Overview of the Alliance for Cellular Signaling (2002)
Gilman, AG, Simon, MI, Bourne, HR, Harris, BA, Long, R, Ross, EM, ...
The Alliance for Cellular Signaling is a large-scale collaboration designed to answer global questions about signalling networks. Pathways will be studied intensively in two cells-B lymphocytes (the...
Van Gaalen, FA, Kasperkovitz, P, Verbeet, N, Alizadeh, AA, Fero, M, ...
No abstract available.
Leung, SY, Chen, X, Chu, KM, Yuen, ST, Mathy, J, Ji, J, ...
We analyzed gene expression patterns in human gastric cancers by using cDNA microarrays representing approximately equal 30,300 genes. Expression of PLA2G2A, a gene previously implicated as a...
Relation of gene expression-based tumor subclasses to clinical phenotypes (2000)
Sørlie, T, Perou, CM, Lønning, PE, Brown, PO, Botstein, D, Børresen-Dale, A-L
No abstract available.
Studying breast cancer on a genomic scale using DNA microarrays (2000)
No abstract available.
Pennica, D., Swanson, T.A., Welsh, J.W., Roy, M.A., Lawrence, D.A., Lee, J., ...
Wnt family members are critical to many developmental processes, and components of the Wnt signaling pathway have been linked to tumorigenesis in familial and sporadic colon carcinomas. Here we...
Pennica, D., Swanson, T.A., Welsh, J.W., Roy, M.A., Lawrence, D.A., Lee, J., ...
Wnt family members are critical to many developmental processes, and components of the Wnt signaling pathway have been linked to tumorigenesis in familial and sporadic colon carcinomas. Here we...
Pennica, D., Swanson, T.A., Welsh, J.W., Roy, M.A., Lawrence, D.A., Lee, J., ...
Wnt family members are critical to many developmental processes, and components of the Wnt signaling pathway have been linked to tumorigenesis in familial and sporadic colon carcinomas. Here we...
The transcriptional program of sporulation in budding yeast (1998)
J. Derisi, M. Eisen, J. Mulholl, D. Botstein, P. O. Brown, S. Chu, ...
Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast...
SGD: Saccharomyces Genome Database (1998)
Cherry, JM, Adler, C, Ball, C, Chervitz, SA, Dwight, SS, Hester, ET, ...
Paoni, N. F., Refino, C. J., Brady, K., Pena, L. C., Nguyen, H. V., Kerr, E. M., ...
The tetra-alanine substitution variant KHRR 296-299 AAAA of tissue-type plasminogen activator (t-PA) was previously shown to have enhanced fibrin specificity and enhanced activity in the presence of...
Bennett, W. F., Paoni, N. F., Keyt, B. A., Botstein, D., Jones, A. J., Presta, L., ...
Sixty-four variants of human tissue-type plasminogen activator (tPA) were produced using recombinant DNA techniques. Charged residues were converted to alanine in clusters of from one to four changes...
Movement of yeast cortical actin cytoskeleton visualized in vivo.
Fusion proteins between the green fluorescent protein (GFP) and the cytoskeleton proteins Act1p (actin), Sac6p (yeast fimbrin homolog), and Abp1p in budding yeast (Saccharomyces cerevisiae) localize...
Genetic footprinting: a genomic strategy for determining a gene's function given its sequence.
Smith, V, Botstein, D, Brown, P O
This report describes an efficient strategy for determining the functions of sequenced genes in microorganisms. A large population of cells is subjected to insertional mutagenesis. The mutagenized...
Conditional lethality of a yeast strain expressing human RHOA in place of RHO1.
Qadota, H, Anraku, Y, Botstein, D, Ohya, Y
The yeast RHO1 GTPase, which has 72% amino acid sequence identity with its human counterpart, RHOA, is essential for growth, although the reason has not been investigated. We report here that yeast...
Kron, S J, Drubin, D G, Botstein, D, Spudich, J A
The yeast Saccharomyces cerevisiae has been used to study the function of components of the actin cytoskeleton in vivo, mainly because it is easy to derive and characterize mutations affecting these...
Chen, Y, Hennessy, K M, Botstein, D, Tye, B K
Saccharomyces cerevisiae cells containing mutations in the cell-division-cycle gene CDC46 arrest with a large bud and a single nucleus with unreplicated DNA at the non-permissive temperature. This...
Molecular sequence accuracy and the analysis of protein coding regions.
Molecular sequences, like all experimental data, have finite error rates. The impact of errors on the information content of molecular sequence data is dependent on the analytic paradigm used to...
GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction.
Baker, D, Wuestehube, L, Schekman, R, Botstein, D, Segev, N
The 21-kDa GTP-binding Ypt1 protein (Ypt1p) is required for protein transport from the endoplasmic reticulum to the Golgi complex in yeast extracts. Ypt1 antibodies block transport; this inhibition...
