Kinetoplast DNA in the insect trypanosomes Crithidia luciliae and Crithidia fasciculata: II. Sequence evolution of the minicircles

Minicircle sequence evolution has been studied by comparison of the minicircles from Crithidia fasciculata and C. luciliae (C. fasciculata, var. luciliae) by restriction enzyme analysis and hybridization experiments. In contrast to the maxicircle sequence, the minicircle sequence of these trypanosomes evolves very rapidly. No conservation of restriction fragments has been observed and cross-hybridization of minicircles, minicircle fragments, and total kDNA is relatively weak. We conclude that no fragment larger than 550 bp is perfectly conserved between all minicircles of the two trypanosomes. Alterations in the minicircle fragment patterns of our stocks of trypanosomes were even apparent in a cultivation period of 1.5 to 2 years. The alterations suggest a random drift of the sequence which supports a noncodogenic function for the minicircles. Double restriction enzyme digestion experiments show that primary fragments are homogeneous with respect to cleavage by the second enzyme. This suggests that sequence rearrangements, rather than point mutations are the basis of the minicircle sequence heterogeneity.     

Kinetoplast DNA of Trypanosoma brucei: Physical map of the maxicircle

Trypanosoma brucei maxicircle DNA in kinetoplast DNA (kDNA) networks was characterized with restriction endonucleases. The data allow the construction of a circular map of a 22.2-kb molecule. Based on these and previous data each T. brucei kDNA network contains about 45 maxicircles which probably have the same sequence. The maxicircle of strain 164 used in this study was slightly larger and had three EcoRI sites compared to two found in other strains. Fragments generated by digestion with BamHI were largely singly cleaved maxicircles that had a density of 1.681 g/cm³ compared to 1.693 g/cm³ for the intact network. This suggests that maxicircles have a higher A + T content than minicircles. Minicircles in the kDNA network were also characterized with restriction endonucleases. Each enzyme cleaved a specific subset of minicircles from the network. However, no single restriction endonuclease or combination of up to three of these enzymes cleaved all molecules in the network. These results are consistent with earlier results of renaturation kinetic experiments and indicate that there are many different sequence classes of mini-circle DNA.     

Large circular mitochondrial DNA in Crithidia luciliae

A novel circular DNA, 11.3 μm in contour length, has been found in a pure kinetoplast DNA fraction of Crithidia luciliae. The mitochondrial nature of the kinetoplast and the absence of these large circular molecules in the nuclear fraction of DNA suggest that they constitute the mitochondrial genome of this species.     

Kinetoplast DNA in the insect trypanosomes Crithidia luciliae and Crithidia fasciculata: III. Heteroduplex analysis of the C. luciliae minicircles

We have investigated the nature of the sequence heterogeneity of the minicircles of Crithidia luciliae kinetoplast DNA by EM heteroduplex analysis of minicircles cleaved with endonuclease HindIII. Approximately 40% of the minicircles showed—after denaturation and reannealing—structures indicative of sequence rearrangements: the majority contained heteroduplex “eyes” interpreted as due to inversions; about 10% of the heteroduplexes yielded structures interpreted as due to translocations and a similar fraction showed insertions and deletions. The category of “eyed” molecules was analyzed in detail: four minicircle segments were found that displayed a high incidence of such eyes indicating that the rearrangements were not scattered at random over the minicircles. Moreover, since also “eyes” were found overlapping two or three of the four regions, we postulate that these segments are capable of recombining with each other. We conclude that specific segmental rearrangements form the main basis of the minicircle sequence heterogeneity in Crithidia.     

