The killing of African trypanosomes by ethidium bromide

Introduced in the 1950s, ethidium bromide (EB) is still used as an anti-trypanosomal drug for African cattle although its mechanism of killing has been unclear and controversial. EB has long been known to cause loss of the mitochondrial genome, named kinetoplast DNA (kDNA), a giant network of interlocked minicircles and maxicircles. However, the existence of viable parasites lacking kDNA (dyskinetoplastic) led many to think that kDNA loss could not be the mechanism of killing. When recent studies indicated that kDNA is indeed essential in bloodstream trypanosomes and that dyskinetoplastic cells survive only if they have a compensating mutation in the nuclear genome, we investigated the effect of EB on kDNA and its replication. We here report some remarkable effects of EB. Using EM and other techniques, we found that binding of EB to network minicircles is low, probably because of their association with proteins that prevent helix unwinding. In contrast, covalently-closed minicircles that had been released from the network for replication bind EB extensively, causing them, after isolation, to become highly supertwisted and to develop regions of left-handed Z-DNA (without EB, these circles are fully relaxed). In vivo, EB causes helix distortion of free minicircles, preventing replication initiation and resulting in kDNA loss and cell death. Unexpectedly, EB also kills dyskinetoplastic trypanosomes, lacking kDNA, by inhibiting nuclear replication. Since the effect on kDNA occurs at a >10-fold lower EB concentration than that on nuclear DNA, we conclude that minicircle replication initiation is likely EB's most vulnerable target, but the effect on nuclear replication may also contribute to cell killing.     

Characterization of the molecular components in kinetoplast- mitochondrial DNA of Trypanosoma equiperdum. Comparative study of the dyskinetoplastic and wild strains

The structure of the kinetoplast DNA of Trypanosoma equiperdum has been studied and compared to the structure of the circular mitochondrial DNA extracted from a dyskinetoplastic strain of T. equiperdum. In T. equiperdum wild type, the kinetoplast DNA constitutes approximately 6% of the total cellular DNA and is composed of approximately 3,000 supercoiled minicircles of 6.4 x 10(5) daltons and approximately 50 circular supercoiled molecules of 15.4 x 10(6) daltons topologically interlocked; The buoyant density in CsCl of the minicircles is 1.691 g/cm 3. The large circles have a buoyant density of 1.684 g/cm 3, are homogeneous in size and are selectively cleaved by several restriction endonucleases which do not cleave the minicircles. The cleavage sites of six different restriction endonucleases have been mapped on the large circle. The minicircles are cleaved by two other restriction endonucleases, and their cleavage sites have been mapped. The mitochondrial DNA extracted from the dyskinetoplastic strain of T. equiperdum represents 7% of the total DNA of the cell and is composed of supercoiled circles, heterogeneous in size, and topologically associated in catenated oligomers. Its buoyant density in CsCl is 1.688 g/cm 3. These molecules are not cleaved by any of the eight restriction endonucleases tested. The reassociation kinetics of in vitro labeled kDNA minicircles and large circles has been studied. The results indicate that the minicircles as well as the large circles are homogeneous in sequence and that the circular DNA of the dyskinetoplastic strain has no sequence in common with the kDNA of the wild strain.     

DNA buoyant densities ofTrypanosoma (Schizotrypanum) species from bats in Ontario,Canada

Summary Two species of trypanosomes,Trypanosoma hedricki andT. myoti, isolated respectively fromEptesicus fuscus andMyotis lucifugus, were cloned.T. hedricki produced long trypomastigotesin vitro (mean length 22.1±0.3 m); the buoyant densities of its kinetoplastic and nuclear deoxyribonucleic acid (kDNA and nDNA) were respectively 1.700 and 1.710 g ml^–1 and it possessed a small amount of a satellite component (C-DNA) of density 1.716 g ml^–1. This species is in this respect closely related toT. dionisii. T. myoti produced long trypomastigotesin vitro (mean length 20.1±0.2 m); its DNA buoyant densities (g ml^–1) were: kDNA 1.700 and nDNA 1.710 (no C-DNA was detected). In this respect, therefore,T. myoti is closer toT. cruzi than the other bat trypanosomes. ac]19830129     

Dual Functions of α-Ketoglutarate Dehydrogenase E2 in the Krebs Cycle and Mitochondrial DNA Inheritance in Trypanosoma brucei

