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Wang JF, Lin RH, Zhang X, Hide G, Lun ZR, Lai DH. Novel insertions in the mitochondrial maxicircle of Trypanosoma musculi, a mouse trypanosome. Parasitology 2022; 149:1546-1555. [PMID: 35924587 PMCID: PMC11093713 DOI: 10.1017/s0031182022001019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 11/07/2022]
Abstract
Trypanosoma musculi is a, globally distributed, mouse-specific haemoflagellate, of the family Trypanosomatidae, which shares similar characteristics in morphology with Trypanosoma lewisi. The kinetoplast (mitochondrial) DNA of Trypanosomatidae flagellates is comprised of catenated maxicircles and minicircles. However, genetic information on the T. musculi kinetoplast remains largely unknown. In this study, the T. musculi maxicircle genome was completely assembled, with PacBio and Illumina sequencing, and the size was confirmed at 34 606 bp. It consisted of 2 distinct parts: the coding region and the divergent regions (DRs, DRI and II). In comparison with other trypanosome maxicircles (Trypanosoma brucei, Trypanosoma cruzi and T. lewisi), the T. musculi maxicircle has a syntenic distribution of genes and shares 73.9, 78.0 and 92.7% sequence identity, respectively, over the whole coding region. Moreover, novel insertions in MURF2 (630 bp) and in ND5 (1278 bp) were found, respectively, which are homologous to minicircles. These findings support an evolutionary scenario similar to the one proposed for insertions in Trypanosoma cruzi, the pathogen of American trypanosomiasis. These novel insertions, together with a deletion (281 bp) in ND4, question the role of Complex I in T. musculi. A detailed analysis of DRII indicated that it contains numerous repeat motifs and palindromes, the latter of which are highly conservative and contain A5C elements. The comprehensively annotated kinetoplast maxicircle of T. musculi reveals a high degree of similarity between this parasite and the maxicircle of T. lewisi and suggests that the DRII could be a valuable marker for distinguishing these evolutionarily related species.
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Affiliation(s)
- Ju-Feng Wang
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Ruo-Hong Lin
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Xuan Zhang
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
| | - Geoff Hide
- Ecosystems and Environment Research Centre and Biomedical Research Centre, School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK
| | - Zhao-Rong Lun
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
- Ecosystems and Environment Research Centre and Biomedical Research Centre, School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK
| | - De-Hua Lai
- Guangdong Provincial Key Laboratory of Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, The People's Republic of China
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Greif G, Rodriguez M, Bontempi I, Robello C, Alvarez-Valin F. Different kinetoplast degradation patterns in American Trypanosoma vivax strains: Multiple independent origins or fast evolution? Genomics 2021; 113:843-853. [PMID: 33418079 DOI: 10.1016/j.ygeno.2020.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/05/2020] [Accepted: 12/28/2020] [Indexed: 01/15/2023]
Abstract
We analyzed the kinetoplast (mitochondrial genome) of Trypanosoma vivax strains from America and Africa to determine their precise architecture and to understand their adaptive response to mechanical transmission. The use of long-read based assemblies that retain individuality of tandem repeats, without erasing inter-copy variability, allowed us to investigate the evolutionary dynamics of repetitive kinetoplast-DNA. This analysis revealed that repeat elements located in edges of repeat clusters are less active in terms of renewal, whereas internal copies appear to undergo a permanent process of birth-and-death. Comparing different American strains with the African Y486 strain, we found that in the former, protein coding genes from the maxicircle contain several function disrupting mutations that with very few exceptions are present in one or the other American strain but not in both, suggesting the absence of common ancestry for most of the genomic changes that led to their loss of oxidative phosphorylation capacity. Analysis of another component of kinetoplast, the minicircles, revealed great loss of diversity, and loss of their encoded guideRNAs. Both groups of American strains retain minimal sets required to edit the still functional A6-APTase and RPS12 genes. The extensive maxi- and minicircle divergence suggests a history of multiple introduction events in America of strains that probably started to degrade their kinetoplast in Africa. The notion that kinetoplast degradation began after incursion in America would imply a pace of accumulation of genetic changes considerably faster than other trypanosomatids.