In vitro Transcription of Kinetoplast and Nuclear DNA in Kinetoplastida*†

SYNOPSIS. DNA-dependent RNA polymerases have been solubilized from homogenates of Crithidia fasciculata using gentle extraction procedures. RNA polymerase I and II are separated on DEAE cellulose at 0.07M (NH₄)₂SO₄ and 0.13M (NH₄)₂SO₄ respectively. RNA polymerase II is inhibited 80% by α-amanitin (25 μg/ml). Both RNA polymerases require DNA as a template, ribonucleoside triphosphates and Mn²⁺. The synthesis of RNA as a product is inhibited by DNase. RNase, pronase and actinomycin D. Purified kinetoplast and nuclear DNA can serve as templates for the RNA polymerases. Denatured DNA templates are preferred. The synthesis of RNA continues for at least an hour and is inhibited by trypanocidal drugs including suramin. antrycide, acriflavine, ethidium bromide and berenil. Complementary RNA synthesized in vitro from C. fasciculata kinetoplast DNA hybridizes with C. fasciculata kinetoplast DNA but not with C. fasciculata nuclear DNA or Blastocrithidia culicis kinetoplast DNA, Escherichia coli, T4 or calf thymus DNAs. The complementary RNA synthesized in vitro from C.fasciculata kinetoplast DNA sediments at 4–5S.     

On the identity of dnaP and dnaF genes of Bacillus subtilis

Summary The dnaP strains of Bacillus subtilis are altered in the initiation of DNA replication at high temperature (Riva et al., 1975). Fine mapping of the gene shows that it is located very close to the dnaF gene, described by Karamata and Gross (1970) and mapped by Love et al. (1976) in the polC region. The phenotype of both mutants is indistinguishable: the DNA synthesis stops at non permissive temperature after synthesizing an amount of DNA equivalent to the completion of the rounds of replication already initiated; at permissive temperature they are abnormally sensitive to MMS and are reduced in the ability to be transformed. Both mutants are to be considered as belonging to the dnaF locus.The dnaF gene is very close to the polC gene, which specifies the DNA polymerase III of B. subtilis. The DNA polymerase III of the dnaF mutants is not temperature sensitive in vitro, however, the level of this enzyme is lower by a factor of 4 or 5 in the dnaF mutants, at the permissive temperature. Following shift of dnaF cultures to the non permissive temperature, the level of DNA polymerase III activity specifically decreases further by a factor of at least 10 in the mutant, whereas the DNA polymerase I level is unaffected.The possible roles of the dnaF gene in the control of the cellular level of the DNA polymerase III, and the possibility of a regulatory role of DNA polymerase III in the initiation of DNA replication in bacteria are discussed.Abbreviations and symbols HPUra 6-(p-hydroxyphenylazo)-uracil; mic, minimum inhibitory concentration - MMS methyl-methanesufonate - Pol I Pol II and Pol III: DNA polymerase I, II and III respectively - PCMB parachloro-mercuri-benzoate     

Kinetoplast-associated DNA topoisomerase in Crithidia fasciculata: crosslinking of mitochondrial topoisomerase II to both minicircles and maxicircles in cells treated with the topoisomerase inhibitor VP16.

The mitochondrial DNA of the trypanosomatid Crithidia fasciculata consists of thousands of copies of a 2.5 kb minicircle and a small number of 37kb maxicircles catenated into a single enormous network. Treatment of C. fasciculata with the type II DNA topoisomerase inhibitor VP16 produces cleavable complexes of a type II DNA topiosomerase with both minicircles and maxicircles. A combined Southern and Western blot analysis of the cleaved DNA species released from the network by SDS treatment has identified topollmt, the kinetoplast-associated topisomerase, in covalent complexes with linear forms of minicircle and maxicircle DNAs. These results directly implicate topollmt in the topological reactions required for the duplication of the kinetoplast network.     

Kinetoplast maxicircle DNA replication in Crithidia fasciculata and Trypanosoma brucei.

Kinetoplast DNA, the mitochondrial DNA of trypanosomatids, is composed of several thousand minicircles and a few dozen maxicircles, all of which are topologically interlocked in a giant network. We have studied the replication of maxicircle DNA, using electron microscopy to analyze replication intermediates from both Crithidia fasciculata and Trypanosoma brucei. Replication intermediates were stabilized against branch migration by introducing DNA interstrand cross-links in vivo with 4,5',8-trimethylpsoralen and UV radiation. Electron microscopy of individual maxicircles resulting from a topoisomerase II decatenation of kinetoplast DNA networks revealed intact maxicircle theta structures. Analysis of maxicircle DNA linearized by restriction enzyme cleavage revealed branched replication intermediates derived from theta structures. Measurements of the linearized branched molecules in both parasites indicate that replication initiates in the variable region (a noncoding segment characterized by repetitive sequences) and proceeds unidirectionally, clockwise on the standard map.     

