Gawryluk, Ryan MR, Gray, Michael W
Abstract Background Analyses based on phylogenetic and ultrastructural data have suggested that euglenids (such as Euglena gracilis ), trypanosomatids and diplonemids are members of a monophyletic...
Iñaki Ruiz-trillo, Andrew J. Roger, Gertraud Burger, Michael W. Gray, Franz Lang
Non standard abbreviations ML: maximum likelihood EST: expressed sequence taq MAGI: membrane-associated guanylate kinase ANTP: Antennapedia PRD: paired
A Phylogenomic Investigation into the Origin of Metazoa (2008)
Ruiz-Trillo, Iñaki, Roger, Andrew J., Burger, Gertraud, Gray, Michael W., Lang, B. Franz
The evolution of multicellular animals (Metazoa) from their unicellular ancestors was a key transition that was accompanied by the emergence and diversification of gene families associated with...
Jackson, Christopher J, Norman, John E, Schnare, Murray N, Gray, Michael W, Keeling, Patrick J, Waller, Ross F
Abstract Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of...
Rogers, Matthew B, Watkins, Russell F, Harper, James T, Durnford, Dion G, Gray, Michael W, Keeling, Patrick J
Abstract Background Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common...
BMC Biology BioMed Central (2007)
Christopher J Jackson, John E Norman, Murray N Schnare, Michael W Gray, Patrick J Keeling, Ross F Waller, ...
Research article Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs) (2007)
O'Brien, Emmet A., Koski, Liisa B., Zhang, Yue, Yang, LiuSong, Wang, Eric, Gray, Michael W., ...
The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and...
Dion G. Durnford, Michael W. Gray
The plastid of Euglena gracilis was acquired secondarily through an endosymbiotic event with a eukaryotic green alga, and as a result, it is surrounded by a third membrane. This membrane complexity...
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs) (2006)
Emmet A. O’brien, Liisa B. Koski, Yue Zhang, Liusong Yang, Eric Wang, Michael W. Gray, ...
The TBestDB database contains 370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and...
Shutt, Timothy E., Gray, Michael W.
Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase...
Shutt, Timothy E., Gray, Michael W.
Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase...
An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia (2005)
Russell, Anthony G, Shutt, Timothy E, Watkins, Russell F, Gray, Michael W
Abstract Background Only one spliceosomal-type intron has previously been identified in the unicellular eukaryotic parasite, Giardia lamblia (a diplomonad). This intron is only 35 nucleotides in...
AutoFACT: An Automatic Functional Annotation and Classification Tool (2005)
Koski, Liisa B, Gray, Michael W, Lang, B Franz, Burger, Gertraud
Abstract Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or...
Russell, Anthony G., Watanabe, Yoh-ichi, Charette, J. Michael, Gray, Michael W.
Box C/D ribonucleoprotein (RNP) particles mediate O2′-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts,...
Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis (2004)
RUSSELL, ANTHONY G., SCHNARE, MURRAY N., GRAY, MICHAEL W.
In eukaryotes, box H/ACA small nucleolar RNAs (snoRNAs) guide sites of pseudouridine (Ψ) formation in rRNA. These snoRNAs reside in RNP complexes containing the putative Ψ synthase, Cbf5p. In this...
Gu, Weifeng, Jackman, Jane E., Lohan, Amanda J., Gray, Michael W., Phizicky, Eric M.
All tRNAHis molecules are unusual in having an extra 5′ GMP residue (G-1) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G-1 residue is a rare example...
Gu, Weifeng, Jackman, Jane E., Lohan, Amanda J., Gray, Michael W., Phizicky, Eric M.
All tRNAHis molecules are unusual in having an extra 5′ GMP residue (G-1) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G-1 residue is a rare example...
Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA (2003)
BULLERWELL, CHARLES E., SCHNARE, MURRAY N., GRAY, MICHAEL W.
Although 5S rRNA is a highly conserved and universal component of eubacterial, archaeal, chloroplast, and eukaryotic cytoplasmic ribosomes, a mitochondrial DNA-encoded 5S rRNA has so far been...
The origin and early evolution of mitochondria (2001)
Gray, Michael W, Burger, Gertraud, Lang, B Franz
Abstract Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial...
Greenwood, Spencer J., Schnare, Murray N., Cook, James R., Gray, Michael W.
We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3′-end of the large subunit ribosomal RNA (rRNA) gene from the 5′-end of the small subunit (SSU) rRNA gene in...
Schnare, Murray N., Collings, James C., Spencer, David F., Gray, Michael W.