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Affiliation(s)
- Gonzalo Greif
- Laboratorio de Interacciones Hospedero-Patógeno/Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Matias Rodriguez
- Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República Uruguay, Montevideo, Uruguay; Institute of Bioinformatics, University of Münster, Germany
| | - Ivan Bontempi
- Laboratorio de Tecnología Inmunológica, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero-Patógeno/Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay; Departamento de Bioquímica, Facultad de Medicina, Universidad de la República Uruguay, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República Uruguay, Montevideo, Uruguay.
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Common Structural Patterns in the Maxicircle Divergent Region of Trypanosomatidae. Pathogens 2020; 9:pathogens9020100. [PMID: 32033466 PMCID: PMC7169413 DOI: 10.3390/pathogens9020100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 12/29/2022] Open
Abstract
Maxicircles of all kinetoplastid flagellates are functional analogs of mitochondrial genome of other eukaryotes. They consist of two distinct parts, called the coding region and the divergent region (DR). The DR is composed of highly repetitive sequences and, as such, remains the least explored segment of a trypanosomatid genome. It is extremely difficult to sequence and assemble, that is why very few full length maxicircle sequences were available until now. Using PacBio data, we assembled 17 complete maxicircles from different species of trypanosomatids. Here we present their large-scale comparative analysis and describe common patterns of DR organization in trypanosomatids.
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Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast. Pathogens 2019; 8:pathogens8030157. [PMID: 31540520 PMCID: PMC6789588 DOI: 10.3390/pathogens8030157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Advancements in next-generation sequencing techniques have led to a substantial increase in the genomic information available for analyses in evolutionary biology. As such, this data requires the exponential growth in bioinformatic methods and expertise required to understand such vast quantities of genomic data. Alignment-free phylogenomics offer an alternative approach for large-scale analyses that may have the potential to address these challenges. The evolutionary relationships between various species within the trypanosomatid family, specifically members belonging to the genera Leishmania and Trypanosoma have been extensively studies over the last 30 years. However, there is a need for a more exhaustive analysis of the Trypanosomatidae, summarising the evolutionary patterns amongst the entire family of these important protists. The mitochondrial DNA of the trypanosomatids, better known as the kinetoplast, represents a valuable taxonomic marker given its unique presence across all kinetoplastid protozoans. The aim of this study was to validate the reliability and robustness of alignment-free approaches for phylogenomic analyses and its applicability to reconstruct the evolutionary relationships between the trypanosomatid family. In the present study, alignment-free analyses demonstrated the strength of these methods, particularly when dealing with large datasets compared to the traditional phylogenetic approaches. We present a maxicircle genome phylogeny of 46 species spanning the trypanosomatid family, demonstrating the superiority of the maxicircle for the analysis and taxonomic resolution of the Trypanosomatidae.
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Abstract
Mitochondrial genomes are often transcribed into polycistronic RNAs punctuated by tRNAs whose excision defines mature RNA boundaries. Although kinetoplast DNA lacks tRNA genes, it is commonly held that in Trypanosoma brucei the monophosphorylated 5' ends of functional molecules typify precursor partitioning by an unknown endonuclease. On the contrary, we demonstrate that individual mRNAs and rRNAs are independently synthesized as 3'-extended precursors. The transcription-defined 5' terminus is converted into a monophosphorylated state by the pyrophosphohydrolase complex, termed the "PPsome." Composed of the MERS1 NUDIX enzyme, the MERS2 pentatricopeptide repeat RNA-binding subunit, and MERS3 polypeptide, the PPsome binds to specific sequences near mRNA 5' termini. Most guide RNAs lack PPsome-recognition sites and remain triphosphorylated. The RNA-editing substrate-binding complex stimulates MERS1 pyrophosphohydrolase activity and enables an interaction between the PPsome and the polyadenylation machinery. We provide evidence that both 5' pyrophosphate removal and 3' adenylation are essential for mRNA stabilization. Furthermore, we uncover a mechanism by which antisense RNA-controlled 3'-5' exonucleolytic trimming defines the mRNA 3' end before adenylation. We conclude that mitochondrial mRNAs and rRNAs are transcribed and processed as insulated units irrespective of their genomic location.
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Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 2018; 146:1-27. [PMID: 29898792 DOI: 10.1017/s0031182018000951] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.
