Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.49 (reverse transcriptase)
31,746 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Two long and uninterrupted reading frames, specifying the ND1 and RTL genes, are embedded within fragmented rRNA genes in the 15.8-kb mitochondrial genome of Chlamydomonas reinhardtii, a unicellular green alga. The ND1 gene encodes a subunit of respiratory NADH dehydrogenase, a standard mitochondrial gene, while the RTL gene is related to the reverse transcriptase-like part of some optional introns and plasmids in fungal mitochondria. The universal genetic code is used in both the ND1 and RTL genes; however, the latter is distinguished from the other protein coding genes of C. reinhardtii mtDNA by several characteristics which suggest that RTL may be a more recently acquired gene. Flanking each of the protein coding genes, whose mRNAs are of similar abundance, are some of the 'scrambled' rRNA gene pieces that are a unique feature of C. reinhardtii mtDNA. These sub-genic modules give rise to high-abundance, small-sized pieces of rRNA, which are not spliced in this genetic system. Judging by the observed juxtaposition of transcripts as they hybridize to the genome, the mature rRNA and mRNA species from this region appear to be generated by precise endonucleolytic cleavages of a long RNA precursor. We suggest a model, involving reverse transcription of rRNAs and insertion of the resulting cDNAs into the mitochondrial genome, that might account for the pattern of dispersed rRNA gene pieces in C. reinhardtii mitochondrial DNA.
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PMID:Genes encoding a subunit of respiratory NADH dehydrogenase (ND1) and a reverse transcriptase-like protein (RTL) are linked to ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. 246 63

We have isolated a 5.7-kbp dispersed moderately repeated DNA sequence (TOC1) from the mutant OEE1 gene of the Chlamydomonas reinhardtii strain FUD44. The copy number (2 to over 30) and genomic locations of TOC1 elements vary widely in different C. reinhardtii strains. Our standard laboratory photosynthetic strain exhibits a high degree of TOC1 instability during short periods of mitotic growth. TOC1 appears to be a retrotransposon: it contains LTRs and an oligonucleotide stretch that corresponds to a conserved pentapeptide of reverse transcriptase. TOC1 is an unusual retrotransposon: it is not flanked by a target site duplication in the OEE1 gene, the left end of TOC1 only contains a fraction of the LTR the remainder of which is present at its right end and TOC1 does not start with a 5' TG and end with a 3' CA. In most cases, TOC1 excision leaves behind a complete solo LTR sequence (577 bp) and in one case a deleted solo LTR sequence (191 bp). Solo LTR sequences form a separate family of repeated sequences in most of the strains tested.
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PMID:A transposon with an unusual arrangement of long terminal repeats in the green alga Chlamydomonas reinhardtii. 284 59

The psbA gene coding for the herbicide binding QB protein of photosystem II has been sequenced previously (Karabin et al. 1984). A herbicide resistant mutant of Euglena, Euglena gracilis ZR, was studied by sequencing part of the psbA gene and its corresponding mRNA. Sequencing reactions were done by annealing a psbA specific, end-labeled DNA-oligomer to total chloroplast DNA or RNA and extending this primer with reverse transcriptase in the presence of the four dideoxynucleotides. An amino acid substitution from serine to alanine at position 265 was detected. All known herbicide resistant higher plants sequenced to date and the Chlamydomonas mutant DCMU-4 show a change at exactly this same position, but the substitution in higher plants is from serine to glycine.
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PMID:The psbA gene of DCMU-resistant Euglena gracilis has an amino acid substitution at serine codon 265. 312 2

The polypeptide product of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase from Euglena gracilis based on the DNA sequence of the chloroplast-encoded gene is described. The large subunit polypeptide of 475 codons is co-linear with the homologous polypeptides from other chloroplasts and cyanobacteria. The amino acid sequence is 92% homologous to that of Chlamydomonas, 84% homologous to spinach, 82% homologous to maize, and 80% homologous to that of the cyanobacterium Anabaena variabilis. Known functional domains of the protein are coded by the larger exons of the gene. Introns in the gene generally occur at coding sequences specifying hydrophilic, presumably surface exposed, regions of the polypeptide. The location of some of the introns may reflect a separation of functional domains. The 5'- and 3'-ends of the rbcL transcript were determined by primer extension sequencing using reverse transcriptase and S1 nuclease protection, respectively. The transcribed but untranslated sequences are quite distinct from those from other rbcL loci.
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PMID:The Euglena gracilis chloroplast ribulose-1,5-bisphosphate carboxylase gene. II. The spliced mRNA and its product. 393 71

