DNA sequence and transcript mapping of MOD5: features of the 5' region which suggest two translational starts

A mutation in the yeast nuclear gene MOD5 drastically reduces the biosynthesis of the modified base isopentenyladenosine in tRNAs located in different cellular compartments: the mitochondria and the nucleus or cytoplasm. Several lines of evidence strongly suggest that MOD5 is the structural gene encoding the tRNA-modifying enzyme delta 2-isopentenyl pyrophosphate:tRNA isopentenyl transferase. DNA sequence analysis of MOD5 reveals an open reading frame of 428 amino acids. A set of mRNAs heterogeneous at both the 5' and 3' termini are transcribed from this gene. Although all of these transcripts initiate upstream of the first AUG codon of the open reading frame, a subset has an extremely short (greater than or equal to 1 base) 5' leader. Furthermore, in positions important for efficient initiation of translation and generally occupied by purines, this first AUG codon is flanked by a U (position -3) and a C (position +4). It is possible that two proteins, one with an amino-terminal extension of basic charge, could be generated from the MOD5 gene via differential translational starts.

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Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader.

Molecular and Cellular Biology ◽

10.1128/mcb.7.8.2728 ◽

1987 ◽

Vol 7 (8) ◽

pp. 2728-2734 ◽

Cited By ~ 31

Author(s):

C A Strick ◽

T D Fox

Keyword(s):

Amino Acids ◽

Regulatory Gene ◽

Mitochondrial Protein ◽

Nuclear Gene ◽

Open Reading Frames ◽

Open Reading Frame ◽

Reading Frame ◽

Amino Terminal ◽

Interesting Pattern ◽

Reading Frames

The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

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Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader

Molecular and Cellular Biology ◽

10.1128/mcb.7.8.2728-2734.1987 ◽

1987 ◽

Vol 7 (8) ◽

pp. 2728-2734

Author(s):

C A Strick ◽

T D Fox

Keyword(s):

Amino Acids ◽

Regulatory Gene ◽

Mitochondrial Protein ◽

Nuclear Gene ◽

Open Reading Frames ◽

Open Reading Frame ◽

Reading Frame ◽

Amino Terminal ◽

Interesting Pattern ◽

Reading Frames

The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

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Identification of a sequence in the unique 5' open reading frame of the gene encoding glycosylated Gag which influences the incubation period of neurodegenerative disease induced by a murine retrovirus.

Journal of Virology ◽

10.1128/jvi.68.6.3879-3887.1994 ◽

1994 ◽

Vol 68 (6) ◽

pp. 3879-3887 ◽

Cited By ~ 28

Author(s):

J L Portis ◽

G J Spangrude ◽

F J McAtee

Keyword(s):

Neurodegenerative Disease ◽

Incubation Period ◽

Open Reading Frame ◽

Gene Encoding ◽

Reading Frame

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GIT1, a Gene Encoding a Novel Transporter for Glycerophosphoinositol in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/149.4.1707 ◽

1998 ◽

Vol 149 (4) ◽

pp. 1707-1715 ◽

Cited By ~ 2

Author(s):

J L Patton-Vogt ◽

S A Henry

Keyword(s):

Saccharomyces Cerevisiae ◽

Regulatory Gene ◽

Sugar Transport ◽

Open Reading Frame ◽

Gene Encoding ◽

Reading Frame ◽

Membrane Spanning ◽

Membrane Spanning Domains ◽

Uptake And Metabolism ◽

Cells Cultured

Abstract Phosphatidylinositol catabolism in Saccharomyces cerevisiae cells cultured in media containing inositol results in the release of glycerophosphoinositol (GroPIns) into the medium. As the extracellular concentration of inositol decreases with growth, the released GroPIns is transported back into the cell. Exploiting the ability of the inositol auxotroph, ino1, to use exogenous GroPIns as an inositol source, we have isolated mutants (Git−) defective in the uptake and metabolism of GroPIns. One mutant was found to be affected in the gene encoding the transcription factor, SPT7. Mutants of the positive regulatory gene INO2, but not of its partner, INO4, also have the Git− phenotype. Another mutant was complemented by a single open reading frame (ORF) termed GIT1 (glycerophosphoinositol). This ORF consists of 1556 bp predicted to encode a polypeptide of 518 amino acids and 57.3 kD. The predicted Git1p has similarity to a variety of S. cerevisiae transporters, including a phosphate transporter (Pho84p), and both inositol transporters (Itr1p and Itr2p). Furthermore, Git1p contains a sugar transport motif and 12 potential membrane-spanning domains. Transport assays performed on a git1 mutant together with the above evidence indicate that the GIT1 gene encodes a permease involved in the uptake of GroPIns.