The segregation of kinetoplast DNA networks in Trypanosoma brucei

The kinetoplast DNA of Trypanosoma brucei consists of 10⁴ minicircles (0.3 μm) and 10² maxicircles (6 μm) held together by catenation in a complex network. In electron micrographs of kinetoplast DNA spread in a protein monolayer we have identified four types of network with the appearance of different stages in network replication and segregation. We show that each network type has characteristic properties with respect to shape, size, number, and location of maxicircle loops and nicked or covalently closed character of minicircles and maxicircles. We propose a detailed model for network segregation that involves a gradual elongation of the network, followed by network cleavage. During this process the basic network structure remains unaltered, implying a complicated mechanism of minicircle rearrangements.     

Kinetoplast DNA minicircles of Trypanosoma brucei share regions of sequence homology

Kinetoplast DNA (kDNA) of Trypanosoma brucei consists of massive networks of 10,000 or more interlocked molecules of maxicircle DNA (about 23 kb each) and minicircle DNA (1.1 kb each). Individual minicircle DNA molecules were released from the network by digestion with HaeIII, HpaII, AluI, HhaI, PstI, or HindIII and cloned in E. coli via the plasmid pBR322 and the poly(dG):poly(dC) tailing technique or the DNA ligase technique. The cloned minicircle DNA molecules were compared (i) by two types of filter hybridization, (ii) by renaturation kinetics, and (iii) by heteroduplex analysis. The sequence complexity of total network kDNA is about 300 times that of a single cloned minicircle kDNA molecule. The filter hybridizations and heteroduplex analyses suggest that minicircle molecules possess sequences in common with each other. The renaturation kinetics indicates that these homologous regions comprise about one-fourth of the 1.1-kb minicircle molecule. Therefore each minicircle molecule appears to have about one-fourth of its sequence in common with a large percentage of the total minicircle population and the remaining three-fourths in common with about 1 out of 300 minicircle molecules.     

Comparison of Six Isoenzymes from 10 Species of Crithidia1

ABSTRACT. The electrophoretic mobility of six isoenzymes from 10 species of Crithidia from insects were compared. Five zymogram patterns emerged. Pattern I was presented by C. acanthocephali and Crithidia sp. from Euryophthalmus davisi; pattern II by C. hutneri and C. luciliae thermophila; pattern III by C. arili; pattern IV by C. luciliae luciliae, Crithidia sp. from Aedes solicitans, C. harmosa, and C. fasciculata; pattern V by C. oncopelti.     

Isolation and characterization of kinetoplast DNA and RNA of Phytomonas davidi

Kinetoplast DNA networks were isolated from stationary-phase culture forms of Phytomonas davidi. The networks banded in CsCl at a density of 1.699 g/ml and consisted of covalently closed circular molecules. The networks were sensitive to shear forces and exhibited several discrete sedimenting components in neutral and alkaline sucrose. Closed monomeric minicircles were isolated from sonicated networks by alkaline band sedimentation. Closed monomers showed a heterogeneous banding pattern on electrophoresis in acrylamide-agarose gels and had sedimentation coefficients of 20.5 S in alkaline sucrose and 11 S in neutral sucrose. The mean minicircle molecular weight as measured by cospreading with φXRF II was 0.70 × 10⁶ or 1064 nucleotide pairs. Minicircles exhibited a sequence microheterogeneity as evidenced by restriction enzyme analysis, melting analysis, and renaturation kinetics. Network maxicircles were evidenced by the appearance of high molecular weight fragments after restriction with several enzymes and by the existence of supertwisted “edge loops” extending out from the periphery of networks. The maxicircle molecular weight was estimated to be approximately 24 × 10⁶. A purified kinetoplast-mitochondrion fraction was found to contain 9 and 12 S RNA species that comigrated with L. tarentolae 9 and 12 S kinetoplast RNAs.     

