Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya.

PubWeight™: 0.86‹?›

🔗 View Article (PMC 1126904)

Published in Nucleic Acids Res on May 13, 2005

Authors

Anthony G Russell1, Yoh-ichi Watanabe, J Michael Charette, Michael W Gray

Author Affiliations

1: Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia, Canada B3H 1X5. russella@dal.ca

Articles cited by this

Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) 38.75

An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res (1995) 8.66

The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell (1997) 6.26

Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene (1994) 5.28

Homologs of small nucleolar RNAs in Archaea. Science (2000) 5.26

tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell (1996) 4.93

Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol Cell (2000) 4.42

A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell (2000) 4.33

Trans splicing of nuclear pre-mRNAs. Cell (1990) 3.85

Transcriptional sequencing: A method for DNA sequencing using RNA polymerase. Proc Natl Acad Sci U S A (1998) 3.78

Purification and partial characterization of a nucleolar scleroderma antigen (Mr = 34,000; pI, 8.5) rich in NG,NG-dimethylarginine. J Biol Chem (1985) 3.60

Gene clusters and polycistronic transcription in eukaryotes. Bioessays (1998) 3.32

Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol Cell Biol (1997) 2.95

trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot Cell (2003) 2.91

Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA. EMBO J (1999) 2.90

Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution. Structure (2004) 2.68

Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol (2003) 2.55

Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability. RNA (1999) 2.48

Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res (2003) 2.44

Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol Cell Biol (2002) 2.37

Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res (2002) 2.23

In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc Natl Acad Sci U S A (2002) 2.07

A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res (1997) 1.99

Box C/D snoRNA-associated proteins: two pairs of evolutionarily ancient proteins and possible links to replication and transcription. RNA (2000) 1.90

Short leader sequences may be transferred from small RNAs to pre-mature mRNAs by trans-splicing in Euglena. EMBO J (1991) 1.85

A new twist in trypanosome RNA metabolism: cis-splicing of pre-mRNA. RNA (2000) 1.79

A spliced leader is present on a subset of mRNAs from the human parasite Schistosoma mansoni. Proc Natl Acad Sci U S A (1990) 1.79

Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria. Nucleic Acids Res (2000) 1.76

A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc Natl Acad Sci U S A (1995) 1.69

mRNA 5'-leader trans-splicing in the chordates. Genes Dev (2001) 1.63

Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP. Chem Biol (2002) 1.58

Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J (2002) 1.51

Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genet (2002) 1.49

Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana. J Biol Chem (2000) 1.36

Introns in protein-coding genes in Archaea. FEBS Lett (2002) 1.29

Trans-spliced leader addition to mRNAs in a cnidarian. Proc Natl Acad Sci U S A (2001) 1.27

Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus? Trends Biochem Sci (2004) 1.24

The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol (2005) 1.23

In vivo analysis of nucleolar proteins modified by the yeast arginine methyltransferase Hmt1/Rmt1p. RNA (2003) 1.09

U1 small nuclear RNA and spliceosomal introns in Euglena gracilis. Proc Natl Acad Sci U S A (1999) 1.04

Structure and expression of Euglena gracilis nuclear rbcS genes encoding the small subunits of the ribulose 1,5-bisphosphate carboxylase/oxygenase: a novel splicing process for unusual intervening sequences? J Mol Biol (1995) 0.99

Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA (2004) 0.97

Analysis of Snu13p mutations reveals differential interactions with the U4 snRNA and U3 snoRNA. RNA (2004) 0.97

Ribosomal protein L7a binds RNA through two distinct RNA-binding domains. Biochem J (2005) 0.96

Analysis of Euglena gracilis alpha-, beta- and gamma-tubulin genes: introns and pre-mRNA maturation. Mol Genet Genomics (2001) 0.95

Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI. Nucleic Acids Res (1992) 0.90

An unusual fibrillarin gene and protein: structure and functional implications. Mol Biol Cell (1997) 0.90

Characterization of the unique intron-exon junctions of Euglena gene(s) encoding the polyprotein precursor to the light-harvesting chlorophyll a/b binding protein of photosystem II. Nucleic Acids Res (1994) 0.88

Chloroplast phosphoglycerate kinase from Euglena gracilis: endosymbiotic gene replacement going against the tide. Eur J Biochem (2004) 0.81

Articles by these authors

AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics (2005) 4.26

The tree of eukaryotes. Trends Ecol Evol (2005) 3.98

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A (2006) 3.85

Mitochondrial genomes: anything goes. Trends Genet (2003) 2.86

A phylogenomic investigation into the origin of metazoa. Mol Biol Evol (2008) 2.32

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature (2012) 2.15

Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol Evol (2013) 1.90

The origins of multicellularity: a multi-taxon genome initiative. Trends Genet (2007) 1.90

tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev (2003) 1.78

Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr Biol (2007) 1.76

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res (2007) 1.55

Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates. J Mol Biol (2002) 1.50

Problems with co-funding in Canada. Science (2005) 1.48

Unique mitochondrial genome architecture in unicellular relatives of animals. Proc Natl Acad Sci U S A (2003) 1.47

Bacteriophage origins of mitochondrial replication and transcription proteins. Trends Genet (2005) 1.38

An early evolutionary origin for the minor spliceosome. Nature (2006) 1.34

How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life (2011) 1.28

Twinkle, the mitochondrial replicative DNA helicase, is widespread in the eukaryotic radiation and may also be the mitochondrial DNA primase in most eukaryotes. J Mol Evol (2006) 1.28

In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus. J Biol Chem (2004) 1.18

The ancient and widespread nature of the ER-mitochondria encounter structure. Mol Biol Evol (2013) 1.17

