scholarly journals Mutations in VPS16 and MRT1Stabilize mRNAs by Activating an Inhibitor of the Decapping Enzyme

1999 ◽  
Vol 19 (11) ◽  
pp. 7568-7576 ◽  
Author(s):  
Shuang Zhang ◽  
Carol J. Williams ◽  
Kevin Hagan ◽  
Stuart W. Peltz
Keyword(s):  
Rna Stability ◽  
Wild Type ◽  
Mrna Decapping ◽  
Hsp70 Family ◽  
Rate Limiting Step ◽  
Nonsense Codon ◽  
Decapping Enzyme ◽  
Rate Limiting

ABSTRACT Decapping is a rate-limiting step in the decay of many yeast mRNAs; the activity of the decapping enzyme therefore plays a significant role in determining RNA stability. Using an in vitro decapping assay, we have identified a factor, Vps16p, that regulates the activity of the yeast decapping enzyme, Dcp1p. Mutations in the VPS16 gene result in a reduction of decapping activity in vitro and in the stabilization of both wild-type and nonsense-codon-containing mRNAs in vivo. The mrt1-3 allele, previously shown to affect the turnover of wild-type mRNAs, results in a similar in vitro phenotype. Extracts from both vps16 and mrt1 mutant strains inhibit the activity of purified Flag-Dcp1p. We have identified a 70-kDa protein which copurifies with Flag-Dcp1p as the abundant Hsp70 family member Ssa1p/2p. Intriguingly, the interaction with Ssa1p/2p is enhanced in strains with mutations in vps16 ormrt1. We propose that Hsp70s may be involved in the regulation of mRNA decapping.

scholarly journals Determining the Rate-Limiting Step for Light-Responsive Redox Regulation in Chloroplasts

Antioxidants ◽  
2018 ◽  
Vol 7 (11) ◽  
pp. 153 ◽  
Author(s):  
Keisuke Yoshida ◽  
Toru Hisabori
Keyword(s):  
Redox Regulation ◽  
Reducing Power ◽  
Rubisco Activase ◽  
Power Transfer ◽  
Target Proteins ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

Thiol-based redox regulation ensures light-responsive control of chloroplast functions. Light-derived signal is transferred in the form of reducing power from the photosynthetic electron transport chain to several redox-sensitive target proteins. Two types of protein, ferredoxin-thioredoxin reductase (FTR) and thioredoxin (Trx), are well recognized as the mediators of reducing power. However, it remains unclear which step in a series of redox-relay reactions is the critical bottleneck for determining the rate of target protein reduction. To address this, the redox behaviors of FTR, Trx, and target proteins were extensively characterized in vitro and in vivo. The FTR/Trx redox cascade was reconstituted in vitro using recombinant proteins from Arabidopsis. On the basis of this assay, we found that the FTR catalytic subunit and f-type Trx are rapidly reduced after the drive of reducing power transfer, irrespective of the presence or absence of their downstream target proteins. By contrast, three target proteins, fructose 1,6-bisphosphatase (FBPase), sedoheptulose 1,7-bisphosphatase (SBPase), and Rubisco activase (RCA) showed different reduction patterns; in particular, SBPase was reduced at a low rate. The in vivo study using Arabidopsis plants showed that the Trx family is commonly and rapidly reduced upon high light irradiation, whereas FBPase, SBPase, and RCA are differentially and slowly reduced. Both of these biochemical and physiological findings suggest that reducing power transfer from Trx to its target proteins is a rate-limiting step for chloroplast redox regulation, conferring distinct light-responsive redox behaviors on each of the targets.

scholarly journals The rate-limiting step of protein synthesis in vivo and in vitro and the distribution of growing peptides between the puromycinlabile and puromycin-non-labile sites on polyribosomes

1971 ◽  
Vol 122 (3) ◽  
pp. 267-276 ◽  
Author(s):  
D. C. N. Earl ◽  
Susan T. Hindley
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Donor Site ◽  
Peptide Bond ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Donor And Acceptor ◽  
Rate Limiting

