Heterologously expressed fungal transient receptor potential channels retain mechanosensitivity in vitro and osmotic response in vivo

The budding yeast Saccharomyces cerevisiae has a mechanosensitive channel, TrpY1, a member of the Trp superfamily of channels associated with various sensations. Upon a hyperosmotic shift, a yeast cell releases Ca²⁺ from the vacuole to the cytoplasm through this channel. The TRPY1 gene has orthologs in other fungal genomes, including TRPY2 of Kluyveromyces lactis and TRPY3 of Candida albicans. We subcloned TRPY2 and TRPY3 and expressed them in the vacuole of S. cerevisiae deleted of TRPY1. The osmotically induced Ca²⁺ transient was restored in vivo as reported by transgenic aequorin. Patch-clamp examination showed that the TrpY2 or the TrpY3 channel was similar to TrpY1 in unitary conductance, rectification properties, Ca²⁺ sensitivity, and mechanosensitivity. The retention of mechanosensitivity of transient receptor potential channels in a foreign setting, shown here both in vitro and in vivo, implies that these mechanosensitive channels, like voltage-gated or ligand-gated channels, do not discriminate their settings. We discuss various mechanisms, including the possibility that stress from the lipid bilayer by osmotic force transmits forces to the transmembrane domains of these channels.     

色氨酸操纵子调控机理详析

色氨酸操纵子是最早被研究的细菌合成代谢调控、基因表达调控的模型之一。其中阻遏蛋白对转录起始的抑制作用、色氨酸作为辅阻遏物的作用以及通过定点突变揭示的弱化作用的分子机制已基本被阐明。此外,色氨酸操纵子RNA结合弱化蛋白、NusA、NusG、TrpY等调节蛋白对细菌色氨酸操纵子弱化作用的调节机制也在近年来得到进一步揭示。特别是在枯草芽孢杆菌中,色氨酸操纵子主要依赖于转录衰减机制调控,包括由色氨酸激活的色氨酸操纵子RNA结合弱化蛋白与新生转录产物结合形成内部终止子,导致5′非翻译区（5′UTR）转录终止。NusA、NusG通过刺激RNA聚合酶在5′UTR的U107和U144位点暂停,释放出RNA聚合酶,最终造成转录终止。不同的是,在U144位点NusA参与的转录弱化机制依赖其发夹结构,且NusA与RNA聚合酶作用促进了RNA结合弱化蛋白与新生转录产物的结合,使转录终止。而NusG是通过与非模板DNA链中的一段富含T碱基序列和RNA聚合酶同时互作,阻止了RNA聚合酶向下游移动,从而引起RNA聚合酶高效停滞。但在细菌操纵子中,绝大多数调节因子参与的弱化机制最终依赖于ρ因子,从而导致多达一半的转录终止事件发生。近年来,随着学科的发展,越来越多关于色氨酸操纵子调节机制新概念被挖掘报道,这也使人类对色氨酸操纵子的表达调控机制的认知愈加详尽。     

Effect of tryptophan on isolated hepatocytes of rats

The addition of tryptophan to adult rat hepatocyte cultures stimulated DNA synthesis. The increase in DNA synthesis as measured by 3H-thymidine incorporation into DNA was observed on treatment of the cultures with tryptophan for 48 h but also as short as for 6 h in comparison with control cultures. An increase was also apparent at 30 h which was maintained for up to 48 h post treatment with tryptophan. The increase in DNA synthesis by tryptophan cannot be attributed to cell injury or to increased DNA degradation. Of the degradative enzymes added after harvesting the hepatocytes, only DNase decreased incorporation of 3H-thymidine. The observed effect was specific for tryptophan since treatment with kynurenine, isoleucine, methionine or serine failed to show a significant effect. Pretreatment of cultured hepatocytes with hydroxyurea prevented the tryptophan stimulated increase in DNA synthesis suggesting that the latter was due to replicative and not to reparative DNA synthesis. Experiments performed with the addition of diethylnitrosamine also alluded to tryptophan's role in replicative DNA synthesis. The mechanism of tryptophan-induced DNA synthesis is discussed.     

Synthesis and DNA binding properties of tryptophan linked monocationic netropsin analogues

One tryptophan (Trp-Net) and two tryptophan (Trp-Trp-Net) residues have been linked to the amino terminus of a minor groove binding Netropsin analogue. DNA metling measurements indicate that Trp-Trp-Net binds significantly stronger than Trp-Net to double helical DNA. Both compounds induce helix extension as measured by changes in DNA viscosity indicating the possibility of intercalation of the tryptophan indole ring.     