ADP-ribosylation factor is functionally and physically associated with the Golgi complex.
Stearns, T, Willingham, M C, Botstein, D, Kahn, R A
ADP-ribosylation factor (ARF) is a ubiquitous, highly conserved 21-kDa GTP-binding protein, first identified in animal cells as the cofactor required for the in vitro ADP-ribosylation of the...
SGD: Saccharomyces Genome Database.
Cherry, J M, Adler, C, Ball, C, Chervitz, S A, Dwight, S S, Hester, E T, ...
The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the...
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.
Chervitz, S A, Hester, E T, Ball, C A, Dolinski, K, Dwight, S S, Harris, M A, ...
The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The latest protein structure and comparison...
Selection of functional signal peptide cleavage sites from a library of random sequences.
Palzkill, T, Le, Q Q, Wong, A, Botstein, D
The export of proteins to the periplasmic compartment of bacterial cells is mediated by an amino-terminal signal peptide. After transport, the signal peptide is cleaved by a processing enzyme, signal...
TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Recently, TEM beta-lactamase variants with amino acid substitutions in the active-site pocket of...
Characterization of amber and ochre suppressors in Salmonella typhimurium.
Winston, F, Botstein, D, Miller, J H
Amber and ochre suppressor mutations in Salmonella typhimurium were selected. The amino acid insertions directed by the suppressors were inferred from suppression patterns of Escherichia coli lacI...
Genetic mapping of mutations in a highly radiation-resistant mutant of Salmonella typhimurium LT2.
Ibe, S N, Sinskey, A J, Botstein, D
The genes involved in the high radiation resistance of mutant R68 of Salmonella typhimurium LT2 were mapped by conjugation. It was observed that the high radiation resistance involved genes localized...
Two alanine racemase genes in Salmonella typhimurium that differ in structure and function.
Wasserman, S A, Walsh, C T, Botstein, D
Mutations were isolated in a previously undescribed Salmonella typhimurium gene encoding an alanine racemase essential for utilization of L-alanine as a source of carbon, energy, and nitrogen. This...
Fusions of bacteriophage P22 late genes to the Escherichia coli lacZ gene.
The late genes of bacteriophage P22 were fused to lacZ to study their differential expression from the late operon transcript. No instances of posttranscriptional regulation were uncovered, thus...
Yeast proteins associated with microtubules in vitro and in vivo.
Barnes, G, Louie, K A, Botstein, D
Conditions were established for the self-assembly of milligram amounts of purified Saccharomyces cerevisiae tubulin. Microtubules assembled with pure yeast tubulin were not stabilized by taxol;...
Preuss, D, Mulholland, J, Franzusoff, A, Segev, N, Botstein, D
The membrane compartments responsible for Golgi functions in wild-type Saccharomyces cerevisiae were identified and characterized by immunoelectron microscopy. Using improved fixation methods, Golgi...
Ohya, Y, Qadota, H, Anraku, Y, Pringle, J R, Botstein, D
Geranylgeranyl transferase I (GGTase I), which modifies proteins containing the sequence Cys-Ali-Ali-Leu (Ali: aliphatic) at their C-termini, is indispensable for growth in the budding yeast...
Ziman, M, Preuss, D, Mulholland, J, O'Brien, J M, Botstein, D, Johnson, D I
The Saccharomyces cerevisiae Cdc42 protein, a member of the Ras superfamily of low-molecular-weight GTP-binding proteins, is involved in the control of cell polarity during the yeast cell cycle. This...
Amberg, D C, Zahner, J E, Mulholland, J W, Pringle, J R, Botstein, D
A search for Saccharomyces cerevisiae proteins that interact with actin in the two-hybrid system and a screen for mutants that affect the bipolar budding pattern identified the same gene, AIP3/BUD6....
Yeast actin cytoskeleton mutants accumulate a new class of Golgi-derived secretary vesicle.
Mulholland, J, Wesp, A, Riezman, H, Botstein, D
Many yeast actin cytoskeleton mutants accumulate large secretory vesicles and exhibit phenotypes consistent with defects in polarized growth. This, together with actin's polarized organization, has...
Bacteriophage P22 gene 23 product acts preferentially in cis.
The expression of the P22 late operon was measured while the activator of the late operon, the product of gene 23, was provided in cis or in trans. It was found that expression of the late operon,...
Dissemination of an antibiotic resistance plasmid in hospital patient flora.
O'Brien, T F, Ross, D G, Guzman, M A, Medeiros, A A, Hedges, R W, Botstein, D
The 2'' aminoglycoside nucleotidyltransferase, AAD (2''), which adenylates gentamicin, tobramycin, and kanamycin, became prevalent over several months in multiple strains and species of...
Nonrandom Mutagenesis of the Escherichia coli Genome by Nitrosoguanidine
The distribution on the genetic map of mutations induced with nitrosoguanidine in stationary-phase cultures of Escherichia coli is nonrandom.