The dihydrolipoyl succinyltransferase (E2) of the multisubunit α-ketoglutarate dehydrogenase complex (α-KD) is an essential Krebs cycle enzyme commonly found in the matrices of mitochondria. African trypanosomes developmentally regulate mitochondrial carbohydrate metabolism and lack a functional Krebs cycle in the bloodstream of mammals. We found that despite the absence of a functional α-KD, bloodstream form (BF) trypanosomes express α-KDE2, which localized to the mitochondrial matrix and inner membrane. Furthermore, α-KDE2 fractionated with the mitochondrial genome, the kinetoplast DNA (kDNA), in a complex with the flagellum. A role for α-KDE2 in kDNA maintenance was revealed in α-KDE2 RNA interference (RNAi) knockdowns. Following RNAi induction, bloodstream trypanosomes showed pronounced growth reduction and often failed to equally distribute kDNA to daughter cells, resulting in accumulation of cells devoid of kDNA (dyskinetoplastic) or containing two kinetoplasts. Dyskinetoplastic trypanosomes lacked mitochondrial membrane potential and contained mitochondria of substantially reduced volume. These results indicate that α-KDE2 is bifunctional, both as a metabolic enzyme and as a mitochondrial inheritance factor necessary for the distribution of kDNA networks to daughter cells at cytokinesis.     

Isolation and characterization of circular DNA molecules heterogeneous in size from a dyskinetoplastic strain of Trypanosoma equiperdum

In a naturally occuring dyskinetoplastic mutant strain of $\text{T. equiperdum}$, covalently closed circular DNA molecules of assumed mitochondrial origin were isolated. These molecules, heterogeneous in size, represent 6–9 % of total DNA and are essentially organized in catenated oligomers composed of molecules of different length. The typical molecular organization of the kinetoplast DNA from kinetoplastic trypanosomes, the network, was not observed.     

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.     

Sex chromosome associated satellite DNA: Evolution and conservation

Satellites visible in female but not in male DNA were isolated from the snakesElaphe radiata (satellite IV, p = 1.708 g · cm^–3) andBungarus fasciatus (BK¹ minor, p=1.709 g · cm^–3). The satellites cross hybridize. Hybridization of³H labelled nick translated BK minor satellite DNA with the total male and female DNA and/or chromosomes in situ of different species of snakes revealed that its sequences are conserved throughout the snake group and are mainly concentrated on the W chromosome. Snakes lacking sex chromosomes do possess related sequences but there is no sex difference and visible related satellites are absent. The following conclusions have been reached on the basis of these results. 1. The W chromosome associated satellite DNA is related to similar sequences scattered in the genome. 2. The origin and increment in the number of the W satellite DNA sequence on the W chromosome is associated with the heterochromatinization of the W. 3. Satellite sequences have become distributed along the length of the W and resulted in morphological differentiation of sex chromosomes. 4. Evolutionary conservation of W satellite DNA strongly suggests that functional constraints may have limited sequence divergence.     

EVIDENCE FOR THE RETENTION OF KINETOPLAST DNA IN AN ACRIFLAVINE-INDUCED DYSKINETOPLASTIC STRAIN OF TRYPANOSOMA BRUCEI WHICH REPLICATES THE ALTERED CENTRAL ELEMENT OF THE KINETOPLAST

A pleomorphic dyskinetoplastic strain of Trypanosoma brucei was produced by repeated acriflavine treatment. No kinetoplastic cells reappeared after 2 yr of maintenance in the absence of acriflavine. These dyskinetoplastic cells retained and therefore replicated the central element of the kinetoplast. This element was present in the "condensed" state typical of acriflavine-treated cells rather than the normal fibrillar state. Whole-cell DNA extracted from both normal and dyskinetoplastic strains revealed three bands upon isopycnic sedimentation, and there was no detectable alteration in buoyant density of any of these DNA components in the dyskinetoplastic strain. It seems likely that the dyskinetoplastic strain has retained its kinetoplast DNA but in an altered state.     

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.     