Solution structural studies of the Saccharomyces cerevisiae TATA binding protein (TBP)

The intrinsic fluorescence of the six tyrosines located within the C-terminal domain of the Saccharomyces cerevisiae TATA binding protein (TBP) and the single tryptophan located in the N-terminal domain has been used to separately probe the structural changes associated with each domain upon DNA binding or oligomerization of the protein. The unusually short-wavelength maximum of TBP fluorescence is shown to reflect the unusually high quantum yield of the tyrosine residues in TBP and not to result from unusual tryptophan fluorescence. The anisotropy of the C-terminal tyrosines is very high in monomeric, octameric, and DNA-complexed TBP and comparable to that observed in much larger proteins. The tyrosines have low accessibility to an external fluorescence quencher. The anisotropy of the single tryptophan located within the N-terminal domain of TBP is much lower than that of the tyrosines and is accessible to an external fluorescence quencher. Tyrosine, but not tryptophan, fluorescence is quenched upon TBP-DNA complex formation. Only the tryptophan fluorescence is shifted to longer wavelengths in the protein-DNA complex. In addition, the accessibility of the tryptophan residue to the external quencher and the internal motion of the tryptophan residue increase upon DNA binding by TBP. These results show the following: (i) The structure of the C-terminal domain structure is unchanged upon TBP oligomerization, in contrast to the N-terminal domain [Daugherty, M. A., Brenowitz, M., and Fried, M. G. (2000) Biochemistry 39, 4869-4880]. (ii) The environment of the tyrosine residues within the C-terminal domain of TBP is structurally rigid and unaffected by oligomerization or DNA binding. (iii) The C-terminal domain of TBP is uniformly in close proximity to bound DNA. (iv) While the N-terminal domain unfolds upon DNA binding by TBP, its increased correlation time shows that the overall structure of the protein is more rigid when complexed to DNA. A model that reconciles these results is proposed.     

Fluorescence and chemical studies on the interaction of Escherichia coli DNA-binding protein with single-stranded DNA.

Nanosecond and steady-state fluorescence spectoscopy were used to probe the environment of the tryptophan residues of Escherichia coli DNA-binding protein. A spectral shift and a change in quantum yield of the protein upon binding to DNA or oligonucleotides indicate that the tryptophan residues are near or at the DNA binding site. The observation of two excited-state lifetimes of the protein indicates that there is heterogeneity in the microenvironments of these tryptophan residues. The "short-lifetime" tryptophan residues are more sensitive to the interaction with DNA than the "long-lifetime" residues. The results of solute-perturbation studies with iodide or acrylamide indicate that there are tryptophan residues near the surface of the protein which are heterogeneous in their accessibility to these quenchers and that they become less accessible after DNA binding. Also, lysine residues of the protein have been shown to be essential to DNA binding by chemical-modification studies. Tyrosine, arginine, and cysteine residues appear not to be involved in this binding process. From studies of the decay of fluorescence anisotropy of the binding protein in the presence and absence of DNA, it has been concluded that (a) the tetrameric binding protein does not dissociate into subuniits upon binding to the oligonucleotide d(pT)16 and (b) the binding protein-fd DNA complex possesses "local flexibility" and, therefore, cannot be described as a continuous, rigid rod.     

Construction and characterization of mutations at codon 751 of the Escherichia coli gyrB gene that confer resistance to the antimicrobial peptide microcin B17 and alter the activity of DNA gyrase

Microcin B17 is a peptide antibiotic that inhibits DNA replication in Escherichia coli by targeting DNA gyrase. Previously, two independently isolated microcin B17-resistant mutants were shown to harbor the same gyrB point mutation that results in the replacement of tryptophan 751 by arginine in the GyrB polypeptide. We used site-directed mutagenesis to construct mutants in which tryptophan 751 was deleted or replaced by other amino acids. These mutants exhibit altered DNA gyrase activity and different levels of resistance to microcin B17.     

Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor

EcoRI endonuclease has two tryptophans at positions 104 and 246 on the protein surface. A single tryptophan mutant containing Trp246 and a single cysteine labeling site at the N-terminus was used to determine the position of the N-terminus in the protein structure. The N-termini of EcoRI endonuclease are essential for tight binding and catalysis yet are not resolved in any of the crystal structures. Resonance energy transfer was used to measure the distance from Trp246 donor to IAEDANS or MIANS acceptors at Cys3. The distance is 36 A in apoenzyme, decreasing to 26 A in the DNA complex. Molecular modeling suggests that the N-termini are located at the dimer interface formed by the loops comprising residues 221-232. Protein conformational changes upon binding of cognate DNA and cofactor Mg(2+) were monitored by tryptophan fluorescence of the single tryptophan mutant and wild-type endonuclease. The fluorescence decay of Trp246 is a triple exponential with lifetimes of 7, 3.5, and 0.7 ns. The decay-associated spectra of the 7- and 3.5-ns components have emission maxima at approximately 345 and approximately 338 nm in apoenzyme, which shift to approximately 340 and approximately 348 nm in the DNA complex. The fluorescence quantum yield of the single tryptophan mutant drops 30% in the DNA complex, as compared to 10% for wild-type endonuclease. Fluorescence changes of Trp104 upon binding of DNA were inferred by comparison of the decay-associated spectra of wild type and single tryptophan mutant. Fluorescence changes are related to changes in proximity and orientation of quenching functional groups in the tryptophan microenvironments, as seen in the crystal structures.     

Indoleamine 2,3-dioxygenase participates in the interferon-gamma-induced cell death process in cultured bovine luteal cells

Interferon-gamma (IFNG) induces apoptotic cell death in bovine luteal cells, but the pathway(s) involved in this process are not well defined. Evidence supporting the involvement of an IFNG-inducible enzymatic pathway that degrades tryptophan in IFNG-induced death of bovine luteal cells is presented in this study. The IFNG-inducible enzyme indoleamine 2,3-dioxygenase (INDO) catalyzes the first step in a metabolic pathway that degrades tryptophan. In the first experiment, RT-PCR revealed the presence of INDO mRNA in luteal cells treated with IFNG, but not in untreated cells. To determine whether INDO participates in IFNG-induced death of bovine luteal cells, an experiment was performed to test the effect of 1-methyl-D-tryptophan (1-MT), an inhibitor of INDO, on IFNG-induced DNA fragmentation in luteal cells. Single-cell gel electrophoresis and microscopic image analysis revealed that 1-MT inhibited DNA fragmentation induced by IFNG. To determine whether supplementation of cell cultures with additional tryptophan could also protect luteal cells from IFNG-induced DNA fragmentation, luteal cells were cultured in the presence of IFNG, and L-tryptophan was added to cultures to achieve final concentrations that were 5-, 10-, or 25-fold higher than the concentration of L-tryptophan found in nonsupplemented culture medium. Supplementation of IFNG-treated luteal cell cultures with elevated concentrations of tryptophan also prevented IFNG-induced DNA fragmentation. We conclude that INDO participates in IFNG-induced death of bovine luteal cells, through a mechanism that involves degradation of tryptophan, thereby reducing tryptophan concentrations to a point insufficient to meet luteal cells needs.     

Human tryptophan oxygenase localized to 4q31: possible implications for alcoholism and other behavioral disorders

A human tryptophan oxygenase clone was isolated by screening a liver cDNA library with a rat tryptophan oxygenase cDNA clone. Analysis showed extensive homology between the rat and the human DNA and protein sequences. The combined use of cell hybrids and in situ hydridization indicated that human tryptophan oxygenase was localized to chromosome band 4q31. The tryptophan oxygenase gene may be important in some human behavior disorders, especially those associated with abnormalities of serotonin metabolism.     

Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis

During industrial production process using yeast, cells are exposed to the stress due to the accumulation of ethanol, which affects the cell growth activity and productivity of target products, thus, the ethanol stress-tolerant yeast strains are highly desired. To identify the target gene(s) for constructing ethanol stress tolerant yeast strains, we obtained the gene expression profiles of two strains of Saccharomyces cerevisiae, namely, a laboratory strain and a strain used for brewing Japanese rice wine (sake), in the presence of 5% (v/v) ethanol, using DNA microarray. For the selection of target genes for breeding ethanol stress tolerant strains, clustering of DNA microarray data was performed. For further selection, the ethanol sensitivity of the knockout mutants in each of which the gene selected by DNA microarray analysis is deleted, was also investigated. The integration of the DNA microarray data and the ethanol sensitivity data of knockout strains suggests that the enhancement of expression of genes related to tryptophan biosynthesis might confer the ethanol stress tolerance to yeast cells. Indeed, the strains overexpressing tryptophan biosynthesis genes showed a stress tolerance to 5% ethanol. Moreover, the addition of tryptophan to the culture medium and overexpression of tryptophan permease gene conferred ethanol stress tolerance to yeast cells. These results indicate that overexpression of the genes for trypophan biosynthesis increases the ethanol stress tolerance. Tryptophan supplementation to culture and overexpression of the tryptophan permease gene are also effective for the increase in ethanol stress tolerance. Our methodology for the selection of target genes for constructing ethanol stress tolerant strains, based on the data of DNA microarray analysis and phenotypes of knockout mutants, was validated.     