Selenium-containing tRNAs from Clostridium sticklandii. Cochromatography of seleno-tRNA I with l-valyl-tRNA

It has been previously shown that Clostridium sticklandii specifically synthesized three readily separable ⁷⁵Se-labeled tRNAs, designated seleno-tRNAs I, II and III, and the partially purified seleno-tRNA II cochromatographed with l-prolyl-tRNA on DEAE-Sephadex A-50 (Chen, C.S. and Stadtman, T.C. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 1403–1407). In the present study a highly purified ⁷⁵Se-labeled tRNA I was obtained by chromatography on benzoylated DEAE-cellulose, DEAE-Sephadex A-50 and Sepharose 4B. The ⁷⁵Se-labeled tRNA I cochromatographed with an l-valine-accepting species on DEAE-Sephadex A-50 and Sepharose 4B. Addition of a 285-fold molar excess of unlabeled l-valine to the l-valine acceptor activity assay mixture markedly decreased the amount of l-[¹⁴C]valine bound to seleno-tRNA I.     

Multiple gene genealogies and species recognition in the ectomycorrhizal fungus Paxillus involutus

Paxillus involutus (basidiomycetes, Boletales) is a common ectomycorrhizal fungus in the Northern Hemisphere. The fungus displays significant variation in phenotypic characters related to morphology, physiology, and ecology. Previous studies have shown that P. involutus contains several intersterility groups and morphological species. In this study, we have used concordance of multiple gene genealogies to identify genetically isolated species of P. involutus. Fragments from five protein coding genes in 50 isolates of P. involutus collected from different hosts and environments in Europe and one location in Canada were analysed using phylogenetic methods. Concordance of the five gene genealogies showed that P. involutus comprises at least four distinct phylogenetic lineages: phylogenetic species I (with nine isolates), II (33 isolates), III (three isolates), and IV (five isolates). The branches separating the four species were long and well supported compared with the species internodes. A low level of shared polymorphisms was observed among the four lineages indicating a long time since the genetic isolation began. Three of the phylospecies corresponded to earlier identified morphological species: I to P. obscurosporus, II to P. involutus s. str., and III to P. validus. The phylogenetic species had an overlapping geographical distribution. Species I and II differed partly in habitat and host preferences.     

Tn5 mutagenesis of Rhizobium trifolii host-specific nodulation genes result in mutants with altered host-range ability

Summary A 14 kb DNA fragment from the Sym plasmid of the Rhizobium trifolii strain ANU843, known to carry common nodulation nod and host specific nodulation hsn genes, was extensively mutagenised with transposon Tn5. A correlation between the site of Tn5 insertion and the induced nodulation defect led to the identification of three specific regions (designated I, II, III) which affected nodulation ability. Twenty-three Tn5 insertions into region I (ca. 3.5 kb) affected normal root hair curling ability and abolished infection thread formation. The resulting mutants were unable to nodulate all tested plant species. Tn5 insertions in regions II and III resulted in mutants which showed an exaggerated root hair curling (Hac⁺⁺) response on clover plants. Ten region II mutants which occurred over a 1.1 kb area showed a greatly reduced nodulation ability on clovers and produced aborted, truncated infection threads. Tn5 insertions into region III (ca. 1.5 kb) altered the outcome of crucial early plant recognition and infection steps by R. trifolii. Seven region III mutants displayed host-range properties which differed from the original parent strain. Region III mutants were able to induce marked root hair distortions, infection threads, and nodules on Pisum sativum including the recalcitrant Afghanistan variety. In addition region III mutants showed a poor nodulation ability on Trifolium repens even though the ability to induce infection threads was retained on this host. The altered host-range properties of region III mutants could only be revealed by mutation and the mutant phenotype was shown to be recessive.     

