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PubMed1989

Transcription and processing of Bacillus subtilis small cytoplasmic RNA.

The 271 nucleotides long scRNA (small cytoplasmic RNA) from Bacillus subtilis is structurally related to the Escherichia coli 4.5 S RNA (114 nucleotides), an essential molecule supposed to be involved in protein biosynthesis, but it possesses an additional moiety completely missing in the E. coli 4.5 S RNA. Both RNAs share a conserved hairpin with the eukaryotic 7SL RNAs, which mediate protein translocation as part of the signal recognition particle (SRP). We have cloned and sequenced the entire scRNA gene region from B. subtilis and have studied transcription and processing of the scRNA in B. subtilis by nuclease S1 mapping. This analysis revealed the scRNA gene to constitute a monofunctional transcription unit, expressed from a single promoter to a rho-independent terminator, yielding a precursor which extends the mature scRNA by approximately 40 nucleotides at both ends. Processing of the scRNA apparently involves only two endonucleolytic cuts and occurs first at the 5' end.

Bacillus subtilis↗

PubMed1998

The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery.

The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed SRalpha for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence similarities between the N-terminal half of SRP54(Ffh) and the C-terminal half of SRalpha(Ftsy). This enables a universal phylogeny based on either protein to be rooted using the second protein as an outgroup. Phylogenetic trees inferred by various methods from an alignment (220 amino acid positions) of the shared SRP54(Ffh) and SRalpha(Ftsy) regions generate two reciprocally rooted universal trees corresponding to the two genes. The root of both trees is firmly positioned between Bacteria and Archaea/Eucarya, thus providing strong support for the notion (Iwabe et al. 1989; Gogarten et al. 1989) that the first bifurcation in the tree of life separated the lineage leading to Bacteria from a common ancestor to Archaea and Eucarya. None of the gene trees inferred from the two paralogues support a paraphyletic Archaea with the crenarchaeota as a sister group to Eucarya.

Algorithms↗

PubMed1999

The rooting of the universal tree of life is not reliable.

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria-Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.

Adenosine Triphosphatases↗

PubMed2000

The vertebrate 7S K RNA separates hagfish (Myxine glutinosa) and lamprey (Lampetra fluviatilis).

7S RNA sequences from the hagfish (Myxiniformes) and lamprey (Petromyzontiformes) were cloned and analyzed. In both species, 7S L RNA (also designated SRP RNA, since it represents the RNA constituent of the signal recognition particle) was clearly detectable. The sequence similarity between the two species was 86%, compared with about 75% similarity between either of these species and mammals. 7S K RNA was also cloned from the lamprey. The similarity between the 7S K RNA of the lamprey and that of mammals was 68%. Interestingly, several interspersed elements were found with nearly 100% similarity compared with mammals. In contrast to the lamprey, no 7S K RNA-related sequences were detectable among hagfish RNA, neither in northern blots nor with the PCR assay. In view of the significant conservation between the 7S K RNA of lamprey and that of mammals (human), this unexpected result clearly separates lamprey and hagfish. In addition, the lack of detectable 7S K RNA sequences in an outgroup, such as amphioxus, indicates that these results do not reflect an autapomorphy of hagfish. Therefore, our data provide additional support to the notion of a sister group relationship between Petromyzontiformes and gnathostomous vertebrates to the exclusion of Myxiniformes.

Animals↗

PubMedDate not supplied

Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis.

