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PubMed1985

Homozygosity, effective number of alleles, and interdeme differentiation in subdivided populations.

The amount and pattern of genetic variability in a geographically structured population at equilibrium under the joint action of migration, mutation, and random genetic drift is studied. The monoecious, diploid population is subdivided into panmictic colonies that exchange migrants. Self-fertilization does not occur; generations are discrete and nonoverlapping; the analysis is restricted to a single locus in the absence of selection; every allele mutates to new alleles at the same rate. It is shown that if the number of demes is finite and migration does not alter the deme sizes, then population subdivision produces interdeme differentiation and the mean homozygosity and the effective number of alleles exceed their panmictic values. A simple relation between the mean probability of identity and the mean homozygosity is established. The results apply to a dioecious population if the migration pattern and mutation rate are sex independent.

Alleles↗
PubMed1993

Cellular interactions implicated in the mechanism of photoreceptor degeneration in transgenic mice expressing a mutant rhodopsin gene.

Photoreceptors of transgenic mice expressing a mutant rhodopsin gene (Pro347-->Ser) slowly degenerate. The mechanism of degeneration was studied by aggregation of embryos of normal and transgenic mice to form chimeras. In these chimeras, mosaicism was observed in the coat color, retinal pigment epithelium, and retina. In the retina, the genotype of adjacent patches of normal and transgenic photoreceptors was determined by in situ hybridization with a transgene-specific RNA probe. Photoreceptors in the chimeric retina degenerated uniformly, independent of the genotype and similar to the photoreceptors in transgenic mice. However, the chimeric retinas showed varying proportions of normal and transgenic cells. The chimeric retina with a nearly even proportion of normal and transgenic photoreceptors displayed uniform but slower degeneration than that observed in a transgenic mouse of the same age. Our results demonstrate non-autonomy of gene action for the mutated rhodopsin gene and imply that cellular interactions between photoreceptors in the retina probably play a role in degeneration.

Amino Acid Sequence↗
PubMed1994

Midline signaling in the primordium of the zebrafish anterior central nervous system.

In all vertebrates the brain develops from the enlarged anterior part of the neural plate. However, in the zebrafish mutant cyclops, the girth of the central nervous system (CNS) is nearly uniform along its length. Changes in expression patterns of homeobox genes and neuronal markers reveal a massive deletion of the ventral forebrain, particularly the diencephalon, as well as its precursor region in the neural plate. The deletion is due to a nonautonomous action of the mutation: very few wild-type cells transplanted to the midline of a mutant embryo can rescue the forebrain phenotype, including cyclopia. Establishment of forebrain ventral positional coordinates may thus require inductive signaling by forebrain midline cells whose specification depends upon the cyclops gene product.

Animals↗
PubMed1999

Enhancement of translation by the downstream box does not involve base pairing of mRNA with the penultimate stem sequence of 16S rRNA.

The downstream box (DB) is a sequence element that enhances translation of several bacterial and phage mRNAs. It has been proposed that the DB enhances translation by base pairing transiently to bases 1469-1483 of 16S rRNA, the so-called anti-DB, during the initiation phase of translation. We have tested this model of enhancer action by constructing mutations in the anti-DB that alter its mRNA base-pairing potential and examining expression of a variety of DB-containing mRNAs in strains expressing the mutant anti-DB 16S rRNA. We found that the rRNA mutant was viable and that expression of all tested DB-containing mRNAs was completely unaffected by radical alterations in the proposed anti-DB. These findings lead us to conclude that enhancement of translation by the DB does not involve mRNA-rRNA base pairing.

Bacterial Proteins↗
PubMed1995

Mutagenic analysis of double-stranded RNA adenosine deaminase, a candidate enzyme for RNA editing of glutamate-gated ion channel transcripts.

Mutagenic analysis of the substrate binding and catalytic domains of double-stranded RNA (dsRNA) adenosine deaminase (DRADA) was carried out. This nuclear enzyme is likely to be involved in the RNA editing of glutamate-gated ion channels that are essential for fast excitatory neurotransmission in mammalian brain. The deletion of the first or the third of the three dsRNA binding motifs within the substrate binding domain dramatically decreases enzyme activity, whereas the second motif seems to be dispensable. The results indicate that the three motifs are not functionally equivalent in the catalytic action of DRADA. Mutation of the putative zinc-coordinating residues, His910, Cys966, and Cys1036, abolished the DRADA activity. Similarly, the Glu912 residue, predicted to be involved in the proton transfer functions of the enzyme, was found to be indispensable. Our results reinforce the previous proposal that the hydrolytic deamination mechanism of DRADA may be more similar to that of the cytidine deaminases than of adenosine deaminases.

