Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Signal Recognition Particle”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources
PubMed1996

Bacillus subtilis Ffh, a homologue of mammalian SRP54, can intrinsically bind to the precursors of secretory proteins.

We analyzed the binding activity of B. subtilis Ffh to the precursors of secretory proteins by purifying mature and precursor proteins of beta-lactamase derived from pUC18 and its derivatives, of which the signal peptide region was replaced with that of E. coli OmpA, B. subtilis AprE, PBP5* or an alkalophilic Bacillus sp. #1011 CGTase. Each of them was mixed with purified B. subtilis Ffh in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC). The tested precursor proteins, including those of E. coli, of which the signal sequences differ from those of B. subtilis in the number of charged amino acids and hydrophobicity, cross-linked with Ffh, whereas mature proteins did not. The addition of scRNA, the B. subtilis counterpart of mammalian SRP 7S RNA, into the mixture did not affect the complex formation. These findings suggest that B. subtilis Ffh intrinsically binds to several precursor proteins.

Amino Acid Sequence↗
PubMed1999

RNA secondary structure prediction based on free energy and phylogenetic analysis.

We describe a computational method for the prediction of RNA secondary structure that uses a combination of free energy and comparative sequence analysis strategies. Using a homology-based sequence alignment as a starting point, all favorable pairings with respect to the Turner energy function are identified. Each potentially paired region within a multiple sequence alignment is scored using a function that combines both predicted free energy and sequence covariation with optimized weightings. High scoring regions are ranked and sequentially incorporated to define a growing secondary structure. Using a single set of optimized parameters, it is possible to accurately predict the foldings of several test RNAs defined previously by extensive phylogenetic and experimental data (including tRNA, 5 S rRNA, SRP RNA, tmRNA, and 16 S rRNA). The algorithm correctly predicts approximately 80% of the secondary structure. A range of parameters have been tested to define the minimal sequence information content required to accurately predict secondary structure and to assess the importance of individual terms in the prediction scheme. This analysis indicates that prediction accuracy most strongly depends upon covariational information and only weakly on the energetic terms. However, relatively few sequences prove sufficient to provide the covariational information required for an accurate prediction. Secondary structures can be accurately defined by alignments with as few as five sequences and predictions improve only moderately with the inclusion of additional sequences.

Algorithms↗
PubMed2002

Expression of green fluorescent protein in Rickettsia conorii.

Rickettsiae are obligate intracellular class III pathogens for which genetic manipulation has only recently been shown to be feasible. Such experiments were restricted to the typhus group rickettsiae, namely R. typhi and R. prowazekii. Here we report the first genetic manipulation of Rickettsia conorii, the bacterial agent responsible for the Mediterranean spotted fever. A gene encoding a variant of the green fluorescent protein under the control of the sterically repressed promoter (srp) from E. coli was integrated into the genome of this bacteria and detected by FACS analysis.

Animals↗
PubMed1989

Two genes encode 7SL RNAs in the yeast Yarrowia lipolytica.

We have identified an abundant cytoplasmic 7S RNA in crude extracts of the yeast Yarrowia lipolytica. A cDNA probe was prepared from this RNA and used to screen a genomic library. The DNA sequence of a positive clone was determined and the end positions of the 7S RNA gene established by comparison with the sequence of the extremities of 7S RNA. This gene, designated SCR2, encodes a 270-nucleotide RNA that can be folded into a secondary structure similar to that of 7SL RNAs. This RNA is 94.4% homologous to a previously identified 7S RNA from this yeast, but is encoded by a separate gene with highly divergent flanking sequences.

Base Sequence↗
PubMed1989

Export of proteins across membranes: the helix reversion hypothesis.

A model is presented which explains the biological role of the leader peptide in protein export. Along the lines of this model, the conformational changes of a protein with environment serves as a general mechanism for translocation. The leader peptide in the cytoplasm takes a hairpin like conformation which reverts to an extended helix upon integration into the membrane. The essential features of this model are in accord with recent results of protein export.

Amino Acids↗
PubMed1994

Emergence of master sequences in families of retroposons derived from 7sl RNA.

The past few years have brought new insight into the evolution of families of retroposons. These are composed of a very small number of master sequences able to duplicate, and a large majority of copies that are inactive for retroposition. During the course of time, successive replacements of master sequences have produced waves of amplification that are recognizable as subfamilies. In the Alu and the B1 families, one can distinguish two evolutionary periods. The first involves only monomeric elements that are now extinguished (fossil elements) and is characterized by deep remodeling of the sequences. This period ends, in primates, with the fusion of a free left and a free right Alu monomer, producing the first modern Alu dimeric element; in rodents it ends with a tandem duplication of 29 bp to create the first modern B1 element. The second period is characterized by a great stability of the master sequences. The observed turn-over of master sequences is still an enigma. However, analysis of the contemporary master sequences and of the oldest master sequences provide some clues. Here, we review the very first stages of the appearance of the Alu and the B1 families in mammalian genomes.

