA Instability in Saccharomyces cerevisiae

The ribosomal RNA (rDNA) sequence is the most abundant repetitive element in the budding yeast genome and forms a tandem cluster of ~100-200 copies. Cells frequently change their rDNA copy number, making rDNA the most unstable region in the budding yeast genome. The rDNA region experiences programmed replication fork arrest and subsequent formation of DNA double-strand breaks (DSBs), which are the main drivers of rDNA instability. The rDNA region offers a unique system to understand the mechanisms that respond to replication fork arrest as well as the mechanisms that regulate repeat instability. This chapter describes three methods to assess rDNA instability.

Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length

Displacement loops (D-loops) are critical intermediates formed during homologous recombination. Rdh54 (a.k.a. Tid1), a Rad54 paralog in Saccharomyces cerevisiae, is well-known for its role with Dmc1 recombinase during meiotic recombination. Yet contrary to Dmc1, Rdh54/Tid1 is also present in somatic cells where its function is less understood. While Rdh54/Tid1 enhances the Rad51 DNA strand invasion activity in vitro, it is unclear how it interplays with Rad54. Here, we show that Rdh54/Tid1 inhibits D-loop formation by Rad51 and Rad54 in an ATPase-independent manner. Using a novel D-loop Mapping Assay, we further demonstrate that Rdh54/Tid1 uniquely restricts the length of Rad51-Rad54-mediated D-loops. The alterations in D-loop properties appear to be important for cell survival and mating-type switch in haploid yeast. We propose that Rdh54/Tid1 and Rad54 compete for potential binding sites within the Rad51 filament, where Rdh54/Tid1 acts as a physical roadblock to Rad54 translocation, limiting D-loop formation and D-loop length.

Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution

Displacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Here, we developed a novel in vitro assay to characterize the length and position of individual D-loops with near base-pair resolution and deep coverage, while also revealing their distribution in a population. Non-denaturing bisulfite treatment modifies the cytosines on the displaced strand of the D-loop to uracil, leaving a permanent signature for the displaced strand. Subsequent single-molecule real-time sequencing uncovers the cytosine conversion patch as a D-loop footprint. The D-loop Mapping Assay is widely applicable with different substrates and donor types and can be used to study factors that influence D-loop properties.

Characterization and proliferation capacity of potentially pathogenic fungi in marine and freshwater fish commercial feeds

In the aquaculture industry, the selection and quality of feed are highly relevant because their integrity and management have an impact on the health and development of organisms. In general, feeds contamination depends on storage conditions and formulation. Furthermore, it has been recognized that filamentous fungi are among the most important contaminating agent in formulated feeds. Therefore, the purpose of this research was to identify saprophytic fungi capable of proliferating in commercial feeds, as well as determining their prevalence, extracellular enzymes profile, ability to assimilate carbon sources, and finally their ability to produce aflatoxins. In order to do that, twenty-two fungi were isolated from commercial fish feeds. After, the species Aspergillus chevalieri, A. cristatus, A. sydowii, A. versicolor, A. flavus, A. creber, and Lichtheimia ramosa were identified. These fungi were able to produce extracellular enzymes, such as phosphatases, esterases, proteases, β-glucosidase, and N-acetyl-β-glucosaminidase. The isolated fungi showed no selective behavior in the assimilation of the different carbon sources, showing a strong metabolic diversity. Prevalence percentages above 85% were recorded. Among all fungi studied, A. flavus M3-C1 had the highest production of aflatoxins when this strain was inoculated directly in the feeds (295 ppb). The aflatoxin production by this strain under the experimental setting is above the permitted levels, and it has been established that high levels of aflatoxins in feeds can cause alterations in fish growth as well as the development of cancerous tumors in the liver, in addition to enhancing mortality.

2D Gel Electrophoresis to Detect DNA Replication and Recombination Intermediates in Budding Yeast

The two-dimensional agarose gel electrophoresis (2D gel) is a powerful method used to detect and analyze rare DNA replication and recombination intermediates within a genomic DNA preparation. The 2D gel method has been extensively applied to the budding yeast Saccharomyces cerevisiae due to its small and well-characterized genome to analyze replication fork dynamics at single DNA loci under both physiological and pathological conditions. Here we describe procedures to extract genomic DNA from in vivo UV-psoralen cross-linked yeast cells, to separate branched DNA replication and recombination intermediates by neutral-neutral 2D gel method and to visualize 2D gel structures by Southern Blot.

Unresolved Recombination Intermediates Cause a RAD9-Dependent Cell Cycle Arrest in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the conserved Sgs1-Top3-Rmi1 helicase-decatenase regulates homologous recombination by limiting accumulation of recombination intermediates that are crossover precursors. In vitro studies have suggested that this may be due to dissolution of double-Holliday junction joint molecules by Sgs1-driven convergent junction migration and Top3-Rmi1 mediated strand decatenation. To ask whether dissolution occurs in vivo, we conditionally depleted Sgs1 and/or Rmi1 during return to growth (RTG), a procedure where recombination intermediates formed during meiosis are resolved when cells resume the mitotic cell cycle. Sgs1 depletion during RTG delayed joint molecule resolution, but, ultimately, most were resolved and cells divided normally. In contrast, Rmi1 depletion resulted in delayed and incomplete joint molecule resolution, and most cells did not divide. rad9 ∆ mutation restored cell division in Rmi1-depleted cells, indicating that the DNA damage checkpoint caused this cell cycle arrest. Restored cell division in Rmi1-depleted rad9 ∆ cells frequently produced anucleate cells, consistent with the suggestion that persistent recombination intermediates prevented chromosome segregation. Our findings indicate that Sgs1-Top3-Rmi1 acts in vivo, as it does in vitro, to promote recombination intermediate resolution by dissolution. They also indicate that, in the absence of Top3-Rmi1 activity, unresolved recombination intermediates persist and activate the DNA damage response, which is usually thought to be activated by much earlier DNA damage-associated lesions.

S. cerevisiae Srs2 helicase ensures normal recombination intermediate metabolism during meiosis and prevents accumulation of Rad51 aggregates

We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilises Rad51-DNA filaments and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction of srs2 mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although in such cells sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalised with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards interhomologue strand invasion characteristic of normal meiosis. srs2 mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division.

Noncanonical Contributions of MutLγ to VDE-Initiated Crossovers During Saccharomyces cerevisiae Meiosis

In Saccharomyces cerevisiae, the meiosis-specific axis proteins Hop1 and Red1 are present nonuniformly across the genome. In a previous study, the meiosis-specific VMA1-derived endonuclease (VDE) was used to examine Spo11-independent recombination in a recombination reporter inserted in a Hop1/Red1-enriched region (HIS4) and in a Hop1/Red1-poor region (URA3). VDE-initiated crossovers at HIS4 were mostly dependent on Mlh3, a component of the MutLγ meiotic recombination intermediate resolvase, while VDE-initiated crossovers at URA3 were mostly Mlh3-independent. These differences were abolished in the absence of the chromosome axis remodeler Pch2, and crossovers at both loci became partly Mlh3-dependent. To test the generality of these observations, we examined inserts at six additional loci that differed in terms of Hop1/Red1 enrichment, chromosome size, and distance from centromeres and telomeres. All six loci behaved similarly to URA3: the vast majority of VDE-initiated crossovers were Mlh3-independent. This indicates that, counter to previous suggestions, levels of meiotic chromosome axis protein enrichment alone do not determine which recombination pathway gives rise to crossovers during VDE-initiated meiotic recombination. In pch2∆ mutants, the fraction of VDE-induced crossovers that were Mlh3-dependent increased to levels previously observed for Spo11-initiated crossovers in pch2∆, indicating that Pch2-dependent processes play an important role in controlling the balance between MutLγ-dependent and MutLγ-independent crossovers.