An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia. BMC Evol Biol (2005) 1.14

Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol (2007) 1.06

A unique serine-specific elongation factor Tu found in nematode mitochondria. Nat Struct Biol (2002) 1.06

Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily. RNA (2012) 1.05

Exploring the mitochondrial proteome of the ciliate protozoon Tetrahymena thermophila: direct analysis by tandem mass spectrometry. J Mol Biol (2007) 1.03

Critical roles of the mitochondrial complex II in oocyst formation of rodent malaria parasite Plasmodium berghei. J Biochem (2012) 1.02

Evolution of the mitochondrial genome: protist connections to animals, fungi and plants. Curr Opin Microbiol (2004) 1.02

Gene discovery in the Acanthamoeba castellanii genome. Protist (2005) 1.02

Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease. Biochem Biophys Res Commun (2006) 0.99

Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont. Mol Biol Evol (2006) 0.98

A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol Biol (2007) 0.98

Mitochondria and apicoplast of Plasmodium falciparum: behaviour on subcellular fractionation and the implication. Mitochondrion (2006) 0.98

Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA (2010) 0.97

Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA (2004) 0.97

A role for tRNA(His) guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5'-tRNA editing. RNA (2011) 0.96

The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa. J Mol Evol (2006) 0.94

Functional reconstitution of a crenarchaeal splicing endonuclease in vitro. Biochem Biophys Res Commun (2005) 0.93

Concatenated mitochondrial DNA of the coccidian parasite Eimeria tenella. Mitochondrion (2010) 0.93

Analysis of Euglena gracilis plastid-targeted proteins reveals different classes of transit sequences. Eukaryot Cell (2006) 0.93

A conserved deubiquitinating enzyme controls cell growth by regulating RNA polymerase I stability. Cell Rep (2012) 0.92

T-armless tRNAs and elongated elongation factor Tu. IUBMB Life (2007) 0.92

Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii. PLoS One (2013) 0.92

Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease. Nucleic Acids Res (2009) 0.91

Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights. Biochim Biophys Acta (2012) 0.90

Assembling a protein-protein interaction map of the SSU processome from existing datasets. PLoS One (2011) 0.90

Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene. BMC Evol Biol (2009) 0.89

Evidence for an early evolutionary emergence of gamma-type carbonic anhydrases as components of mitochondrial respiratory complex I. BMC Evol Biol (2010) 0.88

Ribosomal RNA genes in Euglena gracilis mitochondrial DNA: fragmented genes in a seemingly fragmented genome. Mol Genet Genomics (2010) 0.88

An ancient fission of mitochondrial Cox1. Mol Biol Evol (2010) 0.88

Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii. Nucleic Acids Res (2012) 0.87

Subcomplexes of ancestral respiratory complex I subunits rapidly turn over in vivo as productive assembly intermediates in Arabidopsis. J Biol Chem (2012) 0.85

An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu. Nucleic Acids Res (2006) 0.85

Evolutionary biology: the hydrogenosome's murky past. Nature (2005) 0.85

Analysis of 5'- or 3'-terminal tRNA editing: mitochondrial 5' tRNA editing in Acanthamoeba castellanii as the exemplar. Methods Enzymol (2007) 0.83

Sampling gene diversity across the supergroup Amoebozoa: large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp. Protist (2008) 0.83

A large collection of compact box C/D snoRNAs and their isoforms in Euglena gracilis: structural, functional and evolutionary insights. J Mol Biol (2006) 0.82

A protein extension to shorten RNA: elongated elongation factor-Tu recognizes the D-arm of T-armless tRNAs in nematode mitochondria. Biochem J (2006) 0.82

Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa. Eukaryot Cell (2010) 0.82

Complete modification maps for the cytosolic small and large subunit rRNAs of Euglena gracilis: functional and evolutionary implications of contrasting patterns between the two rRNA components. J Mol Biol (2011) 0.81

Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa? Curr Genet (2011) 0.81

Toward understanding the role of mitochondrial complex II in the intraerythrocytic stages of Plasmodium falciparum: gene targeting of the Fp subunit. Parasitol Int (2012) 0.81

A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi. Mol Microbiol (2010) 0.80

Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA. RNA (2003) 0.80

Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans. Genome Biol Evol (2012) 0.80

Trypanosome alternative oxidase, a potential therapeutic target for sleeping sickness, is conserved among Trypanosoma brucei subspecies. Parasitol Int (2010) 0.80

Methods for analysis of mitochondrial tRNA editing in Acanthamoeba castellanii. Methods Mol Biol (2004) 0.79

Comment on "Does constructive neutral evolution play an important role in the origin of cellular complexity?" DOI 10.1002/bies.201100010. Bioessays (2011) 0.78

A split and rearranged nuclear gene encoding the iron-sulfur subunit of mitochondrial succinate dehydrogenase in Euglenozoa. BMC Res Notes (2009) 0.78

Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7. Gene (2011) 0.78

U3 snoRNA genes are multi-copy and frequently linked to U5 snRNA genes in Euglena gracilis. BMC Genomics (2009) 0.78

Identification of the residues involved in the unique serine specificity of Caenorhabditis elegans mitochondrial EF-Tu2. Biochemistry (2006) 0.77

Arabidopsis thaliana mitochondrial EF-G1 functions in two different translation steps. J Biochem (2013) 0.75

Functional reconstitution of an archaeal splicing endonuclease in vitro. Nucleic Acids Symp Ser (Oxf) (2005) 0.75

Detection of enzymatic activities related to the tRNA splicing pathway in Methanosarcina acetivorans cell extract. Nucleic Acids Symp Ser (Oxf) (2009) 0.75