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P Sloof

Publications and source records attributed to P Sloof.

At least 19 recordsLinked to original sources
PubMed2000

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status.

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Animals↗
PubMed2000

Mitochondrial minicircles in the free-living bodonid Bodo saltans contain two gRNA gene cassettes and are not found in large networks.

In trypanosomatids, the majority of the guide (g) RNAs that provide the information for U-insertion/deletion RNA editing are encoded by minicircles that are catenated into large networks. In contrast, in the distantly related cryptobiid Trypanoplasma borreli, gRNA genes appear to reside in large 180-kb noncatenated DNA circles. To shed light on the evolutionary history and function of the minicircle network, we have analyzed minicircle organization in the free-living bodonid Bodo saltans, which is more closely related to trypanosomatids than T. borreli. We identified 1.4-kb circular DNAs as the B. saltans equivalent of minicircles via sequence analysis of 4 complete minicircles, 14 minicircle fragments, and 14 gRNAs. We show that each minicircle harbors two gRNA gene cassettes of opposite polarity residing in variable regions of about 200 nt in otherwise highly conserved molecules. In the conserved region, B. saltans minicircles contain a putative bent helix sequence and a degenerate dodecamer motif (CSB-3). Electron microscopy, sedimentation, and gel electrophoresis analyses showed no evidence for the existence of large minicircle networks in B. saltans, the large majority of the minicircles being present as circular and linear monomers (85-90%) with small amounts of catenated dimers and trimers. Our results provide the first example of a kinetoplastid species with noncatenated, gRNA gene-containing minicircles, which implies that the creation of minicircles and minicircle networks are separate evolutionary events.

Amino Acid Sequence↗
PubMed1999

MitBASE: a comprehensive and integrated mitochondrial DNA database.

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects all available information from different organisms and from intraspecie variants and mutants. Research institutions from different countries are involved, each in charge of developing, collecting and annotating data for the organisms they are specialised in. The design of the actual structure of the database and its implementation in a user-friendly format are the care of the European Bioinformatics Institute. The database can be accessed on the Web at the following address: http://www.ebi.ac. uk/htbin/Mitbase/mitbase.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecie diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Animals↗
PubMed1998

RNA editing in the free-living bodonid Bodo saltans.

In parasitic kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g) RNAs. In order to further explore the role and evolutionary history of this process, we searched for editing in mt RNAs of the free-living bodonid Bodo saltans. We found extensive editing in the transcript for NADH dehydrogenase (ND) subunit 5, which is unedited in trypanosomatids. In contrast, B.saltans cytochrome c oxidase (cox) subunit 2 and maxicircle unidentified reading frame (MURF) 2 RNAs display limited editing in the same regions as their trypanosomatid counterparts. A putative intramolecular cox2 gRNA and the gene for gMURF2-I directing the insertion of only one U in the 5' editing domain of MURF2 RNA, are conserved in B.saltans. This lends (further) evolutionary support to the proposed role of these sequences as gRNAs. Phylogenetic analysis showed that B.saltans is more closely related to trypanosomatids than the cryptobiids Trypanoplasma borreli and Cryptobia helicis, in line with the trypanosomatid-like cox2 and MURF2 RNA editing patterns. Nevertheless, other features like the apparent absence of a catenated mtDNA network, are shared with bodonid and cryptobiid species. ND5 RNA editing may represent yet another example of editing 'on the way out' during kinetoplastid evolution, but in view of the fact that cox2 RNA is unedited in T. borreli and C.helicis, we infer that the editing of this RNA may have arisen relatively recently. Our results provide the first examples of RNA editing in a free-living kinetoplastid, indicating that there is no direct link between U-insertion/deletion editing and a parasitic lifestyle.

Amino Acid Sequence↗
PubMed1997

Glucocerebrosidase genotype of Gaucher patients in The Netherlands: limitations in prognostic value.