Methods for Controlled Protein Depletion to Study Protein Function during Meiosis

Proteins with potential roles in meiotic recombination often have essential or important functions during the mitotic cell cycle. In addition, proteins may have different functions at different times during meiosis. In such cases, it can be challenging to precisely determine protein function during meiosis using null or hypomorphic mutants. One example is the Sgs1-Top3-Rmi1 helicase-decatenase complex, which is required for normal vegetative growth and genome stability. In such cases, conditional loss-of-function mutants can be useful. In this chapter, we describe the construction of two types of conditional mutants, meiotic depletion alleles and auxin-induced degradation alleles, that allow protein depletion specifically during budding yeast meiosis, and illustrate their use with Sgs1. We also describe a modified method for the isolation of meiotic recombination intermediates that combines previous psoralen cross-linking and cetyltrimethylammonium bromide isolation methods.

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis

The budding yeast genome contains regions where meiotic recombination initiates more frequently than in others. This pattern parallels enrichment for the meiotic chromosome axis proteins Hop1 and Red1. These proteins are important for Spo11-catalyzed double strand break formation; their contribution to crossover recombination remains undefined. Using the sequence-specific VMA1-derived endonuclease (VDE) to initiate recombination in meiosis, we show that chromosome structure influences the choice of proteins that resolve recombination intermediates to form crossovers. At a Hop1-enriched locus, most VDE-initiated crossovers, like most Spo11-initiated crossovers, required the meiosis-specific MutLγ resolvase. In contrast, at a locus with lower Hop1 occupancy, most VDE-initiated crossovers were MutLγ-independent. In pch2 mutants, the two loci displayed similar Hop1 occupancy levels, and VDE-induced crossovers were similarly MutLγ-dependent. We suggest that meiotic and mitotic recombination pathways coexist within meiotic cells, and that features of meiotic chromosome structure determine whether one or the other predominates in different regions.

DOI:http://dx.doi.org/10.7554/eLife.19669.001

Inside the cells of many species, double-stranded DNA is packaged together with specialized proteins to form structures called chromosomes. Breaks that span across both strands of the DNA can cause cell death because if the break is incorrectly repaired, a segment of the DNA may be lost. Cells use a process known as homologous recombination to repair such breaks correctly. This uses an undamaged DNA molecule as a template that can be copied to replace missing segments of the DNA sequence. During the repair of double-strand breaks, connections called crossovers may form. This results in the damaged and undamaged DNA molecules swapping a portion of their sequences.

In meiosis, a type of cell division that produces sperm and eggs, cells deliberately break their chromosomes and then repair them using homologous recombination. The crossovers that form during this process are important for sharing chromosomes between the newly forming cells. It is crucial that the crossovers form at the right time and place along the chromosomes.

Chromosomes have different structures depending on whether a cell is undergoing meiosis or normal (mitotic) cell division. This structure may influence how and where crossovers form. Enzymes called resolvases catalyze the reactions that occur during the last step in homologous recombination to generate crossovers. One particular resolvase acts only during meiosis, whereas others are active in both mitotic and meiotic cells. However, it is not known whether local features of the chromosome structure – such as the proteins packaged in the chromosome alongside the DNA – influence when and where meiotic crossover occurs.

Medhi et al. have now studied how recombination occurs along different regions of the chromosomes in budding yeast cells, which undergo meiosis in a similar way to human cells. The results of the experiments reveal that the mechanism by which crossovers form depends on proteins called axis proteins, one type of which is specifically found in meiotic chromosomes. In regions that had high levels of meiotic axis proteins, crossovers mainly formed using the meiosis-specific resolvase enzyme. In regions that had low levels of meiotic axis proteins, crossovers formed using resolvases that are active in mitotic cells. Further experiments demonstrated that altering the levels of one of the meiotic axis proteins changed which resolvase was used.

Overall, the results presented by Medhi et al. show that differences in chromosome structure, in particular the relative concentration of meiotic axis proteins, influence how crossovers form in yeast. Future studies will investigate whether this is observed in other organisms such as humans, and whether local chromosome structure influences other steps of homologous recombination in meiosis.

DOI:http://dx.doi.org/10.7554/eLife.19669.002

Analysis and description of the stages of Aspergillus fumigatus biofilm formation using scanning electron microscopy

Background

Biofilms are a highly structured consortia of microorganisms that adhere to a substrate and are encased within an extracellular matrix (ECM) that is produced by the organisms themselves. Aspergillus fumigatus is a biotechnological fungus that has a medical and phytopathogenic significance, and its biofilm occurs in both natural and artificial environments; therefore, studies on the stages observed in biofilm formation are of great significance due to the limited knowledge that exists on this specific topic and because there are multiple applications that are being carried out.

Results

Growth curves were obtained from the soil and clinical isolates of the A. fumigatus biofilm formation. The optimal conditions for both of the isolates were inocula of 1 × 10⁶ conidia/mL, incubated at 28 °C during 24 h; these showed stages similar to those described in classic microbial growth: the lag, exponential, and stationary phases. However, the biofilms formed at 37 °C were uneven.

The A. fumigatus biofilm was similar regardless of the isolation source, but differences were presented according to the incubation temperature. The biofilm stages included the following: 1) adhesion to the plate surface (4 h), cell co-aggregation and exopolymeric substance (EPS) production; 2) conidial germination into hyphae (8-12 h), development, hyphal elongation, and expansion with channel formation (16-20 h); and 3) biofilm maturation as follows: mycelia development, hyphal layering networks, and channels formation, and high structural arrangement of the mycelia that included hyphal anastomosis and an extensive production of ECM (24 h); the ECM covered, surrounded and strengthened the mycelial arrangements, particular at 37 °C. In the clinical isolate, irregular fungal structures, such as microhyphae that are short and slender hyphae, occurred; 4) In cell dispersion, the soil isolate exhibited higher conidia than the clinical isolate, which had the capacity to germinate and generate new mycelia growth (24 h). In addition, we present images on the biofilm’s structural arrangement and chemical composition using fluorochromes to detect metabolic activity (FUNI) and mark molecules, such as chitin, DNA, mannose, glucose and proteins.

Conclusions

To our knowledge, this is the first time that, in vitro, scanning electronic microscopy (SEM) images of the stages of A. fumigatus biofilm formation have been presented with a particular emphasis on the high hyphal organization and in diverse ECM to observe biofilm maturation.

Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1

Xue et al. identified Mte1 as a multifunctional regulator of S. cerevisiae Mph1. Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination.

We identified Mte1 (Mph1-associated telomere maintenance protein 1) as a multifunctional regulator of Saccharomyces cerevisiae Mph1, a member of the FANCM family of DNA motor proteins important for DNA replication fork repair and crossover suppression during homologous recombination. We show that Mte1 interacts with Mph1 and DNA species that resemble a DNA replication fork and the D loop formed during recombination. Biochemically, Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Consistent with this activity, genetic analysis reveals that Mte1 functions with Mph1 and the associated MHF complex in replication fork repair. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We further show that the influence of Mte1 on Mph1 activities requires its binding to Mph1 and DNA. Thus, Mte1 differentially regulates Mph1 activities to achieve distinct outcomes in recombination and replication fork repair.

Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils

Yeasts were quantified and isolated from the rhizospheres of 5 plant species grown at 2 sites of a Mexican region contaminated with arsenic, lead, and other heavy metals. Yeast abundance was about 10(2) CFU/g of soil and 31 isolates were obtained. On the basis of the phylogenetic analysis of 26S rRNA and internal transcribed spacer fragment, 6 species were identified within the following 5 genera: Cryptococcus (80.64%), Rhodotorula (6.45%), Exophiala (6.45%), Trichosporon (3.22%), and Cystobasidium (3.22%). Cryptococcus spp. was the predominant group. Pectinases (51.6%), proteases (51.6%), and xylanases (41.9%) were the enzymes most common, while poor production of siderophores (16.1%) and indole acetic acid (9.67%) was detected. Isolates of Rhodotorula mucilaginosa and Cystobasidium sloffiae could promote plant growth and seed germination in a bioassay using Brassica juncea. Resistance of isolates by arsenic and heavy metals was as follows: As(3+) ≥ 100 mmol/L, As(5+) ≥ 30 mmol/L, Zn(2+) ≥ 2 mmol/L, Pb(2+) ≥ 1.2 mmol/L, and Cu(2+) ≥ 0.5 mmol/L. Strains of Cryptococcus albidus were able to reduce arsenate (As(5+)) into arsenite (As(3+)), but no isolate was capable of oxidizing As(3+). This is the first study on the abundance and identification of rhizosphere yeasts in a heavy-metal- and arsenic-contaminated soil, and of the reduction of arsenate by the species C. albidus.

Top3-Rmi1 DNA single-strand decatenase is integral to the formation and resolution of meiotic recombination intermediates

The topoisomerase III (Top3)-Rmi1 heterodimer, which catalyzes DNA single-strand passage, forms a conserved complex with the Bloom's helicase (BLM, Sgs1 in budding yeast). This complex has been proposed to regulate recombination by disassembling double Holliday junctions in a process called dissolution. Top3-Rmi1 has been suggested to act at the end of this process, resolving hemicatenanes produced by earlier BLM/Sgs1 activity. We show here that, to the contrary, Top3-Rmi1 acts in all meiotic recombination functions previously associated with Sgs1, most notably as an early recombination intermediate chaperone, promoting regulated crossover and noncrossover recombination and preventing aberrant recombination intermediate accumulation. In addition, we show that Top3-Rmi1 has important Sgs1-independent functions that ensure complete recombination intermediate resolution and chromosome segregation. These findings indicate that Top3-Rmi1 activity is important throughout recombination to resolve strand crossings that would otherwise impede progression through both early steps of pathway choice and late steps of intermediate resolution.

Antibiosis interaction of Staphylococccus aureus on Aspergillus fumigatus assessed in vitro by mixed biofilm formation

Background

Microorganisms of different species interact in several ecological niches, even causing infection. During the infectious process, a biofilm of single or multispecies can develop. Aspergillus fumigatus and Staphyloccocus aureus are etiologic agents that can cause infectious keratitis. We analyzed in vitro single A. fumigatus and S. aureus, and mixed A. fumigatus-S. aureus biofilms. Both isolates were from patients with infectious keratitis. Structure of the biofilms was analyzed through microscopic techniques including scanning electron microscopy (SEM), transmission electron microscopy (TEM), confocal, and fluorescence microscopy (CLSM) in mixed biofilm as compared with the single A. fumigatus biofilm.

Results

To our knowledge, this is the first time that the structural characteristics of the mixed biofilm A. fumigatus-A. fumigatus were described and shown. S. aureus sharply inhibited the development of biofilm formed by A. fumigatus, regardless of the stage of biofilm formation and bacterial inoculum. Antibiosis effect of bacterium on fungus was as follows: scarce production of A. fumigatus biofilm; disorganized fungal structures; abortive hyphae; and limited hyphal growth; while conidia also were scarce, have modifications in their surface and presented lyses. Antagonist effect did not depend on bacterial concentration, which could probably be due to cell-cell contact interactions and release of bacterial products. In addition, we present images about the co-localization of polysaccharides (glucans, mannans, and chitin), and DNA that form the extracellular matrix (ECM). In contrast, single biofilms showed extremely organized structures: A. fumigatus showed abundant hyphal growth, hyphal anastomosis, and channels, as well as some conidia, and ECM. S. aureus showed microcolonies and cell-to-cell bridges and ECM.

Conclusions

Herein we described the antibiosis relationship of S. aureus against A. fumigatus during in vitro biofilm formation, and report the composition of the ECM formed.

Visualization of recombination-mediated damage bypass by template switching

Template switching (TS) mediates damage-bypass via a recombination-related mechanism involving PCNA polyubiquitylation and Polymerase δ-dependent DNA synthesis. Using two-dimensional gel electrophoresis and electron microscopy, here we characterize TS intermediates arising in Saccharomyces cerevisiae at a defined chromosome locus, identifying five major families of intermediates. Single-stranded DNA gaps in the range of 150-200 nucleotides, and not DNA ends, initiate TS by strand invasion. This causes re-annealing of the parental strands and exposure of the non-damaged newly synthesized chromatid as template for replication by the other blocked nascent strand. Structures resembling double Holliday Junctions, postulated to be central double-strand break repair intermediates, but so far only visualized in meiosis, mediate late stages of TS, before being processed to hemicatenanes. Our results reveal the DNA transitions accounting for recombination-mediated DNA damage tolerance in mitotic cells and for replication under conditions of genotoxic stress.

Unique genome replication mechanism of the archaeal virus AFV1

The exceptional genomic content and genome organization of the Acidianus filamentous virus 1 (AFV1) that infects the hyperthermophilic archaeon Acidianus hospitalis suggest that this virus might exploit an unusual mechanism of genome replication. An analysis of replicative intermediates of the viral genome by two-dimensional (2D) agarose gel electrophoresis revealed that viral genome replication starts by the formation of a D-loop and proceeds via strand displacement replication. Characterization of replicative intermediates using dark-field electron microscopy, in combination with the 2D agarose gel electrophoresis data, suggests that recombination plays a key role in the termination of AFV1 genome replication through the formation of terminal loops. A terminal protein was found to be attached to the ends of the viral genome. The results allow us to postulate a model of genome replication that relies on recombination events for initiation and termination.

Smc5/6-Mms21 prevents and eliminates inappropriate recombination intermediates in meiosis

Repairing broken chromosomes via joint molecule (JM) intermediates is hazardous and therefore strictly controlled in most organisms. Also in budding yeast meiosis, where production of enough crossovers via JMs is imperative, only a subset of DNA breaks are repaired via JMs, closely regulated by the ZMM pathway. The other breaks are repaired to non-crossovers, avoiding JM formation, through pathways that require the BLM/Sgs1 helicase. “Rogue” JMs that escape the ZMM pathway and BLM/Sgs1 are eliminated before metaphase by resolvases like Mus81-Mms4 to prevent chromosome nondisjunction. Here, we report the requirement of Smc5/6-Mms21 for antagonizing rogue JMs via two mechanisms; destabilizing early intermediates and resolving JMs. Elimination of the Mms21 SUMO E3-ligase domain leads to transient JM accumulation, depending on Mus81-Mms4 for resolution. Absence of Smc6 leads to persistent rogue JMs accumulation, preventing chromatin separation. We propose that the Smc5/6-Mms21 complex antagonizes toxic JMs by coordinating helicases and resolvases at D-Loops and HJs, respectively.