Adenosine Deaminase↗
PubMed1994

Dictyostelium discoideum mutants with conditional defects in phagocytosis.

We have isolated and characterized Dictyostelium discoideum mutants with conditional defects in phagocytosis. Under suspension conditions, the mutants exhibited dramatic reductions in the uptake of bacteria and polystyrene latex beads. The initial binding of these ligands was unaffected, however, indicating that the defect was not in a plasma membrane receptor: Because of the phagocytosis defect, the mutants were unable to grow when cultured in suspensions of heat-killed bacteria. The mutants exhibited normal capacities for fluid phase endocytosis and grew as rapidly as parental (AX4) cells in axenic medium. Both the defects in phagocytosis and growth on bacteria were corrected when the mutant Dictyostelium cells were cultured on solid substrates. Reversion and genetic complementation analysis suggested that the mutant phenotypes were caused by single gene defects. While the precise site of action of the mutations was not established, the mutations are likely to affect an early signaling event because the binding of bacteria to mutant cells in suspension was unable to trigger the localized polymerization of actin filaments required for ingestion; other aspects of actin function appeared normal. This class of conditional phagocytosis mutant should prove to be useful for the expression cloning of the affected gene(s).

Animals↗
PubMed2005

LIS-less neurons don't even make it to the starting gate.

The manuscript by Tsai et al. (935-945) is a tour de force analysis of a controversial issue in developmental neurobiology, namely the molecular basis of the devastating human brain malformation, type I lissencephaly (Lis1) (Jellinger, K., and A. Rett. 1976. Neuropadiatrie. 7:66-91). For several decades, defects in neuronal migration have been assumed to underlie all defects in cortical histogenesis. In the paper by Tsai et al., the authors use a variety of elegant approaches, including the first real-time imaging of cortical neurons with reduced levels of LIS1, to demonstrate that LIS1 and dynactin act as regulators of dynein during cortical histogenesis. A loss of LIS1 results in both a failure to exit the cortical germinal zone and abnormal neuronal process formation. Thus, the primary action of the mutation is to disrupt the production of neurons in the developing brain as well as their migration.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗
PubMed1999

New yeast genes important for chromosome integrity and segregation identified by dosage effects on genome stability.

Phenotypes produced by gene overexpression may provide important clues to gene function. Here, we have performed a search for genes that affect chromo-some stability when overexpressed in the budding yeast Saccharomyces cerevisiae. We have obtained clones encompassing 30 different genes. Twenty-four of these genes have been previously characterized. Most of them are involved in chromatin dynamics, cell cycle control, DNA replication or mitotic chromosome segregation. Six novel genes obtained in this screen were named CST (chromosome stability). Based on the pattern of genomic instability, inter-action with checkpoint mutations and sensitivity to chromosome replication or segregation inhibitors, we conclude that overexpression of CST4 specifically interferes with mitotic chromosome segregation, and CST6 affects some aspect of DNA metabolism. The other CST genes had complex pleiotropic phenotypes. We have created deletions of five genes obtained in this screen, CST9, CST13, NAT1, SBA1 and FUN30. None of these genes is essential for viability, and deletions of NAT1 and SBA1 cause chromosome instability, a phenotype not previously associated with these genes. This work shows that analysis of dosage effects is complementary to mutational analysis of chromosome transmission fidelity, as it allows the identification of chromosome stability genes that have not been detected in mutational screens.

Aneuploidy↗
PubMed2001

Enhancement of translation by the epsilon element is independent of the sequence of the 460 region of 16S rRNA.