Evolution of the alcohol dehydrogenase (ADH) genes in yeast: characterization of a fourth ADH in Kluyveromyces lactis

Summary Three alcohol dehydrogenase (ADH) genes have recently been characterized in the yeast Kluyveromyces lactis. We report on a fourth ADH in K. lactis (KADH II: KADH2 gene) which is highly similar to other ADHs in K. lactis and Saccharomyces cerevisiae. KADH II appears to be a cytoplasmic enzyme, and after expression of KADH2 in S. cerevisiae enzyme activity comigrated with a K. lactis ADH present in cells grown in glucose or in ethanol. KADH I was also expressed in S. cerevisiae and it comigrated with a major ADH species expressed under glucose growth conditions in K. lactis. The substrate specificities for KADH I and KADH II were shown to be more similar to that of SADH II than to SADH I. SADH I cannot efficiently utilize long chain alcohols, in contrast to other cytoplasmic yeast ADHs, presumably because of the presence of a methionine (residue 271) in its substrate binding cleft. A comparison of the DNA sequences of ADHs among K. lactis, S. cerevisiae and Schizosaccharomyces pombe suggests that the ancestral yeast species contained one cytoplasmic ADH. After divergence from S. pombe, the ADH in the ancestor to K. lactis and S. cerevisiae was duplicated, and one ADH became localized to the mitochondrion, presumably for the oxidative use of ethanol. Following the speciation of S. cerevisiae and K. lactis, the gene encoding the cytoplasmic ADH in S. cerevisiae duplicated, which resulted in the development of the SADH II protein as the primary oxidative enzyme in place of SADH III. In contrast, the K. lactis mitochondrial ADH duplicated to give rise to the highly expressed KADH3 and KADH4 genes, both of which may still play primary roles in oxidative metabolism. These data suggest that K. lactis and S. cerevisiae use different compartments for their metabolism of ethanol. Our results also indicate that the complex regulatory circuits controlling the glucose-repressible SADH2 in S. cerevisiae are a recent acquisition from regulatory networks used for the control of genes other than SADH2.

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Seven new calochroid and fulvoid species of Cortinarius

We describe seven new European species of Cortinarius. All species are based on analyses of morphological and DNA sequence data. They all belong to a well-supported clade comprising most species traditionally treated in Cortinarius subgenus Phlegmacium sections Fulvi and Calochroi (i.e. the/Calochroi clade). All taxa are either fulvoid (containing anthraquinoid pigments) or calochroid (without these pigments). Morphological and ecological data are presented for all species and compared with similar species. A dichotomous key is presented for C. calochrous and similar species, including all six newly described calochroid species. The calochroid species C. albertii, C. chailluzii, C. cisticola, C. sancti-felicis, C. selandicus and C. vesterholtii spp. nov., and the fulvoid species C. langeorum sp. nov. are described.     

DNA Synthesis and Fos and Jun Protein Expression in Mitotic and Postmitotic WI-38 Fibroblasts in Vitro

Normal human embryonic lung fibroblasts WI-38 differentiate spontaneously along the cell lineage mitotic fibroblasts (MF) I, II, and III and postmitotic fibroblasts (PMF) IV, V, VI, and VII in the fibroblast stem cell system in vitro, when appropriate methods are applied. The mitotic fibroblasts can be induced to shift to postmitotic fibroblasts by two treatments with mitomycin C (2× MMC) in a short period of time compared to spontaneous development. Mitotic and postmitotic fibroblast cell types have specific morphological and biochemical properties, e.g., [³⁵S]methionine polypeptide markers in 2D PAGE. Spontaneously arisen and experimentally induced (2× MMC) PMF have the same morphological and biochemical characteristics. Mitotic fibroblasts have 2n DNA and undergo DNA synthesis for reduplication. Postmitotic cells undergo, on average, two rounds of DNA synthesis for endoreduplication (polyploidization). Spontaneously arisen and experimentally induced postmitotic populations are composed of postmitotic fibroblasts PMF IV, V, and VI with 2n, 4n, and 8n DNA. DNA synthesis of mitotic and postmitotic WI-38 cell populations may be regulated by the expression of Fos and Jun proteins. The Fos level of MFs was higher by a factor of 15-24 and the Jun level of MFs by a factor of 4.2-6.3 than those of spontaneously arisen PMFs. In 2× MMC-induced PMFs, the Fos level was about 4.4-7.5 times higher and the Jun level 1.7-3.3 times higher than that of spontaneously arisen PMFs. The down-regulation of these two parameters is a normal event in the development of mitotic to postmitotic WI-38 fibroblasts in the fibroblast stem cell system and is not related to cellular aging.