Fitts, R, Reuveny, Z, Van Amsterdam, J, Mulholland, J, Botstein, D
Six independent secretion-defective mutations were found that result in failure to release protein from the membrane into the periplasmic space of Salmonella typhimurium after removal of the signal...
Yeast genes fused to beta-galactosidase in Escherichia coli can be expressed normally in yeast.
Rose, M, Casadaban, M J, Botstein, D
A plasmid was constructed that allows the selection in vivo of gene fusions between the Escherichia coli beta-galactosidase gene and the yeast (Saccharomyces cerevisiae) URA3 gene. A large yeast DNA...
Stachelek, C, Stachelek, J, Swan, J, Botstein, D, Konigsberg, W
The hexokinase A (HKA) and hexokinase B (HKB) genes of Saccharomyces cerevisiae have been cloned from a library of yeast genomic DNA. Using an in vitro glucose phosphorylation assay, the HKB gene was...
Shortle, D, Grisafi, P, Benkovic, S J, Botstein, D
Short single-stranded gaps can be constructed by limited exonuclease action at single-stranded breaks (nicks) placed at predetermined sites on closed circular DNA molecules. As efficient...
Single-copy sequence hybridizes to polymorphic and homologous loci on human X and Y chromosomes.
Page, D, De Martinville, B, Barker, D, Wyman, A, White, R, Francke, U, ...
Use of a 4.5-kilobase-pair (kb) segment of single-copy DNA from a human genomic library as a hybridization probe of genomic human DNAs revealed allelic Taq I restriction fragments 10.6, 11.8, and...
Shortle, D, Koshland, D, Weinstock, G M, Botstein, D
A general method for efficiently mutagenizing a predetermined segment of a closed circular duplex DNA molecule was used to construct mutations in two specific regions of the beta-lactamase (bla) gene...
Efficiency and diversity of protein localization by random signal sequences.
Three randomly derived sequences that can substitute for the signal peptide of Saccharomyces cerevisiae invertase were tested for the efficiency with which they can translocate invertase or...
Hoyt, M A, Stearns, T, Botstein, D
By using a multiply marked supernumerary chromosome III as an indicator, we isolated mutants of Saccharomyces cerevisiae that display increased rates of chromosome loss. In addition to mutations in...
DNA topoisomerase II must act at mitosis to prevent nondisjunction and chromosome breakage.
Holm, C, Stearns, T, Botstein, D
The hypothesis that DNA topoisomerase II facilitates the separation of replicated sister chromatids was tested by examining the consequences of chromosome segregation in the absence of topoisomerase...
Intragenic revertants of yeast invertase variants with secretion-defective leader sequences.
Several secretion-defective variants of invertase from Saccharomyces cerevisiae were generated by replacement of the wild-type signal sequence codons with DNA fragments with random sequences. Strains...
Stearns, T, Kahn, R A, Botstein, D, Hoyt, M A
ADP ribosylation factor (ARF) is a ubiquitous 21-kDa GTP-binding protein in eucaryotes. ARF was first identified in animal cells as the protein factor required for the efficient ADP-ribosylation of...
Isolation and characterization of mutations in the HXK2 gene of Saccharomyces cerevisiae.
Ma, H, Bloom, L M, Zhu, Z M, Walsh, C T, Botstein, D
Several hundred new mutations in the gene (HXK2) encoding hexokinase II of Saccharomyces cerevisiae were isolated, and a subset of them was mapped, resulting in a fine-structure genetic map. Among...
Ma, H, Bloom, L M, Walsh, C T, Botstein, D
Saccharomyces cerevisiae mutants containing different point mutations in the HXK2 gene were used to study the relationship between phosphorylation by hexokinase II and glucose repression in yeast...
The ras-like yeast YPT1 gene is itself essential for growth, sporulation, and starvation response.
The Saccharomyces cerevisiae gene YPT1 encodes a protein that exhibits significant homology to the mammalian ras proteins. Using gene disruption techniques, we have shown that the intact YPT1 gene is...
Two functional alpha-tubulin genes of the yeast Saccharomyces cerevisiae encode divergent proteins.
Schatz, P J, Pillus, L, Grisafi, P, Solomon, F, Botstein, D
Two alpha-tubulin genes from the budding yeast Saccharomyces cerevisiae were identified and cloned by cross-species DNA homology. Nucleotide sequencing studies revealed that the two genes, named TUB1...
Schatz, P J, Solomon, F, Botstein, D
Microtubules in yeast are essential components of the mitotic and meiotic spindles and are essential for nuclear movement during cell division and mating. The relative importance in these processes...
Saccharomyces cerevisiae has two homologous hexokinases, I and II; they are 78% identical at the amino acid level. Either enzyme allows yeast cells to ferment fructose. Mutant strains without any...
Secretion-defective mutations in the signal sequence for Saccharomyces cerevisiae invertase.