A number of group II introns from eukaryotic organelles and prokaryotes contain open reading frames for polypeptides with homology to retroviral reverse transcriptases (RTs). We have used the yeast transposon (Ty) system to express ORFs for RTs from eukaryotic organelles. This includes the mitochondrial coxI intron i1 from the fungus Podospora anserina, the plastid petD intron from the alga Scenedesmus obliquus and the mitochondrial RTL gene from the alga Chlamydomonas reinhardtii. The ORFs were fused with the TYA ORF from the yeast retrotransposon Ty to produce virus-like particles in the recipient strains with detectable amounts of the RT-like polypeptides. Analysis of the heterologous gene products revealed biochemical evidence that the P. anserina intron encodes an RNA-directed DNA polymerase with properties typically found for RTs of viral or retrotransposable origin. In vitro assays showed that the intron encoded RT is sensitive to RT inhibitors such as N-ethylmaleimide and dideoxythymidine triphosphate but is insensitive against the DNA polymerase inhibitor aphidicolin. The direct biochemical evidence provided here supports the idea that intron encoded RTs are involved in intron transposition events.
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PMID:Reverse transcriptase activity of an intron encoded polypeptide. 751 30

The complete nucleotide sequence of the Chlamydomonas eugametos (Chlamydomonadales, Chlorophyceae, sensu Mattox and Stewart) mitochondrial genome has been determined (22,897 bp, 34.6% G + C). The genes identified in this circular-mapping genome include those for apocytochrome b, subunit 1 of the cytochrome oxidase complex, subunits 1, 2, 4, 5, and 6 of the NADH dehydrogenase complex, discontinuous large and small subunit ribosomal rRNAs and three tRNAs whose anticodons CAU, CCA and UUG are specific for methionine, tryptophan and glutamine, respectively. The C. eugametos mitochondrial DNA (mtDNA), therefore, shares almost the same reduced set of coding functions and similar unusual features of rRNA gene organization with the linear 15.8 kb mtDNA of Chlamydomonas reinhardtii, the only other completely sequenced chlamydomonadalean mtDNA. However, sequence analysis of the C. eugametos mtDNA has revealed the following distinguishing features relative to those of C. reinhardtii: (1) the absence of a reverse transcriptase-like gene homologue, (2) the presence of an additional gene for tRNA(met) that may be a pseudogene, (3) a completely different gene order, (4) transcription of all genes from the same mtDNA strand, (5) a lower G + C content, (6) less pronounced bias in codon usage, and (7) nine group I introns, several of which contain open reading frames coding for potential maturases/endonucleases and two have a nucleotide at the 5' or 3' splice site of the deduced precursor RNAs that deviates from highly conserved nucleotides reported in other group I introns. The features of mitochondrial genome organization and gene content shared by C. eugametos and C. reinhardtii contrast with those of other green algal mtDNAs that have been characterized in detail. The deep evolutionary divergence between these two Chlamydomonas taxa within the Chlamydomonadales suggests that their shared features of mitochondrial genome organization evolved prior to the origin of this group.
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PMID:Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos. 948 40

A gene for chloroplast omega6 desaturase, which catalyzes the desaturation of monoenoic to dienoic acids in chloroplasts, was isolated from Chlamydomonas reinhardtii. We first performed reverse transcriptase-polymerase chain reaction with oligonucleotide primers corresponding to regions conserved among plastid omega6 desaturases of higher plants and delta12 desaturases of cyanobacteria, using C. reinhardtii poly(A)+ RNA. An amplified DNA fragment of 0.5 kb, containing a frame for a protein homologous to these desaturases, was used as a probe for screening cDNA and genomic DNA libraries of C. reinhardtii. The cDNA clone of 2.2 kb obtained contained an open reading frame encoding a protein of 424 amino acids with a putative molecular mass of 48.4 kDa, the amino acid sequence of which showed 46-51% homology to those of higher plant plastid omega6 and cyanobacterial delta12 desaturases. Introduction of the cloned genomic counterpart of this cDNA, designated as des6, into a Chlamydomonas mutant with defects in chloroplast omega6 desaturation and in the activities of photosystems I and II (PSI and PSII) complemented the desaturation mutation, indicating that the des6 gene codes for chloroplast omega6 desaturase. The complemented strains did not recover from the photosynthetic lesions, but showed lower PSII activity at 45 degrees C than the desaturation mutant, proving that the photosynthetic lesions in hf-9 are not caused by the desaturation mutation, and that the lowered unsaturation level of chloroplast lipids in the mutant is responsible for the expression at this high temperature of PSII activity, one of the thylakoid membrane functions.
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PMID:Cloning of a gene for chloroplast omega6 desaturase of a green alga, Chlamydomonas reinhardtii. 949 69