The kinetoplast ultrastructural organization of endosymbiont-bearing trypanosomatids as revealed by deep-etching, cytochemical and immunocytochemical analysis

The endosymbiont-bearing trypanosomatids present a typical kDNA arrangement, which is not well characterized. In the majority of trypanosomatids, the kinetoplast forms a bar-like structure containing tightly packed kDNA fibers. On the contrary, in trypanosomatids that harbor an endosymbiotic bacterium, the kDNA fibers are disposed in a looser arrangement that fills the kinetoplast matrix. In order to shed light on the kinetoplast structural organization in these protozoa, we used cytochemical and immunocytological approaches. Our results showed that in endosymbiont-containing species, DNA and basic proteins are distributed not only in the kDNA network, but also in the kinetoflagellar zone (KFZ), which corresponds to the region between the kDNA and the inner mitochondrial membrane nearest the flagellum. The presence of DNA in the KFZ is in accordance with the actual model of kDNA replication, whereas the detection of basic proteins in this region may be related to the basic character of the intramitochondrial filaments found in this area, which are part of the complex that connects the kDNA to the basal body. The kinetoplast structural organization of Bodo sp. was also analyzed, since this protozoan lacks the highly ordered kDNA-packaging characteristic of trypanosomatid and represents an evolutionary ancestral of the Trypanosomatidae family.     

Expression and subcellular localization of kinetoplast-associated proteins in the different developmental stages of Trypanosoma cruzi

Background  

The kinetoplast DNA (kDNA) of trypanosomatids consists of an unusual arrangement of circular molecules catenated into a single network. The diameter of the isolated kDNA network is similar to that of the entire cell. However, within the kinetoplast matrix, the kDNA is highly condensed. Studies in Crithidia fasciculata showed that kinetoplast-associated proteins (KAPs) are capable of condensing the kDNA network. However, little is known about the KAPs of Trypanosoma cruzi, a parasitic protozoon that shows distinct patterns of kDNA condensation during their complex morphogenetic development. In epimastigotes and amastigotes (replicating forms) the kDNA fibers are tightly packed into a disk-shaped kinetoplast, whereas trypomastigotes (non-replicating) present a more relaxed kDNA organization contained within a rounded structure. It is still unclear how the compact kinetoplast disk of epimastigotes is converted into a globular structure in the infective trypomastigotes.     

Transkinetoplastidy—A Novel Phenomenon Involving Bulk Alterations of Mitochondrion-Kinetoplast DNA of a Trypanosomatid Protozoan1,2

ABSTRACT. Dramatic and consistent changes of mitochondrial or kinetoplast DNA (kDNA) were observed in certain variants of Leishmania amazonensis (A variants) selected in vitro for arsenite-resistance. This was found initially by comparing different lots of wild-type cells and their respective A variants resistant to 30 μM arsenite. The kDNAs isolated from these two groups had different restriction patterns and hybridized poorly to each other, whereas those from different lots within each of the two groups were identical. Hybridization data showed an overall identity of less than 10^?3 between total kDNAs of the two groups. This difference was further examined in three independent series of variants, which were selected from three different clones for resistance to graded concentrations of arsenite (5–30 μM). In all three series, their kDNAs were found to change abruptly in an identical pattern at a late step of the selection process, i.e. A variants resistant to 15 μM or 30 μM arsenite. There was no apparent loss of kDNA in the process. Most of the changes observed appear to involve a shift in either the dominance or the copy number of different minicircle subclasses. Surprisingly, the kDNAs of tunicamycin-resistant variants (T variants) were also found to undergo similar changes. Genetic changes previously described in both A and T variants are limited to their nuclei. Namely, different chromosomal regions are amplified to produce large DNA circles which are responsible for the drug-resistant phenotypes. Interestingly, other arsenite-resistant clones without such chromosomal DNA amplification (A'variants) had kDNA of the wild-type pattern. The profound changes of kDNA observed are unprecedented. We propose the term “transkinetoplastidy” for this phenomenon to distinguish it from dyskinetoplastidy or the loss of kDNA described previously in trypanosomatid protozoa. This phenomenon is discussed with respect to the possible mechanisms of its generation, regulation and relation to the drug-resistant phenotypes.     

Mitochondrial DNA polymerase POLIB is essential for minicircle DNA replication in African trypanosomes

The unique mitochondrial DNA of trypanosomes is a catenated network of minicircles and maxicircles called kinetoplast DNA (kDNA). The network is essential for survival, and requires an elaborate topoisomerase‐mediated release and reattachment mechanism for minicircle theta structure replication. At least seven DNA polymerases (pols) are involved in kDNA transactions, including three essential proteins related to bacterial DNA pol I (POLIB, POLIC and POLID). How Trypanosoma brucei utilizes multiple DNA pols to complete the topologically complex task of kDNA replication is unknown. To fill this gap in knowledge we investigated the cellular role of POLIB using RNA interference (RNAi). POLIB silencing resulted in growth inhibition and progressive loss of kDNA networks. Additionally, unreplicated covalently closed precursors become the most abundant minicircle replication intermediate as minicircle copy number declines. Leading and lagging strand minicircle progeny similarly declined during POLIB silencing, indicating POLIB had no apparent strand preference. Interestingly, POLIB RNAi led to the accumulation of a novel population of free minicircles that is composed mainly of covalently closed minicircle dimers. Based on these data, we propose that POLIB performs an essential role at the core of the minicircle replication machinery.     