1. At 3 min after an intravenous injection of radioactive amino acids into the rat, the bulk of radioactivity associated with liver polyribosomes can be interpreted as growing peptides. 2. In an attempt to identify the rate-limiting step of protein synthesis in vivo and in vitro, use was made of the action of puromycin at 0°C, in releasing growing peptides only from the donor site, to study the distribution of growing peptides between the donor and acceptor sites. 3. Evidence is presented that all growing peptides in a population of liver polyribosomes labelled in vivo are similarly distributed between the donor and acceptor sites, and that the proportion released by puromycin is not an artifact of methodology. 4. The proportion released by puromycin is about 50% for both liver and muscle polyribosomes labelled in vivo, suggesting that neither the availability nor binding of aminoacyl-tRNA nor peptide bond synthesis nor translocation can limit the rate of protein synthesis in vivo. Attempts to alter this by starvation, hypophysectomy, growth hormone, alloxan, insulin and partial hepatectomy were unsuccessful. 5. Growing peptides on liver polyribosomes labelled in a cell-free system in vitro or by incubating hemidiaphragms in vitro were largely in the donor site, suggesting that either the availability or binding of aminoacyl-tRNA, or peptide bond synthesis, must be rate limiting in vitro and that the rate-limiting step differs from that in vivo. 6. Neither in vivo nor in the hemidiaphragm system in vitro was a correlation found between the proportion of growing peptides in the donor site and changes in the rate of incorporation of radioactivity into protein. This could indicate that the intracellular concentration of amino acids or aminoacyl-tRNA limits the rate of protein synthesis and that the increased incorporation results from a rise to a higher but still suboptimum concentration.

scholarly journals The In Vivo Association of BiP with Newly Synthesized Proteins Is Dependent on the Rate and Stability of Folding and Not Simply on the Presence of Sequences That Can Bind to BiP

1999 ◽  
Vol 144 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Rachel Hellman ◽  
Marc Vanhove ◽  
Annabelle Lejeune ◽  
Fred J. Stevens ◽  
Linda M. Hendershot
Keyword(s):  
Secretory Pathway ◽  
Variable Region ◽  
Wild Type ◽  
Mutant Proteins ◽  
Protein Subunits ◽  
Hsp70 Family ◽  
Nascent Chain ◽  
Kinetic Traps

Immunoglobulin heavy chain-binding protein (BiP) is a member of the hsp70 family of chaperones and one of the most abundant proteins in the ER lumen. It is known to interact transiently with many nascent proteins as they enter the ER and more stably with protein subunits produced in stoichiometric excess or with mutant proteins. However, there also exists a large number of secretory pathway proteins that do not apparently interact with BiP. To begin to understand what controls the likelihood that a nascent protein entering the ER will associate with BiP, we have examined the in vivo folding of a murine λI immunoglobulin (Ig) light chain (LC). This LC is composed of two Ig domains that can fold independent of the other and that each possess multiple potential BiP-binding sequences. To detect BiP binding to the LC during folding, we used BiP ATPase mutants, which bind irreversibly to proteins, as “kinetic traps.” Although both the wild-type and mutant BiP clearly associated with the unoxidized variable region domain, we were unable to detect binding of either BiP protein to the constant region domain. A combination of in vivo and in vitro folding studies revealed that the constant domain folds rapidly and stably even in the absence of an intradomain disulfide bond. Thus, the simple presence of a BiP-binding site on a nascent chain does not ensure that BiP will bind and play a role in its folding. Instead, it appears that the rate and stability of protein folding determines whether or not a particular site is recognized, with BiP preferentially binding to proteins that fold slowly or somewhat unstably.

scholarly journals Coassembly of SecYEG and SecA Fully Restores the Properties of the Native Translocon

2018 ◽  
Vol 201 (1) ◽  
Author(s):  
Priya Bariya ◽  
Linda L. Randall
Keyword(s):  
Lipid Bilayers ◽  
Rate Constant ◽  
Apparent Rate Constant ◽  
Membrane Vesicles ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Secretory System ◽  
Rate Limiting