Analysis of trp repressor-operator interaction by filter binding.

A filter binding assay was developed that allows measurement of specific binding of trp repressor to operator DNA. The most important feature of this procedure is the concentration and type of salt present in the binding buffer. Using this assay the dissociation constant of the repressor-operator complex was determined to be 2.6 X 10(-9) M, and 1.34 repressor dimers were found to be bound to each operator-containing DNA molecule. These values agree with those obtained by more complex methods. The dissociation constant of the repressor for the corepressor L-tryptophan in the presence of operator DNA was shown to be 2.5 X 10(-5) M. A synthetic 48 bp operator fragment was used to determine the repressor-operator dissociation constant in the presence of tryptophan or tryptophan analogs which have higher or lower affinities for aporepressor. The rate of dissociation of repressor from operator DNA also was determined. Our findings indicate that dissociation is influenced by the concentration of tryptophan or tryptophan analogs and suggest that release of the corepressor may be the first step in dissociation of the repressor-operator complex.     

Vitamin E protects against methyl ethyl ketone peroxide-induced peroxidative damage to rat brain DNA

Peroxidative damage to DNA initiated by methyl ethyl ketone peroxide, a potent initiator of lipid peroxidation, and protection against this damage by vitamin E were studied in rats. Groups of rats were fed a casein-based diet that contained 10% tocopherol-stripped corn oil and either 0, 3, 5, or 10 IU of DL-alpha-tocopherol acetate/kg; the groups were named 0, 3, 5, or 10, respectively. DNA isolated from the brains of these rats was analyzed for template activity, bound tryptophan, and malondialdehyde-type DNA-protein and interstrand DNA crosslinks. The DNA of groups 5 and 10 had significantly higher template activity, less bound tryptophan, and fewer crosslinks than that of groups 3 and 5, respectively. The DNA of group 3 had significantly fewer interstrand DNA crosslinks than that of group 0, and the most significant differences were between groups 3 and 5. Loss of template activity correlated best with interstrand DNA crosslinks, and bound tryptophan correlated best with DNA-protein crosslinks. Electrophoresis of the RNA transcribed from the isolated DNA showed that a significantly higher percentage of longer RNA was made from the DNA of groups 5 and 10 than from that of group 0. The apparent molecular weight of the DNA of group 0 was less than that of group 10 and was more heterogeneous, which suggests fragmentation and/or crosslinking. The DNA from group 10 had maximum observed template activity; therefore, 10 IU of vitamin E/kg of diet appeared to be adequate to protect brain DNA against the damage measured in this study.     

Tryptophan in alpha-helix 3 of Tet repressor forms a sequence-specific contact with tet operator in solution

The Tn10-encoded Tet repressor contains two tryptophan residues at positions 43 and 75. The typical tryptophan fluorescence is decreased upon binding of tet operator. The Tet repressor gene was engineered to replace either or both of the Trp codons by Phe codons. The resulting single tryptophan mutants are called F43 and F75 and the double mutant F43F75. The mutant proteins were purified to homogeneity. They recognize tet operator DNA only in the absence of the inducer tetracycline, indicating an intact tertiary structure of the engineered proteins. F75 and wild-type bind tet operator with the same association constant. The association constants of F43 and F43F75 with tet operator are about 3 orders of magnitude smaller. This indicates that Trp43 is important for tet operator recognition. Trp43 fluorescence is completely quenched in the complex with tet operator DNA while Trp75 remains unaffected. Binding to nonspecific DNA leads only to a 40% decrease of Trp43 fluorescence. This is interpreted as the contribution of the changed environment while the complete quench reflects a tight sequence-specific contact of tryptophan 43 to tet operator DNA. Trp43 is solvent-exposed, while Trp75 is buried in the hydrophobic interior of the protein. These results are discussed in light of the alpha-helix turn-alpha-helix DNA binding motif deduced from homology to other repressor proteins.