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PubMedDate not supplied

Alu sequences are processed 7SL RNA genes.

7SL RNA is an abundant cytoplasmic RNA which functions in protein secretion as a component of the signal recognition particle. Alu sequences are the most abundant family of human and rodent middle repetitive DNA sequences (reviewed in ref. 2). The primary structure of human 7SL RNA consists of an Alu sequence interrupted by a 155-base pair (bp) sequence that is unique to 7SL RNA. In order to obtain information about the evolution of the Alu domain of 7SL RNA, we have determined the nucleotide sequence of a cDNA copy of Xenopus laevis 7SL RNA and of the 7SL RNA gene of Drosophila melanogaster. We find that the Xenopus sequence is 87% homologous with its human counterpart and the Drosophila 7SL RNA is 64% homologous to both the human and amphibian molecules. Despite the evolutionary distance between the species, significant blocks of homology to both the Alu and 7SL-specific portions of mammalian 7SL RNA can be found in the insect sequence. These results clearly demonstrate that the Alu sequence in 7SL RNA appeared in evolution before the mammalian radiation. We suggest that mammalian Alu sequences were derived from 7SL RNA (or DNA) by a deletion of the central 7SL-specific sequence, and are therefore processed 7SL RNA genes.

Animals↗
PubMed2000

YidC mediates membrane protein insertion in bacteria.

The basic machinery for the translocation of proteins into or across membranes is remarkably conserved from Escherichia coli to humans. In eukaryotes, proteins are inserted into the endoplasmic reticulum using the signal recognition particle (SRP) and the SRP receptor, as well as the integral membrane Sec61 trimeric complex (composed of alpha, beta and gamma subunits). In bacteria, most proteins are inserted by a related pathway that includes the SRP homologue Ffh, the SRP receptor FtsY, and the SecYEG trimeric complex, where Y and E are related to the Sec61 alpha and gamma subunits, respectively. Proteins in bacteria that exhibit no dependence on the Sec translocase were previously thought to insert into the membrane directly without the aid of a protein machinery. Here we show that membrane insertion of two Sec-independent proteins requires YidC. YidC is essential for E. coli viability and homologues are present in mitochondria and chloroplasts. Depletion of YidC also interferes with insertion of Sec-dependent membrane proteins, but it has only a minor effect on the export of secretory proteins. These results provide evidence for an additional component of the translocation machinery that is specialized for the integration of membrane proteins.

ATP-Binding Cassette Transporters↗
PubMed1995

Reconstitution of the initial steps of mitochondrial protein import.

We have reconstituted the initial steps of mitochondrial protein import with a purified precursor protein, a purified, ATP-dependent, cytosolic chaperone selective for mitochondrial precursors (mitochondrial import stimulating factor; MSF), and either intact mitochondria or intact or solubilized mitochondrial outer membranes. We show that the precursor-MSF complex first binds to the Mas37p/Mas70p subunits of the mitochondrial import receptor. After ATP-dependent release of MSF, the precursor is transferred from Mas37p/Mas70p to the Mas20p/Mas22p subunits of the receptor, and finally delivered to the import channel in the outer membrane. Import in the absence of the MSF bypasses Mas37p/Mas70p. The ATP-mediated transfer of a precursor from MSF to specific subunits of the import receptor is similar to the GTP-mediated transfer of precursors from the signal recognition particle to its receptor on the endoplasmic reticulum.

14-3-3 Proteins↗
PubMed1991

Insulin secretory granule biogenesis. Co-ordinate regulation of the biosynthesis of the majority of constituent proteins.

Two-dimensional gel-electrophoretic analysis combined with fluorography and densitometric quantification was used to examine the effects of glucose on the biosynthesis of rat pancreatic islet proteins. An increase in the medium glucose concentration from 2.8 to 16.7 mM produced a 10-20 fold stimulation in the synthesis of 10 out of 260 detected islet proteins, as judged by incorporation of [35S]methionine during a 20 min incubation. The synthetic rates of the majority of the remaining proteins were stimulated by 2-4-fold. Greater resolution achieved by pulse-chase labelling and subcellular fractionation showed that, of 32 major proteins localized to insulin secretory granules, the biosynthesis of 25 were stimulated 15-30-fold by glucose. By contrast, only eight of 160 proteins in the soluble fraction showed a response of similar magnitude. It is concluded that there is a major and co-ordinated activation of the biosyntheses of proteins destined for secretory granules, which most likely occurs at the level of translational initiation and signal-recognition-particle-mediated translocation into the endoplasmic reticulum lumen. However, it is clear that not all granule proteins, or the majority of proteins translocated across the endoplasmic reticulum membrane, are affected in an equivalent manner. In addition, the synthesis of a small number of cytosolic proteins may be increased markedly by insulinotropic stimuli.