ABSTRACTIn all cells, a highly conserved channel transports proteins across membranes. InEscherichia coli, that channel is SecYEG. Many investigations of this protein complex have used purified SecYEG reconstituted into proteoliposomes. How faithfully do activities of reconstituted systems reflect the properties of SecYEG in the native membrane environment? We investigated by comparing threein vitrosystems: the native membrane environment of inner membrane vesicles and two methods of reconstitution. One method was the widely used reconstitution of SecYEG alone into lipid bilayers. The other was our method of coassembly of SecYEG with SecA, the ATPase of the translocase. For nine different precursor species we assessed parameters that characterize translocation: maximal amplitude of competent precursor translocated, coupling of energy to transfer, and apparent rate constant. In addition, we investigated translocation in the presence and absence of chaperone SecB. For all nine precursors, SecYEG coassembled with SecA was as active as SecYEG in native membrane for each of the parameters studied. Effects of SecB on transport of precursors faithfully mimicked observations madein vivo. From investigation of the nine different precursors, we conclude that the apparent rate constant, which reflects the step that limits the rate of translocation, is dependent on interactions with the translocon of portions of the precursors other than the leader. In addition, in some cases the rate-limiting step is altered by the presence of SecB. Candidates for the rate-limiting step that are consistent with our data are discussed.IMPORTANCEThis work presents a comprehensive quantification of the parameters of transport by the Sec general secretory system in the threein vitrosystems. The standard reconstitution used by most investigators can be enhanced to yield six times as many active translocons simply by adding SecA to SecYEG during reconstitution. This robust system faithfully reflects the properties of translocation in native membrane vesicles. We have expanded the number of precursors studied to nine. This has allowed us to conclude that the rate constant for translocation varies with precursor species.

Glycosaminoglycan-bound and free inter-α-trypsin inhibitor components of follicular fluid

Zygote ◽  
2001 ◽  
Vol 9 (4) ◽  
pp. 283-288 ◽  
Author(s):  
Lars Ødum ◽  
Torben E. Jessen ◽  
Claus Yding Andersen
Keyword(s):  
Extracellular Matrix ◽  
Trypsin Inhibitor ◽  
Follicular Fluid ◽  
Normal Female ◽  
Heavy Chains ◽  
Rate Limiting Step ◽  
Fluid Concentration ◽  
Rate Limiting

The proteinase inhibitor inter-α trypsin inhibitor (ITI) is a blood-derived protein necessary for normal female fertility. Absence of ITI leads to ovulation of naked oocytes that cannot fertilise. ITI consists of two heavy chains (ITI-HC) and bikunin linked by a chrondroitin sulphate. By binding to hyaluronate, ITI-HC stabilises the extracellular matrix, but ITI-HC also binds to proteoglycans in follicular fluid. In vivo concentrations of ITI components in preovulatory follicular fluid, free as well as bound to hyaluronate or proteoglycan, are unknown. In order to quantify these components, 58 follicular fluids and 13 blood samples were collected in connection with in vitro fertilisation and embryo transfer treatment of 13 women. Quantitation of glycosaminoglycan-bound ITI-HC was performed after separation from free ITI in agarose gel. ITI components were determined by immunoelectrophoresis and hyaluronate by an ELISA method. The follicular fluid concentration of ITI was on average 70% of that in plasma and the concentration of hyaluronate remained low despite follicular production, suggesting that the production of hyaluronate is the rate-limiting step in the formation of the extracellular matrix of the oocyte-cumulus complex. In follicular fluid, the concentration of free ITI-HC was higher than that of glycosaminoglycan-bound ITI-HC. Addition of exogeneous hyaluronate doubled the amount of hyaluronate-bound ITI-HC, further supporting the notion that ITI in follicular fluid is not rate-limiting for cumulus expansion in vivo.

scholarly journals The regulation of phosphatidylcholine biosynthesis in rye (Secale cereale) roots. Stimulation of the nucleotide pathway by low temperature