Homologous recombination allows repair of DNA breaks from intact templates of identical sequence by a “copy-and-paste” like mechanism. However, the double Holliday Junction (dHJ) is a hazardous intermediate that can form during homologous recombination, if single stranded DNA from both ends of a lesion pair with the template. Once the primary lesion is eliminated, the dHJ connects the chromosomes stably and if unresolved can prevent segregation during cell division. In order to prevent chromosome non-disjunction, resolvases will cut any HJ before division. However, genomes contain many multi-copy DNA sequences as transposons or repetitive elements. If dHJs form between such non-allelic loci, cleavage by resolvases can result in chromosome translocations and deletions. Therefore, stabilization of dHJs is sought to be avoided in the first instance by anti-recombinogenic helicases on early intermediates. Analysis of Smc5/6-Mms21 mutants in meiosis revealed that it antagonizes unregulated dHJs both by prevention and resolution. Elimination of the Mms21 SUMO E3-ligase domain leads to inappropriate dHJ accumulation still resolved by Mus81-Mms4. Disruption of the whole complex results in persistent dHJ accumulation and dysfunction of resolvases, preventing chromatin segregation. These results provide a first unified view on the function of Smc5/6-Mms21 as an antagonist of dangerous dHJs.

Inhibition of the Smc5/6 complex during meiosis perturbs joint molecule formation and resolution without significantly changing crossover or non-crossover levels

Meiosis is a specialized cell division used by diploid organisms to form haploid gametes for sexual reproduction. Central to this reductive division is repair of endogenous DNA double-strand breaks (DSBs) induced by the meiosis-specific enzyme Spo11. These DSBs are repaired in a process called homologous recombination using the sister chromatid or the homologous chromosome as a repair template, with the homolog being the preferred substrate during meiosis. Specific products of inter-homolog recombination, called crossovers, are essential for proper homolog segregation at the first meiotic nuclear division in budding yeast and mice. This study identifies an essential role for the conserved Structural Maintenance of Chromosomes (SMC) 5/6 protein complex during meiotic recombination in budding yeast. Meiosis-specific smc5/6 mutants experience a block in DNA segregation without hindering meiotic progression. Establishment and removal of meiotic sister chromatid cohesin are independent of functional Smc6 protein. smc6 mutants also have normal levels of DSB formation and repair. Eliminating DSBs rescues the segregation block in smc5/6 mutants, suggesting that the complex has a function during meiotic recombination. Accordingly, smc6 mutants accumulate high levels of recombination intermediates in the form of joint molecules. Many of these joint molecules are formed between sister chromatids, which is not normally observed in wild-type cells. The normal formation of crossovers in smc6 mutants supports the notion that mainly inter-sister joint molecule resolution is impaired. In addition, return-to-function studies indicate that the Smc5/6 complex performs its most important functions during joint molecule resolution without influencing crossover formation. These results suggest that the Smc5/6 complex aids primarily in the resolution of joint molecules formed outside of canonical inter-homolog pathways.

Most eukaryotic cells are diploid, which means that they contain two copies of each chromosome – one from each parent. In order to preserve the chromosome number from generation to generation, diploid organisms employ a process called meiosis to form gametes containing only one copy of each chromosome. During sexual reproduction, two gametes (sperm and eggs in mammals) fuse to form a zygote with the same chromosome number as the parents. This zygote will develop into a new organism that has genetic characteristics unique from, but still related to, both parents. The reduction of chromosome number and the reshuffling of genetic traits during meiosis depend on the repair of naturally occurring DNA breaks. Improper break repair during meiosis may block meiosis altogether or form genetically instable gametes, leading to fertility problems or defects in the offspring. The study presented here demonstrates the importance of the evolutionarily conserved Smc5/6 protein complex in upholding the integrity of meiotic repair processes. Our results show that cells deficient in components of the Smc5/6 complex lead to inviable meiotic products. Cells lacking functional Smc5/6 complex are unable to direct DNA repair to the proper template and accumulate abnormal repair intermediates, which inhibit the reductive division.

Timeless-dependent DNA replication-coupled recombination promotes Kaposi's Sarcoma-associated herpesvirus episome maintenance and terminal repeat stability

Kaposi's Sarcoma-associated herpesvirus (KSHV) is maintained as a stable episome in latently infected pleural effusion lymphoma (PEL) cells. Episome maintenance is conferred by the binding of the KSHV-encoded LANA protein to the viral terminal repeats (TR). Here, we show that DNA replication in the KSHV TR is coupled with DNA recombination and mediated in part through the cellular replication fork protection factors Timeless (Tim) and Tipin. We show by two-dimensional (2D) agarose gel electrophoresis that replication forks naturally stall and form recombination-like structures at the TR during an unperturbed cell cycle. Chromatin immunoprecipitation (ChIP) assays revealed that Tim and Tipin are selectively enriched at the KSHV TR during S phase and in a LANA-dependent manner. Tim depletion inhibited LANA-dependent TR DNA replication and caused the loss of KSHV episomes from latently infected PEL cells. Tim depletion resulted in the aberrant accumulation of recombination structures and arrested MCM helicase at TR. Tim depletion did not induce the KSHV lytic cycle or apoptotic cell death. We propose that KSHV episome maintenance requires Tim-assisted replication fork protection at the viral terminal repeats and that Tim-dependent recombination-like structures form at TR to promote DNA repeat stability and viral genome maintenance.

Unusual chromatin structure associated with monoparalogous transcription of the Babesia bovis ves multigene family

Rapid antigenic variation in Babesia bovis involves the variant erythrocyte surface antigen-1 (VESA1), a heterodimeric protein with subunits encoded by two branches of the ves multigene family. The ves1α and ves1β gene pair encoding VESA1a and 1b, respectively, are transcribed in a monoparalogous manner from a single locus of active ves transcription (LAT), just one of many quasi-palindromic ves loci. To determine whether this organization plays a role in transcriptional regulation, chromatin structure was first assessed. Limited treatment of isolated nuclei with micrococcal nuclease to assay nucleosomal patterning revealed a periodicity of 156-159 bp in both bulk chromatin and specific gene coding regions. This pattern also was maintained in the intergenic regions (IGr) of non-transcribed ves genes. In contrast, the LAT IGr adopts a unique pattern, yielding an apparent cluster of five closely-spaced hypersensitive sites flanked by regions of reduced nucleosomal occupancy. ves loci fall into three patterns of overall sensitivity to micrococcal nuclease or DNase I digestion, with only the LAT being consistently very sensitive. Non-transcribed ves genes are inconsistent in their sensitivity to the two enzymatic probes. Non-linear DNA structure in chromatin was investigated to determine whether unique structure arising as a result of the quasi-palindromic nature of the LAT may effect transcriptional control. The in vitro capacity of ves IGr sequences to adopt stable higher-order DNA structure is demonstrated here, but the presence of such structure in vivo was not supported. Based upon these results a working model is proposed for the chromatin structural remodeling responsible for the sequential expression of ves multigene family members from divergently-organized loci.

Biochemical and molecular analysis of some commercial samples of chilli peppers from Mexico

The genus Capsicum provides antioxidant compounds, such as phenolics and carotenoids, into the diet. In Mexico, there is a wide diversity of species and varieties of chilli peppers, a fruit which has local cultural and gastronomic importance. In the present study, the relationship of the carotenoid and phenolic profiles with the RAPD fingerprint of three different commercial cultivars of chilli peppers of seven regions of Mexico was investigated. Through RAPD, the species of chilli were differentiated by means of different primers (OPE-18, MFG-17, MFG-18, C51, and C52). The genetic distance found with OPE 18 was in the order of 2.6. The observed differences were maintained when the chromatographic profile of carotenoids, and the molecular markers were analyzed, which suggest a close relationship between carotenoids and the genetic profile. While the chromatographic profile of phenols and the molecular markers were unable to differentiate between genotypes of chilli peppers. In addition, by using infrared spectroscopy and statistical PCA, differences explained by geographic origin were found. Thus, this method could be an alternative for identification of chilli species with respect to their geographic origin.