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Flegontov PN, Guo Q, Ren L, Strelkova MV, Kolesnikov AA. Conserved repeats in the kinetoplast maxicircle divergent region of Leishmania sp. and Leptomonas seymouri. Mol Genet Genomics 2006; 276:322-33. [PMID: 16909285 DOI: 10.1007/s00438-006-0145-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 06/22/2006] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Pavel N Flegontov
- Department of Molecular Biology, Lomonosov Moscow State University, Vorobjevy Gory 1, build. 12, 119992, Moscow, Russia
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Flegontov PN, Kolesnikov AA. Radically different maxicircle classes within the same kinetoplast: an artefact or a novel feature of the kinetoplast genome? KINETOPLASTID BIOLOGY AND DISEASE 2006; 5:5. [PMID: 16978422 PMCID: PMC1578572 DOI: 10.1186/1475-9292-5-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 09/18/2006] [Indexed: 11/27/2022]
Abstract
We discuss here some results which suggest that radically different maxicircle classes coexist within the same kinetoplast. These data, although tentative and incomplete, may provide a new outlook on the kinetoplast genome structure and expression.
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Affiliation(s)
- Pavel N Flegontov
- Department of Molecular Biology, Lomonosov Moscow State University, Vorobjevy Gory 1, Build. 12, 119992 Moscow, Russia
| | - Alexander A Kolesnikov
- Department of Molecular Biology, Lomonosov Moscow State University, Vorobjevy Gory 1, Build. 12, 119992 Moscow, Russia
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Flegontov PN, Strelkova MV, Kolesnikov AA. The Leishmania major maxicircle divergent region is variable in different isolates and cell types. Mol Biochem Parasitol 2006; 146:173-9. [PMID: 16442169 DOI: 10.1016/j.molbiopara.2005.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 12/05/2005] [Accepted: 12/13/2005] [Indexed: 11/20/2022]
Abstract
The maxicircle divergent region (DR) was partially sequenced in several isolates of Leishmania major. The sequence contains various repeated elements: two types of long GC-rich repeats alternating with clusters of short AT-rich repeats. The arrangement of repeats appears to be similar in the studied Leishmania species and their relative Leptomonas seymouri. Furthermore, a conserved sequence containing putative promoters within a palindrome was revealed in the DRs of these species. Unexpectedly, the DR sequence proved to be dissimilar in promastigotes and amastigotes of the same isolate perhaps through selection of parasites with particular maxicircle variants in the course of the promastigote-amastigote differentiation. Different number of repeats and numerous single nucleotide polymorphisms are observed in the compared sequences. We have also investigated the DR structure in 21 L. major isolates by PCR and demonstrated its great variability. We suppose, however, that different variants of the DR structure are generated by combination of several highly conserved domains.
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10
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Brewster S, Barker DC. The ATPase subunit 6 gene sequence predicts that RNA editing is conserved between lizard- and human-infecting Leishmania. Gene 1999; 235:77-84. [PMID: 10415335 DOI: 10.1016/s0378-1119(99)00207-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Here we investigate the similarities in the kinetoplastid RNA editing process between human- and lizard-infecting Leishmania species. We present the sequence of the maxicircle-encoded ATPase subunit 6 gene from L. (V.) panamensis, L. (L.) mexicana and L. (L.) donovani species of human-infecting Leishmania. These represent the first available sequences of this gene from Leishmania species other than the lizard-infecting L. tarentolae. The gene sequences are highly conserved, both over the edited and unedited parts of the gene, implying that the RNA editing process is likely to be highly conserved between Leishmania species. Indeed, the first editing domain is absolutely conserved in all three Leishmania species studied and L. tarentolae. A phylogeny based on part of the ATPase subunit 6 gene placed the lizard-infecting Leishmania within the monophyletic Leishmania genus, supporting previous data which suggest that lizard- and human-infecting Leishmania species are closely related.
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Affiliation(s)
- S Brewster
- Molteno Outstation of NIMR, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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11
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Myler PJ, Glick D, Feagin JE, Morales TH, Stuart KD. Structural organization of the maxicircle variable region of Trypanosoma brucei: identification of potential replication origins and topoisomerase II binding sites. Nucleic Acids Res 1993; 21:687-94. [PMID: 8382804 PMCID: PMC309170 DOI: 10.1093/nar/21.3.687] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The maxicircle of the parasitic protozoan Trypanosoma brucei, one component of the mitochondrial genome, has size differences among isolates that localize to the variable region (VR) between the ND5 and 12S rRNA genes. We present here the nucleotide sequence of this entire region, thus completing the sequence of the maxicircle genome. We also find heterogeneously sized transcripts from throughout most of the VR. The VR has three distinct sections, each with characteristic repeated sequences. The repeated sequences in two sections are short and highly reiterated; the intraspecies size variation occurs within this region. The third section contains non-repetitive sequences and a large duplication immediately upstream of the 12S rRNA gene. Two repeat units within section I contain a sequence that has homology to the DNA replication origin of minicircles. This region also contains sequences with homology to topoisomerase II binding and cleavage sites. These findings suggest a role for the VR in DNA replication of the maxicircle.