1987 ◽  
Vol 242 (3) ◽  
pp. 755-759 ◽  
Author(s):  
A J Kinney ◽  
D T Clarkson ◽  
B C Loughman
Keyword(s):  
Secale Cereale ◽  
Choline Chloride ◽  
Rate Limiting Step ◽  
Phosphatidylcholine Biosynthesis ◽  
Secale Cereale L ◽  
Choline Phosphate ◽  
Relative Differences ◽  
Rate Limiting

The incorporation of [14C]choline chloride and [14C]glycerol into segments taken from rye (Secale cereale L., cv. Rheidal) roots was greater in segments from roots grown at 5 degrees C than in segments taken from roots growing at 20 degrees C. The incorporation was measured at the temperature at which the root had been growing. Measurements in vitro of the enzymes of the nucleotide pathway showed activity of choline kinase (EC 2.7.1.32), choline-phosphate cytidylyltransferase (EC 2.7.7.15) and cholinephosphotransferase (EC 2.7.8.2) to be higher in homogenates from the cooler roots when assayed at 5 degrees C than the activities assayed at 20 degrees C in the 20 degrees C-root homogenates. Changes in vivo in the pool sizes of the CDP-base intermediates with temperature, relative differences in nucleotide-pathway-enzyme activities and a pulse-chase experiment with [14C]choline indicated that the rate-limiting step for phosphatidylcholine biosynthesis in this tissue, at both temperatures, was the reaction catalysed by cytidylyltransferase.

scholarly journals Analysis of Mutations in the Yeast mRNA Decapping Enzyme

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1273-1285 ◽  
Author(s):  
Sundaresan Tharun ◽  
Roy Parker
Keyword(s):  
Specific Activity ◽  
Temperature Sensitive ◽  
Loss Of Function ◽  
Alanine Scanning Mutagenesis ◽  
Mrna Decapping ◽  
Nonsense Codons ◽  
Decapping Enzyme ◽  
Decapping Enzymes

Abstract A major mechanism of mRNA decay in yeast is initiated by deadenylation, followed by mRNA decapping, which exposes the transcript to 5′ to 3′ exonucleolytic degradation. The decapping enzyme that removes the 5′ cap structure is encoded by the DCP1 gene. To understand the function of the decapping enzyme, we used alanine scanning mutagenesis to create 31 mutant versions of the enzyme, and we examined the effects of the mutations both in vivo and in vitro. Two types of mutations that affected mRNA decapping in vivo were identified, including a temperature-sensitive allele. First, two mutants produced decapping enzymes that were defective for decapping in vitro, suggesting that these mutated residues are required for enzymatic activity. In contrast, several mutants that moderately affected mRNA decapping in vivo yielded decapping enzymes that had at least the same specific activity as the wild-type enzyme in vitro. Combination of alleles within this group yielded decapping enzymes that showed a strong loss of function in vivo, but that still produced fully active enzymes in vitro. This suggested that interactions of the decapping enzyme with other factors may be required for efficient decapping in vivo, and that these particular mutations may be disrupting such interactions. Interestingly, partial loss of decapping activity in vivo led to a defect in normal deadenylation-dependent decapping, but it did not affect the rapid deadenylation-independent decapping triggered by early nonsense codons. This observation suggested that these two types of mRNA decapping differ in their requirements for the decapping enzyme.

scholarly journals ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions

2016 ◽  
Author(s):  
Haythem Latif ◽  
Stephen Federowicz ◽  
Ali Ebrahim ◽  
Janna Tarasova ◽  
Richard Szubin ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Receptor Protein ◽  
Elongation Complex ◽  
Template Strand ◽  
Rate Limiting Step ◽  
Dna Motif ◽  
Genome Scale ◽  
Rate Limiting

ABSTRACTNumerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70 are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.

