DNA Organization of
            <i>Methanobacterium thermoautotrophicum</i>

Mitchell, Ralph; Loeblich, Laurel A.; Klotz, Lynn C.; Loeblich, Alfred R.

doi:10.1126/science.377486

Cited by 51 publications

(13 citation statements)

References 16 publications

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“…The Cot value for half complexity value differing from the computed reassociation, (Cot)112, is read from the curve as value by a factor of 2. The computer-assisted the value at which the hyperchromicity falls by statistical analysis of Pearson et al (31) was one-third from its maximum value (21). The ratio used to make such an assessment.…”

Section: Resultsmentioning

confidence: 99%

DNA content, kinetic complexity, and the ploidy question in Candida albicans.

Riggsby¹,

Torres-Bauza²,

Wills³

et al. 1982

Mol. Cell. Biol.

152

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Candida albicans is a dimorphic fungus that is pathogenic for humans. No sexual cycle has been reported for this fungus, and earlier reports have differed on whether typical strains of C. albicans are haploid or diploid. Previous estimates of the DNA content of C. albicans varied by one order of magnitude. We used three independent methods to measure the kinetic complexity of the single-copy DNA from a typical strain of C. albicans (strain H317) to determine the DNA content per haploid genote; we obtained values of 15 and 20 fg per cell by using S1 nuclease and hydroxyapatite assays, respectively. Optical assays for DNA reassociation kinetics, although not definitive in themselves, yielded values in this range. Chemical measurements of the DNA content of several typical strains, including strain H317, yielded values clustered about a mean of 37 fg per cell. We concluded that these strains are diploid.Candida albicans is a dimorphic fungus, classified among the fungi imperfecti because no sexual cycle has been observed in strains of the species. Most members of the species exist in the yeast form, but the mycelial form may develop under certain conditions (23,24). Both forms of the species are pathogenic for human hosts, although the details of the pathogenicity of the two forms may be very different. Candida is the most common fungal pathogen of humans (1); clinical reports concerning the genus number in the hundreds each year (23).In contrast to the clinical reports, biochemical studies of Candida are relatively sparse. In particular, little has been established concerning the nature and organization of Candida genomes, including those of the most extensively studied species, C. albicans. Even the ploidy of C. albicans is in dispute (27,32,35,46). Several recent reports (27,28,45,46) conclude that at least some C. albicans strains are diploid, whereas results from other reports (32,35), are more simply interpreted in terms of haploidy.There have also been confficting reports of the DNA content of C. albicans strains; even values published during the last 2 years (35,39,46) disagree by nearly one order of magnitude. We present direct measurements of the total DNA content and sequence complexity of C. albicans.The determination reported here was designed specifically to include a large number of measurements to ensure a high degree of precision (2) or Stewart (41); the former procedure was modified by replacing the 0.2 M PCA wash with a 0.2 M PCA extraction (10 to 15 min on ice). We refer to these two extraction procedures as method A and method B, respectively. The supernatants of the hot PCA extractions from both methods were centrifuged at 20,000 x g for 30 min to remove substances that interfered with the diphenylamine assay. DNA was assayed colorimetrically with a diphenylamine reagent (5) and, for some experiments, also with diaminobenzoic acid reagent (37). Highly polymerized calf thymus DNA (type V, Sigma Chemical Co., St. Louis, Mo.) was used as a standard. The DNA was dried by heating at 70°C overnight...

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Section: Resultsmentioning

confidence: 99%

DNA content, kinetic complexity, and the ploidy question in Candida albicans.

Riggsby¹,

Torres-Bauza²,

Wills³

et al. 1982

Mol. Cell. Biol.

152

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“…The size of the T. ferrooxidans genome (2.8 x 106 bp) is about two-thirds that of E. coli (4 x 106 bp) but is larger than those of two members of the archaebacterial group, Thermoplasma acidophilum (1.2 x 106 bp) and Methanobacterium thermoautotrophicum (1.7 x 10' bp) (16,21,28 The reiteration frequency of family 1 has also been determined by kinetic analysis. This was done by determining the CoT112 of a radioactively labeled fragment of a repeated DNA sequence derived from family 1 reassociated with an excess of unlabeled total DNA (Fig.…”

Section: Discussionmentioning

confidence: 99%

Two families of repeated DNA sequences in Thiobacillus ferrooxidans

Yates¹,

Holmes²

1987

J Bacteriol

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The genome of Thiobacillus ferrooxidans ATCC 19859 is about 2.8 X 10(6) base pairs as determined by analysis of reassociation kinetics of sheared DNA. This is 70% of the size of the genome of Escherichia coli. About 6% of the genome of T. ferrooxidans consists of moderately repetitive DNA sequences that are repeated an average of 20 times per genome. Two distinct repeated sequences, designated family 1 and family 2, have been analyzed in more detail. Both families are approximately 1 kilobase in length and are repeated 20 to 30 times per genome. Preliminary evidence from restriction enzyme analysis, Southern blotting experiments, and thermal melting analysis indicates that members of both families are conserved and are interspersed with single-copy DNA. Six copies of one family are present on the 45-kilobase-pair plasmid of strain ATCC 19859.

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“…In this connection, we have studied DNA organization in several organisms that may be near the major prokaryote-eukaryote evolutionary splite.g., dinoflagellates (16), blue-green algae (17), yeast (18,19), and methanobacteria (20). We wish to determine the evolutionary tree topology and root for these organisms with respect to this major split by using 5S RNA sequences.…”

Section: The Methodsmentioning

confidence: 99%

Calculation of evolutionary trees from sequence data.

Klotz¹,

Komar²,

Blanken³

et al. 1979

Proc. Natl. Acad. Sci. U.S.A.

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Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences. from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot.define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct tree topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular fox the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences. The recent proliferation of protein and nucleic acid sequences, due in part to the development of new sequencing techniques (1, 2), has led to a renewed interest in the evolution of these sequences and the organisms from which they came. We wish to discuss here some problems with the commonly used method (3, 4) (the matrix method) for calculating evolutionary trees from molecular sequence data and to present an alternative method that, in theory, eliminates these problems. Because the analytic proof of our method depends on a knowledge of existing methods, we will briefly review what is necessary from the existing literature, then discuss the problems with the matrix method in some detail.An evolutionary tree representation of nucleic acid or protein sequence differences among several organisms should give the following information: (I) the correct pattern of branching of the various present-day organisms from one another (that is, the correct tree "topology"); (ii) the correct position on the tree of the common ancestor to all the present-day organisms (that is, the correct tree "root"); and (iii) of secondary importance, a reasonable estimate of the number of mutations along each of the tree branches (branch mutations).One type of such a representation is presented in Fig. la for five hypothetical present-day organisms, A, B, C, D, and E, and their common ancestor X. In this representation, the topology is shown by the order in which the branches connect: C and D are most closely related in the sense that they connect first, then CD connects to E, and A connects to B. The root of the tree with the common ancestor X is shown to be between the groups AB and CDE. This pictorial representation may also be represented...

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DNA Organization of Methanobacterium thermoautotrophicum

Cited by 51 publications

References 16 publications

DNA content, kinetic complexity, and the ploidy question in Candida albicans.

DNA content, kinetic complexity, and the ploidy question in Candida albicans.

Two families of repeated DNA sequences in Thiobacillus ferrooxidans

Calculation of evolutionary trees from sequence data.

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