Nine mutations in the signal sequence region of the gene specifying the secreted Saccharomyces cerevisiae enzyme invertase were constructed in vitro. The consequences of these mutations were studied...
Insertions of up to 17 amino acids into a region of alpha-tubulin do not disrupt function in vivo.
Schatz, P J, Georges, G E, Solomon, F, Botstein, D
Microtubules in yeasts are essential components of the mitotic and meiotic spindle and are necessary for nuclear movement during cell division and mating. The yeast Saccharomyces cerevisiae has two...
Organization of the SUC gene family in Saccharomyces.
The SUC gene family of yeast (Saccharomyces) includes six structural genes for invertase (SUC1 through SUC5 and SUC7) found at unlinked chromosomal loci. A given yeast strain does not usually carry...
Carlson, M, Taussig, R, Kustu, S, Botstein, D
The SUC2 gene of Saccharomyces cerevisiae encodes two differently regulated mRNAs (1.8 and 1.9 kilobases) that differ at their 5' ends. The larger RNA encodes a secreted, glycosylated form of...
Regulation of HIS4-lacZ fusions in Saccharomyces cerevisiae.
Silverman, S J, Rose, M, Botstein, D, Fink, G R
The beginning of the Saccharomyces cerevisiae HIS4 gene has been fused to the structural gene for Escherichia coli beta-galactosidase. This construction, which contains HIS4 DNA from -732 to +30...
Bach, M L, Lacroute, F, Botstein, D
From a large population of strains of Escherichia coli carrying shear fragments of yeast (Saccharomyces cerevisiae) DNA attached by in vitro recombination to the plasmid vector pMB9, two hybrid...
Simple single-gene disorders in humans can be genetically mapped by using traditional methods of linkage analysis and increasingly abundant restriction fragment length polymorphisms (RFLPs). Many...
Shortle, D, Novick, P, Botstein, D
Two temperature-sensitive mutations have been constructed in the single actin gene (ACT1) of the yeast Saccharomyces cerevisiae by in vitro mutagenesis of the cloned gene followed by integrative...
Wyman, A R, Wolfe, L B, Botstein, D
The growth of clones of human genomic DNA fragments in a bacteriophage lambda vector has been examined in a number of different Escherichia coli hosts. A large proportion (8.9%) of the phages...
Simple Mendelian inheritance of the reiterated ribosomal DNA of yeast.
A diploid strain of yeast (Saccharomyces cerevisiae) was found to be heterozygous for two forms of the highly repetitious ribosomal DNA. These forms could be distinguished by the pattern of fragments...
An analysis of revertants of missense mutants in phage P22 has shown: (i) New temperature-sensitive (TS) and cold-sensitive (CS) phenotypes are often acquired concomitant with reversion. (ii) In many...
Ross, D G, Grisafi, P, Kleckner, N, Botstein, D
By heteroduplex and hybridization analysis we showed that the inverted repetition (here called IS10) at the ends of the translocatable tetracycline resistance element Tn10 is not IS3, as had...
Mutations in genes of Saccharomyces cerevisiae that code for proteins that interact with β-tubulin were sought by screening for unlinked mutations that fail to complement mutations in the single...
Schatz, P. J., Solomon, F., Botstein, D.
Microtubules in yeast are functional components of the mitotic and meiotic spindles and are essential for nuclear movement during cell division and mating. We have isolated 70 conditional-lethal...
Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps
The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic...
Suppressors of Yeast Actin Mutations
Novick, P., Osmond, B. C., Botstein, D.
Suppressors of a temperature-sensitive mutation (act1-1) in the single actin gene of Saccharomyces cerevisiae were selected that had simultaneously acquired a cold-sensitive growth phenotype. Five...
Dominant Suppressors of Yeast Actin Mutations That Are Reciprocally Suppressed
A gene whose product is likely to interact with yeast actin was identified by the isolation of pseudorevertants carrying dominant suppressors of the temperature-sensitive (Ts) act1-1 mutation. Of 30...
Synapsis-Mediated Fusion of Free DNA Ends Forms Inverted Dimer Plasmids in Yeast
Kunes, S., Botstein, D., Fox, M. S.
When yeast (Saccharomyces cerevisiae) is transformed with linearized plasmid DNA and the ends of the plasmid do not share homology with the yeast genome, circular inverted (head-to-head) dimer...
Yeast Mutants Sensitive to Antimicrotubule Drugs Define Three Genes That Affect Microtubule Function
Stearns, T., Hoyt, M. A., Botstein, D.
Three new genes affecting microtubule function in Saccharomyces cerevisiae were isolated by screening for mutants displaying supersensitivity to the antimicrotubule drug benomyl. Such mutants fall...
Systematic Mutational Analysis of the Yeast Act1 Gene
Wertman, K. F., Drubin, D. G., Botstein, D.