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Cloning, Nucleotide Sequence, and Expression of the Gene Encoding the Bacteriocin Boticin B from Clostridium botulinum Strain 213B

Applied and Environmental Microbiology ◽

10.1128/aem.66.12.5480-5483.2000 ◽

2000 ◽

Vol 66 (12) ◽

pp. 5480-5483 ◽

Cited By ~ 16

Author(s):

Sean S. Dineen ◽

Marite Bradshaw ◽

Eric A. Johnson

Keyword(s):

Amino Acids ◽

Nucleotide Sequence ◽

Clostridium Botulinum ◽

Shuttle Vector ◽

Open Reading Frame ◽

Gene Encoding ◽

Reading Frame ◽

Heat Stable ◽

Group I

ABSTRACT Boticin B is a heat-stable bacteriocin produced byClostridium botulinum strain 213B that has inhibitory activity against various strains of C. botulinum and related clostridia. The gene encoding the bacteriocin was localized to a 3.0-kb HindIII fragment of an 18.8-kb plasmid, cloned, and sequenced. DNA sequencing revealed the boticin B structural gene,btcB, to be an open reading frame encoding 50 amino acids. A C. botulinum strain 62A transconjugant containing theHindIII fragment inserted into a clostridial shuttle vector expressed boticin B, although at much lower levels than those observed in C. botulinum 213B. To our knowledge, this is the first demonstration and characterization of a bacteriocin from toxigenic group I C. botulinum.

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Molecular and genetic analysis of the gene encoding the Saccharomyces cerevisiae strand exchange protein Sep1

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2593-2608.1991 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2593-2608 ◽

Cited By ~ 1

Author(s):

D X Tishkoff ◽

A W Johnson ◽

R D Kolodner

Keyword(s):

Saccharomyces Cerevisiae ◽

Open Reading Frame ◽

Strand Exchange ◽

Wild Type ◽

Homologous Pairing ◽

Gene Encoding ◽

Reading Frame ◽

Cloned Gene ◽

Diploid Cells ◽

Exchange Protein

Vegetatively grown Saccharomyces cerevisiae cells contain an activity that promotes a number of homologous pairing reactions. A major portion of this activity is due to strand exchange protein 1 (Sep1), which was originally purified as a 132,000-Mr species (R. Kolodner, D. H. Evans, and P. T. Morrison, Proc. Natl. Acad. Sci. USA 84:5560-5564, 1987). The gene encoding Sep1 was cloned, and analysis of the cloned gene revealed a 4,587-bp open reading frame capable of encoding a 175,000-Mr protein. The protein encoded by this open reading frame was overproduced and purified and had a relative molecular weight of approximately 160,000. The 160,000-Mr protein was at least as active in promoting homologous pairing as the original 132,000-Mr species, which has been shown to be a fragment of the intact 160,000-Mr Sep1 protein. The SEP1 gene mapped to chromosome VII within 20 kbp of RAD54. Three Tn10LUK insertion mutations in the SEP1 gene were characterized. sep1 mutants grew more slowly than wild-type cells, showed a two- to fivefold decrease in the rate of spontaneous mitotic recombination between his4 heteroalleles, and were delayed in their ability to return to growth after UV or gamma irradiation. Sporulation of sep1/sep1 diploids was defective, as indicated by both a 10- to 40-fold reduction in spore formation and reduced spore viability of approximately 50%. The majority of sep1/sep1 diploid cells arrested in meiosis after commitment to recombination but prior to the meiosis I cell division. Return-to-growth experiments showed that sep1/sep1 his4X/his4B diploids exhibited a five- to sixfold greater meiotic induction of His+ recombinants than did isogenic SEP1/SEP1 strains. sep1/sep1 mutants also showed an increased frequency of exchange between HIS4, LEU2, and MAT and a lack of positive interference between these markers compared with wild-type controls. The interaction between sep1, rad50, and spo13 mutations suggested that SEP1 acts in meiosis in a pathway that is parallel to the RAD50 pathway.

