Localization of kinetoplast DNA maxicircle transcripts in bloodstream and procyclic form Trypanosoma brucei

Identification of a bacterial-like HslVU protease in the mitochondria of Trypanosoma brucei and its role in mitochondrial DNA replication

ATP-dependent protease complexes are present in all living organisms, including the 26S proteasome in eukaryotes, Archaea, and Actinomycetales, and the HslVU protease in eubacteria. The structure of HslVU protease resembles that of the 26S proteasome, and the simultaneous presence of both proteases in one organism was deemed unlikely. However, HslVU homologs have been identified recently in some primordial eukaryotes, though their potential function remains elusive. We characterized the HslVU homolog from Trypanosoma brucei, a eukaryotic protozoan parasite and the causative agent of human sleeping sickness. TbHslVU has ATP-dependent peptidase activity and, like its bacterial counterpart, has essential lysine and N-terminal threonines in the catalytic subunit. By epitope tagging, TbHslVU localizes to mitochondria and is associated with the mitochondrial genome, kinetoplast DNA (kDNA). RNAi of TbHslVU dramatically affects the kDNA by causing over-replication of the minicircle DNA. This leads to defects in kDNA segregation and, subsequently, to continuous network growth to an enormous size. Multiple discrete foci of nicked/gapped minicircles are formed on the periphery of kDNA disc, suggesting a failure in repairing the gaps in the minicircles for kDNA segregation. TbHslVU is a eubacterial protease identified in the mitochondria of a eukaryote. It has a novel function in regulating mitochondrial DNA replication that has never been observed in other organisms.

ATP-dependent protein-hydrolyzing enzyme complexes are present in all living organisms, including the 26S proteasome in eukaryotes and the HslVU complex in bacteria. A simultaneous presence of both complexes in an organism was originally deemed unlikely until some HslVU homologs were found in certain ancient eukaryotes, though their potential function in these organisms remains unclear. We characterized an HslVU complex in Trypanosoma brucei, a protozoan parasite that causes human sleeping sickness in Africa. The complex is an active enzyme localized to the mitochondria of the parasite and closely associated with the mitochondrial DNA complex, which consists of several thousand small circular DNAs and a few dozen mitochondrial genomic DNAs. Depletion of this HslVU from the parasite resulted in a continuous synthesis of the small circular DNA, which led to aberrant segregation and incessant growth of the mitochondrial DNA complex to an enormous size that eventually blocks cell division. This novel HslVU function, which has not been observed in other organisms previously, could be a potential target for anti-sleeping sickness chemotherapy.

Conserved repeats in the kinetoplast maxicircle divergent region of Leishmania sp. and Leptomonas seymouri

The maxicircle control region [also termed divergent region (DR)] composed of various repeat elements remains the most poorly studied part of the kinetoplast genome. Only three extensive DR sequences demonstrating no significant similarity were available for trypanosomatids (Leishmania tarentolae, Crithidia oncopelti, Trypanosoma brucei). Recently, extensive DR sequences have been obtained for Leishmania major and Trypanosoma cruzi. In this work we have sequenced DR fragments of Leishmania turanica, Leishmania mexicana, Leishmania chagasi and two monogenetic trypanosomatids Leptomonas seymouri and Leptomonas collosoma. With the emergence of the additional extensive sequences some conserved features of DR structure become evident. A conserved palindromic sequence has been revealed in the DRs of the studied Leishmania species, L. seymouri, and T. cruzi. The overall DR structure appears to be similar in all the Leishmania species, their relative L. seymouri, and T. brucei: long relatively GC-rich repeats are interspersed with clusters of short AT-rich repeats. C. oncopelti, L. collosoma, and T. cruzi have a completely different DR structure. Identification of conserved sequences and invariable structural features of the DR may further our understanding of the functioning of this important genome fragment.