I attempt to sketch a unified picture of the origin of living organisms in their genetic, bioenergetic, and structural aspects. Only selection at a higher level than for individual selfish genes could power the cooperative macromolecular coevolution required for evolving the genetic code. The protein synthesis machinery is too complex to have evolved before membranes. Therefore a symbiosis of membranes, replicators, and catalysts probably mediated the origin of the code and the transition from a nucleic acid world of independent molecular replicators to a nucleic acid/protein/lipid world of reproducing organisms. Membranes initially functioned as supramolecular structures to which different replicators attached and were selected as a higher-level reproductive unit: the proto-organism. I discuss the roles of stereochemistry, gene divergence, codon capture, and selection in the code's origin. I argue that proteins were primarily structural not enzymatic and that the first biological membranes consisted of amphipathic peptidyl-tRNAs and prebiotic mixed lipids. The peptidyl-tRNAs functioned as genetically-specified lipid analogues with hydrophobic tails (ancestral signal peptides) and hydrophilic polynucleotide heads. Protoribosomes arose from two cooperating RNAs: peptidyl transferase (large subunit) and mRNA-binder (small subunit). Early proteins had a second key role: coupling energy flow to the phosphorylation of gene and peptide precursors, probably by lithophosphorylation by membrane-anchored kinases scavenging geothermal polyphosphate stocks. These key evolutionary steps probably occurred on the outer surface of an 'inside out-cell' or obcell, which evolved an unambiguous hydrophobic code with four prebiotic amino acids and proline, and initiation by isoleucine anticodon CAU; early proteins and nucleozymes were all membrane-attached. To improve replication, translation, and lithophosphorylation, hydrophilic substrate-binding and catalytic domains were later added to signal peptides, yielding a ten-acid doublet code. A primitive proto-ecology of molecular scavenging, parasitism, and predation evolved among obcells. I propose a new theory for the origin of the first cell: fusion of two cup-shaped obcells, or hemicells, to make a protocell with double envelope, internal genome and ribosomes, protocytosol, and periplasm. Only then did water-soluble enzymes, amino acid biosynthesis, and intermediary metabolism evolve in a concentrated autocatalytic internal cytosolic soup, causing 12 new amino acid assignments, termination, and rapid freezing of the 22-acid code. Anticodons were recruited sequentially: GNN, CNN, INN, and *UNN. CO2 fixation, photoreduction, and lipid synthesis probably evolved in the protocell before photophosphorylation. Signal recognition particles, chaperones, compartmented proteases, and peptidoglycan arose prior to the last common ancestor of life, a complex autotrophic, anaerobic green bacterium.

Anticodon↗

PubMed1997

A high-resolution map of the regulator of the complement activation gene cluster on 1q32 that integrates new genes and markers.

Sixteen microsatellite markers, including two described here, were used to construct a high-resolution map of the 1q32 region encompassing the regulator of the complement activation (RCA) gene cluster. The RCA genes are a group of related genes coding for plasma and membrane associated proteins that collectively control activation of the complement component C3. We provide here the location of two new genes within the RCA gene cluster. These genes are PFKFB2 that maps 15 kilobases (kb) upstream of the C4BPB gene, and a gene located 4 kb downstream of C4BPA, which seems to code for the 72 000 Mr component of the signal recognition particle (SRP72). Neither of these two genes is related structurally or functionally to the RCA genes. In addition, our map shows the centromere-telomere orientation of the C4BPB/MCP linkage group, which is: centromere-PFKFB2-C4BPB-C4BPA-SRP72-C4BPAL1++ +-C4BPAL2-telomere, and outlines an interval with a significant female-male recombination difference which suggests the presence of a female-specific hotspot(s) of recombination.

Chromosome Mapping↗

PubMed2002

Idiopathic inflammatory myopathy: autoantibody update.