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The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1

Molecular and Cellular Biology ◽

10.1128/mcb.8.4.1432-1442.1988 ◽

1988 ◽

Vol 8 (4) ◽

pp. 1432-1442 ◽

Cited By ~ 4

Author(s):

J D Boeke ◽

D Eichinger ◽

D Castrillon ◽

G R Fink

Keyword(s):

Saccharomyces Cerevisiae ◽

Long Terminal Repeat ◽

Missense Mutation ◽

Dna Sequence ◽

Open Reading Frame ◽

Yeast Genome ◽

Reading Frame ◽

Ty Elements ◽

Ty Element ◽

Repeat Sequences

Saccharomyces cerevisiae Ty elements are transposons closely related to retroviruses. The DNA sequence of a functional Ty element (TyH3) is presented. The long terminal repeat sequences are different, suggesting that TyH3 is a recombinant Ty element. A chromosomal Ty element near the LYS2 gene, Ty173, was found to be nonfunctional, even though it has no detectable insertions or deletions. The defect in Ty173 transposition is caused by a missense mutation giving rise to a Leu-to-Ile substitution in the TYB (pol) open reading frame. Several chromosomal Ty elements carry this lesion in their DNA, indicating that nonfunctional Ty elements are common in the yeast genome.

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Sequences required for delivery and localization of the ADP/ATP translocator to the mitochondrial inner membrane.

Molecular and Cellular Biology ◽

10.1128/mcb.6.2.626 ◽

1986 ◽

Vol 6 (2) ◽

pp. 626-634 ◽

Cited By ~ 159

Author(s):

G S Adrian ◽

M T McCammon ◽

D L Montgomery ◽

M G Douglas

Keyword(s):

Transmembrane Protein ◽

Nuclear Gene ◽

Translocator Protein ◽

Gene Encoding ◽

Inner Membrane ◽

Amino Terminal ◽

Mitochondrial Inner Membrane ◽

Membrane Anchoring ◽

High Degree

The ADP/ATP translocator, a transmembrane protein of the mitochondrial inner membrane, is coded in Saccharomyces cerevisiae by the nuclear gene PET9. DNA sequence analysis of the PET9 gene showed that it encoded a protein of 309 amino acids which exhibited a high degree of homology with mitochondrial translocator proteins from other sources. This mitochondrial precursor, in contrast to many others, does not contain a transient presequence which has been shown to direct the posttranslational localization of proteins in the organelle. Gene fusions between the PET9 gene and the gene encoding beta-galactosidase (lacZ) were constructed to define the location of sequences necessary for the mitochondrial delivery of the ADP/ATP translocator protein in vivo. These studies reveal that the information to target the hybrid molecule to the mitochondria is present within the first 115 residues of the protein. In addition, these studies suggest that the "import information" of the amino-terminal region of the ADP/ATP translocator precursor is twofold. In addition to providing targeting function of the precursor to the organelle, these amino-terminal sequences act to prevent membrane-anchoring sequences located between residues 78 and 98 from stopping import at the outer mitochondrial membrane. These results are discussed in light of the function of distinct protein elements at the amino terminus of mitochondrially destined precursors in both organelle delivery and correct membrane localization.

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The Apoptosis Inhibitor Gene API2 and a Novel 18q Gene,MLT, Are Recurrently Rearranged in the t(11;18)(q21;q21) Associated With Mucosa-Associated Lymphoid Tissue Lymphomas

Blood ◽

10.1182/blood.v93.11.3601.411a47_3601_3609 ◽

1999 ◽

Vol 93 (11) ◽

pp. 3601-3609 ◽

Cited By ~ 10

Author(s):

Judith Dierlamm ◽

Mathijs Baens ◽

Iwona Wlodarska ◽

Margarita Stefanova-Ouzounova ◽

Jesus Maria Hernandez ◽

...

Keyword(s):

Lymphoid Tissue ◽

Marginal Zone ◽

Open Reading Frame ◽

Inhibitor Of Apoptosis ◽

Low Grade ◽

Gene Encoding ◽

Reading Frame ◽

Genetic Lesion ◽

Zone Cell ◽

Apoptosis Inhibitor

Marginal zone cell lymphomas of the mucosa-associated lymphoid tissue (MALT) are the most common subtype of lymphoma arising at extranodal sites. The t(11;18)(q21;q21) appears to be the key genetic lesion and is found in approximately 50% of cytogenetically abnormal low-grade MALT lymphomas. We show that the API2 gene, encoding an inhibitor of apoptosis also known as c-IAP2, HIAP1, andMIHC, and a novel gene on 18q21 characterized by several Ig-like C2-type domains, named MLT, are recurrently rearranged in the t(11;18). In both MALT lymphomas analyzed, the breakpoint inAPI2 occurred in the intron separating the exons coding respectively for the baculovirus IAP repeat domains and the caspase recruitment domain. The breakpoints within MLT differed but the open reading frame was conserved in both cases. In one case, the translocation was accompanied by a cryptic deletion involving the 3′ part of API2. As a result, the reciprocal transcript was not present, strongly suggesting that the API2-MLT fusion is involved in the oncogenesis of MALT lymphoma.

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