We report the isolation and characterization of a synoptic set of site-directed mutations distributed throughout the single actin gene of Saccharomyces cerevisiae. Mutations were systematically...
Isolation and Characterization of Chromosome-Gain and Increase-in-Ploidy Mutants in Yeast
We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it...
Conditional-lethal mutations of the single calmodulin gene in Saccharomyces cerevisiae have been very difficult to isolate by random and systematic methods, despite the fact that deletions cause...
Identification of functional connections between calmodulin and the yeast actin cytoskeleton.
Sekiya-Kawasaki, M, Botstein, D, Ohya, Y
One of four intragenic complementing groups of temperature-sensitive yeast calmodulin mutations, cmd1A, results in a characteristic functional defect in actin organization. We report here that among...
A deletion map of the human Y chromosome based on DNA hybridization.
Vergnaud, G, Page, D C, Simmler, M C, Brown, L, Rouyer, F, Noel, B, ...
The genomes of 27 individuals (19 XX males, two XX hermaphrodites, and six persons with microscopically detectable anomalies of the Y chromosome) were analyzed by hybridization for the presence or...
Construction of a genetic linkage map in man using restriction fragment length polymorphisms.
Botstein, D, White, R L, Skolnick, M, Davis, R W
We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy...
Movement of yeast cortical actin cytoskeleton visualized in vivo.
Fusion proteins between the green fluorescent protein (GFP) and the cytoskeleton proteins Act1p (actin), Sac6p (yeast fimbrin homolog), and Abp1p in budding yeast (Saccharomyces cerevisiae) localize...
Genetic footprinting: a genomic strategy for determining a gene's function given its sequence.
Smith, V, Botstein, D, Brown, P O
This report describes an efficient strategy for determining the functions of sequenced genes in microorganisms. A large population of cells is subjected to insertional mutagenesis. The mutagenized...
Conditional lethality of a yeast strain expressing human RHOA in place of RHO1.
Qadota, H, Anraku, Y, Botstein, D, Ohya, Y
The yeast RHO1 GTPase, which has 72% amino acid sequence identity with its human counterpart, RHOA, is essential for growth, although the reason has not been investigated. We report here that yeast...
Kron, S J, Drubin, D G, Botstein, D, Spudich, J A
The yeast Saccharomyces cerevisiae has been used to study the function of components of the actin cytoskeleton in vivo, mainly because it is easy to derive and characterize mutations affecting these...
Chen, Y, Hennessy, K M, Botstein, D, Tye, B K
Saccharomyces cerevisiae cells containing mutations in the cell-division-cycle gene CDC46 arrest with a large bud and a single nucleus with unreplicated DNA at the non-permissive temperature. This...
Molecular sequence accuracy and the analysis of protein coding regions.
Molecular sequences, like all experimental data, have finite error rates. The impact of errors on the information content of molecular sequence data is dependent on the analytic paradigm used to...
GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction.
Baker, D, Wuestehube, L, Schekman, R, Botstein, D, Segev, N
The 21-kDa GTP-binding Ypt1 protein (Ypt1p) is required for protein transport from the endoplasmic reticulum to the Golgi complex in yeast extracts. Ypt1 antibodies block transport; this inhibition...
ADP-ribosylation factor is functionally and physically associated with the Golgi complex.
Stearns, T, Willingham, M C, Botstein, D, Kahn, R A
ADP-ribosylation factor (ARF) is a ubiquitous, highly conserved 21-kDa GTP-binding protein, first identified in animal cells as the cofactor required for the in vitro ADP-ribosylation of the...
SGD: Saccharomyces Genome Database.
Cherry, J M, Adler, C, Ball, C, Chervitz, S A, Dwight, S S, Hester, E T, ...
The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the...
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.
Chervitz, S A, Hester, E T, Ball, C A, Dolinski, K, Dwight, S S, Harris, M A, ...
The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The latest protein structure and comparison...
Selection of functional signal peptide cleavage sites from a library of random sequences.
Palzkill, T, Le, Q Q, Wong, A, Botstein, D
The export of proteins to the periplasmic compartment of bacterial cells is mediated by an amino-terminal signal peptide. After transport, the signal peptide is cleaved by a processing enzyme, signal...
TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Recently, TEM beta-lactamase variants with amino acid substitutions in the active-site pocket of...
Ross, D G, Grisafi, P, Kleckner, N, Botstein, D
By heteroduplex and hybridization analysis we showed that the inverted repetition (here called IS10) at the ends of the translocatable tetracycline resistance element Tn10 is not IS3, as had...
Characterization of amber and ochre suppressors in Salmonella typhimurium.
Winston, F, Botstein, D, Miller, J H
Amber and ochre suppressor mutations in Salmonella typhimurium were selected. The amino acid insertions directed by the suppressors were inferred from suppression patterns of Escherichia coli lacI...
Genetic mapping of mutations in a highly radiation-resistant mutant of Salmonella typhimurium LT2.