Animals↗
PubMed1998

Membrane integration of Sec61alpha: a core component of the endoplasmic reticulum translocation complex.

The Sec61 complex is a central component of the endoplasmic reticulum (ER) translocation site. The complex consists of three subunits: Sec61alpha, Sec61beta and Sec61gamma, at least two of which (alpha and beta) are adjacent to nascent proteins during membrane insertion. Another component of the translocation machinery is the translocating chain-associating membrane (TRAM) protein, which is also adjacent to many nascent proteins during membrane insertion. Sec61alpha functions as the major component of a transmembrane channel formed by oligomers of the Sec61 complex. This channel is the site of secretory protein translocation and membrane protein integration at the ER membrane. Sec61alpha is a polytopic integral membrane protein, and we have studied its biosynthesis and membrane integration in vitro. Using a cross-linking approach to analyse the environment of a series of discrete Sec61alpha membrane-integration intermediates, we find: (i) newly synthesized Sec61alpha is adjacent to known components of the ER membrane-insertion site, namely Sec61alpha, Sec61beta and TRAM, and thus the integration of Sec61alpha appears to require a pre-existing Sec61 complex; (ii) a site-specific cross-linking analysis indicates that the first transmembrane domain of Sec61alpha remains adjacent to protein components of the ER-insertion site (specifically TRAM and Sec61beta) during the insertion of at least three subsequent transmembrane domains; and (iii) the membrane integration of Sec61alpha requires ER targeting by the signal-recognition particle.

Animals↗
PubMed2003

Getting to the membrane: how is co-translational protein targeting to the endoplasmic reticulum regulated?

Co-translational protein targeting to the endoplasmic reticulum requires the signal-recognition particle, its cognate receptor and the translocation channel. Co-ordination of the targeting process necessitates the interaction of these components with each other and with the ribosome. These interactions are regulated by three GTPases, which act in concert, ensuring the fidelity of the targeting process.

Endoplasmic Reticulum↗
PubMed2005

The complexity of pathways for protein import into thylakoids: it's not easy being green.

Numerous proteins are transported into or across the chloroplast thylakoid membrane. To date, two major pathways have been identified for the transport of luminal proteins (the Sec- and Tat-dependent pathways) and it is now clear that these protein translocases use fundamentally different transport mechanisms. Integral membrane proteins are inserted by means of at least two further pathways. One involves the input of numerous targeting factors, including SRP (signal recognition particle), FtsY and Albino3. Surprisingly, the other pathway does not involve any of the known chloroplastic targeting factors, and insertion is energy-independent, raising the possibility of an unusual 'spontaneous' insertion mechanism.

Intracellular Membranes↗
PubMed1999

Molecular characterization of Escherichia coli FtsE and FtsX.

The genes ftsE and ftsX are organized in one operon together with ftsY. FtsY codes for the receptor of the signal recognition particle (SRP) that functions in targeting a subset of inner membrane proteins. We have found no indications for a structural relationship between FtsE/X and FtsY. Evidence is presented that FtsE and FtsX form a complex in the inner membrane that bears the characteristics of an ATP-binding cassette (ABC)-type transporter. FtsE is a hydrophilic nucleotide-binding protein that has a tendency to dimerize and associates with the inner membrane through an interaction with the integral membrane protein FtsX. An FtsE null mutant showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport.

ATP-Binding Cassette Transporters↗
PubMed2000

The G-protein FlhF has a role in polar flagellar placement and general stress response induction in Pseudomonas putida.

The flhF gene of Pseudomonas putida, which encodes a GTP-binding protein, is part of the flagellar-motility-chemotaxis operon. Its disruption leads to a random flagellar arrangement in the mutant (MK107) and loss of directional motility in contrast to the wild type, which has polar flagella. The return of a normal flhF allele restores polar flagella and normal motility to MK107; its overexpression triples the flagellar number but does not restore directional motility. As FlhF is homologous to the receptor protein of the signal recognition particle (SRP) pathway of membrane protein translocation, this pathway may have a role in polar flagellar placement in P. putida. MK107 is also compromised in the development of the starvation-induced general stress resistance (SGSR) and effective synthesis of several starvation and exponential phase proteins. While somewhat increased protein secretion in MK107 may contribute to its SGSR impairment, the altered protein synthesis pattern also appears to have a role.