Trypanosoma brucei mitochondrial CR4 gene encodes an extensively edited mRNA with completely edited sequence only in bloodstream forms

Several kinetoplastid mitochondrial genes cannot be expressed without RNA editing of their transcripts to create a functional open reading frame. We have examined one such mitochondrial gene, CR4, in Trypanosoma brucei EATRO164 and find extensive editing of transcripts in both bloodstream and procyclic life cycle stages. However, a consensus edited sequence for the entire mRNA occurs only in the bloodstream stage. The unedited CR4 transcript is 283 nucleotides in length, not including the poly(A) tail. A total of 325 uridines are inserted, and 40 uridines deleted, to create the mature mRNA which encodes a very hydrophobic protein.

Characterization of sequence changes in kinetoplast DNA maxicircles of drug-resistant Leishmania

We have compared kinetoplast DNA maxicircles of tunicamycin- and arsenite-resistant variants of repeatedly cloned Leishmania mexicana amazonensis showing DNA amplification with wild-type and arsenite-resistant variants of the same lineage that do not show DNA amplification. DNA restriction patterns and the degree of cross-hybridization between maxicircle DNA fragments of parasites displaying DNA amplification and those of parasites without amplification were examined. In addition, the nucleotide sequence of the cytochrome b (Cyb) gene from the coding region was compared between these two groups of parasites. Extensive changes were found in the nucleotide sequences and the amino acid sequences of the cytochrome gene of the maxicircles of variants with DNA amplification. The Cyb genes from both groups had much shorter open reading frames than the same gene from Leishmania tarentolae and Trypanosoma brucei. The simultaneous changes in maxicircles and minicircles of these variants suggest that they may confer the advantage of maintaining viable mitochondrial function under selective pressure.

Editing of kinetoplastid mitochondrial mRNAs by uridine addition and deletion generates conserved amino acid sequences and AUG initiation codons

RNA editing is a novel type of mRNA processing in the kinetoplastid mitochondrion that involves the co- or posttranscriptional addition of uridine residues within transcripts. The result is an mRNA nucleotide sequence which differs from that of the corresponding gene. We have found that RNA editing may also occur through the deletion of genome-encoded uridines from the RNA sequence. Uridine additions and deletions in the 5' ends of the COIII, MURF2, and MURF3 transcripts create new N-terminal amino acid sequences that are conserved between species, and new AUG initiation codons in several cases. These results suggest that the creation of new amino acid sequences and methionine initiation codons may be important functions of RNA editing in the kinetoplastid mitochondrion.

The variable region of the Trypanosoma brucei kinetoplast maxicircle: sequence and transcript analysis of a repetitive and a non-repetitive fragment

The sequence of two fragments derived from the variable region of the kinetoplast maxicircle of Trypanosoma brucei has been determined. One fragment (1334 nucleotides, situated immediately upstream of the 12S and 9S ribosomal RNA genes) consists of non-repetitious DNA, which does not hybridize to other maxicircle regions. The other (844 nt, located between 1.7 and 2.55 kb downstream of the NADH-dehydrogenase subunit 5 gene) contains arrays of repetitive sequences which are also found outside this area. Hybridization analysis suggests that approximately 60% of the remaining part of the divergent region, which has not yet been fully analyzed, consists of similar sequences. Neither segment contains genes for mitochondrial proteins or tRNAs, as judged from computer analysis. This conclusion is supported by the fact that maxicircle DNA of trypanosome species other than T. brucei does not cross-hybridize to either fragment. Northern blot analysis and S1 nuclease experiments demonstrate, however, that both maxicircle regions are transcribed into RNAs of varying length (100-3000 nt), albeit at a low level. The function of these transcripts, that are derived from both DNA strands, and the likely absence of protein and tRNA genes from the variable region of the T. brucei maxicircle is discussed.