The epsilon enhancer element is a pyrimidine-rich sequence that increases expression of T7 gene 10 and a number of Escherichia coli mRNAs during initiation of translation and inhibits expression of the recF mRNA during elongation. Based on its complementarity to the 460 region of 16S rRNA, it has been proposed that epsilon exerts its enhancer activity by base pairing to this complementary rRNA sequence. We have tested this model of enhancer action by constructing mutations in the 460 region of 16S rRNA and examining expression of epsilon-containing CAT reporter genes and recF-lacZ fusions in strains expressing the mutant rRNAs. Replacement of the 460 E.coli stem-loop with that of Salmonella enterica serovar Typhimurium or a stem-loop containing a reversal of all 8 bp in the helical region produced fully functional rRNAs with no apparent effect on cell growth or expression of any epsilon-containing mRNA. Our experiments confirm the reported effects of the epsilon elements on gene expression but show that these effects are independent of the sequence of the 460 region of 16S rRNA, indicating that epsilon-rRNA base pairing does not occur.

Bacterial Proteins↗
PubMed1988

Cation channels from ciliary membrane of Tetrahymena reconstituted into planar lipid bilayer. Comparison between the channels from the wild T. thermophila and from its mutant which does not show ciliary reversal.

Cation channels in ciliary membrane vesicles from wild type Tetrahymena thermophila and from its mutant which does not show ciliary reversal or avoiding reaction were reconstituted into a planar lipid bilayer. Since the mutant does not produce the regenerative Ca2+ action potential, the mutation was expected to have occurred at the Ca-channel in the ciliary membrane. In the sample from the mutant, the channel most frequently observed was selective for cations over anions. The single channel conductance shows Michaelis-Menten type dependency on the cation concentration. The maximum conductance and dissociation constants (in parenthesis) for K+, Mg2+, Ca2+, and Ba2+ were 371 pS (23.3 mM), 17 pS (0.49 mM), 18 pS (0.52 mM), and 25 pS (0.82 mM), respectively, when the anion was gluconate. The properties of the corresponding channel from the wild type are similar to those from the mutant. No essential difference was detected, which indicates that the predominant channel is not the putative Ca channel responsible for the avoiding reaction of Tetrahymena. Some other channels than the predominant channel were also observed.

Animals↗
PubMed2001

The case for large-size mutations.

There are no laws of physics or chemistry that forbid large mutations. Therefore, the "size" of a random mutation should fit the mathematics of a Poisson point process: The number of mutations (N), versus mutation size (MS), should obey an exponential relationship. Three examples are examined: A simple 15-mutation sequence; actual experimental data involving a sequence of 56,611 random action potentials (rather than mutations); and a synthetic sequence of 65,535 random mutations. In the latter example, with an average MS of 2.22 units, the largest MS is a 25-unit giant that would be associated with major changes.

Evolution, Molecular↗
PubMed2004

Relations between substrate affinities and charge equilibration rates in the rat GABA cotransporter GAT1.

The relations between apparent affinity for substrates and operating rates have been investigated by two-electrode voltage clamp in the GABA transporter rGAT1 expressed in Xenopus oocytes. We have measured the transport current induced by the presence of GABA, as well as the charge equilibration rate in the absence of the neurotransmitter, in various experimental conditions known to affect the transporter characteristics. The apparent affinities for GABA and for Na(+) were also determined in the same conditions. Two pharmacological actions and three mutated isoforms have been examined. In all cases significant correlations were found between the charge equilibration rates and apparent affinities for both substrates. In particular in the transport process, the apparent affinity for GABA appears to be inversely related to the sum of the unidirectional charge equilibration rates (alpha+beta), while the Na(+) apparent affinity is directly related to their ratio (beta/alpha). Together these observations suggest a kinetic basis for GABA affinity with higher turnover rates resulting in lower affinity, and indicate that an efficient uptake requires a compromise between these two parameters.

Animals↗
PubMed2003

Crucial role of extracellular signal-regulated kinase pathway in reactive oxygen species-mediated endothelin-1 gene expression induced by endothelin-1 in rat cardiac fibroblasts.