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Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, WA 98109-1651
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12
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Affiliation(s)
- K Stuart
- Seattle Biomedical Research Institute, Washington 98109
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13
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Muhich ML, Iida CT, Horikoshi M, Roeder RG, Parker CS. cDNA clone encoding Drosophila transcription factor TFIID. Proc Natl Acad Sci U S A 1990; 87:9148-52. [PMID: 2123550 PMCID: PMC55121 DOI: 10.1073/pnas.87.23.9148] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Proper initiation of transcription by RNA polymerase II requires the TATA-consensus-binding transcription factor TFIID. A cDNA clone encoding the Drosophila TFIID protein has been isolated and characterized. The deduced amino acid sequence reveals an open reading frame of 353 residues. The carboxyl-terminal 180 amino acids are approximately 80% identical to yeast TFIID and 88% identical to human TFIID. The amino-terminal portions of the yeast and Drosophila TFIID proteins lack appreciable homology, whereas the Drosophila and human amino termini appear qualitatively similar. In addition, the amino-terminal region of the Drosophila TFIID contains several sequence motifs that are found in other Drosophila proteins which appear to regulate transcription.
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Affiliation(s)
- M L Muhich
- Division of Chemistry, California Institute of Technology, Pasadena 91125
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Kolesnikov A, Maslov D, Podlipaev S. Comparative Restriction Enzyme Cleavage Analysis of Kinetoplast DNA from the Lower Trypanosomatids Isolated in the North-West Region of the USSR. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0003-9365(11)80167-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Polycistronic transcripts in trypanosomes and their accumulation during heat shock: evidence for a precursor role in mRNA synthesis. Mol Cell Biol 1989. [PMID: 3221866 DOI: 10.1128/mcb.8.9.3837] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Maturation of mRNA precursors in trypanosomes involves an apparent trans splicing event in which a 39-nucleotide miniexon sequence, common to all trypanosome mRNAs, is joined to the 5' end of a protein-coding exon. We demonstrate that the processing machinery responsible for the maturation of tubulin mRNA precursors in Trypanosoma brucei can be disrupted by heat shock. This results in an accumulation of polycistronic RNA species and a decrease in the abundance of branched splicing intermediates. At normal temperatures, tubulin polycistronic transcripts were also detected and were shown in pulse-chase experiments to be abundantly synthesized and very rapidly turned over. These results, combined with results of the heat shock experiments, suggest that these polycistronic transcripts are the precursors of the (monocistronic) tubulin mRNAs of trypanosomes.
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Muhich ML, Boothroyd JC. Polycistronic transcripts in trypanosomes and their accumulation during heat shock: evidence for a precursor role in mRNA synthesis. Mol Cell Biol 1988; 8:3837-46. [PMID: 3221866 PMCID: PMC365442 DOI: 10.1128/mcb.8.9.3837-3846.1988] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Maturation of mRNA precursors in trypanosomes involves an apparent trans splicing event in which a 39-nucleotide miniexon sequence, common to all trypanosome mRNAs, is joined to the 5' end of a protein-coding exon. We demonstrate that the processing machinery responsible for the maturation of tubulin mRNA precursors in Trypanosoma brucei can be disrupted by heat shock. This results in an accumulation of polycistronic RNA species and a decrease in the abundance of branched splicing intermediates. At normal temperatures, tubulin polycistronic transcripts were also detected and were shown in pulse-chase experiments to be abundantly synthesized and very rapidly turned over. These results, combined with results of the heat shock experiments, suggest that these polycistronic transcripts are the precursors of the (monocistronic) tubulin mRNAs of trypanosomes.