In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains...
Watanabe, Yoh-ichi, Gray, Michael W.
A reverse transcription–polymerase chain reaction (RT–PCR) approach was used to clone a cDNA encoding the Euglena gracilis homolog of yeast Cbf5p, a protein component of the box H/ACA class...
Genome structure and gene content in protist mitochondrial DNAs (1998)
Michael W. Gray, B. Franz Lang, Robert Cedergren, G. Brian Golding, Claude Lemieux, David Sankoff, ...
Although the collection of completely sequenced mitochondrial genomes is expanding rapidly, only recently has a phylogenetically broad representation of mtDNA sequences from protists (mostly...
The Organelle Genome Database Project (GOBASE (1998)
Maria Korab-laskowska, Pierre Rioux, Nicolas Brossard, Timothy G. Littlejohn, Michael W. Gray, B. Franz Lang, ...
The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the...
The Organelle Genome Database Project (GOBASE) (1998)
Maria Korab-Laskowska, Pierre Rioux, Nicolas Brossard, Timothy G. Littlejohn, Michael W. Gray, B. Franz Lang, ...
The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the...
Schnare, Murray N., Yepiz-Plascencia, Gloria M., Copertino, Donald W., Hallick, Richard B., Gray, Michael W.
Chloroplast-like transfer RNA genes expressed in wheat mitochondria (1989)
Joyce, Paul B.M., Gray, Michael W.
In the course of a systematic survey of wheat mitochondria] tRNA genes, we have sequenced chloroplast−like serine (trnS-GGA), phenylalanine (trnF-GAA) and cysteine (trnC-GCA) tRNA genes and their...
Joyce, Paul B. M., Gray, Michael W.
We have identified genes encoding a “native” tRNAAsp (trnD-GTC) and a c“hloroplast-like” tRNAAsn (trnN-GTT) on opposite strands and 633 bp apart within a sequenced 1640 bp RsaI restriction...
Nucleotide sequence of the wheat mitochondrial gene for subunit I of cytochrome oxidase (1987)
Bonen, Linda, Boer, Poppo H., McIntosh, John E., Gray, Michael W.
Boer, Poppo H., McIntosh, John E., Gray, Michael W., Bonen, Linda
The wheat mitochondrial gene for apocytochrome b (CYB) has been identified by its hybridization to a yeast CYB probe and its nucleotide sequence has been determined. The wheat CYB sequence predicts a...
Gray, Michael W., Sankoff, David, Cedergren, Robert J.
To probe the earliest evolutionary events attending the origin of the five known genome types (archaebacterial, eubacterial, nuclear, mitochondrial and plastid), we have analyzed sequences...
Nucleotide sequence of an exceptionally long 5.8S ribosomal RNA from Crithidia fasciculata (1982)
Schnare, Murray N., Gray, Michael W
In Crithidia fasciculata, a trypanosomatid protozoan, the large ribosomal subunit contains five small RNA species (e, f, g, i, j) in addition to 5S rRNA [Gray, M.W. (1981) Mol. Cell, Biol. 1,...
Schnare, Murray N., Gray, Michael W.
We have determined the sequences of the 3′-terminal {small tilde}100 nucleotides of [5{small tilde}-32P]pCp-labeled wheat mitochondrial, wheat cytosol, and E. coli small subunit rRNAs. Sequence...
Nucleotide sequence of Crithidia fasciculata cytosol 5S ribosomal ribonucleic acid (1980)
MacKay, Ron M., Gray, Michael W., Doolittle, W.Ford
The complete nucleotide sequence of the cytosol 5S ribosomal ribonucleic acid of the trypanosomatid protozoan Crithidia fasciculata has been determined by a combination of T1-oligonucleotide...
U1 small nuclear RNA and spliceosomal introns in Euglena gracilis
Breckenridge, David G., Watanabe, Yoh-ichi, Greenwood, Spencer J., Gray, Michael W., Schnare, Murray N.
In the flagellated protozoon Euglena gracilis, characterized nuclear genes harbor atypical introns that usually are flanked by short repeats, adopt complex secondary structures in pre-mRNA, and do...
Greenwood, Spencer J., Schnare, Murray N., Cook, James R., Gray, Michael W.
We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3′-end of the large subunit ribosomal RNA (rRNA) gene from the 5′-end of the small subunit (SSU) rRNA gene in...
Characterization of a DNA-Binding Protein Implicated in Transcription in Wheat Mitochondria
Ikeda, Tatsuya M., Gray, Michael W.