Transcripts of the maxicircle kinetoplast DNA of Crithidia oncopelti

Functional organization of mitochondrial genome (maxicircle kinetoplast DNA (kDNA)) from a flagellate protozoan Crithidia oncopelti was studied by Northern hybridization. A set of overlapping transcripts were mapped in the conserved region of the maxicircle. Several large (3-4 kb) RNAs, overlapping two or more smaller transcripts were found. Four regions produce a couple of RNAs differing in size 50-100 bases. Southern hybridization with several probes from the maxicircle kDNA of Leishmania tarentolae allowed identification of some of the found transcripts as corresponding to NADH dehydrogenase, subunit IV (Nd IV), cytochrome oxidase, subunits I-II (Cox I-II), cytochrome b (Cyt. b), ORF6-genes. Regions, homologous to the probes used are arranged in the same fashion in C. oncopelti kDNA as related genes in L. tarentolae. The divergent region was proved to be poorly transcribed and to produce a set of RNAs from 0.5 to 2.3 kb. Some transcripts of the divergent region seem to hybridize with distant maxicircular fragments. Cross-hybridization of such fragments has shown the absence of the regions of continuous homology.

Transcription of kinetoplast DNA minicircles

The mitochondrial DNA of trypanosomes is organized as a network of catenated circular DNA molecules called the kinetoplast. The minicircles of the kinetoplast are 1 kb circular DNA molecules present at 5,000-10,000 copies per network. The maxicircles are 20 kb circular molecules present at 50-100 copies per network. Maxicircles are transcribed and are thus analogous to mitochondrial DNAs. Here we show that, contrary to previous reports, the minicircles of T. brucei are also transcribed. A minicircle transcript of approximately 240 nucleotides is present in bloodstream and insect developmental stages of the parasite, is enriched in purified mitochondrial preparations, and is efficiently synthesized in vitro. The minicircle cDNA overlaps the conserved region of the T. brucei minicircle and is juxtaposed to a 12 base sequence common to all minicircles. These findings indicate that minicircles, in addition to their previously proposed structural role, are transcribed.

Developmentally regulated addition of nucleotides within apocytochrome b transcripts in Trypanosoma brucei

Production of the mitochondrial respiratory system and expression of mitochondrial genes are developmentally regulated in T. brucei. We have found three classes of apocytochrome b (CYb) transcripts. Two of these contain U's within their 5' sequence that are not found in the CYb gene. They occur in procyclic forms, which have a complete mitochondrial respiratory system, but are absent in bloodstream forms, which lack this respiratory system. The third transcript has the sequence predicted from the genomic sequence and is present in both life cycle stages. These findings suggest that there is developmentally regulated posttranscriptional addition of U's to CYb transcripts. This process may contribute to the developmentally regulated production of the mitochondrial respiratory system.

Variation of G-rich mitochondrial transcripts among stocks of Trypanosoma brucei

We have compared maxicircle transcripts from eight stocks of subspecies of Trypanosoma brucei. Transcripts from the rRNA and protein genes have a constant size among stocks and exhibit only minor variation in abundance. In contrast, four of the G+C rich sequences encode multiple transcripts that very markedly in size or abundance. Maxicircle nucleotide sequence comparison of three stocks shows very limited sequence divergence suggesting that sequence divergence may not explain the transcript variability. These results suggest that the G-rich transcripts do not encode proteins and that their variability among stocks may result from posttranscriptional processing events.

Trypanosoma cruzi: structure and transcription of kinetoplast DNA maxicircles of cloned stocks

Restriction endonuclease mapping of the Trypanosoma cruzi kinetoplast DNA maxicircle was performed in nine cloned stocks using maxicircle probes from T. brucei. Analysis of the maxicircle 13-15-kbp encoding region allowed cloned stocks to be divided into three groups: A, B, and C. Parasites from groups A and B had 3% sequence divergence while parasites from group C showed 16-17% sequence divergence with regard to parasites from groups A and B. Cross-hybridization experiments demonstrated that the 23-25-kbp maxicircle divergent region was similar in sequence in group A and B, but different in group C parasites. The high homology of the T. cruzi and T. brucei encoding regions allowed the use of T. brucei probes to detect T. cruzi transcripts, whose overall picture did not differ for parasites from any of the nine assayed clones.