BLM helicase ortholog Sgs1 is a central regulator of meiotic recombination intermediate metabolism

The BLM helicase has been shown to maintain genome stability by preventing accumulation of aberrant recombination intermediates. We show here that the Saccharomyces cerevisiae BLM ortholog, Sgs1, plays an integral role in normal meiotic recombination, beyond its documented activity limiting aberrant recombination intermediates. In wild-type meiosis, temporally and mechanistically distinct pathways produce crossover and noncrossover recombinants. Crossovers form late in meiosis I prophase, by polo kinase-triggered resolution of Holliday junction (HJ) intermediates. Noncrossovers form earlier, via processes that do not involve stable HJ intermediates. In contrast, sgs1 mutants abolish early noncrossover formation. Instead, both noncrossovers and crossovers form by late HJ intermediate resolution, using an alternate pathway requiring the overlapping activities of Mus81-Mms4, Yen1, and Slx1-Slx4, nucleases with minor roles in wild-type meiosis. We conclude that Sgs1 is a primary regulator of recombination pathway choice during meiosis and suggest a similar function in the mitotic cell cycle.

Meiotic recombination intermediates are resolved with minimal crossover formation during return-to-growth, an analogue of the mitotic cell cycle

Accurate segregation of homologous chromosomes of different parental origin (homologs) during the first division of meiosis (meiosis I) requires inter-homolog crossovers (COs). These are produced at the end of meiosis I prophase, when recombination intermediates that contain Holliday junctions (joint molecules, JMs) are resolved, predominantly as COs. JM resolution during the mitotic cell cycle is less well understood, mainly due to low levels of inter-homolog JMs. To compare JM resolution during meiosis and the mitotic cell cycle, we used a unique feature of Saccharomyces cerevisiae, return to growth (RTG), where cells undergoing meiosis can be returned to the mitotic cell cycle by a nutritional shift. By performing RTG with ndt80 mutants, which arrest in meiosis I prophase with high levels of interhomolog JMs, we could readily monitor JM resolution during the first cell division of RTG genetically and, for the first time, at the molecular level. In contrast to meiosis, where most JMs resolve as COs, most JMs were resolved during the first 1.5–2 hr after RTG without producing COs. Subsequent resolution of the remaining JMs produced COs, and this CO production required the Mus81/Mms4 structure-selective endonuclease. RTG in sgs1-ΔC795 mutants, which lack the helicase and Holliday junction-binding domains of this BLM homolog, led to a substantial delay in JM resolution; and subsequent JM resolution produced both COs and NCOs. Based on these findings, we suggest that most JMs are resolved during the mitotic cell cycle by dissolution, an Sgs1 helicase-dependent process that produces only NCOs. JMs that escape dissolution are mostly resolved by Mus81/Mms4-dependent cleavage that produces both COs and NCOs in a relatively unbiased manner. Thus, in contrast to meiosis, where JM resolution is heavily biased towards COs, JM resolution during RTG minimizes CO formation, thus maintaining genome integrity and minimizing loss of heterozygosity.

Cell proliferation involves DNA replication followed by a mitotic division, producing two cells with identical genomes. Diploid organisms, which contain two genome copies per cell, also undergo meiosis, where DNA replication followed by two divisions produces haploid gametes, the equivalent sperm and eggs, with a single copy of the genome. During meiosis, the two copies of each chromosome are brought together and connected by recombination intermediates (joint molecules, JMs) at sites of sequence identity. During meiosis, JMs frequently resolve as crossovers, which exchange flanking sequences, and crossovers are required for accurate chromosome segregation. JMs also form during the mitotic cell cycle, but resolve infrequently as crossovers. To understand how JMs resolve during the mitotic cell cycle, we used a property of budding yeast, return to growth (RTG), in which cells exit meiosis and resume the mitotic cell cycle. By returning to growth cells with high levels of JMs, we determined how JMs resolve in a mitotic cell cycle-like environment. We found that, during RTG, most JMs are taken apart without producing crossovers by Sgs1, a DNA unwinding enzyme. Because Sgs1 is homologous to the mammalian BLM helicase, it is likely that similar mechanisms reduce crossover production in mammals.

Timeless links replication termination to mitotic kinase activation

The mechanisms that coordinate the termination of DNA replication with progression through mitosis are not completely understood. The human Timeless protein (Tim) associates with S phase replication checkpoint proteins Claspin and Tipin, and plays an important role in maintaining replication fork stability at physical barriers, like centromeres, telomeres and ribosomal DNA repeats, as well as at termination sites. We show here that human Tim can be isolated in a complex with mitotic entry kinases CDK1, Auroras A and B, and Polo-like kinase (Plk1). Plk1 bound Tim directly and colocalized with Tim at a subset of mitotic structures in M phase. Tim depletion caused multiple mitotic defects, including the loss of sister-chromatid cohesion, loss of mitotic spindle architecture, and a failure to exit mitosis. Tim depletion caused a delay in mitotic kinase activity in vivo and in vitro, as well as a reduction in global histone H3 S10 phosphorylation during G2/M phase. Tim was also required for the recruitment of Plk1 to centromeric DNA and formation of catenated DNA structures at human centromere alpha satellite repeats. Taken together, these findings suggest that Tim coordinates mitotic kinase activation with termination of DNA replication.

The replisome pausing factor Timeless is required for episomal maintenance of latent Epstein-Barr virus

The Epstein-Barr virus (EBV) genome is maintained as an extrachromosomal episome during latent infection of B lymphocytes. Episomal maintenance is conferred by the interaction of the EBV-encoded nuclear antigen 1 (EBNA1) with a tandem array of high-affinity binding sites, referred to as the family of repeats (FR), located within the viral origin of plasmid replication (OriP). How this nucleoprotein array confers episomal maintenance is not completely understood. Previous studies have shown that DNA replication forks pause and terminate with high frequency at OriP. We now show that cellular DNA replication fork pausing and protection factors Timeless (Tim) and Tipin (Timeless-interacting protein) accumulate at OriP during S phase of the cell cycle. Depletion of Tim inhibits OriP-dependent DNA replication and causes a complete loss of the closed-circular form of EBV episomes in latently infected B lymphocytes. Tim depletion also led to the accumulation of double-strand breaks at the OriP region. These findings demonstrate that Tim is essential for sustaining the episomal forms of EBV DNA in latently infected cells and suggest that DNA replication fork protection is integrally linked to the mechanism of plasmid maintenance.

Separable roles for Exonuclease I in meiotic DNA double-strand break repair

Exo1 is a member of the Rad2 protein family and possesses both 5'-3' exonuclease and 5' flap endonuclease activities. In addition to performing a variety of functions during mitotic growth, Exo1 is also important for the production of crossovers during meiosis. However, its precise molecular role has remained ambiguous and several models have been proposed to account for the crossover deficit observed in its absence. Here, we present physical evidence that the nuclease activity of Exo1 is essential for normal 5'-3' resection at the Spo11-dependent HIS4 hotspot in otherwise wild-type cells. This same activity was also required for normal levels of gene conversion at the locus. However, gene conversions were frequently observed at a distance beyond that at which resection was readily detectable arguing that it is not the extent of the initial DNA end resection that limits heteroduplex formation. In addition to these nuclease-dependent functions, we found that an exo1-D173A mutant defective in nuclease activity is able to maintain crossing-over at wild-type levels in a number of genetic intervals, suggesting that Exo1 also plays a nuclease-independent role in crossover promotion.