To investigate the transcriptional apparatus in wheat mitochondria, mitochondrial extracts were subjected to column chromatography and protein fractions were analyzed by in vitro transcription and...
Watanabe, Yoh-ichi, Gray, Michael W.
A reverse transcription–polymerase chain reaction (RT–PCR) approach was used to clone a cDNA encoding the Euglena gracilis homolog of yeast Cbf5p, a protein component of the box H/ACA class of...
Schnare, Murray N., Collings, James C., Spencer, David F., Gray, Michael W.
In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains...
The origin and early evolution of mitochondria
Gray, Michael W, Burger, Gertraud, Lang, B Franz
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial...
On the evolutionary origin of the plant mitochondrion and its genome
Gray, Michael W., Cedergren, Robert, Abel, Yvon, Sankoff, David
Higher plants occupy very different positions in the mitochondrial and nuclear lineages of global phylogenetic trees based on conserved regions of small subunit (SSU) and large subunit (LSU) rRNA...
Gu, Weifeng, Jackman, Jane E., Lohan, Amanda J., Gray, Michael W., Phizicky, Eric M.
All tRNAHis molecules are unusual in having an extra 5′ GMP residue (G-1) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G-1 residue is a rare example...
Unique mitochondrial genome architecture in unicellular relatives of animals
Burger, Gertraud, Forget, Lise, Zhu, Yun, Gray, Michael W., Lang, B. Franz
Animal mtDNAs are typically small (≈16 kbp), circular-mapping molecules that encode 37 or fewer tightly packed genes. Here we investigate whether similarly compact mitochondrial genomes are also...
Nedelcu, Aurora M., Lee, Robert W., Lemieux, Claude, Gray, Michael W., Burger, Gertraud
Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced–derived, Chlamydomonas-like type and an ancestral, Prototheca-like type....
Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata
Spencer, David F., Collings, James C., Schnare, Murray N., Gray, Michael W.
In Crithidia fasciculata, a trypanosomatid protozoan, the nuclear-encoded `28S' rRNA is multiply fragmented, comprising two large (c and d) and four small (e, f, g and j) RNA species. We have...
Falconet, Denis, Lejeune, Bernard, Quetier, Francis, Gray, Michael W.
Closely linked genes for 18S and 5S rRNAs have been located on four different cloned SalI restriction fragments of wheat (Triticum aestivum L.) mitochondrial DNA. Restriction analysis has revealed...
Bonen, Linda, Boer, Poppo H., Gray, Michael W.
We have determined the sequence of the wheat mitochondrial gene for cytochrome oxidase subunit II (COII) and find that its derived protein sequence differs from that of maize at only three amino acid...
Russell, Anthony G., Watanabe, Yoh-ichi, Charette, J. Michael, Gray, Michael W.
Box C/D ribonucleoprotein (RNP) particles mediate O2′-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts,...
AutoFACT: An Automatic Functional Annotation and Classification Tool
Koski, Liisa B, Gray, Michael W, Lang, B Franz, Burger, Gertraud
An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia
Russell, Anthony G, Shutt, Timothy E, Watkins, Russell F, Gray, Michael W
Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA
BULLERWELL, CHARLES E., SCHNARE, MURRAY N., GRAY, MICHAEL W.
Although 5S rRNA is a highly conserved and universal component of eubacterial, archaeal, chloroplast, and eukaryotic cytoplasmic ribosomes, a mitochondrial DNA-encoded 5S rRNA has so far been...
Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis
RUSSELL, ANTHONY G., SCHNARE, MURRAY N., GRAY, MICHAEL W.
In eukaryotes, box H/ACA small nucleolar RNAs (snoRNAs) guide sites of pseudouridine (Ψ) formation in rRNA. These snoRNAs reside in RNP complexes containing the putative Ψ synthase, Cbf5p. In this...
U1 small nuclear RNA and spliceosomal introns in Euglena gracilis
Breckenridge, David G., Watanabe, Yoh-ichi, Greenwood, Spencer J., Gray, Michael W., Schnare, Murray N.
In the flagellated protozoon Euglena gracilis, characterized nuclear genes harbor atypical introns that usually are flanked by short repeats, adopt complex secondary structures in pre-mRNA, and do...
Greenwood, Spencer J., Schnare, Murray N., Cook, James R., Gray, Michael W.
We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3′-end of the large subunit ribosomal RNA (rRNA) gene from the 5′-end of the small subunit (SSU) rRNA gene in...