Endothelin-1 (ET-1) has been implicated in fibroblast proliferation. However, the mechanism involving ET-1 is not clear. The present study was performed to examine the role of endogenous ET-1 in ET-1-stimulated fibroblast proliferation and to investigate the regulatory mechanism of ET-1-induced ET-1 gene expression in cardiac fibroblasts. Both ET(A) receptor antagonist [(hexahydro-1H-azepinyl)carbonyl-Leu-D-Trp-D-OH (BQ485)] and endothelin-converting enzyme inhibitor (phosphoramidon) inhibited the increased DNA synthesis caused by ET-1. ET-1 gene was induced by ET-1, as revealed with Northern blotting and ET-1 promoter activity assay. ET-1 increased intracellular reactive oxygen species (ROS), which were significantly inhibited by BQ485 and antioxidants. Antioxidants suppressed ET-1 gene expression and DNA synthesis stimulated by ET-1. ET-1 activated mitogen-activated protein kinases (MAPK), including extracellular signal-regulated kinase (ERK), p38 MAPK, and c-Jun N-terminal kinase, which were significantly inhibited by antioxidants. Only ERK inhibitor U0126 could inhibit ET-1-induced transcription of the ET-1 gene. Cotransfection of dominant-negative mutant of Ras, Raf, and MEK1 decreased the ET-1-induced increase in ET-1 transcription, suggesting that the Ras-Raf-ERK pathway is required for ET-1 action. Truncation and mutational analysis of the ET-1 gene promoter showed that the activator protein-1 (AP-1) binding site was an important cis-element in ET-1-induced ET-1 gene expression. Antioxidants attenuated the ET-1-stimulated AP-1 binding activity. Our data suggest that ROS were involved in ET-1-induced fibroblast proliferation and mediated ET-1-induced activation of ERK pathways, which culminated in ET-1 gene expression.

Animals↗
PubMed2006

Protease activity, secretion, cell entry, cytotoxicity, and cellular targets of secreted autotransporter toxin of uropathogenic Escherichia coli.

The secreted autotransporter toxin (Sat), found predominantly in uropathogenic Escherichia coli, is a member of the SPATE (serine protease autotransporters of Enterobacteriaceae) family and, as such, has serine protease activity and causes cytopathic effects on various cell types. To assess the contribution of the serine protease active site to the mechanism of action of Sat, mutations were made in the first (S256I), in the second (S258A), or in both (S256I/S258A) serine residues within the active site motif. Mutations in the first or both serines reduced protease activity to background levels (P<0.001); a single mutation in the second serine reduced activity by 60% compared to wild type (P<0.001). After reversion of the S256I mutation to wild type (I256S), we confirmed S256 as the catalytically active serine. None of these mutations affected secretion of the mature passenger domain or release into the supernatant. The S256I mutation, however, abrogated the cytotoxicity of Sat on human bladder (UM-UC-3) and kidney (HEK 293) epithelial cells, characterized by rounding and elongation, respectively, and a high level of cell detachment. Moreover, S256 is essential for Sat to mediate cytoskeletal contraction and actin loss in host cells as well as to degrade specific membrane/cytoskeletal (fodrin and leukocyte function-associated molecule 1) and nuclear [microtubule-associated proteins, LIM domain-only protein 7, Rap GTPase-activating protein, poly(ADP-ribose) polymerase] proteins in vitro. Lastly, Sat was internalized by host cells and localized to the cytoskeletal fraction where membrane/cytoskeletal target proteins reside.

Bacterial Toxins↗
PubMed1970

Elimination of sex factors in Escherichia coli by urea.

Eliminatory action of urea on the sex factor (F) in Escherichia coli K-12 strains is reported. Growth of E. coli harboring F or F'8 (F-gal) factors in Penassay Broth containing urea led to the loss of these genetic elements and yielded F(-) cells. Appearance of F(-) cells among survivors was already observed when the culture was in the very early stage of exponential phase. However, frequencies of F(-) cells formed did not increase much as a function of the incubation time. Unusual F(+) or F'8 cells which retained the ability of genetic transfer but showed resistance to M12 phage were also isolated. Addition of sucrose to broth with urea led to the favorable growth of cells in the culture and the increase, if little, of elimination frequencies of F factors by urea. These findings, coupled with other observations, suggest that urea has two separate actions in enhancing the frequency of F(-) bacteria, namely, (i) to inactivate F by direct action, such as mutation, and (ii) to select the F(-) variants by differentially inhibiting the growth of F(+).

Bacteriological Techniques↗
PubMed2002

Mutant forms of the Azotobacter vinelandii transcriptional activator NifA resistant to inhibition by the NifL regulatory protein.