Frequent and efficient use of the sister chromatid for DNA double-strand break repair during budding yeast meiosis

Studies of DNA double-strand break repair during meiosis reveal that a substantial fraction of recombination occurs between sister chromatids.

Recombination between homologous chromosomes of different parental origin (homologs) is necessary for their accurate segregation during meiosis. It has been suggested that meiotic inter-homolog recombination is promoted by a barrier to inter-sister-chromatid recombination, imposed by meiosis-specific components of the chromosome axis. Consistent with this, measures of Holliday junction–containing recombination intermediates (joint molecules [JMs]) show a strong bias towards inter-homolog and against inter-sister JMs. However, recombination between sister chromatids also has an important role in meiosis. The genomes of diploid organisms in natural populations are highly polymorphic for insertions and deletions, and meiotic double-strand breaks (DSBs) that form within such polymorphic regions must be repaired by inter-sister recombination. Efforts to study inter-sister recombination during meiosis, in particular to determine recombination frequencies and mechanisms, have been constrained by the inability to monitor the products of inter-sister recombination. We present here molecular-level studies of inter-sister recombination during budding yeast meiosis. We examined events initiated by DSBs in regions that lack corresponding sequences on the homolog, and show that these DSBs are efficiently repaired by inter-sister recombination. This occurs with the same timing as inter-homolog recombination, but with reduced (2- to 3-fold) yields of JMs. Loss of the meiotic-chromosome-axis-associated kinase Mek1 accelerates inter-sister DSB repair and markedly increases inter-sister JM frequencies. Furthermore, inter-sister JMs formed in mek1Δ mutants are preferentially lost, while inter-homolog JMs are maintained. These findings indicate that inter-sister recombination occurs frequently during budding yeast meiosis, with the possibility that up to one-third of all recombination events occur between sister chromatids. We suggest that a Mek1-dependent reduction in the rate of inter-sister repair, combined with the destabilization of inter-sister JMs, promotes inter-homolog recombination while retaining the capacity for inter-sister recombination when inter-homolog recombination is not possible.

In diploid organisms, which contain two parental sets of chromosomes, double-stranded breaks in DNA can be repaired by recombination, either with a copy of the chromosome produced by replication (the sister chromatid), or with either chromatid of the other parental chromosome (the homolog). During meiosis, recombination with the homolog ensures faithful segregation of chromosomes to gametes (sperm or egg). It has been suggested that use of the spatially distant homolog, as opposed to the nearby sister chromatid, results from a meiosis-specific barrier to recombination between sister chromatids. However, there are situations where meiotic recombination must occur between sister chromatids, such as when recombination initiates in sequences that are absent from the homolog. By studying such a situation, we show that meiotic recombination with the sister chromatid occurs with similar timing and efficiency as recombination with the homolog. Further analysis indicates that inter-sister recombination is more common than was previously thought, although still far less prevalent than in somatic cells, where inter-sister recombination predominates. We suggest that meiosis-specific factors act to roughly equalize repair from the sister and homolog, which both allows the establishment of physical connections between homologs and ensures timely repair of breaks incurred in regions lacking corresponding sequences on the homolog.

Microcystis toxigenic strains in urban lakes: a case of study in Mexico City

Microcystis is a bloom-forming, common cyanobacterium in urban lakes of Mexico City. To assess the presence of potentially cyanotoxin-producing Microcystis, molecular techniques were applied and acute toxicity bioassays were performed with Daphnia magna neonates exposed to cyanobacterial crude extracts. Toxigenic potential of isolated strains was inferred by amplifying the mcyA-Cd genes and their identity as Microcystis was confirmed through the 16S rDNA and phycocyanin operon amplification. Microcystins synthesized under culture conditions were quantified through ELISA. The acute toxicity bioassays revealed that mortality was independent from the cyanotoxin concentration in some strains; this suggests the presence of other metabolites (different from microcystins) that also exerted an important biological effect. Isolated strains had the mcyA-Cd gene and most of them produced variable amounts of microcystins in the culture conditions used, confirming their toxigenic potential. Results warn about possible toxic effect risks for aquatic biota, neighboring areas, visitors and users of these sites, due to the constant presence of these blooms in the studied water bodies.

Evidence that MEK1 positively promotes interhomologue double-strand break repair

During meiosis there is an imperative to create sufficient crossovers for homologue segregation. This can be achieved during repair of programmed DNA double-strand breaks (DSBs), which are biased towards using a homologue rather than sister chromatid as a repair template. Various proteins contribute to this bias, one of which is a meiosis specific kinase Mek1. It has been proposed that Mek1 establishes the bias by creating a barrier to sister chromatid repair, as distinct from enforcing strand invasion with the homologue. We looked for evidence that Mek1 positively stimulates strand invasion of the homologue. This was done by analysing repair of DSBs induced by the VMA1-derived endonuclease (VDE) and flanked by directly repeated sequences that can be used for intrachromatid single-strand annealing (SSA). SSA competes with interhomologue strand invasion significantly more successfully when Mek1 function is lost. We suggest the increase in intrachromosomal SSA reflects an opportunistic default repair pathway due to loss of a MEK1 stimulated bias for strand invasion of the homologous chromosome. Making use of an inhibitor sensitive mek1-as1 allele, we found that Mek1 function influences the repair pathway throughout the first4–5 h of meiosis. Perhaps reflecting a particular need to create bias for successful interhomologue events before chromosome pairing is complete.

Essential global role of CDC14 in DNA synthesis revealed by chromosome underreplication unrecognized by checkpoints in cdc14 mutants

The CDC14 family of multifunctional evolutionarily conserved phosphatases includes major regulators of mitosis in eukaryotes and of DNA damage response in humans. The CDC14 function is also crucial for accurate chromosome segregation, which is exemplified by its absolute requirement in yeast for the anaphase segregation of nucleolar organizers; however the nature of this essential pathway is not understood. Upon investigation of the rDNA nondisjunction phenomenon, it was found that cdc14 mutants fail to complete replication of this locus. Moreover, other late-replicating genomic regions (10% of the genome) are also underreplicated in cdc14 mutants undergoing anaphase. This selective genome-wide replication defect is due to dosage insufficiency of replication factors in the nucleus, which stems from two defects, both contingent on the reduced CDC14 function in the preceding mitosis. First, a constitutive nuclear import defect results in a drastic dosage decrease for those replication proteins that are regulated by nuclear transport. Particularly, essential RPA subunits display both lower mRNA and protein levels, as well as abnormal cytoplasmic localization. Second, the reduced transcription of MBF and SBF-controlled genes in G1 leads to the reduction in protein levels of many proteins involved in DNA replication. The failure to complete replication of late replicons is the primary reason for chromosome nondisjunction upon CDC14 dysfunction. As the genome-wide slow-down of DNA replication does not trigger checkpoints [Lengronne A, Schwob E (2002) Mol Cell 9:1067-1078], CDC14 mutations pose an overwhelming challenge to genome stability, both generating chromosome damage and undermining the checkpoint control mechanisms.