A family of dispersed repeats in the genome of Vicia faba: structure, chromosomal organization, redundancy modulation, and evolution

A family of repeated DNA sequences of about 1200 bp in length and bordered by well-conserved, 18 bp inverted repeats (VfB family) was found in the nuclear genome of Vicia faba. The structure, chromosomal organization, redundancy modulation and evolution of these sequences were investigated. They are enriched in A+T base pairs (about 40% G+C) and lack any obvious internally repeated motif. A 64%–73% nucleotide sequence identity was found when pairwise comparisons between VfB sequences were carried out (average 69%). Direct repeats were not found to flank the inverted repeats that border these DNA sequences. The results obtained by hybridizing VfB repeats to Southern blots of V. faba genomic DNA digested with EcoRI indicated that these DNA elements are interspersed in the genome. The appearance of bands in these Southern blots and comparison of the structure of the sequences that flank different VfB elements showed that these repeats might be part of other, longer repeated DNA sequences. A high degree of dispersion throughout the genome was confirmed by cytological hybridization, which showed VfB sequences to be scattered along the length of all chromosomes and to be absent or rare only at heterochromatic chromosomal regions. These sequences contribute to intraspecific alterations of genomic size. Indeed, dot-blot hybridizations proved that their redundancy, which is positively correlated with the overall amount of nuclear DNA in each accession, varies between V. faba land races (27×10³–230×10³ copies per 1C DNA). Southern blot hybridization of VfB repeats to restriction endonuclease-digested genomic DNAs of V. faba, V. narbonensis, V. sativa, Phaseolus coccineus, Populus deltoides, and Triticum durum revealed nucleotide sequence homology of these DNA elements, whatever the stringency conditions, only to the DNAs of Vicia species, and to a reduced extent to the DNAs of V. narbonensis and V. sativa compared with that of V. faba. It is concluded that VfB repeats might be descended from mobile DNA elements and contribute to change genomic size and organization during evolution. Received: 10 September 1998; in revised form: 12 May 1999 / Accepted: 19 May 1999     

Kinetoplast DNA permits characterization of pathogenic plant trypanosomes of economic importance

Summary— Twelve Phytomonas isolates were obtained from different plants originating from several countries and cultured in vitro in complex media. The kinetoplast DNA (kDNA) was purified and observed by electron microscopy. The structure of kDNA from all isolates appeared as a large network of interlocked minicircles with some maxicircles extruding from the network, as has often been shown for Trypanosomatidae. Topoisomerase II resolved the kDNA network into free minicircles which were then analyzed by electron microscopy and by electrophoresis in agarose gel. The minicircle sizes varied from 1.3 to 2.8 kilobase pairs according to the Phytomonas isolate. The analysis by restriction endonucleases revealed a base sequence heterogeneity in the minicircles of 10 of these Phytomonas isolates. By contrast, in 2 Phytomonas isolates, more than 90% of their minicircle content was found to be homogeneous. Most interestingly, the minicircle cleavage patterns were found to be different between Phytomonas isolates and thus could be used to distinguish them.     

Novel class of rDNA repeat units in somatic hybrids between Nicotiana and Atropa

Summary Behavior of ribosomal RNA genes in the process of somatic hybridization was analyzed using hybrids Nicotiana tabacum + Atropa belladonna. Blothybridization of parental species DNAs to ³²P-rDNA specific probes revealed two classes of ribosomal repeats in both tobacco and nightshade; their length was 11.2 kb, 10.4 kb (tobacco) and 9.4 kb, 10.2 kb (night-shade). For analysis of hybrids, labelled ³²P rDNA specific probes were hybridized to DNA of parental species and somatic hybrids digested with restriction endonucleases EcoR1, EcoRV and BamH1. A new class of ribosomal DNA repeat, absent in parental species, was found in hybrid line NtAb-1. Possible mechanisms of appearence of a new rDNA class in the process of somatic cell fusion are discussed.     