Ibe, S N, Sinskey, A J, Botstein, D
The genes involved in the high radiation resistance of mutant R68 of Salmonella typhimurium LT2 were mapped by conjugation. It was observed that the high radiation resistance involved genes localized...
Two alanine racemase genes in Salmonella typhimurium that differ in structure and function.
Wasserman, S A, Walsh, C T, Botstein, D
Mutations were isolated in a previously undescribed Salmonella typhimurium gene encoding an alanine racemase essential for utilization of L-alanine as a source of carbon, energy, and nitrogen. This...
Fusions of bacteriophage P22 late genes to the Escherichia coli lacZ gene.
The late genes of bacteriophage P22 were fused to lacZ to study their differential expression from the late operon transcript. No instances of posttranscriptional regulation were uncovered, thus...
Yeast proteins associated with microtubules in vitro and in vivo.
Barnes, G, Louie, K A, Botstein, D
Conditions were established for the self-assembly of milligram amounts of purified Saccharomyces cerevisiae tubulin. Microtubules assembled with pure yeast tubulin were not stabilized by taxol;...
Preuss, D, Mulholland, J, Franzusoff, A, Segev, N, Botstein, D
The membrane compartments responsible for Golgi functions in wild-type Saccharomyces cerevisiae were identified and characterized by immunoelectron microscopy. Using improved fixation methods, Golgi...
Ohya, Y, Qadota, H, Anraku, Y, Pringle, J R, Botstein, D
Geranylgeranyl transferase I (GGTase I), which modifies proteins containing the sequence Cys-Ali-Ali-Leu (Ali: aliphatic) at their C-termini, is indispensable for growth in the budding yeast...
Ziman, M, Preuss, D, Mulholland, J, O'Brien, J M, Botstein, D, Johnson, D I
The Saccharomyces cerevisiae Cdc42 protein, a member of the Ras superfamily of low-molecular-weight GTP-binding proteins, is involved in the control of cell polarity during the yeast cell cycle. This...
Amberg, D C, Zahner, J E, Mulholland, J W, Pringle, J R, Botstein, D
A search for Saccharomyces cerevisiae proteins that interact with actin in the two-hybrid system and a screen for mutants that affect the bipolar budding pattern identified the same gene, AIP3/BUD6....
Yeast actin cytoskeleton mutants accumulate a new class of Golgi-derived secretary vesicle.
Mulholland, J, Wesp, A, Riezman, H, Botstein, D
Many yeast actin cytoskeleton mutants accumulate large secretory vesicles and exhibit phenotypes consistent with defects in polarized growth. This, together with actin's polarized organization, has...
Bacteriophage P22 gene 23 product acts preferentially in cis.
The expression of the P22 late operon was measured while the activator of the late operon, the product of gene 23, was provided in cis or in trans. It was found that expression of the late operon,...
Dissemination of an antibiotic resistance plasmid in hospital patient flora.
O'Brien, T F, Ross, D G, Guzman, M A, Medeiros, A A, Hedges, R W, Botstein, D
The 2'' aminoglycoside nucleotidyltransferase, AAD (2''), which adenylates gentamicin, tobramycin, and kanamycin, became prevalent over several months in multiple strains and species of...
Nonrandom Mutagenesis of the Escherichia coli Genome by Nitrosoguanidine
The distribution on the genetic map of mutations induced with nitrosoguanidine in stationary-phase cultures of Escherichia coli is nonrandom.
Fitts, R, Reuveny, Z, Van Amsterdam, J, Mulholland, J, Botstein, D
Six independent secretion-defective mutations were found that result in failure to release protein from the membrane into the periplasmic space of Salmonella typhimurium after removal of the signal...
Yeast genes fused to beta-galactosidase in Escherichia coli can be expressed normally in yeast.
Rose, M, Casadaban, M J, Botstein, D
A plasmid was constructed that allows the selection in vivo of gene fusions between the Escherichia coli beta-galactosidase gene and the yeast (Saccharomyces cerevisiae) URA3 gene. A large yeast DNA...
Stachelek, C, Stachelek, J, Swan, J, Botstein, D, Konigsberg, W
The hexokinase A (HKA) and hexokinase B (HKB) genes of Saccharomyces cerevisiae have been cloned from a library of yeast genomic DNA. Using an in vitro glucose phosphorylation assay, the HKB gene was...
Shortle, D, Grisafi, P, Benkovic, S J, Botstein, D
Short single-stranded gaps can be constructed by limited exonuclease action at single-stranded breaks (nicks) placed at predetermined sites on closed circular DNA molecules. As efficient...
Single-copy sequence hybridizes to polymorphic and homologous loci on human X and Y chromosomes.
Page, D, De Martinville, B, Barker, D, Wyman, A, White, R, Francke, U, ...