Conservation of kinetoplastid minicircle characteristics without nucleotide sequence conservation

The nucleotide sequence and restriction fragment electrophoretic mobility of four minicircles from the kinetoplast DNA of Trypanosoma brucei were determined. Each minicircle possesses an approximately 130 base pair conserved sequence which occurs in other African trypanosome minicircles and contains a 13 base pair sequence that is conserved among kinetoplastid genera [Kidane et al. (1984) Gene 27, 265-277]. A sequence located adjacent to the conserved sequence conserves purine versus pyrimidine strand bias, but not nucleotide sequence, and contains periodic oligo(dA) tracts. Minicircle fragments containing the conserved sequence and adjacent segment exhibited anomalous electrophoretic mobility in polyacrylamide gels. The position of the oligo(dA) tracts in the fragments appears to influence this anomalous mobility. The presence of conserved features independent of conserved nucleotide sequence and the lack of conserved open reading frames among these minicircles suggests that minicircles may have a function other than encoding protein.

Identification of mitochondrial genes in Trypanosoma brucei and homology to cytochrome c oxidase II in two different reading frames

We have determined the nucleotide sequence of a 3.3 kilobase segment of the kDNA maxicircle of Trypanosoma brucei brucei 164. The nucleotide sequence and its predicted translated sequence have homology to cytochrome c oxidase subunits I and II (CO I and II) and mammalian unidentified reading frame 1 (URF 1). Amino acid homology to CO II extends for 170 residues from the amino terminus in one reading frame and then continues in another reading frame for 39 residues to the carboxyl terminus. Similar results have been obtained for Leishmania tarentolae [de la Cruz, V.F., Neckelmann, N. and Simpson, L. (1984) J. Biol. Chem., in press] and T. brucei 427 [Hensgens, L.A.M., Brackenhoff, J., De Vries, B.F., Sloof, P., Tromp, M.C., Van Boom, J.H. and Benne, R. (1984) Nucleic Acids Res. 12, 7327-7344]. This may indicate that novel events are required for expression of this gene. Amino acid homology to URF 1 exists predominantly at the amino terminal end although no corresponding AUG codon occurs in this area. An alternative initiation codon may therefore be utilized by trypanosome mitochondria. Two other open reading frames (ORFs) were detected and these are discussed with reference to transcripts from this region. ORFs corresponding to transcripts are organized compactly and are distributed more equally on both strands compared to ORFs of other mitochondrial systems.

The maxicircle of Trypanosoma brucei kinetoplast DNA encodes apocytochrome b

The region of the maxicircle of Trypanosoma brucei kinetoplast DNA which hybridizes at low stringency with the apocytochrome b gene of Saccharomyces cerevisiae has been identified and cloned. The nucleotide sequence of a 1.7 kb segment of this region is reported. This segment contains a single long open reading from capable of coding for a 350 amino acid protein with substantial homology to apocytochromes b of other species. The trypanosome protein is considerably more distantly related to other apocytochromes b than they are to each other. Several short unassigned open reading frames (300 nucleotides or shorter) also are described. If polypeptides are synthesized from these regions, they are more hydrophilic than known mitochondrially coded proteins.

Conservative and divergent base sequence regions in the maxicircle kinetoplast DNA of several trypanosomatid flagellates

The structure of kinetoplast maxicircle DNA from trypanosomatids Crithidia oncopelti, C. luciliae, Leptomonas pessoai and Leishmania gymnodactyli was compared by the blot hybridization method. The sizes of these molecules are 24.5, 34, 31 and 38 kilobase pairs (kbp), respectively. Labelled maxicircle fragments from C. oncopelti were used as probes. A general model of the structural organization of maxicircles is proposed according to which this molecule is composed of a 17kbp conservative region and a divergent one occupying the rest of the molecule. The conservative region contains the sequences homologous to those in all trypanosomatids. The sequence of the divergent region exhibits no cross homology detectable by high stringency hybridization. The main size differences between the maxicircle molecules from different trypanosomatid species are explained by the length variability of their divergent regions.