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Affiliation(s)
- M L Muhich
- Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305
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Simpson L, Neckelmann N, de la Cruz V, Simpson A, Feagin J, Jasmer D, Stuart J. Comparison of the maxicircle (mitochondrial) genomes of Leishmania tarentolae and Trypanosoma brucei at the level of nucleotide sequence. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45555-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Muhich ML, Hughes DE, Simpson AM, Simpson L. The monogenetic kinetoplastid protozoan, Crithidia fasciculata, contains a transcriptionally active, multicopy mini-exon sequence. Nucleic Acids Res 1987; 15:3141-53. [PMID: 3562248 PMCID: PMC340916 DOI: 10.1093/nar/15.7.3141] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A repeated sequence from the Crithidia fasciculata nuclear genome has been isolated which is homologous to the mini-exon genes of other kinetoplastid protozoa. Sequence analysis of the 417 bp monomeric unit confirmed the presence of a 35 nt sequence within the repeat that is 77% homologous with the Trypanosoma brucei 35-mer mini-exon or spliced leader sequence. The repeat is present at approximately 250 copies per cell and is organized into one, or a few, large head to tail tandem clusters predominantly on a single chromosome. The mini-exon repeat unit hybridizes to a major 84 nt and a minor 87 nt poly (A)- steady state transcript, the first 35 nts of which comprise the mini-exon sequence found at the 5' end of mRNAs in several other kinetoplastid species. The 3'-termini of the transcripts map to positions on the DNA sense strand directly preceeding a stretch of 8 thymidine residues. Crithidia represents the most primitive kinetoplastid species which apparently possesses a discontinuous type of mRNA processing, implying that this represents a conserved feature in possibly all genera of kinetoplastid protozoa.
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Sloof P, van den Burg J, Voogd A, Benne R. The nucleotide sequence of a 3.2 kb segment of mitochondrial maxicircle DNA from Crithidia fasciculata containing the gene for cytochrome oxidase subunit III, the N-terminal part of the apocytochrome b gene and a possible frameshift gene; further evidence for the use of unusual initiator triplets in trypanosome mitochondria. Nucleic Acids Res 1987; 15:51-65. [PMID: 3029678 PMCID: PMC340397 DOI: 10.1093/nar/15.1.51] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A 3.2 kb segment of the maxicircle of Crithidia fasciculata mitochondrial (mt) DNA contains the gene for cytochrome oxidase subunit III (coxIII), the N-terminal portion of the gene for apocytochrome b (cytb) and two partially overlapping Unassigned Reading Frames (C.URF2/1). Transcript analysis of the segment reveals that both the coxIII gene and the C.URF2/1 area are transcribed into a pair of RNA products. With the C. fasciculata gene version as a probe, a coxIII gene could not be detected in nuclear and mtDNA of Trypanosoma brucei, indicating that the cytochrome oxidases of these two closely related trypanosome species may differ. The nucleotide homology in the N-terminal region of the coxIII and cytb genes in T. brucei, Leishmania tarentolae and C. fasciculata starts at a UUA leucine codon, which adds further support to the hypothesis that apart from AUG, other initiator triplets are used in trypanosomal mitochondria: UUG, CUG and UUA, all triplets coding for leucine in the universal code. Finally, the possibility is discussed that the two overlapping URFs (C.URF2/1) in fact represent a single, frameshift containing, gene.
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Affranchino JL, Sanchez DO, Engel JC, Frasch AC, Stoppani AO. Trypanosoma cruzi: structure and transcription of kinetoplast DNA maxicircles of cloned stocks. THE JOURNAL OF PROTOZOOLOGY 1986; 33:503-7. [PMID: 3025435 DOI: 10.1111/j.1550-7408.1986.tb05650.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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.
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Tarassoff IA, Kuzmin EV, Levchenko IV, Zaitseva GN. Repeated sequences with unusual properties from the divergent region of Crithidia oncopelti maxicircle kinetoplast DNA. MOLECULAR & GENERAL GENETICS : MGG 1986; 205:122-6. [PMID: 3025554 DOI: 10.1007/bf02428041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The occurrence of bacterial promoter-like sequences was shown in the divergent region of Crithidia oncopelti maxicircular kinetoplast DNA. A promoter-cloning vector based on the neomycin phosphotransferase II (NPT II) gene was used to localize promoters in three homologous blocks of repeated sequences. The elements found displayed greater promoter strength in Escherichia coli than the normal promoter of the NPT II gene. Sequences of three promoter-containing inserts from different blocks were determined and typical prokaryotic promoter sequences were localized.