Gaucher disease is a recessively inherited lysosomal storage disorder that is caused by a deficiency in glucocerebrosidase activity. The clinical expression is markedly heterogeneous with respect to age of onset, progression, severity, and neurological involvement. The relative incidence of glucocerebrosidase (GC) mutations has been studied extensively for Jewish but not for non-Jewish Caucasian patient populations. The present survey on mutant GC genotypes prevalent in Gaucher disease in The Netherlands was taken of 72 patients from different genetic backgrounds. This number is more than half the total number of affected Gaucher patients to be expected on the basis of the incidence of the disorder in this country. Analysis of nine GC mutations led to the identification of 74% of the mutant GC alleles in patients from 44 unrelated Dutch families (i.e., families that have lived in The Netherlands for at least several generations) and of 44% of the mutant GC alleles in patients from nine unrelated families that recently immigrated from both European and non-European countries. The N370S (cDNA 1226G) GC mutation proved to occur most frequently (41%) in the unrelated Dutch patients and less frequently (6%) in the unrelated immigrant patients and was always associated with the nonneuronopathic (Type 1) form of the disease. Apart from the association of the N370S mutation with Type 1 Gaucher disease, the prognostic value of GC genotyping was limited, since a particular GC genotype did not correlate closely to a specific clinical course, or to a specific relative responsiveness to enzyme-supplementation therapy.

Blotting, Southern↗
PubMed1997

RNA editing in kinetoplastid parasites: what to do with U.

The editing of the mitochondrial RNAs of kinetoplastid protozoa is a bizarre form of transcript maturation that involves insertion and deletion of uridylate residues. Editing leads to the formation of translational initiation and termination codons, the correction of gene-encoded reading frame shifts and the creation of complete reading frames in mRNAs. It is therefore an essential step in mitochondrial gene expression.

Animals↗
PubMed1995

A possible role for the guide RNA U-tail as a specificity determinant in formation of guide RNA-messenger RNA chimeras in mitochondrial extracts of Crithidia fasciculata.

Chimeric g(uide) RNA:pre-mRNA molecules are potential intermediates of the RNA editing process in kinetoplastid mitochondria. We have studied the characteristics of chimeric molecules formed in mitochondrial extracts of the insect trypanosomatid Crithidia fasciculata which had been supplied with synthetic NADH dehydrogenase (ND) subunit-7 gRNA and pre-mRNA variants. The ability of a gRNA to participate in chimera formation in this system depends on the possibility of base pairing with the pre-mRNA via the anchor sequence, but not on the presence of a U-tail or a full-length informational part. Chimeras formed with a specific gRNA:pre-mRNA pair displayed a large variation in length, due to variably sized 3' end truncations of the gRNA moieties and variation in the sites in the pre-mRNA to which the gRNAs were attached. Surprisingly, the presence of a U-tail in the gRNA for a large part determined the specificity of the linkage. In 60% of the cases gRNAs possessing a U-tail of at least one residue were attached to an editing site, whereas 75% of the gRNAs without Us were attached to non-editing sites. Furthermore, the chimera forming activity was greatly stimulated by the addition of ATP but not by AMP-CPP, an ATP-analogue with a non-hydrolyzable alpha-beta phosphate bond. This suggests the involvement in the chimera formation of an RNA ligase.

Adenosine Triphosphate↗
PubMed1994

Novel pattern of editing regions in mitochondrial transcripts of the cryptobiid Trypanoplasma borreli.

In mitochondria of Kinetoplastida belonging to the suborder Trypanosomatina, the nucleotide sequence of transcripts is post-transcriptionally edited via insertion and deletion of uridylate residues. In order to shed more light on the evolutionary history of this process we have searched for editing in mitochondrial RNAs of Trypanoplasma borreli, an organism belonging to the suborder Bodonina. We have cloned and sequenced a 5.3 kb fragment derived from a 37 kb mitochondrial DNA molecule which does not appear to be a part of a network structure and have found genes encoding cytochrome c oxidase (cox) subunit 1, cox 2 and apocytochrome (cyt) b, and genes encoding the small and large subunit mitoribosomal RNAs. The order in which these genes occur is completely different from that of trypanosomatid maxicircle genes. The 5' and 3' termini of both the cytb and cox1 gene are cryptic, the protein coding sequences being created by extensive insertion/deletion of Us in the corresponding mRNA sections. Phylogenetic analyses of the protein and ribosomal RNA sequences demonstrated that the separation between T.borreli and Trypanosomatina was an early event, implying that U-insertion/deletion processes are ancient. Different patterns of editing have persisted in different lineages, however, since editing of cox1 RNA and of relatively small 3'-terminal RNA sections is not found in trypanosomatids. In contrast, cox2 RNA which is edited in trypanosomatids by the insertion of four Us, is unedited in T.borreli.