Sequence heterogeneity and anomalous electrophoretic mobility of kinetoplast minicircle DNA from Leishmania tarentolae

Several unit-length minicircles from the kinetoplast DNA of Leishmania tarentolae were cloned into pBR322 and into M13 phage vectors. The complete nucleotide sequences of three different partially homologous minicircles were obtained. The molecules contained a region of approx. 80% sequence homology extending for 160-270 bp and a region unique to each minicircle . A 14-mer was found to be conserved in all kinetoplast minicircle sequences reported to date. The frequency distributions of various minicircle sequence classes in L. tarentolae were obtained by quantitative gel electrophoresis and by examination of the "T ladder" patterns of minicircles randomly cloned into M13 at several sites. By these methods we could assign approx. 50% of the total minicircle DNA into a minimum of five sequence classes. A sequence-dependent polyacrylamide gel migration abnormality was observed with several minicircle fragments both cloned and uncloned. The abnormality was dependent on the presence of a portion of the conserved region of the minicircle .

Replication of kinetoplast DNA maxicircles

The kinetoplast DNA of Crithidia fasciculata is a massive network composed of thousands of topologically interlocked circles. Most of these circles are minicircles (2.5 kb), and about 50 are maxicircles (37 kb). Previous studies showed that minicircles replicate, after release from the network, via Cairns (theta) intermediates. Here we show that maxicircles replicate, while attached to the network, by an entirely different mechanism involving rolling circle intermediates. After the network-bound maxicircle has finished replication, the branch of the rolling circle is apparently cleaved off to form a linear free maxicircle. A restriction map of the linearized free maxicircles shows that these molecules have unique termini, one of which presumably corresponds to the replication origin.

Kinetoplast DNA, mitochondrial DNA with a difference

Kinetoplast DNA occurs in flagellated protozoa belonging to the order Kinetoplastida. Kinetoplast DNA contains tens of maxicircles and thousands of minicircles which are catenated into a single network in each cell. Maxicircles contain genetic information analogous to that in other mitochondrial DNAs. Maxicircles encode mitochondrial ribosomal RNAs and hybridize with mitochondrial gene sequences from other organisms. Minicircles evolve rapidly, may not be transcribed, and vary greatly in total complexity among genera. The functions of minicircles and the network structure are unknown.

Mitochondrial DNA of an African trypanosome

The maxicircles of African trypanosome kDNA are the genetic equivalent of other mitochondrial DNAs, but the function of minicircles is unknown. The maxicircle of Trypanosoma brucei 164 encodes conventional mitochondrial gene products and is largely but not completely transcribed. Nucleotide sequence analysis of a region not found to be transcribed revealed numerous translation termination codons in all three reading frames of both strands and numerous inverted repeats, suggesting that this segment does not have polypeptide-coding function. This segment may encode a t-RNA and has a sequence resembling a consensus sequence found in mitochondrial introns, thus implying that transcript processing occurs in trypanosome mitochondria. While several cloned minicircles had distinct restriction maps reflecting T brucei minicircle heterogeneity, one segment of the minicircle contained a sequence that was conserved by minicircles from other trypanosome strains and species. Of nine mutants unable to grow as the respiring procyclic forms, seven were devoid of kDNA. The other two mutants retained normal amounts of all maxicircle restriction fragments and normal amounts of those minicircle sequences tested. Minicircle alterations probably occur in these mutants, since the kDNA does not stain with Giemsa and bands at an altered density in cesium chloride/ethidium bromide density gradients.

The maxicircle of Trypanosoma brucei kinetoplast DNA hybridizes with a mitochondrial gene encoding cytochrome oxidase subunit II

A restriction endonuclease fragment of the maxicircle of Trypanosoma brucei brucei kinetoplast DNA hybridizes with a cloned mitochondrial DNA sequence which encodes cytochrome oxidase subunit II of Zea mays. A cloned mitochondrial DNA sequence encoding cytochrome oxidase subunit II of Saccharomyces cerevisiae also hybridized with kDNA, but exhibits less homology with the maxicircle than does the maize gene. The hybridizing maxicircle DNA was localized to a 2.8 kbp segment which is bounded by TaqI restriction endonuclease sites and nearby HindIII and EcoRI restriction sites. The TaqI restriction fragment is conserved between T. brucei brucei, T. brucei rhodesiense and T. brucei gambiense and hybridizes with the Zea mays probe in each case.