Transposon-facilitated DNA sequencing.

Strathmann, Michael; Hamilton, Bruce A.; Mayeda, Carol A.; Simon, Melvin I.; Meyerowitz, Elliot M.; Palazzolo, Michael J.

doi:10.1073/pnas.88.4.1247

Cited by 186 publications

(102 citation statements)

References 19 publications

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“…The plasmid 3-kb libraries were transformed concurrently in 96-well format into pox38UR. The transformants were mated subsequently with JGM in 96-well format (Strathmann et al 1991). All matings of the 3-kb clones within the tiling path were streaked on LB-carbenicillin-kanamycin plates and a random selection of 12 colonies per 3-kb clone were prepped in the AGCT system.…”

Section: Genomic Sequencingmentioning

confidence: 99%

A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus

Ruddy¹,

Kronmal²,

Lee³

et al. 1997

Genome Res.

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In the process of positionally cloning a candidate gene responsible for hereditary hemochromatosis (HH), we constructed a 1.1-Mb transcript map of the region of human chromosome 6p that lies 4.5 Mb telomeric to HLA-A. A combination of three gene-finding techniques, direct cDNA selection, exon trapping, and sample sequencing, were used initially for a saturation screening of the 1.1-Mb region for expressed sequence fragments. As genetic analysis further narrowed the HH candidate locus, we sequenced completely 0.25 Mb of genomic DNA as a final measure to identify all genes. Besides the novel MHC class 1-like HH candidate gene HLA-H, we identified a family of five butyrophilin-related sequences, two genes with structural similarity to a type 1 sodium phosphate transporter, 12 novel histone genes, and a gene we named RoRet based on its strong similarity to the 52-kD Ro/SSA lupus and Sjogren’s syndrome auto-antigen and the RET finger protein. Several members of the butyrophilin family and the RoRet gene share an exon of common evolutionary origin called B30-2. The B30-2 exon was originally isolated from the HLA class 1 region, yet has apparently “shuffled” into several genes along the chromosome telomeric to the MHC. The conservation of the B30-2 exon in several novel genes and the previously described amino acid homology of HLA-H to MHC class 1 molecules provide further support that this gene-rich region of 6p21.3 is related to the MHC. Finally, we performed an analysis of the four approaches for gene finding and conclude that direct selection provides the most effective probes for cDNA screening, and that as much as 30% of ESTs in this 1.1-Mb region may be derived from noncoding genomic DNA.[The sequence data described in this paper have been submitted to GenBank under accession nos. U90543–U90548,U90550–U90552, and U91328.]

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Section: Genomic Sequencingmentioning

confidence: 99%

A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus

Ruddy¹,

Kronmal²,

Lee³

et al. 1997

Genome Res.

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“…For each strand, nucleotide sequence analysis was performed on overlapping segments, either by subcloning small fragments into Bluescript pSKj, and subsequently sequencing using T3 and T7 primers, or by subcloning larger fragments into pMOB, generating nested γδ insertions and sequencing using transposon-specific primers as described by Strathmann et al (1991). A combination of manual (Sanger et al, 1977) and automated (Applied Biosystems) sequencing methods was used for the analysis of the complete φCPG1 genome.…”

Section: Methodsmentioning

confidence: 99%

Microvirus of Chlamydia psittaci strain Guinea pig Inclusion Conjunctivitis: isolation and molecular characterization The GenBank accession number for the sequence reported in this paper is U41758.

2000

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The authors report the isolation and molecular characterization of a bacteriophage, φCPG1, which infects Chlamydia psittaci strain Guinea pig Inclusion Conjunctivitis. Purified virion preparations contained isometric particles of 25 nm diameter, superficially similar to spike-less members of the φX174 family of bacteriophages. The single-stranded circular DNA genome of φCPG1 included five large ORFs, which were similar to ORFs in the genome of a previously described Chlamydia bacteriophage (Chp1) that infects avian C. psittaci. Three of the ORFs encoded polypeptides that were similar to those in a phage infecting the mollicute Spiroplasma melliferum , a pathogen of honeybees. Lesser sequence similarities were seen between two ORF products and the major capsid protein of the φX174 coliphage family and proteins mediating rolling circle replication initiation in phages, phagemids and plasmids. Phage φCPG1 is the second member of the genus Chlamydiamicrov irus, the first to infect a member of a Chlamydia species infecting mammals. Similarity searches of the nucleotide sequence further revealed a highly conserved (75 % identity) 375 base sequence integrated into the genome of the human pathogen Chlamydia pneumoniae. This genomic segment encodes a truncated 113 residue polypeptide, the sequence of which is 72 % identical to the amino-terminal end of the putative replication initiation protein of φCPG1. This finding suggests that C. pneumoniae has been infected by a phage related to φCPG1 and that infection resulted in integration of some of the phage genome into the C. pneumoniae genome.

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“…DNA was sequenced by the dideoxynucleotide chain-terminating method (Sanger et a]., 1977) using the Pharmacia T7 sequencing-kit (Pharmacia) with double-stranded templates. The TNlOOO kit (Angewandte Gentechnologie Systeme GmbH) was employed to obtain overlapping sequencing priming sites (Strathmann et al, 1991). The DNASIS/PROSIS program (Pharmacia) was used for DNA and protein analysis.…”

Section: Molecular Biology Techniquesmentioning

confidence: 99%

Characterization of the essential yeast gene encoding N‐acetylglucosamine‐phosphate mutase

Hofmann

Boles

Zimmermann

1994

European Journal of Biochemistry

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A previously cloned gene of Saccharomyces cerevisiae, which complements the growth defect of a phosphoglucomutase (pgm1Δ/pgm2Δ) double deletion mutant on a pure galactose medium [Boles, E., Liebetrau, W., Hofmann, M. & Zimmermann, F. K. (1994) Eur. J. Biochem. 220, 83–96], was identified as the structural gene encoding N‐acetylglucosamine‐phosphate mutase. The complete nucleotide sequence of the gene, AGM1, and surrounding regions was determined. AGM1 codes for a predicted 62‐kDa protein with 557 amino acids and is located on chromosome V adjacent to the known gene PRB1 encoding protease B. No extended nucleotide or amino acid sequence similarities could be found in the databases, except for a small region of amino acids with high similarity to the active‐site consensus sequence of hexosephosphate mutases. Three putative pheromone‐responsive elements have been identified in the upstream region of the AGM1 gene. The gene is essential for cell viability. An agm1 deletion mutant progresses through only approximately five cell cycles to form a ‘string' of undivided cells with an abnormal cell morphology resembling glucosamine auxotrophic mutants. Expression of the AGM1 gene on a multi‐copy plasmid led to a significantly increased N‐acetylglucosamine‐phosphate mutase activity. Unlike over‐expression of the AGM1 gene in a pgm1/pgm2 double deletion mutant which could restore phosphoglucomutase activity, over‐expression of the PGM2 gene encoding the major isoenzyme of phosphoglucomutase did not increase N‐acetylglucosamine‐phosphate‐mutase activity and did not restore growth of agm1 deletion mutant cells. Our observations indicate that the different hexosephosphate mutases of S. cerevisiae have partially overlapping substrate specifities but, nevertheless, distinct physiological functions.

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Transposon-facilitated DNA sequencing.

Cited by 186 publications

References 19 publications

A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus

A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus

Microvirus of Chlamydia psittaci strain Guinea pig Inclusion Conjunctivitis: isolation and molecular characterization The GenBank accession number for the sequence reported in this paper is U41758.

Characterization of the essential yeast gene encoding N‐acetylglucosamine‐phosphate mutase

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