The Azotobacter vinelandii sigma(54)-dependent transcriptional activator protein NifA is regulated by the NifL protein in response to redox, carbon, and nitrogen status. Under conditions inappropriate for nitrogen fixation, NifL inhibits transcription activation by NifA through the formation of the NifL-NifA protein complex. NifL inhibits the ATPase activity of the central AAA+ domain of NifA required to drive open complex formation by sigma(54)-RNA polymerase and may also inhibit the activator-polymerase interaction. To analyze the mechanism of inhibition in greater detail, we isolated NifA mutants which are resistant to the inhibitory action of NifL. Mutations in both the amino-terminal GAF domain and the catalytic AAA+ domain of NifA were isolated. Several mutants blocked inhibition by NifL in response to both nitrogen and redox status, whereas some of the mutant NifA proteins were apparently able to discriminate between the forms of NifL present under different environmental conditions. One mutant protein, NifA-Y254N, was resistant to NifL under conditions of anaerobic nitrogen excess but was relatively sensitive to NifL under aerobic growth conditions. The properties of the purified mutant protein in vitro were consistent with the in vivo phenotype and indicate that NifA-Y254N is not responsive to the nitrogen signal conveyed by the interaction of NifL with A. vinelandii GlnK but is responsive to the oxidized form of NifL when ADP is present. Our observations suggest that different conformers of NifL may be generated in response to discrete signal transduction events and that both the GAF and AAA+ domains of NifA are involved in the response to NifL.

Adenosine Triphosphate↗
PubMed1986

Product of Saccharomyces cerevisiae nuclear gene PET494 activates translation of a specific mitochondrial mRNA.

The product of Saccharomyces cerevisiae nuclear gene PET494 is known to be required for a posttranscriptional step in the accumulation of one mitochondrial gene product, subunit III of cytochrome c oxidase (coxIII). Here we show that the PET494 protein probably acts in mitochondria by demonstrating that both a PET494-beta-galactosidase fusion protein and unmodified PET494 are specifically associated with mitochondria. To define the PET494 site of action, we isolated mutations that suppress a pet494 deletion. These mutations were rearrangements of the mitochondrial gene oxi2 that encodes coxIII. The suppressor oxi2 genes had acquired the 5'-flanking sequences of other mitochondrial genes and gave rise to oxi2 transcripts carrying the 5'-untranslated leaders of their mRNAs. These results demonstrate that in wild-type cells PET494 specifically promotes coxIII translation, probably by interacting with the 5'-untranslated leader of the oxi2 mRNA.

Base Sequence↗
PubMed2005

Carbonic anhydrase IX expression and tumor oxygenation status do not correlate at the microregional level in locally advanced cancers of the uterine cervix.

PURPOSE: Carbonic anhydrase IX (CA IX) can be induced by hypoxia in vitro and shows an immunohistochemical expression pattern that is predominantly found in perinecrotic tumor areas and correlates with exogenous markers of hypoxia, such as pimonidazole. CA IX might therefore serve as an endogenous marker of tumor hypoxia, although comparisons of CA IX immunostaining with direct oxygenation measurements using pO2 microsensors have thus far yielded contradictory results. EXPERIMENTAL DESIGN: Because tumor heterogeneity may be among the factors responsible for the discrepancy between the two methods, CA IX expression in tissue samples originating from oxygen microelectrode tracks of locally advanced cervical cancers was assessed in this study. Seventy-seven biopsy specimens were analyzed immunohistochemically using an anti-CA IX rabbit polyclonal antibody and semiquantitative scoring. RESULTS: CA IX expression showed no correlation with the oxygenation variables median pO2 and hypoxic fraction 2.5, 5, or 10. Cases with higher International Federation of Gynecology and Obstetrics stages (IIb-IVa) exhibited stronger expression of CA IX (P = 0.035) and CA IX expression tended to be more prevalent in node-positive patients (P = 0.051). CONCLUSIONS: These data indicate that CA IX cannot be recommended as a substitute for oxygen microelectrode measurements. That the expression of CA IX does not correlate with the oxygenation status may be due to the degree to which other factors, such as nutrient (e.g., glucose) deficiency or the action of oncogenic mutations, can modulate the in vivo expression of this protein, rendering a strict association with tumor hypoxia too unreliable for clinical use.

Antigens, Neoplasm↗