Use of a 4.5-kilobase-pair (kb) segment of single-copy DNA from a human genomic library as a hybridization probe of genomic human DNAs revealed allelic Taq I restriction fragments 10.6, 11.8, and...
Shortle, D, Koshland, D, Weinstock, G M, Botstein, D
A general method for efficiently mutagenizing a predetermined segment of a closed circular duplex DNA molecule was used to construct mutations in two specific regions of the beta-lactamase (bla) gene...
Efficiency and diversity of protein localization by random signal sequences.
Three randomly derived sequences that can substitute for the signal peptide of Saccharomyces cerevisiae invertase were tested for the efficiency with which they can translocate invertase or...
Hoyt, M A, Stearns, T, Botstein, D
By using a multiply marked supernumerary chromosome III as an indicator, we isolated mutants of Saccharomyces cerevisiae that display increased rates of chromosome loss. In addition to mutations in...
DNA topoisomerase II must act at mitosis to prevent nondisjunction and chromosome breakage.
Holm, C, Stearns, T, Botstein, D
The hypothesis that DNA topoisomerase II facilitates the separation of replicated sister chromatids was tested by examining the consequences of chromosome segregation in the absence of topoisomerase...
Intragenic revertants of yeast invertase variants with secretion-defective leader sequences.
Several secretion-defective variants of invertase from Saccharomyces cerevisiae were generated by replacement of the wild-type signal sequence codons with DNA fragments with random sequences. Strains...
Stearns, T, Kahn, R A, Botstein, D, Hoyt, M A
ADP ribosylation factor (ARF) is a ubiquitous 21-kDa GTP-binding protein in eucaryotes. ARF was first identified in animal cells as the protein factor required for the efficient ADP-ribosylation of...
Isolation and characterization of mutations in the HXK2 gene of Saccharomyces cerevisiae.
Ma, H, Bloom, L M, Zhu, Z M, Walsh, C T, Botstein, D
Several hundred new mutations in the gene (HXK2) encoding hexokinase II of Saccharomyces cerevisiae were isolated, and a subset of them was mapped, resulting in a fine-structure genetic map. Among...
Ma, H, Bloom, L M, Walsh, C T, Botstein, D
Saccharomyces cerevisiae mutants containing different point mutations in the HXK2 gene were used to study the relationship between phosphorylation by hexokinase II and glucose repression in yeast...
The ras-like yeast YPT1 gene is itself essential for growth, sporulation, and starvation response.
The Saccharomyces cerevisiae gene YPT1 encodes a protein that exhibits significant homology to the mammalian ras proteins. Using gene disruption techniques, we have shown that the intact YPT1 gene is...
Two functional alpha-tubulin genes of the yeast Saccharomyces cerevisiae encode divergent proteins.
Schatz, P J, Pillus, L, Grisafi, P, Solomon, F, Botstein, D
Two alpha-tubulin genes from the budding yeast Saccharomyces cerevisiae were identified and cloned by cross-species DNA homology. Nucleotide sequencing studies revealed that the two genes, named TUB1...
Schatz, P J, Solomon, F, Botstein, D
Microtubules in yeast are essential components of the mitotic and meiotic spindles and are essential for nuclear movement during cell division and mating. The relative importance in these processes...
Saccharomyces cerevisiae has two homologous hexokinases, I and II; they are 78% identical at the amino acid level. Either enzyme allows yeast cells to ferment fructose. Mutant strains without any...
Secretion-defective mutations in the signal sequence for Saccharomyces cerevisiae invertase.
Nine mutations in the signal sequence region of the gene specifying the secreted Saccharomyces cerevisiae enzyme invertase were constructed in vitro. The consequences of these mutations were studied...
Insertions of up to 17 amino acids into a region of alpha-tubulin do not disrupt function in vivo.
Schatz, P J, Georges, G E, Solomon, F, Botstein, D
Microtubules in yeasts are essential components of the mitotic and meiotic spindle and are necessary for nuclear movement during cell division and mating. The yeast Saccharomyces cerevisiae has two...
Organization of the SUC gene family in Saccharomyces.
The SUC gene family of yeast (Saccharomyces) includes six structural genes for invertase (SUC1 through SUC5 and SUC7) found at unlinked chromosomal loci. A given yeast strain does not usually carry...
Carlson, M, Taussig, R, Kustu, S, Botstein, D
The SUC2 gene of Saccharomyces cerevisiae encodes two differently regulated mRNAs (1.8 and 1.9 kilobases) that differ at their 5' ends. The larger RNA encodes a secreted, glycosylated form of...
Regulation of HIS4-lacZ fusions in Saccharomyces cerevisiae.
Silverman, S J, Rose, M, Botstein, D, Fink, G R
The beginning of the Saccharomyces cerevisiae HIS4 gene has been fused to the structural gene for Escherichia coli beta-galactosidase. This construction, which contains HIS4 DNA from -732 to +30...