Alleles↗
PubMed2000

Endoribonuclease RNase III is essential in Bacillus subtilis.

The rncS gene of Bacillus subtilis encodes Bs-RNase III, a narrow-specificity endoribonuclease. Previous attempts to disrupt rncS were unsuccessful. Here, a strain was constructed in which Bs-RNase III expression was dependent upon transcription of rncS from a temperature-sensitive plasmid. Growth of this strain at the non-permissive temperature resulted in 90-95% cell death, and virtually all the cells that survived retained the rncS-expressing plasmid. Thus, we conclude that rncS is essential in B. subtilis. The rncS conditional strain also revealed that Bs-RNase III participates in the processing of ribosomal RNA, in addition to processing small cytoplasmic RNA, a member of the signal recognition particle RNA family. Most significantly, a rare rncS null strain was isolated that will aid further study of the critical role Bs-RNase III plays in B. subtilis.

Bacillus subtilis↗
PubMed2000

In vivo targeting of a sunflower oil body protein in yeast secretory (sec) mutants.

A sunflower oleosin was expressed in yeast to study the in vivo insertion of the protein into the endoplasmic reticulum (ER) and subsequent transfer to lipid bodies. The oleosin cDNA was expressed in a range of yeast secretory (sec) mutants to determine the precise targeting pathway of the oleosin to the ER. Subcellular fractionation experiments indicated that the signal recognition particle (SRP) is required for oleosin targeting to the ER and hence subsequent deposition on the lipid bodies in vivo. The expression of oleosin in a range of sec61 mutant alleles confirmed the role of the SEC61 translocon in insertion of oleosin into the ER membrane, as well as indicating an unusual substrate/translocon interaction for one particular allele (sec61-3). Mistargeting of the oleosin due to impaired SRP function resulted in enhanced proteolysis of the plant protein in the transformed yeast, as determined by pulse-chase analysis. These data therefore provide the first in vivo evidence for the SRP-dependent targeting of the oleosin to the ER, and the subsequent requirement for a functional SEC61 translocon to mediate the correct insertion of the protein into the membrane.

Cloning, Organism↗
PubMed2000

Insertion of light-harvesting chlorophyll a/b protein into the thylakoid topographical studies.

The major light-harvesting chlorophyll a/b-binding protein (Lhcb1,2) of photosystem II is inserted into the thylakoid via the signal recognition particle dependent pathway. However, the mechanism by which the protein enters the membrane is at this time unknown. In order to define some topographical restrictions for this process, we constructed several recombinant derivatives of Lhcb1 carrying hexahistidine tags at either protein terminus or in the stromal loop domain. Additionally, green fluorescent protein (GFP) was fused to either terminus. None of the modifications significantly impair the pigment-binding properties of the protein in the in vitro reconstitution of LHCII. With the exception of the C-terminal GFP fusion, all mutants stably insert into isolated thylakoids in the absence of Ni2+ ions. The addition of low concentrations of Ni2+ ions abolishes the thylakoid insertion of C-terminally His-tagged mutants whereas the other His-tagged proteins fail to insert only at higher Ni2+ concentrations. The C-terminus of Lhcb1 must cross the membrane during protein insertion whereas the other sites of Lhcb1 modification are positioned on the stromal side of LHCII. We conclude that a Ni2+-complexed His tag and fusion to GFP inhibit translocation of the protein C-terminus across the thylakoid. Our observations indicate that the N-terminal and stromal domain of Lhcb1 need not traverse the thylakoid during protein insertion and are consistent with a loop mechanism in which only the C-terminus and the lumenal loop of Lhcb1 are translocated across the thylakoid.

Biological Transport↗
PubMedDate not supplied

Gene expression analysis in cucumber leaves primed by root colonization with Pseudomonas chlororaphis O6 upon challenge-inoculation with Corynespora cassiicola.