Characterization of Pyrenophora Isolates Associated with Spot and Net Type Lesions on Barley in South Africa

Single-spored isolates of Pyrenophora associated with spot and net type net blotch of barley were compared using total DNA banding patterns, morphological and cultural characteristics, symptomatology and mating studies. Isolates of spot and net type net blotch were found to vary regarding conidium length and cultural growth rate. Mating studies among and between ascospore, spot and net type isolates proved unsuccessful under the conditions studied. Total DNA polymorphisms of the net spot and ascospore isolates digested with the restriction enzymes HpaII and HaeIII showed that the isolates have similar banding patterns. Random amplified polymorphic DNA (RAPD) showed that the banding patterns of the spot and net type isolates were again similar but were distinct from outgroups such as P. semeniperda and P. triticirepentis. The homology in DNA banding patterns of local isolates indicated that the difference in conidium length is insufficient to separate them as two species. It is concluded that spot and net type isolates occurring in South Africa belong to P. teres. Therefore spot type lesions are caused by P. teres f. sp. maculata and not by P. japonica as reported previously.     

MITOCHONDRIAL DNA VARIATION IN THE FUNGUS ATKINSONELLA HYPOXYLON INFECTING SYMPATRIC DANTHONIA GRASSES

The purpose of this study was to determine how host identity and geographic proximity were related to genetic variation in the fungus Atkinsonella hypoxylon infecting four sympatric Danthonia grasses. We analyzed 192 A. hypoxylon isolates from 48 geographic sites for mitochondrial DNA (mtDNA) variation by restriction digestion of total DNA with EcoRI, BamHI, and PstI, and subsequent hybridization with purified A. hypoxylon mtDNA. Thirtynine haplotypes were identified. UPGMA cluster analysis showed that mtDNA type is highly correlated with host-species group; isolates from Danthonia compressa and D. spicata formed one branch of the phenogram, and isolates from D. epilis and D. sericea formed the other. Restriction maps of the most common mtDNA haplotypes infecting each host-species pair revealed a 30-kb size difference and a minimum of eight length changes and one restrictionsite change between them. Mapping of the mutation differences among all haplotypes occurring at North Carolina sites resulted in two distinct gene trees corresponding to the two Danthonia species groups, corroborating the phenetic analysis. The results indicate a high degree of host-dependent isolation and establish the existence of host races in A. hypoxylon. Possible mechanisms responsible for this isolation are discussed. Little differentiation existed between isolates from within a Danthonia species pair, and some variation was explained by geographic origin. Analysis of progeny from a natural sexual cross revealed that mitochondria are maternally inherited in A. hypoxylon.     

Length–weight and length–length relationships of fish species from the Chi River,northeastern Thailand

The relationships of total length (TL), fork length (FL) and standard length (SL) are presented for four fish species and the relationships between TL and wet weight for 23 fish species from the Chi River in northeastern Thailand. All length–length relationships were linear (r² > 0.95). Slope (b) of the length–weight relationships showed values between 2.5073 and 3.4896.     

Reproductive features of Celmisia species (Asteraceae) in relation to altitude and geographical range in New Zealand

A range of seed and flower characters was examined in 37 species of the New Zealand genus Celmisia (Asteraceae) to determine whether there were any relationships between reproductive features and the geographic or altitudinal ranges of the species. Using published sources and herbarium material, flower attractiveness to pollinators was measured in terms of capitulum size and ray/disc length ratio. Dispersibility was measured in terms of seed dry weight, seed terminal velocity, pappus/seed length ratio, and scape/leaf length ratio. Altitude (minimum and maximum) and geographic ranges (number of 1^o latitude x 1^o longitude squares occupied) were obtained from published sources. A multivariate principal components analysis using 12 morphological characters revealed the presence of five groups of species differing in capitulum size, seed weight, pappus length, number of pappus bristles, leaf length and scape length. Linear regressions showed that altitude was significantly and negatively related to seed dry weight and capitulum size, and positively to scape/leaf length ratio. Geographic range is negatively related to capitulum size, and positively to ray/disc ratio and altitudinal range. Amongst the seed features measured, seed weight was the best predictor of terminal velocity (an inverse measure of dispersability), but lighter seeds also had a higher pappus/seed length ratio. The frequency distribution of the geographic ranges of the species is highly skewed, with many local species (86% occurring in 15 or fewer one‐degree squares) and very few common ones. Two species (C. gracilenta and C. graminifolia) are notably more common than all the others. A comparison of these species with the others shows that, on average, they have lighter seeds with more bristles, taller scapes and higher ray/disc ratios, but have smaller capitula. The low geographic abundance of the rare species could not readily be attributed to any specific reproductive feature, possibly because of the multiple types of rarity represented within the genus.