Bach, M L, Lacroute, F, Botstein, D
From a large population of strains of Escherichia coli carrying shear fragments of yeast (Saccharomyces cerevisiae) DNA attached by in vitro recombination to the plasmid vector pMB9, two hybrid...
Simple single-gene disorders in humans can be genetically mapped by using traditional methods of linkage analysis and increasingly abundant restriction fragment length polymorphisms (RFLPs). Many...
Shortle, D, Novick, P, Botstein, D
Two temperature-sensitive mutations have been constructed in the single actin gene (ACT1) of the yeast Saccharomyces cerevisiae by in vitro mutagenesis of the cloned gene followed by integrative...
Wyman, A R, Wolfe, L B, Botstein, D
The growth of clones of human genomic DNA fragments in a bacteriophage lambda vector has been examined in a number of different Escherichia coli hosts. A large proportion (8.9%) of the phages...
Simple Mendelian inheritance of the reiterated ribosomal DNA of yeast.
A diploid strain of yeast (Saccharomyces cerevisiae) was found to be heterozygous for two forms of the highly repetitious ribosomal DNA. These forms could be distinguished by the pattern of fragments...
An analysis of revertants of missense mutants in phage P22 has shown: (i) New temperature-sensitive (TS) and cold-sensitive (CS) phenotypes are often acquired concomitant with reversion. (ii) In many...
Mutations in genes of Saccharomyces cerevisiae that code for proteins that interact with β-tubulin were sought by screening for unlinked mutations that fail to complement mutations in the single...
Schatz, P. J., Solomon, F., Botstein, D.
Microtubules in yeast are functional components of the mitotic and meiotic spindles and are essential for nuclear movement during cell division and mating. We have isolated 70 conditional-lethal...
Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps
The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic...
Suppressors of Yeast Actin Mutations
Novick, P., Osmond, B. C., Botstein, D.
Suppressors of a temperature-sensitive mutation (act1-1) in the single actin gene of Saccharomyces cerevisiae were selected that had simultaneously acquired a cold-sensitive growth phenotype. Five...
Dominant Suppressors of Yeast Actin Mutations That Are Reciprocally Suppressed
A gene whose product is likely to interact with yeast actin was identified by the isolation of pseudorevertants carrying dominant suppressors of the temperature-sensitive (Ts) act1-1 mutation. Of 30...
Synapsis-Mediated Fusion of Free DNA Ends Forms Inverted Dimer Plasmids in Yeast
Kunes, S., Botstein, D., Fox, M. S.
When yeast (Saccharomyces cerevisiae) is transformed with linearized plasmid DNA and the ends of the plasmid do not share homology with the yeast genome, circular inverted (head-to-head) dimer...
Yeast Mutants Sensitive to Antimicrotubule Drugs Define Three Genes That Affect Microtubule Function
Stearns, T., Hoyt, M. A., Botstein, D.
Three new genes affecting microtubule function in Saccharomyces cerevisiae were isolated by screening for mutants displaying supersensitivity to the antimicrotubule drug benomyl. Such mutants fall...
Systematic Mutational Analysis of the Yeast Act1 Gene
Wertman, K. F., Drubin, D. G., Botstein, D.
We report the isolation and characterization of a synoptic set of site-directed mutations distributed throughout the single actin gene of Saccharomyces cerevisiae. Mutations were systematically...
Isolation and Characterization of Chromosome-Gain and Increase-in-Ploidy Mutants in Yeast
We have developed a colony papillation assay for monitoring the copy number of genetically marked chromosomes II and III in Saccharomyces cerevisiae. The unique feature of this assay is that it...
Conditional-lethal mutations of the single calmodulin gene in Saccharomyces cerevisiae have been very difficult to isolate by random and systematic methods, despite the fact that deletions cause...
Identification of functional connections between calmodulin and the yeast actin cytoskeleton.
Sekiya-Kawasaki, M, Botstein, D, Ohya, Y
One of four intragenic complementing groups of temperature-sensitive yeast calmodulin mutations, cmd1A, results in a characteristic functional defect in actin organization. We report here that among...
A deletion map of the human Y chromosome based on DNA hybridization.
Vergnaud, G, Page, D C, Simmler, M C, Brown, L, Rouyer, F, Noel, B, ...
The genomes of 27 individuals (19 XX males, two XX hermaphrodites, and six persons with microscopically detectable anomalies of the Y chromosome) were analyzed by hybridization for the presence or...
Construction of a genetic linkage map in man using restriction fragment length polymorphisms.
Botstein, D, White, R L, Skolnick, M, Davis, R W
We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy...
A locus for Fanconi anemia on 16q determined by homozygosity mapping.
Gschwend, M., Levran, O., Kruglyak, L., Ranade, K., Verlander, P. C., Shen, S., ...
We report the results of a genomewide scan using homozygosity mapping to identify genes causing Fanconi anemia, a genetically heterogeneous recessive disorder. By studying 23 inbred families, we...