Animals↗
PubMed2001

Molecular biology of chloroplast biogenesis: gene expression, protein import and intraorganellar sorting.

The chloroplast is the hallmark organelle of plants. It performs photosynthesis and is therefore required for photoautotrophic plant growth. The chloroplast is the most prominent member of a family of related organelles termed plastids which are ubiquitous in plant cells. Biogenesis of the chloroplast from undifferentiated proplastids is induced by light. The generally accepted endosymbiont hypothesis states that chloroplasts have arisen from an internalized cyanobacterial ancestor. Although chloroplasts have maintained remnants of the ancestral genome (plastome), the vast majority of the genes encoding chloroplast proteins have been transferred to the nucleus. This poses two major challenges to the plant cell during chloroplast biogenesis: First, light and developmental signals must be interpreted to coordinately express genetic information contained in two distinct compartments. This is to ensure supply and stoichiometry of abundant chloroplast components. Second, developing chloroplasts must efficiently import nuclear encoded and cytosolically synthesized proteins. A subset of proteins, including such encoded by the plastome, must further be sorted to the thylakoid compartments for assembly into the photosynthetic apparatus.

Biological Transport↗
PubMed1998

Relics from the RNA world.

An RNA world is widely accepted as a probable stage in the early evolution of life. Two implications are that proteins have gradually replaced RNA as the main biological catalysts and that RNA has not taken on any major de novo catalytic function after the evolution of protein synthesis, that is, there is an essentially irreversible series of steps RNA --> RNP --> protein. This transition, as expected from a consideration of catalytic perfection, is essentially complete for reactions when the substrates are small molecules. Based on these principles we derive criteria for identifying RNAs in modern organisms that are relics from the RNA world and then examine the function and phylogenetic distribution of RNA for such remnants of the RNA world. This allows an estimate of the minimum complexity of the last ribo-organism-the stage just preceding the advent of genetically encoded protein synthesis. Despite the constraints placed on its size by a low fidelity of replication (the Eigen limit), we conclude that the genome of this organism reached a considerable level of complexity that included several RNA-processing steps. It would include a large protoribosome with many smaller RNAs involved in its assembly, pre-tRNAs and tRNA processing, an ability for recombination of RNA, some RNA editing, an ability to copy to the end of each RNA strand, and some transport functions. It is harder to recognize specific metabolic reactions that must have existed but synthetic and bio-energetic functions would be necessary. Overall, this requires that such an organism maintained a multiple copy, double-stranded linear RNA genome capable of recombination and splicing. The genome was most likely fragmented, allowing each "chromosome" to be replicated with minimum error, that is, within the Eigen limit. The model as developed serves as an outgroup to root the tree of life and is an alternative to using sequence data for inferring properties of the earliest cells.

Evolution, Molecular↗
PubMed2002

Nascent-polypeptide-associated complex.

Nascent-polypeptide-associated complex (NAC) is a heterodimeric complex which can reversibly bind to eukaryotic ribosomes. NAC is located in direct proximity to newly synthesized polypeptide chains as they emerge from the ribosome. Although its function is thought to be conserved from yeast to humans our current knowledge about what NAC actually does in a living cell is incomplete. It has been suggested that NAC is a (i) dynamic component of the ribosomal exit tunnel, providing a shield for nascent polypeptides, (ii) negative regulator of translocation into the endoplasmic reticulum and (iii) positive regulator of translocation into the mitochondria. However, none of these hypotheses is generally accepted. Moreover, the individual subunits of NAC have been implicated in processes related to transcription rather than translation, and it is currently under debate whether NAC might be a protein of dual function. This review attempts to summarize the data from different fields and to discuss the partly controversial results in a common context.

Amino Acid Sequence↗
PubMed1997

Hydrophobin gene srh1, expressed during sporulation of the biocontrol agent Trichoderma harzianum.

A cDNA clone encoding a spore-related hydrophobin, SRHI, was isolated from a cDNA bank prepared from mRNA induced in sporulating cultures of Trichoderma harzianum by heterologous hybridization using the hfb2 gene encoding a spore-bound hydrophobin of Trichoderma reesei as a probe. Based on sequence similarity the predicted protein was identified as a new member of the class-II hydrophobin family. Including the signal sequences, SRHI has 65% and 56% amino-acid similarity with the T. reesei hydrophobins HFBII and HFBI, respectively, being less similar with other hydrophobins. srh1 is present as one copy in the T. harzianum genome. It is highly expressed under sporulating conditions, both in submerged as well as in aerial cultures. Moreover, nutrient limitation induces srh1 expression.

Fungal Proteins↗
PubMed2001

Recent findings in the modern RNA world.

It is assumed that modern life forms arose from a molecular ancestor in which RNA molecules both stored genetic information and catalyzed biochemical reactions. In modern cells, these functions are carried out, respectively, by DNA and proteins, but diverse cellular RNAs are also involved in key cellular functions. In this paper, we review the cellular RNAs that are ubiquitous and/or that perform essential biological functions, and we discuss the evolutionary relationships of such RNAs with a prebiotic RNA world. This unexpected biological diversity of cellular RNAs and the crucial functions they perform in cellular metabolism demonstrate the complexity of an RNA-driven metabolism in an ancient RNA world and in modern life. Cellular RNAs are involved in translation (tRNA and rRNA) but also in ribosome maturation (snoRNA) and more generally in RNA processing (snRNA and snoRNA), replication (telomerase RNA), editing, protein translocation (SRP RNA), cellular transport (vRNA) and translation quality control (tmRNA). In addition, the function of many other cellular RNAs has not yet been determined. Future investigations of RNA function will allow us to better understand not only early evolutionary biological processes but also the central metabolism of modern cells.

Biological Evolution↗
PubMed1988

The human docking protein does not associate with the membrane of the rough endoplasmic reticulum via a signal or insertion sequence-mediated mechanism.

Docking protein (DP, or SRP receptor) is an essential component of the cellular machinery that mediates the targeting of nascent secretory and membrane proteins to the rough endoplasmic reticulum (ER). In this study we have investigated the nature of its own targeting to its site of function, the rough ER. Using an in vitro transcription-translation system we demonstrate that DP is not inserted into the membrane via a classical SRP/DP-mediated process (in contrast to human ribophorins), nor via hydrophobic insertion sequences (in contrast to cytochrome b5). Instead, we suggest that membrane assembly of DP is receptor-mediated; requiring the presence in the membrane of other proteins that mediate its targeting and insertion.

Animals↗
PubMed1993

Do cytosolic factors prevent promiscuity at the membrane surface?

From the point of view of a preprotein, escaping from the cytosol into a specific organelle must seem an arduous, almost impossible task. How is it that preproteins resist the temptation to fold prematurely, to avoid the multiple membrane surfaces in the cell, and manage instead to enter only the translocation apparatus of a single organelle?

Biological Transport↗
PubMed1996

Structure of a methionine-rich segment of Escherichia coli Ffh protein.

The methionine-rich segments of the Ffh protein of Escherichia coli and its eukaryotic counterpart SRP54 are thought to bind signal sequences of secretory proteins. The structure of a chemically synthesized 25-residue-long peptide corresponding to one of the proposed methionine-rich amphiphilic helices of Ffh was determined in water and in aqueous trifluroethanol (TFE) solution using CD and NMR. An appreciable alpha-helix conformation exists even in water and this peptide assumes a stable alpha-helix along most of its length in aqueous TFE solution. It is clear that this segment of Ffh protein has a very strong propensity to form alpha-helical structure.

Amino Acid Sequence↗
PubMed1989

PrlC, a suppressor of signal sequence mutations in Escherichia coli, can direct the insertion of the signal sequence into the membrane.

The prlC gene product of Escherichia coli can be altered by mutation so that it restores export of proteins with defective signal sequences. The strongest suppressor, prlC8, restores processing of a mutant signal sequence to a rate indistinguishable from the wild-type. Data obtained by changing gene dosage of the dominant suppressor and its specificity for different signal sequence mutations suggest that PrlC8 interacts directly with the hydrophobic core of the signal sequence. Despite the fact that signal sequence processing appears to be mediated by leader peptidase, the processed mature protein is not translocated efficiently from the cytoplasm. Results obtained with various double mutants indicate that PrlC8-mediated processing of mutant signal sequences does not require components of the cellular export machinery such as SecA, SecB or PrlA (SecY) and that the block in translocation from the cytoplasm occurs because PrlA (SecY) fails to recognize the defective signal sequence. We suggest that PrlC8 directs insertion of the mutant signal sequence into the membrane bilayer to an extent that processing by leader peptidase can occur. This reaction is novel in that it has not been observed previously in vivo.

Bacterial Outer Membrane Proteins↗
PubMed1986

In vitro protein translocation across the yeast endoplasmic reticulum: ATP-dependent posttranslational translocation of the prepro-alpha-factor.

The in vitro synthesized precursor of the alpha-factor pheromone, prepro-alpha-factor, of Saccharomyces cerevisiae was translocated across yeast microsomal membranes in either a homologous or a wheat germ cell free system. Translocated prepro-alpha-factor was glycosylated, sedimented with yeast microsomal vesicles, and was protected from digestion by added protease, but was soluble after alkaline sodium carbonate treatment. Thus prepro-alpha-factor was properly sequestered within yeast microsomal vesicles, but was not integrated into the lipid bilayer. In marked contrast to protein translocation across mammalian microsomal membranes, translocation of prepro-alpha-factor across yeast microsomal membranes could occur posttranslationally. This reaction required protein components in the yeast microsomal fraction that could be inactivated by alkylation or proteolysis, was ATP-dependent, and was insensitive to the presence of a variety of uncouplers and ionophores.

Adenosine Triphosphate↗