Several defined, specific autoantibodies have been associated with polymyositis and dermatomyositis. These include autoantibodies to at least six of the aminoacyl-transfer-ribonucleic-acid synthetases; to the signal recognition particle; to the protein complexes labeled Mi-2 and PM-Scl; and several autoantibodies, such as anti-U1nRNP and anti-Ro/SSA, that have recognized associations with other conditions. These autoantibodies are a continuing area of interest. Recent studies have involved the clinical implications of these autoantibodies, and their potential significance for etiology and pathogenesis of the disease. This report will review recent studies of myositis autoantibodies and their clinical associations, both extramuscular features, such as interstitial lung disease and aspects of the myositis itself. New myositis autoantibodies continue to emerge, which may have clinical utility. Several have been associated with dermatomyositis, including juvenile dermatomyositis, which has a low frequency of traditional myositis autoantibodies. There is also new information regarding the antigenic targets of anti-Mi-2 and anti-PM-Scl, two of the earliest recognized myositis autoantibodies. New evidence over the past few years has challenged old concepts of the relationship of autoantibodies to the pathogenesis of myositis, and has suggested potential new mechanisms for the origin of the associated autoantibodies. Despite this progress, the reason for production of the autoantibodies and their role in tissue injury remain unknown.

Amino Acyl-tRNA Synthetases↗

PubMed1993

Drug therapy of the idiopathic inflammatory myopathies: predictors of response to prednisone, azathioprine, and methotrexate and a comparison of their efficacy.

PURPOSE: To identify factors associated with responses to treatment with prednisone, methotrexate, or azathioprine in patients with idiopathic inflammatory myopathy, and to compare the efficacy of these drugs. PATIENTS AND METHODS: Data were collected on 113 adult patients meeting criteria for definite idiopathic inflammatory myopathy in this retrospective cohort study. Patients were categorized as responding completely, partially, or not at all to each therapeutic trial based upon clinical and laboratory criteria. RESULTS: Clinical group, presence of certain myositis-specific autoantibodies, and time from disease onset to diagnosis influenced rates of complete clinical response to these therapeutic agents. Patients with inclusion body myositis responded comparatively poorly to prednisone and the other drugs: 43% had no clinical response to prednisone and none responded completely to any medication. Patients with autoantibodies to aminoacyl-tRNA synthetases or to signal recognition particle proteins were likely to respond partially, but not completely, to prednisone. No patient with a long delay to diagnosis (greater than 18 months) responded completely, compared with 34% of those with a short delay (less than 3 months). A patient's response to the first course of prednisone predicted subsequent responses to prednisone and to azathioprine better than response to methotrexate. Men responded to methotrexate better than women. Among certain subgroups of patients, responses to methotrexate were better than to either azathioprine or retreatment with prednisone. CONCLUSION: Determining the clinical group, autoantibody status, and time from disease onset to diagnosis of patients with myositis provides useful information in predicting clinical responses to therapy, and these factors should be considered in designing future therapeutic trials. Methotrexate therapy may be superior to either azathioprine or further steroid treatment alone in certain patients who do not respond completely to an initial adequate course of prednisone.

Adult↗

PubMed1994

The membrane proteins TRAMp and sec61 alpha p may be involved in post-translational transport of presecretory proteins into mammalian microsomes.

The presecretory protein ppcecDHFR, a hybrid between preprocecropinA and dihydrofolate reductase, is transported into mammalian microsomes post-translationally, i.e. independent of ribosome and signal recognition particle. Here, the involvement of microsomal proteins in ribonucleoparticle-independent transport of ppcecDHFR was analyzed by transport into trypsin-pretreated microsomes and by transport of a truncated version of ppcecDHFR and subsequent chemical cross-linking. We observed that post-translational transport of ppcecDHFR can occur into microsomes which had been pretreated with trypsin (final concentration, 100 micrograms/ml) and that of the known transport components only TRAMp and sec61 alpha p are still present under these conditions. Furthermore, we found that the truncated ppcecDHFR, ppcecDHFR-98mer', can be cross-linked to 36 kDa microsomal membrane proteins during post-translational transport. Therefore, the two microsomal membrane proteins with molecular masses of about 36 kDa, TRAMp and sec61 alpha p, appear to be involved in the post-translational transport of ppcecDHFR and ppcecDHFR-98mer.

Adenosine Triphosphate↗

PubMed1995

The 3' untranslated region of bovine preprolactin contains a transferable non-poly(A) mRNA sequence that prolongs translation.