Identificação diferencial de Rhodococcus equi e Dietzia maris em bubalinos

Foram analisados 24 isolados bacterianos oriundos de leite e pele de búfalas (Bubalus bubalis), os quais foram previamente identificados como Rhodococcus equi com o auxílio de fenotipia concisa. Testes fenotípicos complementares e ferramentas moleculares foram utilizados com o objetivo de caracterizar esses isolados, bem como diferenciá-los de outros microrganismos intimamente relacionados. Observaram-se três fenótipos distintos, porém a identificação dos isolados foi inconclusiva. Apenas um dos isolados foi comprovado como sendo R. equi com a realização da PCR espécie-específica, sequenciamento e análise dos fragmentos de DNA. Os demais isolados só foram identificados pelo sequenciamento de fragmento do gene que codifica a região 16S do rRNA universal de bactérias, indicando tratar-se de Dietzia maris. O perfil de susceptibilidade aos antimicrobianos revelou maior resistência dos isolados de D. maris para oxacilina (96%) e rifampicina (87%). O isolado de R. equi apresentou resistência à amicacina, oxacilina, penicilina, rifampicina e tetraciclina. Alerta-se para o risco da incorreta identificação dos isolados baseados em testes fenotípicos concisos e para a necessidade de utilização de testes complementares para diferenciação entre R. equi e D. maris.

The stress-activated protein kinase Hog1 mediates S phase delay in response to osmostress

Control of cell cycle progression by stress-activated protein kinases (SAPKs) is essential for cell adaptation to extracellular stimuli. Exposure of yeast to osmostress activates the Hog1 SAPK, which modulates cell cycle progression at G1 and G2 by the phosphorylation of elements of the cell cycle machinery, such as Sic1 and Hsl1, and by down-regulation of G1 and G2 cyclins. Here, we show that upon stress, Hog1 also modulates S phase progression. The control of S phase is independent of the S phase DNA damage checkpoint and of the previously characterized Hog1 cell cycle targets Sic1 and Hsl1. Hog1 uses at least two distinct mechanisms in its control over S phase progression. At early S phase, the SAPK prevents firing of replication origins by delaying the accumulation of the S phase cyclins Clb5 and Clb6. In addition, Hog1 prevents S phase progression when activated later in S phase or cells containing a genetic bypass for cyclin-dependent kinase activity. Hog1 interacts with components of the replication complex and delays phosphorylation of the Dpb2 subunit of the DNA polymerase. The two mechanisms of Hog1 action lead to delayed firing of origins and prolonged replication, respectively. The Hog1-dependent delay of replication could be important to allow Hog1 to induce gene expression before replication.

Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae

Esc2 is a member of the RENi family of SUMO-like domain proteins and is implicated in gene silencing in Saccharomyces cerevisiae. Here, we identify a dual role for Esc2 during S-phase in mediating both intra-S-phase DNA damage checkpoint signaling and preventing the accumulation of Rad51-dependent homologous recombination repair (HRR) intermediates. These roles are qualitatively similar to those of Sgs1, the yeast ortholog of the human Bloom's syndrome protein, BLM. However, whereas mutation of either ESC2 or SGS1 leads to the accumulation of unprocessed HRR intermediates in the presence of MMS, the accumulation of these structures in esc2 (but not sgs1) mutants is entirely dependent on Mph1, a protein that shows structural similarity to the Fanconi anemia group M protein (FANCM). In the absence of both Esc2 and Sgs1, the intra-S-phase DNA damage checkpoint response is compromised after exposure to MMS, and sgs1esc2 cells attempt to undergo mitosis with unprocessed HRR intermediates. We propose a model whereby Esc2 acts in an Mph1-dependent process, separately from Sgs1, to influence the repair/tolerance of MMS-induced lesions during S-phase.

Stabilization and electrophoretic analysis of meiotic recombination intermediates in Saccharomyces cerevisiae

Joint Molecule (JM) recombination intermediates result from DNA strand-exchange between homologous chromosomes. Physical monitoring of JM formation in budding yeast has provided a wealth of information about the timing and mechanism of meiotic recombination. These assays are especially informative when applied to the analysis of mutants for which genetic analysis of recombination is impossible, i.e. mutants that die during meiosis. This chapter describes three distinct methods to stabilize JMs against thermally driven dissolution as well as electrophoretic approaches to resolve and detect JMs at two well-characterized recombination hotspots.

Mus81/Mms4 endonuclease and Sgs1 helicase collaborate to ensure proper recombination intermediate metabolism during meiosis

Budding yeast lacking the Sgs1 helicase and the Mus81/Mms4 endonuclease are inviable, and indirect studies implicate homologous recombination gone awry as the cause of death. We show that mutants lacking both enzymes have profound defects in meiotic recombination intermediate metabolism and crossover (CO) formation. Recombination intermediates (joint molecules, JMs) accumulate in these cells, many with structures that are infrequent in wild-type cells. These JMs persist, preventing nuclear division. Using an inducible expression system, we restored Mus81 or Sgs1 to sgs1 mus81 cells at a time when JMs are forming. Mus81 expression did not prevent JM formation but did restore JM resolution, CO formation, and nuclear division. In contrast, Sgs1 expression reduced the extent of JM accumulation. These results indicate that Sgs1 and Mus81/Mms4 collaborate to direct meiotic recombination toward interhomolog interactions that promote proper chromosome segregation, and also indicate that Mus81/Mms4 promotes JM resolution in vivo.

A role for MRE11, NBS1, and recombination junctions in replication and stable maintenance of EBV episomes

Recombination-like structures formed at origins of DNA replication may contribute to replication fidelity, sister chromatid cohesion, chromosome segregation, and overall genome stability. The Epstein-Barr Virus (EBV) origin of plasmid replication (OriP) provides episomal genome stability through a poorly understood mechanism. We show here that recombinational repair proteins MRE11 and NBS1 are recruited to the Dyad Symmetry (DS) region of OriP in a TRF2- and cell cycle-dependent manner. Depletion of MRE11 or NBS1 by siRNA inhibits OriP replication and destabilized viral episomes. OriP plasmid maintenance was defective in MRE11 and NBS1 hypomorphic fibroblast cell lines and only integrated, non-episomal forms of EBV were detected in a lympoblastoid cell line derived from an NBS1-mutated individual. Two-dimensional agarose gel analysis of OriP DNA revealed that recombination-like structures resembling Holliday-junctions form at OriP in mid S phase. MRE11 and NBS1 association with DS coincided with replication fork pausing and origin activation, which preceded the formation of recombination structures. We propose that NBS1 and MRE11 promote replication-associated recombination junctions essential for EBV episomal maintenance and genome stability.

Evidence that a RecQ helicase slows senescence by resolving recombining telomeres

RecQ helicases, including Saccharomyces cerevisiae Sgs1p and the human Werner syndrome protein, are important for telomere maintenance in cells lacking telomerase activity. How maintenance is accomplished is only partly understood, although there is evidence that RecQ helicases function in telomere replication and recombination. Here we use two-dimensional gel electrophoresis (2DGE) and telomere sequence analysis to explore why cells lacking telomerase and Sgs1p (tlc1 sgs1 mutants) senesce more rapidly than tlc1 mutants with functional Sgs1p. We find that apparent X-shaped structures accumulate at telomeres in senescing tlc1 sgs1 mutants in a RAD52- and RAD53-dependent fashion. The X-structures are neither Holliday junctions nor convergent replication forks, but instead may be recombination intermediates related to hemicatenanes. Direct sequencing of examples of telomere I-L in senescing cells reveals a reduced recombination frequency in tlc1 sgs1 compared with tlc1 mutants, indicating that Sgs1p is needed for tlc1 mutants to complete telomere recombination. The reduction in recombinants is most prominent at longer telomeres, consistent with a requirement for Sgs1p to generate viable progeny following telomere recombination. We therefore suggest that Sgs1p may be required for efficient resolution of telomere recombination intermediates, and that resolution failure contributes to the premature senescence of tlc1 sgs1 mutants.

Because telomeres are situated at the ends of chromosomes, they are both essential for chromosome integrity and particularly susceptible to processes that lead to loss of their own DNA sequences. The enzyme telomerase can counter these losses, but there are also other means of telomere maintenance, some of which depend on DNA recombination. The RecQ family of DNA helicases process DNA recombination intermediates and also help ensure telomere integrity, but the relationship between these activities is poorly understood. Family members include yeast Sgs1p and human WRN and BLM, which are deficient in the Werner premature aging syndrome and the Bloom cancer predisposition syndrome, respectively. We have found that the telomeres of yeast cells lacking both telomerase and Sgs1p accumulate structures that resemble recombination intermediates. Further, we provide evidence that the inability of cells lacking Sgs1p to process these telomere recombination intermediates leads to the premature arrest of cell division. We predict that similar defects in the processing of recombination intermediates may contribute to telomere defects in human Werner and Bloom syndrome cells.

Yeast cells lacking the RecQ helicase Sgs1p show an accumulation of telomere recombination intermediates associated with premature senescence.

Shu proteins promote the formation of homologous recombination intermediates that are processed by Sgs1-Rmi1-Top3

CSM2, PSY3, SHU1, and SHU2 (collectively referred to as the SHU genes) were identified in Saccharomyces cerevisiae as four genes in the same epistasis group that suppress various sgs1 and top3 mutant phenotypes when mutated. Although the SHU genes have been implicated in homologous recombination repair (HRR), their precise role(s) within this pathway remains poorly understood. Here, we have identified a specific role for the Shu proteins in a Rad51/Rad54-dependent HRR pathway(s) to repair MMS-induced lesions during S-phase. We show that, although mutation of RAD51 or RAD54 prevented the formation of MMS-induced HRR intermediates (X-molecules) arising during replication in sgs1 cells, mutation of SHU genes attenuated the level of these structures. Similar findings were also observed in shu1 cells in which Rmi1 or Top3 function was impaired. We propose a model in which the Shu proteins act in HRR to promote the formation of HRR intermediates that are processed by the Sgs1-Rmi1-Top3 complex.

Replication fork reversal occurs spontaneously after digestion but is constrained in supercoiled domains

Replication fork reversal was investigated in undigested and linearized replication intermediates of bacterial DNA plasmids containing a stalled fork. Two-dimensional agarose gel electrophoresis, a branch migration and extrusion assay, electron microscopy, and DNA-psoralen cross-linking were used to show that extensive replication fork reversal and extrusion of the nascent-nascent duplex occurs spontaneously after DNA nicking and restriction enzyme digestion but that fork retreat is severely limited in covalently closed supercoiled domains.

Topological locking restrains replication fork reversal

Two-dimensional agarose gel electrophoresis, psoralen cross-linking, and electron microscopy were used to study the effects of positive supercoiling on fork reversal in isolated replication intermediates of bacterial DNA plasmids. The results obtained demonstrate that the formation of Holliday-like junctions at both forks of a replication bubble creates a topological constraint that prevents further regression of the forks. We propose that this topological locking of replication intermediates provides a biological safety mechanism that protects DNA molecules against extensive fork reversals.

Top3 processes recombination intermediates and modulates checkpoint activity after DNA damage

Mutation of TOP3 in Saccharomyces cerevisiae causes poor growth, hyperrecombination, and a failure to fully activate DNA damage checkpoints in S phase. Here, we report that overexpression of a dominant-negative allele of TOP3, TOP3(Y356F), which lacks the catalytic (decatenation) activity of Top3, causes impaired S-phase progression and the persistence of abnormal DNA structures (X-shaped DNA molecules) after exposure to methylmethanesulfonate. The impaired S-phase progression is due to a persistent checkpoint-mediated cell cycle delay and can be overridden by addition of caffeine. Hence, the catalytic activity of Top3 is not required for DNA damage checkpoint activation, but it is required for normal S-phase progression after DNA damage. We also present evidence that the checkpoint-mediated cell cycle delay and persistence of X-shaped DNA molecules resulting from overexpression of TOP3(Y356F) are downstream of Rad51 function. We propose that Top3 functions in S phase to both process homologous recombination intermediates and modulate checkpoint activity.

Formation and processing of stalled replication forks--utility of two-dimensional agarose gels

Replication forks can be stalled by tightly bound proteins, DNA damage, nucleotide deprivation, or defects in the replication machinery. It is now appreciated that processing of stalled replication forks is critical for completion of DNA replication and maintenance of genome stability. In this chapter, we detail the use of two-dimensional (2D) agarose gels with Southern hybridization for the detection and analysis of blocked replication forks in vivo. This kind of 2D gel electrophoresis has been used extensively for analysis of replication initiation mechanisms for many years, and more recently has become a valuable tool for analysis of fork stalling. Although the method can provide valuable information when forks are stalled in random locations (e.g., after UV damage or nucleotide deprivation), it is even more informative with site-specific fork blockage, for example, blocks caused by tightly bound replication terminator proteins or by drug-stabilized topoisomerase cleavage complexes.

Molecular mechanism and thermodynamics study of plasmid DNA and cationic surfactants interactions

The molecular mechanism and thermodynamics of the interactions between plasmid DNA and cationic surfactants were investigated by isothermal titration calorimetry (ITC), dynamic light scattering, surface tension measurements, and UV spectroscopy. The cationic surfactants studied include benzyldimethyldodecylammonium chloride, benzyldimethyltetradecylammonium chloride, cetylpyridinium chloride, and cetyltrimethylammonium chloride. The results indicate a critical aggregation concentration (cac) of a surfactant: above the cac the surfactant forms aggregates with plasmid DNA; below the cac, however, there is no detectable interaction between DNA and surfactant. Surfactants with longer hydrocarbon chains have smaller cac, indicating that hydrophobic interaction plays a key role in DNA-surfactant complexation. Moreover, an increase in ionic strength (I) increases the cac but decreases the critical micellization concentration (cmc). These opposite effects lead to a critical ionic strength (I(c)) at which cac = cmc; when I < I(c), cac < cmc; when I > I(c), DNA does not form complexes with surfactant micelles. In the interaction DNA exhibits a pseudophase property as the cac is a constant over a wide range of DNA concentrations. ITC data showed that the reaction is solely driven by entropy because both deltaH(o) (approximately 2-6 kJ mol(-1)) and deltaS(o) (approximately 70-110 J K(-1) mol(-1)) have positive values. In the complex, the molar ratio of DNA phosphate to surfactant is in the range of 0.63-1.05. The reaction forms sub-micrometer-sized primary particles; those aggregate at high surfactant concentrations. Taken together, the results led to an inference that there is no interaction between surfactant monomers and DNA molecules and demonstrated that DNA-cationic surfactant interactions are mediated by the hydrophobic interactions of surfactant molecules and counterion binding of DNA phosphates to the cationic surfactant aggregates.

Methods to study replication fork collapse in budding yeast

Replication of the eukaryotic genome is a difficult task, as cells must coordinate chromosome replication with chromatin remodeling, DNA recombination, DNA repair, transcription, cell cycle progression, and sister chromatid cohesion. Yet, DNA replication is a potentially genotoxic process, particularly when replication forks encounter a bulge in the template: forks under these conditions may stall and restart or even break down leading to fork collapse. It is now clear that fork collapse stimulates chromosomal rearrangements and therefore represents a potential source of DNA damage. Hence, the comprehension of the mechanisms that preserve replication fork integrity or that promote fork collapse are extremely relevant for the understanding of the cellular processes controlling genome stability. Here we describe some experimental approaches that can be used to physically visualize the quality of replication forks in the yeast S. cerevisiae and to distinguish between stalled and collapsed forks.