Amino Acid Sequence↗
PubMed1994

RNA editing in mitochondria of cultured trypanosomatids: translatable mRNAs for NADH-dehydrogenase subunits are missing.

RNA editing in mitochondria of kinetoplastid protozoa involves the posttranscriptional insertion and deletion of uridylate residues in protein encoding regions of pre-mRNAs. Editing is required to remove gene-encoded translational defects or to convert a nonsense sequence into a sense message. In cultured trypanosomatids, however, translationally defective pre-mRNAs for a number of NADH-dehydrogenase subunits are not converted into functional mRNAs by editing. In this report, the available data are discussed in the context of current models for RNA editing.

Animals↗
PubMed1993

RNA editing in trypanosome mitochondria: guidelines for models.

Mitochondrial RNAs in trypanosomes are post-transcriptionally altered by uridine insertion and deletion. The information for these RNA editing processes, which are essential for the production of functional messengers, is provided by small guide RNAs. This article discusses how features of partially edited RNAs, gRNAs and chimeric RNAs, in which a gRNA is covalently linked to an editing site of pre-mRNA, have been used for the construction of models.

Animals↗
PubMed1993

Implications of novel guide RNA features for the mechanism of RNA editing in Crithidia fasciculata.

We have determined the relative steady state concentration of the two Crithidia fasciculata guide (g)RNAs involved in editing the two domains of mRNAs for NADH dehydrogenase (ND) subunit 7. We found that, although there was an 8-fold difference between the molar ratio of these two gRNAs relative to the (pre)-mRNA, the two domains are edited with a very similar frequency (around 50%). Also, for the editing of a given domain, many gRNA species exist with the same 5' end but with a different 3' uridylation site. Approximately 20% of these short gRNAs do not contain the information required for editing a complete domain, which may explain the high incidence of partially edited RNAs. Remarkably, genomically encoded Us are missing from two sites of a few of the gRNAs involved in editing apocytochrome b RNA. We speculate that these species are created by editing-like events. Both the short and complete forms of the ND7 gRNAs are found in chimeric molecules, in which the gRNA is covalently linked via its 3'-terminus to an editing site of pre-edited ND7 RNA. Some features of the chimeric molecules are at odds with current models of RNA editing: (i) U residues are completely absent from the connecting sequence of a number of these molecules, (ii) the ND7 gRNAs are frequently hooked up to the wrong editing domain of ND7 RNA, although other gRNAs are not found at these positions and (iii) in some chimeric molecules the gRNA appears to be linked to the 5' end of pre-edited RNA.

Animals↗
PubMed1992

The nucleotide sequence of the variable region in Trypanosoma brucei completes the sequence analysis of the maxicircle component of mitochondrial kinetoplast DNA.

The nucleotide sequence of two non-contiguous DNA fragments of 4.0 and 2.2 kb, respectively, of the kinetoplast maxicircle of Trypanosoma brucei brucei EATRO strain 427 has been determined, completing the sequence analysis of the so-called variable region (see also de Vries et al., 1988, Mol. Biochem. Parasitol. 27, 71-82). Analysis of the entire 8-kb variable region sequence revealed the presence of a 5.2-kb cluster of imperfect, tandemly repeated sequences, flanked by DNA of unique sequence. Both repetitive and unique DNA evolve rapidly, but comparison to the closely related strain EATRO 164 indicated that the repetitive cluster is more prone to sequence and size divergence. The variable region is transcribed into RNAs of varying lengths but appears to be devoid of genes encoding mitochondrial proteins or tRNAs, as judged from computer analysis. Moreover, genes that could encode guide RNAs involved in producing the known edited mitochondrial mRNA sequences are also absent. The repetitive DNA cluster within this region consists of 14 blocks each containing one 130 bp repeat and a variable number of 19 bp repeats. A duplicated sequence was identified (5'-GGGGTTGGTGT) which proved to be identical to the eleven 5'-terminal residues of the universal minicircle dodecamer involved in initiation of leading strand synthesis. This suggests a role for these sequences in the initiation of maxicircle DNA replication. With the data presented in this report, the nucleotide sequence analysis of the 23016 bp maxicircle of T. brucei brucei EATRO strain 427 has been completed.