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Muhich ML, Simpson L. Specific cleavage of kinetoplast minicircle DNA from Leishmania tarentolae by mung bean nuclease and identification of several additional minicircle sequence classes. Nucleic Acids Res 1986; 14:5531-56. [PMID: 3016649 PMCID: PMC311557 DOI: 10.1093/nar/14.13.5531] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Multiple sequence classes of kinetoplast minicircle DNA from Leishmania tarentolae were cleaved by mung bean nuclease in the presence of formamide, yielding unit length linear molecules which retained the anomalous electrophoretic mobility in acrylamide characteristic of minicircle DNA. No specific cleavage site sequence common to all minicircle sequence classes was apparent, although the main region of nuclease cleavage was localized approximately 350 bp from the unique SmaI restriction site of the conserved region found in all minicircle sequence classes. Covalent closure of the minicircle substrate was not a requirement for cleavage, as linearized network-derived or cloned minicircles were also cleaved by mung bean nuclease at similar locations. The partial sequences of several new minicircle sequence classes released from the network by mung bean nuclease are also reported.
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Simpson AM, Neckelmann N, de la Cruz VF, Muhich ML, Simpson L. Mapping and 5' end determination of kinetoplast maxicircle gene transcripts from Leishmania tarentolae. Nucleic Acids Res 1985; 13:5977-93. [PMID: 2994021 PMCID: PMC321927 DOI: 10.1093/nar/13.16.5977] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Transcripts for six Leishmania tarentolae maxicircle structural genes (cytochrome oxidase subunits I, II and III, cytochrome b, human mitochondrial unidentified reading frames 4 and 5) and several unidentified open reading frames were mapped, and the locations of the 5' ends determined by primer runoff analysis. All genes studied here are transcribed from the same strand as the 12S and 9S ribosomal RNAs except for the cytochrome oxidase subunit I gene. In two cases (ORF3 and ORF4, ORF5 and ORF6), a single transcript covers two contiguous overlapping reading frames. The 5' ends of the RNAs are located 20-64 nt from the putative translation initiation codons. Primary transcripts from a mitochondrial RNA preparation were 5' end-labeled with guanylyltransferase and alpha -32P-GTP; the major labeled species comigrated with the 12S and 9S mitochondrial rRNAs, and in addition there were at least four higher molecular weight labeled species.
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Muhich ML, Neckelmann N, Simpson L. The divergent region of the Leishmania tarentolae kinetoplast maxicircle DNA contains a diverse set of repetitive sequences. Nucleic Acids Res 1985; 13:3241-60. [PMID: 2987878 PMCID: PMC341232 DOI: 10.1093/nar/13.9.3241] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A 2.76 kb segment of the 12 kb divergent region of the Leishmania tarentolae kinetoplast maxicircle DNA consists almost entirely of repeated sequences. The repeats can be grouped into six families, some of which are present throughout the remainder of the divergent region. The repeats are oriented in a head-to-tail fashion with the three simplest repeats clustered into large arrays. A 47 bp palindrome and two copies of a "supercluster" of three different types of repeats are also present in the sequenced region. A sequence change in the divergent region is described for a clonal strain of L. tarentolae which was passaged continuously for several years. The repetitive sequences found in the divergent region appear to be appropriate substrates for the presumed deletion/insertion/recombination events occurring in this rapidly evolving portion of the maxicircle.
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Kuzmin EV, Tarassoff IA, Zaitseva GN. Kinetoplast DNA segments function as promoters in Escherichia coli cells. MOLECULAR & GENERAL GENETICS : MGG 1985; 198:323-8. [PMID: 2984521 DOI: 10.1007/bf00383014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
By means of coupled transcription-translation in Escherichia coli cell-free system, an open reading frame was found in the Crithidia oncopelti maxi-circle kDNA segment cloned in the hybrid plasmid pCo1. Subfragments from this region were tested for their ability to function as promoters in E. coli cells. For this purpose the vector pVE8 was constructed using the aminoglycoside phosphotransferase II (APTII) gene from the Tn5 transposon, and the pHC79 cosmid. After cloning of Sau3A fragments of pCo1 by insertion into pVE8 three types of plasmids containing promoter sequences were obtained. Two of these plasmids displayed promoter strength in E. coli cells greater than that of the normal promoter of the APTII gene. However the promoters found are not necessary for the coupled transcription-translation of kDNA in the E. coli cell-free system.
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de la Cruz VF, Neckelmann N, Simpson L. Sequences of six genes and several open reading frames in the kinetoplast maxicircle DNA of Leishmania tarentolae. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42525-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Abstract
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.
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