Preprolactin transcripts, synthesized in vitro, were actively translated for a prolonged period when injected into Xenopus oocytes. As a result, prolactin continued to be secreted into the media for up to 6 days after injection of the transcript. To investigate the role of the preprolactin 3' untranslated sequence in stabilizing transcripts, it was fused to coding regions derived from signal recognition particle receptor alpha-subunit or preproinsulin receptor. The translational half-life of the chimeric RNA was increased for both coding regions, suggesting that a sequence within the preprolactin 3' untranslated region that prolongs translation is transferable. Deletion mutagenesis of this untranslated region demonstrated that a sequence of 98 nucleotides immediately following the prolactin stop codon was sufficient to prolong translation of RNAs injected into Xenopus oocytes.

Animals↗

PubMed1995

The functioning of the SRP receptor FtsY in protein-targeting in E. coli is correlated with its ability to bind and hydrolyse GTP.

In this study, we have established that FtsY, the E. coli homolog of the mammalian signal recognition particle (SRP) receptor, is a GTP-binding protein which displays intrinsic GTPase activity. GTP was found to influence the protease sensitivity of FtsY indicative of a conformational change. FtsY mutated in the 4th GTP-binding consensus element displayed reduced GTP-binding and -hydrolysis which correlated with a reduced ability to interact with SRP. Overexpression of the mutant proteins had a stronger inhibitory effect on protein translocation than overexpression of wild-type FtsY. These observations suggest that in E. coli GTP is important for proper functioning of FtsY in protein-targeting.

Base Sequence↗

PubMed1992

Expression of Alu and 7SL RNA in Alzheimer's and control brains.

We investigated whether changes in expression of RNA polymerase III (pol III) or heterodisperse RNA polymerase II (pol II) transcripts hybridizing to Alu could be detected in Alzheimer's disease (AD). RNA samples obtained from AD and control brain tissues were examined by Northern analysis for Alu and 7SL RNA expression. All RNA samples contained a prominent band of approximately 300 nucleotides which corresponds to 7SL RNA, the Alu-homologous RNA component of the signal recognition particle. In addition, three small (i.e. less than 300 nucleotide) 7SL/Alu-hybridizing transcripts were detected. The two larger of the low molecular weight transcripts hybridized preferentially to the 7SL RNA probe, while the smallest transcript hybridized to the Alu probe. These transcripts and the heterodisperse RNA were variable in quantity and displayed a lack of correlation with AD.

Alzheimer Disease↗

PubMed1991

Identification of deletion mutations and three new genes at the familial polyposis locus.

Small (100-260 kb), nested deletions were characterized in DNA from two unrelated patients with familial adenomatous polyposis coli (APC). Three candidate genes located within the deleted region were ascertained and a previous candidate gene, MCC, was shown to be located outside the deleted region. One of the new genes contained sequence identical to SRP19, the gene coding for the 19 kd component of the ribosomal signal recognition particle. The second, provisionally designated DP1 (deleted in polyposis 1), was found to be transcribed in the same orientation as MCC. Two other cDNAs, DP2 and DP3, were found to overlap, forming a single gene, DP2.5, that is transcribed in the same orientation as SRP19.

Adenomatous Polyposis Coli↗

PubMed1993

Protein translocation into proteoliposomes reconstituted from purified components of the endoplasmic reticulum membrane.

We have reproduced the process of protein transport across and of protein integration into the mammalian endoplasmic reticulum membrane by the use of proteoliposomes reconstituted from pure phospholipids and purified membrane proteins. The transport of some proteins requires only two membrane protein complexes: the signal recognition particle receptor, needed for targeting of a nascent chain to the membrane, and a novel complex, the Sec61p complex, that consists of Sec61p and two smaller polypeptides. The translocation of other proteins also needs the presence of the translocating chain-association membrane (TRAM) protein. The integration of two membrane proteins of different topologies into the membrane does not require additional components. These results indicate a surprising simplicity of the basic translocation machinery. They suggest that the Sec61p complex binds the ribosome during translocation and forms the postulated protein-conducting channel.