Characterization of a DNA-Binding Protein Implicated in Transcription in Wheat Mitochondria
Ikeda, Tatsuya M., Gray, Michael W.
To investigate the transcriptional apparatus in wheat mitochondria, mitochondrial extracts were subjected to column chromatography and protein fractions were analyzed by in vitro transcription and...
Watanabe, Yoh-ichi, Gray, Michael W.
A reverse transcription–polymerase chain reaction (RT–PCR) approach was used to clone a cDNA encoding the Euglena gracilis homolog of yeast Cbf5p, a protein component of the box H/ACA class of...
Schnare, Murray N., Collings, James C., Spencer, David F., Gray, Michael W.
In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from ∼11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains...
The origin and early evolution of mitochondria
Gray, Michael W, Burger, Gertraud, Lang, B Franz
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial...
On the evolutionary origin of the plant mitochondrion and its genome
Gray, Michael W., Cedergren, Robert, Abel, Yvon, Sankoff, David
Higher plants occupy very different positions in the mitochondrial and nuclear lineages of global phylogenetic trees based on conserved regions of small subunit (SSU) and large subunit (LSU) rRNA...
Gu, Weifeng, Jackman, Jane E., Lohan, Amanda J., Gray, Michael W., Phizicky, Eric M.
All tRNAHis molecules are unusual in having an extra 5′ GMP residue (G-1) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G-1 residue is a rare example...
Unique mitochondrial genome architecture in unicellular relatives of animals
Burger, Gertraud, Forget, Lise, Zhu, Yun, Gray, Michael W., Lang, B. Franz
Animal mtDNAs are typically small (≈16 kbp), circular-mapping molecules that encode 37 or fewer tightly packed genes. Here we investigate whether similarly compact mitochondrial genomes are also...
Nedelcu, Aurora M., Lee, Robert W., Lemieux, Claude, Gray, Michael W., Burger, Gertraud
Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced–derived, Chlamydomonas-like type and an ancestral, Prototheca-like type....
Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata
Spencer, David F., Collings, James C., Schnare, Murray N., Gray, Michael W.
In Crithidia fasciculata, a trypanosomatid protozoan, the nuclear-encoded `28S' rRNA is multiply fragmented, comprising two large (c and d) and four small (e, f, g and j) RNA species. We have...
Falconet, Denis, Lejeune, Bernard, Quetier, Francis, Gray, Michael W.
Closely linked genes for 18S and 5S rRNAs have been located on four different cloned SalI restriction fragments of wheat (Triticum aestivum L.) mitochondrial DNA. Restriction analysis has revealed...
Bonen, Linda, Boer, Poppo H., Gray, Michael W.
We have determined the sequence of the wheat mitochondrial gene for cytochrome oxidase subunit II (COII) and find that its derived protein sequence differs from that of maize at only three amino acid...
Russell, Anthony G., Watanabe, Yoh-ichi, Charette, J. Michael, Gray, Michael W.
Box C/D ribonucleoprotein (RNP) particles mediate O2′-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts,...
AutoFACT: An Automatic Functional Annotation and Classification Tool
Koski, Liisa B, Gray, Michael W, Lang, B Franz, Burger, Gertraud
An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia
Russell, Anthony G, Shutt, Timothy E, Watkins, Russell F, Gray, Michael W
Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA
BULLERWELL, CHARLES E., SCHNARE, MURRAY N., GRAY, MICHAEL W.
Although 5S rRNA is a highly conserved and universal component of eubacterial, archaeal, chloroplast, and eukaryotic cytoplasmic ribosomes, a mitochondrial DNA-encoded 5S rRNA has so far been...
Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis
RUSSELL, ANTHONY G., SCHNARE, MURRAY N., GRAY, MICHAEL W.
In eukaryotes, box H/ACA small nucleolar RNAs (snoRNAs) guide sites of pseudouridine (Ψ) formation in rRNA. These snoRNAs reside in RNP complexes containing the putative Ψ synthase, Cbf5p. In this...
Durnford, Dion G., Gray, Michael W.
The plastid of Euglena gracilis was acquired secondarily through an endosymbiotic event with a eukaryotic green alga, and as a result, it is surrounded by a third membrane. This membrane complexity...
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
O'Brien, Emmet A., Koski, Liisa B., Zhang, Yue, Yang, LiuSong, Wang, Eric, Gray, Michael W., ...
The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and...
A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer
Rogers, Matthew B, Watkins, Russell F, Harper, James T, Durnford, Dion G, Gray, Michael W, Keeling, Patrick J