Three classes of RNA, represented by atpB and petD mRNAs, Arg and Glu tRNAs, and 5S rRNA, were found to exist in polyadenylated form in Chlamydomonas reinhardtii chloroplasts. Sequence analysis of cDNA clones derived from reverse transcriptase-polymerase chain reaction protocols used to select polyadenylated RNAs revealed that, at least for the mRNAs and tRNAs, there are three apparent types of polyadenylation. In the first case, the poly(A) tail is added at or near the mature 3' end, even when this follows a strong secondary structure. In the second case, the tail is added to pre-mRNA or pre-tRNA, suggesting a possible competition between polyadenylation and RNA-processing pathways. Finally, in all cases, the poly(A) tail can be added internally, possibly as a part of an RNA-decay pathway. The tails found in Chlamydomonas chloroplasts differ from those of spinach chloroplasts in adenine content, being nearly homopolymeric (>98% adenine) versus 70% in spinach, and are similar in length to those of Escherichia coli, being mostly between 20 and 50 nt. In vitro assays using a Chlamydomonas chloroplast protein extract showed that a 3' end A25 tail was sufficient to stimulate rapid degradation of atpB RNA in vitro, with a lesser effect for petD, and only minor effects on trnE. We therefore propose that polyadenylation contributes to mRNA degradation in Chlamydomonas chloroplasts, but that its effect may vary.
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PMID:Polyadenylation of three classes of chloroplast RNA in Chlamydomonas reinhadtii. 1078 50

Polyadenylation of synthetic RNAs stimulates rapid degradation in vitro by using either Chlamydomonas or spinach chloroplast extracts. Here, we used Chlamydomonas chloroplast transformation to test the effects of mRNA homopolymer tails in vivo, with either the endogenous atpB gene or a version of green fluorescent protein developed for chloroplast expression as reporters. Strains were created in which, after transcription of atpB or gfp, RNase P cleavage occurred upstream of an ectopic tRNA(Glu) moiety, thereby exposing A(28), U(25)A(3), [A+U](26), or A(3) tails. Analysis of these strains showed that, as expected, polyadenylated transcripts failed to accumulate, with RNA being undetectable either by filter hybridization or reverse transcriptase-PCR. In accordance, neither the ATPase beta-subunit nor green fluorescent protein could be detected. However, a U(25)A(3) tail also strongly reduced RNA accumulation relative to a control, whereas the [A+U] tail did not, which is suggestive of a degradation mechanism that does not specifically recognize poly(A), or that multiple mechanisms exist. With an A(3) tail, RNA levels decreased relative to a control with no added tail, but some RNA and protein accumulation was observed. We took advantage of the fact that the strain carrying a modified atpB gene producing an A(28) tail is an obligate heterotroph to obtain photoautotrophic revertants. Each revertant exhibited restored atpB mRNA accumulation and translation, and seemed to act by preventing poly(A) tail exposure. This suggests that the poly(A) tail is only recognized as an instability determinant when exposed at the 3' end of a message.
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PMID:Evidence for in vivo modulation of chloroplast RNA stability by 3'-UTR homopolymeric tails in Chlamydomonas reinhardtii. 1189 Dec 97

Retrotransposons commonly encode a reverse transcriptase (RT), but other functional domains are variable. The acquisition of new domains is the dominant evolutionary force that brings structural variety to retrotransposons. Non-long-terminal-repeat (non-LTR) retrotransposons are classified into two groups by their structure. Early branched non-LTR retrotransposons encode a restriction-like endonuclease (RLE), and recently branched non-LTR retrotransposons encode an apurinic/apyrimidinic endonuclease-like endonuclease (APE). In this study, we report a novel non-LTR retrotransposon family Dualen, identified from the Chlamydomonas reinhardtii genome. Dualen encodes two endonucleases, RLE and APE, with RT, ribonuclease H, and cysteine protease. Phylogenetic analyses of the RT domains revealed that Dualen is positioned at the midpoint between the early-branched and the recently branched groups. In the APE tree, Dualen was branched earlier than the I group and the Jockey group. The ribonuclease H domains among the Dualen family and other non-LTR retrotransposons are monophyletic. Phylogenies of three domains revealed the monophyly of the Dualen family members. The domain structure and the phylogeny of each domain imply that Dualen is a retrotransposon conserving the domain structure just after the acquisition of APE. From these observations, we discuss the evolution of domain structure of non-LTR retrotransposons.
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PMID:An extraordinary retrotransposon family encoding dual endonucleases. 1607 10


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