Animals↗

PubMed1986

Translocation of murine interleukin 2 into microsomes during translation in a cell-free system.

Interleukin 2 (IL2) is a lymphokine which stimulates the growth of T lymphocytes. Although IL2 mRNA is translated into biologically active IL2 relatively efficiently in microinjected Xenopus laevis oocytes, it has been difficult to establish reproducible cell-free translation systems for this lymphokine. Such systems would be useful for the analysis of translational and post-translational events. In this paper, we show that a wheat germ extract will translate IL2 mRNA into biologically active murine IL2, most of which is translocated into dog pancreas microsomes when these are present. Translocation occurs only during translation, but wheat germ extracts translate IL2 mRNA whether microsomes are present or not. Surprisingly, reticulocyte lysates do not readily translate IL2 mRNA, and strongly inhibit its translation in wheat germ extracts. This inhibition can be partially alleviated by adding dog pancreas microsomes to the system. The inhibition seen with reticulocyte lysate may be attributable to the action of the signal recognition particle, which binds nascent secretory proteins, and blocks their further translation in the absence of the docking protein present in microsomes.

Animals↗

PubMed1992

The 7SL RNA homologue of Trypanosoma brucei is closely related to mammalian 7SL RNA.

In eukaryotes, protein translocation across the endoplasmic reticulum is mediated by a signal recognition particle, a small ribonucleoprotein (RNP) containing 7SL RNA. We have cloned and sequenced the gene coding for the Trypanosoma brucei 7SL RNA homologue and found that its sequence shows the highest degree of similarity to the human 7SL RNA sequence. In keeping with the prototype secondary structure of eukaryotic 7SL RNA, the trypanosome 7SL RNA secondary structure can be folded into four domains. The 7SL RNP, which sediments at approximately 11S on sucrose density gradients, was partially purified using column chromatography. A particle containing a 76-nucleotide-long RNA co-purified with the 7SL RNP; however, these particles did not co-fractionate by non-denaturing polyacrylamide gel electrophoresis.

Animals↗

PubMed1990

Characterization of a 17 kDa protein gene upstream from the small cytoplasmic RNA gene of Bacillus subtilis.

The Bacillus subtilis small cytoplasmic RNA (scRNA) is the structural homologue of both the RNA component of the eukaryotic signal recognition particle (SRP) and the Escherichia coli 4.5S RNA, and it can complement the essential function of the latter RNA in vivo. In the course of characterization of the single-copy scRNA gene locus (scr) we identified an open reading frame, termed ORF17, upstream from scr that encodes an acidic 17 kDa protein of unknown function. This analysis involved DNA sequencing, monitoring expression of transcriptional and translational ORF17-cat and ORF17-lacZ fusions, respectively, and purification and sequencing of the ORF17-lacZ fusion protein. Apparently, transcription of ORF17 proceeds into scr. A small portion of the 17 kDa protein shows homology to deoxycytidylate (DCMP) deaminase of bacteriophagphage T2, but no similarity exists to the sequenced SRP-polypeptides or any other known protein sequences.

Amino Acid Sequence↗

PubMed1988

Molecular sorting of proteins into the cisternal secretory pathway.

Cotranslational translocation of exportable proteins across the RER membrane prior to their release into the extracellular space has been essentially described by use of canine pancreatic microsomal membranes. Intracisternal segregation of nascent secretory proteins was observed to be irreversible and proteolytic removal of signal sequences resulted in conformationally mature and stable proteins. Structural studies on various translocation peptides from both eukaryotic and prokaryotic preparations showed that many of them have a comparable three-domain organization. A hydrophilic amino-terminal domain is followed by a core region of hydrophobic amino acids and by the region in which the proteolytic cleavage occurs. