Evidence for protected regions of DNA in the mitochondrial nucleoid ofSaccharomyces cerevisiae

Analysis of the Persistence and Particle Size Distributional Shift of Sperm-Derived Environmental DNA to Monitor Jack Mackerel Spawning Activity

Environmental DNA (eDNA) analysis holds great promise as an efficient and noninvasive method to monitor not only the distribution of organisms but also their spawning activity. In eDNA analysis-based monitoring of spawning activity, the detection of sperm-derived eDNA is a key point; however, its characteristics and dynamics are completely unknown. The present study focuses on the persistence and particle size distribution (PSD) of eDNA derived from the sperm of Japanese jack mackerel. First, we investigated the time-dependent degradation and the PSD of sperm-derived eDNA by artificially adding sperm to seawater. Next, we kept fish in tanks and examined the changes in eDNA concentration and PSD before and after spawning. The results of two experiments showed that the degradation of sperm-derived eDNA proceeded rapidly, with PSD shifting to a smaller size regardless of the DNA region (Cyt b or ITS1). Additionally, it was shown that the nuclei and mitochondria released from sperm through degradation had a size distribution that was not simply dependent on each organelle size. These results will contribute to elucidating the characteristics and dynamics of eDNA specifically during the spawning season and to further developing eDNA analysis as a powerful tool for the monitoring of spawning activity.

The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance

Environmental DNA (eDNA) analysis has enabled more sensitive and efficient biological monitoring than traditional methods. However, since the target species is not directly observed, interpretation of results cannot preclude process Type I errors. Specifically, there may be a spatial or temporal gap between the target eDNA and the eDNA source in the sampled area. Moreover, eDNA surveillance lacks the ability to distinguish whether eDNA originated from a living or non-living source. This kind of Type I error is difficult to control for, in part, because the relationship between the state of eDNA (i.e., intracellular or extracellular) and the degradation rate is still unclear. Here, we applied PMA (Propidium monoazide) to eDNA analysis which enabled us to differentiate “intact cells” from “disrupted cells.” PMA is a dye that has a high affinity for double-stranded DNA and forms a covalent bond with double-stranded DNA and inhibits amplification of the bonded DNA molecules by PCR. Since PMA is impermeable to the cell membrane, DNA protected by an intact cell membrane can be selectively detected. In this study, we investigated the workability of PMA on vertebrate eDNA using zebrafish, Danio rerio. Aquarium water was incubated for 1 week to monitor the eDNA degradation process of both intracellular and extracellular eDNA. We developed ten species-specific quantitative PCR assays for D. rerio with different amplification lengths that enabled independent quantification of total eDNA (sum of intracellular and extracellular eDNA, commonly measured in other studies) and intracellular eDNA (DNA in intact cells) and allow for analyses of sequence length-dependent eDNA degradation in combination with PMA. We confirmed that PMA is effective at differentiating “intact” and “disrupted” fish cells. We found that total eDNA and intracellular eDNA have different degradation processes that are dependent on the length of target sequence. For future conservation efforts using eDNA analyses, it is necessary to increase the reliability of the analysis results. The research presented here provides new analysis tools that expand our understanding of the ecology of eDNA, so that more accurate and reliable conclusions can be determined.

Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular

Environmental DNA analysis has emerged as a key component of biodiversity and environmental monitoring. However, the state and fate of eDNA in natural environments is still poorly understood for many ecological systems. Here we assess the state and fate of eDNA derived from the water flea, Daphnia magna, using a full factorial mesocosm experiment. We measured the quantity and degradation of eDNA over a two month period across a range of filters differing in pore size (0, 0.2, 1 and 10 µm), which spans the range of eDNA source material including subcellular, cellular and tissue. We also used two primer sets targeting mitochondrial (COI) and nuclear (18S) genomic regions. Our findings demonstrated that eDNA was most prevalent in the effluent water, but also reliably detected on the 0.2 μm filter, suggesting subcellular material is the predominate state of eDNA. Temporal eDNA quantity dynamics followed an exponential decay function over the course of 6-17 days, demonstrating a predictable decline in eDNA concentration. Nuclear eDNA was more abundant than mitochondrial eDNA, which may be a result of greater primer affinity, or indicate greater availability of nuclear eDNA gene targets in the environment. In contrast to two previous size-sorting experiments, which utilizing fish eDNA, our findings suggest that the state of invertebrate eDNA is much smaller than previously suspected. Overall, our data suggest that the detection of eDNA greatly depends on our knowledge of the state and fate of eDNA, which differ among species, and likely across environmental conditions.

Use of the nuc1 null mutant for analysis of yeast mitochondrial nucleoids

Mitochondrial DNA (mtDNA) of the yeast Saccharomyces cerevisiae is organized to form mitochondrial nucleoids (mt-nucleoids) by association with specific proteins. The sensitivity of DNA-protein complexes to nuclease digestion is a useful means for examining DNA packaging and organization. However, the mt-nucleoids isolated from wild-type cells of S. cerevisiae demonstrated a significant amount of endogenous nuclease activity. In order to minimize the nuclease activity associated with the isolated mt-nucleoids, we isolated the mt-nucleoids from a mutant strain that lacked the mitochondrial nuclease, Nuc1p. In this manner, we succeeded in isolating mt-nucleoids that showed a low level of the nuclease activity. Micrococcal nuclease treatment of these mt-nucleoids led to the continuous digestion of mtDNA in the presence of Ca(2+) ions. MtDNA in the mt-nucleoids also showed the continuous digestion pattern when treated with DNase II. These results suggest that mtDNA in the mt-nucleoids is protected from nuclease digestion by association with proteins, but the organization of the mtDNA-protein complexes is different from that of nuclear chromatin, in which the unit of DNA packaging is regularly repeated.

A novel DNA-binding protein bound to the mitochondrial inner membrane restores the null mutation of mitochondrial histone Abf2p in Saccharomyces cerevisiae

The yeast mitochondrial HMG-box protein, Abf2p, is essential for maintenance of the mitochondrial genome. To better understand the role of Abf2p in the maintenance of the mitochondrial chromosome, we have isolated a multicopy suppressor (YHM2) of the temperature-sensitive defect associated with an abf2 null mutation. The function of Yhm2p was characterized at the molecular level. Yhm2p has 314 amino acid residues, and the deduced amino acid sequence is similar to that of a family of mitochondrial carrier proteins. Yhm2p is localized in the mitochondrial inner membrane and is also associated with mitochondrial DNA in vivo. Yhm2p exhibits general DNA-binding activity in vitro. Thus, Yhm2p appears to be novel in that it is a membrane-bound DNA-binding protein. A sequence that is similar to the HMG DNA-binding domain is important for the DNA-binding activity of Yhm2p, and a mutation in this region abolishes the ability of YHM2 to suppress the temperature-sensitive defect of respiration of the abf2 null mutant. Disruption of YHM2 causes a significant growth defect in the presence of nonfermentable carbon sources such as glycerol and ethanol, and the cells have defects in respiration as determined by 2,3,5,-triphenyltetrazolium chloride staining. Yhm2p may function as a member of the protein machinery for the mitochondrial inner membrane attachment site of mitochondrial DNA during replication and segregation of mitochondrial genomes.

SHM1: a multicopy suppressor of a temperature-sensitive null mutation in the HMG1-like abf2 gene

HM, an HMG1-like mitochondrial DNA-binding protein, is required for maintenance of the yeast mitochondrial genome when cells are grown in glucose. To better understand the role of HM in mitochondria, we have isolated several multicopy suppressors of the temperature-sensitive defect associated with an abf2 null mutation (lacking HM protein). One of these suppressors, SHM1, has been characterized at the molecular level and is described herein. SHM1 encodes a protein (SHM1p) that shares sequence similarity to a family of mitochondrial carrier proteins. On glycerol medium, where mitochondrial function is required for growth, shm1 deletion mutants are able to grow whereas shm1 abf2 double mutants are severely inhibited. These results suggest the SHM1p plays an accessory role to HM in the mitochondrion.

The mitochondrial histone HM: an evolutionary link between bacterial HU and nuclear HMG1 proteins

The mitochondrial histone HM is a very abundant protein in yeast mitochondria that wraps DNA and activates transcription in vitro and is required within the cell for proper maintenance of the mitochondrial chromosome. HM and the bacterial histone-like protein HU have similar activities in vitro and can substitute for each other in E coli cells and in yeast mitochondria. HM also appears to be functionally homologous to nuclear HMG1 proteins, with which it shares a high degree of sequence homology. We report here the isolation of extragenic suppressors of the yeast HM mutant temperature-sensitive phenotype. We also examined the effects of the lack of HM protein and of respiration deficiency on yeast cells mutant for the NHP6 proteins, the putative yeast nuclear HMG1 homologues.

Characterisation of RNA polymerase activity in yeast mitochondria

This paper reports on the optimal incubation conditions for in vitro transcription in isolated yeast mitochondria. The mitochondrial RNA polymerase has an absolute requirement for all four nucleoside triphosphates and Mg2+. The enzyme is inhibited by Mn2+, Ca2+, Cd2+ and KCl while low concentrations of NaCl stimulate activity. Transcription is maximal in Tris/HCl buffer at pH 7.9 and the optimum incubation temperature is 28 degrees C.

Characterization of DNA-protein complexes from the mitochondria of Xenopus laevis oocytes

Mitochondrial DNA (mtDNA)-protein complexes (nucleoids) from Xenopus laevis oocytes were purified either on rate-zonal sucrose or isopyknic metrizamide gradients. From electron microscopic studies and staphylococcal nuclease digestion experiments mtDNA appears to be packaged into regular beaded structures. Protein electrophoretic analysis and M banding results show that mtDNA is associated with the membrane structures and also with few specific proteins including one acid-soluble polypeptide of 28 kD.