Animals↗
PubMed1991

Conserved genes encode guide RNAs in mitochondria of Crithidia fasciculata.

RNA editing is the post-transcriptional alteration of the nucleotide sequence of RNA, which in trypanosome mitochondria is characterized by the insertion and deletion of uridine residues. It has recently been proposed that the information for the sequence alteration in Leishmania tarentolae is provided by small guide (g) RNAs encoded in the mitochondrial DNA [Blum et al. (1990) Cell, 60, 189-198]. We are studying the mechanism of RNA editing in the insect trypanosome Crithidia fasciculata and report that: (i) a full length, conventional DNA gene or an independently replicating RNA gene that could encode the edited MURF3 transcript is absent when probed for in sensitive, calibrated assay systems; (ii) in all cases (seven) investigated in C. fasciculata so far, putative gRNA genes are found in a position in the mitochondrial DNA virtually identical to that in L. tarentolae and (iii) also in C. fasciculata, the putative gRNA genes are transcribed into small RNAs with discrete 5' ends. These results provide strong evolutionary evidence in support of the participation of gRNAs in RNA editing. Remarkably, in C. fasciculata the basepaired region of some putative gRNA:mRNA hybrids contains a C:A non-Watson-Crick basepair.

Animals↗
PubMed1990

RNA editing in transcripts of the mitochondrial genes of the insect trypanosome Crithidia fasciculata.

With the aid of cDNA and RNA sequence analysis, we have determined to what extent transcripts of mitochondrial maxicircle genes of the insect trypanosome Crithidia fasciculata are altered by RNA editing, a novel mechanism of gene expression which operates via the insertion and deletion of uridine residues. Editing of cytochrome c oxidase (cox) subunit II and III transcripts and of maxicircle unidentified reading frame (MURF) 2 RNA is limited to a small section and results in the creation of a potential AUG translational initiation codon (coxIII, MURF2) or the removal of a frameshift (coxII). No differences with the genomic sequences were observed in the remainder of these RNAs. Surprisingly, NADH dehydrogenase subunit I transcripts were completely unedited in the coding region, implying that an AUG translational initiation codon is absent. The partial ribosomal RNA sequences determined also conform to the gene sequences. Together these results lead to the conclusion that the unusual sequences predicted by the protein and rRNA genes must indeed be present in the gene products. Editing also occurred in the poly(A) tail of RNAs from all protein genes, including those that are unedited in the coding region. The tails display a large variation in AU sequence motifs. Finally, some cDNAs contained sequences absent from both the DNA and the edited RNA. Some of these may represent intermediates in the RNA editing process. We argue, however, that long runs of T may be artefacts of cDNA synthesis.

Animals↗
PubMed1988

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.

Animals↗
PubMed1988

Transcripts from the frameshifted MURF3 gene from Crithidia fasciculata are edited by U insertion at multiple sites.

In trypanosome mitochondria an RNA editing process is operative, which co- or post-transcriptionally alters the nucleotide sequence of transcripts by insertion and/or deletion of U residues at specific sites. To increase our understanding of the mechanism of this process we have compared the nucleotide sequence of the frameshifted mitochondrial MURF3 gene from Crithidia fasciculata to that of a large number of MURF3 cDNAs. We found cDNAs derived from transcripts edited at two different sites in the protein coding sequence: (i) at the frameshift position five extra U residues connect the two reading frames and (ii) at the 5' terminus 22 inserted Us shift a putative initiator codon out of phase. The collection also contained cDNAs that were derived from non-edited transcripts. Partially edited sequences were not found, except in one cDNA, which contained an edited frameshift site in combination with a non-edited 5' terminus. The analysis further showed that MURF3 transcripts have a 3'-terminal poly(AU) extension, which varies in sequence. The implications of these results are discussed.

Amino Acid Sequence↗
PubMed1987

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.

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.

Amino Acid Sequence↗