Root colonization by Pseudomonas chlororaphis O6, a non-pathogenic rhizobacterium, induced systemic resistance in cucumber against target leaf spot caused by Corynespora cassiicola. A cDNA library was constructed using mRNA extracted from cucumber leaves 12 h after inoculation with C. cassiicola, using plants colonized by O6. To identify genes involved in O6-mediated induced systemic resistance (ISR), we employed a subtractive hybridization method using mRNAs extracted from pathogen-challenged cucumber leaves of plants lacking colonization. Differential screening of the cDNA library led to the isolation of six distinct genes encoding a GTP binding protein, a 60S ribosomal protein, a hypersensitive-induced reaction protein, a ubiquitin extension protein, a pyridine nucleotide-disulfide oxidoreductase, and a signal recognition particle receptor. Expression of these genes was not induced by O6 colonization alone. Rather, transcript accumulation of these genes increased significantly faster and stronger in the O6 colonized than in non-colonized plants after challenge infection. Therefore, O6-mediated ISR may be associated with an enhanced capacity for the rapid and effective activation of cellular defence responses after challenge inoculation.

Ascomycota↗
PubMed2004

MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.

We present a highly accurate method for identifying genes with conserved RNA secondary structure by searching multiple sequence alignments of a large set of candidate orthologs for correlated arrangements of reverse-complementary regions. This approach is growing increasingly feasible as the genomes of ever more organisms are sequenced. A program called msari implements this method and is significantly more accurate than existing methods in the context of automatically generated alignments, making it particularly applicable to high-throughput scans. In our tests, it discerned clustalw-generated multiple sequence alignments of signal recognition particle or RNaseP orthologs from controls with 89.1% sensitivity at 97.5% specificity and with 74.4% sensitivity with no false positives in 494 controls. We used msari to conduct a comprehensive scan for secondary structure in mRNAs of coding genes, and we found many genes with known mRNA secondary structure and compelling evidence for secondary structure in other genes. msari uses a method for coping with sequence redundancy that is likely to have applications in a large set of other comparison-based search methods. The program is available for download from http://theory.csail.mit.edu/MSARi.

Algorithms↗
PubMed2006

Homodimerization of the G protein SRbeta in the nucleotide-free state involves proline cis/trans isomerization in the switch II region.

Protein translocation across and insertion into membranes is essential to all life forms. Signal peptide-bearing nascent polypeptide chains emerging from the ribosome are first sampled by the signal-recognition particle (SRP), then targeted to the membrane via the SRP receptor (SR), and, finally, transferred to the protein-conducting channel. In eukaryotes, this process is tightly controlled by the concerted action of three G proteins, the 54-kD subunit of SRP and the alpha- and beta-subunits of SR. We have determined the 2.2-A crystal structure of the nucleotide-free SRbeta domain. Unexpectedly, the structure is a homodimer with a highly intertwined interface made up of residues from the switch regions of the G domain. The remodeling of the switch regions does not resemble any of the known G protein switch mechanisms. Biochemical analysis confirms homodimerization in vitro, which is incompatible with SRalpha binding. The switch mechanism involves cis/trans isomerization of a strictly conserved proline, potentially implying a new layer of regulation of cotranslational transport.

Amino Acid Sequence↗
PubMed1985

Secretory S complex of Bacillus subtilis forms a large, organized structure when released from ribosomes.

The S complex of Bacillus subtilis, a set of four proteins that appears to be involved in protein secretion, is shown to be attached to 70S ribosomes: antibody to its 64-kDa component can aggregate these ribosomes, and the complex can be chemically crosslinked to ribosomal proteins. Low Mg2+ or prolonged high-speed centrifugation in a sucrose gradient releases the S complex from the ribosomes, and it is recovered as an aggregate with an S value of 76. Electron microscopy shows that these aggregates have a regular structure, somewhat resembling clathrin cages, with a diameter of about 45 nm. If these aggregates are physiological, their function would differ significantly from that of the signal recognition particle of eukaryotes.

Bacillus subtilis↗
PubMed1989

Genetic analysis of Schizosaccharomyces pombe 7SL RNA: a structural motif that includes a conserved tetranucleotide loop is important for function.

We have studied the effects of mutations in a 6-base segment of Schizosaccharomyces pombe 7SL RNA, which lies within a 35-nucleotide domain whose sequence and secondary structure are conserved in RNAs from many divergent organisms, including the 7SL component of human signal recognition particle (SRP). Surprisingly, many changes in this region can be tolerated under normal growth conditions. An exception is the lethality of several mutations at positions 159 and 160, 2 nucleotides previously shown to be protected from RNase digestion by the 19-kDa canine SRP protein. Nucleotide 160 is, in addition, the most highly conserved base in a consensus sequence for the most common tetranucleotide loop in ribosomal RNAs. Mutations that are likely to affect the stability and/or conformation of the RNA give rise to a conditional phenotype: when osmolarity of the medium is raised, the RNAs become partially or completely defective in function at high temperature.

Base Sequence↗