Potential Role of Intercellular Communication in the Rate-Limiting Step in Carcinogenesis

1983 ◽  
Vol 2 (3) ◽  
pp. 5-22 ◽  
Author(s):  
James E. Trosko ◽  
Chia-cheng Chang
Keyword(s):  
Intercellular Communication ◽  
Critical Mass ◽  
Epidemiological Data ◽  
Malignant Cell ◽  
Dna Lesions ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

In order to ascertain whether there might be a scientific basis for determining practical “thresholds” for “carcinogens,” the concepts of thresholds and carcinogens were examined in the context of some current ideas on cardnogenesis. The observation that cardnogenesis seems to involve the donal expansion of a pre-malignant cell through a series of pheno-typic changes was explained by the initiation/promotion model of cardnogenesis. Unrepaired DNA lesions, acting as substrates for mutations in dividing cells, were speculated to play a role in the initiation phase of cardnogenesis (and indirectly to the promotion phase if the lesions lead to significant cell killing, forcing “compensatory hyperplasia”). Inhibition of intercellular communication, either by cell removal, cell death, growth factors or chemical promoters, was speculated to allow the donal expansion of initiated cells to reach a “critical mass.” During that donal expansion of initiated cells, additional phenotypic changes were speculated to occur during cell replication by mutational and/or epigenetic events. Therefore, it was concluded, on the basis of this model, that conditions which prevented the inhibition of intercellular communication between normal cells and the initiated cell(s) contributed to the rate limiting step of cardnogenesis. Assuming the initiation and promotion model of cardnogenesis, the classical concepts of “thresholds” and “carcinogens” were viewed as grossly inadequate because they did not symbolically represent the known determinants of the complex carcinogenic process. Unless genetic, developmental stage, tissue, nutritional, stress, life style, as well as concurrent antagonists and/or synergists, factors are known, extrapolation about the potential carcinogenicity of a given chemical from molecular, in vitro or even in vivo experiments or epidemiological data would be extremely risky. It was concluded that, at this stage of our understanding of the mech-anism(s) of carcinogenesis, attempts to determine “thresholds” for “carcinogens” naively assume “carcinogens” are the single determinants for carcinogenesis, and that all chemicals which might influence the appearance of tumors act the same way.

scholarly journals The GTPase Effector Domain Sequence of the Dnm1p GTPase Regulates Self-Assembly and Controls a Rate-limiting Step in Mitochondrial Fission

2001 ◽  
Vol 12 (9) ◽  
pp. 2756-2766 ◽  
Author(s):  
Noelle H. Fukushima ◽  
Ellen Brisch ◽  
Brian R. Keegan ◽  
William Bleazard ◽  
Janet M. Shaw
Keyword(s):  
Mitochondrial Fission ◽  
Yeast Two Hybrid ◽  
Effector Domain ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Gtpase Effector Domain ◽  
Rate Limiting ◽  
Two Hybrid

Dnm1p belongs to a family of dynamin-related GTPases required to remodel different cellular membranes. In budding yeast, Dnm1p-containing complexes assemble on the cytoplasmic surface of the outer mitochondrial membrane at sites where mitochondrial tubules divide. Our previous genetic studies suggested that Dnm1p's GTPase activity was required for mitochondrial fission and that Dnm1p interacted with itself. In this study, we show that bacterially expressed Dnm1p can bind and hydrolyze GTP in vitro. Coimmunoprecipitation studies and yeast two-hybrid analysis suggest that Dnm1p oligomerizes in vivo. With the use of the yeast two-hybrid system, we show that this Dnm1p oligomerization is mediated, in part, by a C-terminal sequence related to the GTPase effector domain (GED) in dynamin. The Dnm1p interactions characterized here are similar to those reported for dynamin and dynamin-related proteins that form higher order structures in vivo, suggesting that Dnm1p assembles to form rings or collars that surround mitochondrial tubules. Based on previous findings, a K705A mutation in the Dnm1p GED is predicted to interfere with GTP hydrolysis, stabilize active Dnm1p-GTP, and stimulate a rate-limiting step in fission. Here we show that expression of the Dnm1 K705A protein in yeast enhances mitochondrial fission. Our results provide evidence that the GED region of a dynamin-related protein modulates a rate-limiting step in membrane fission.

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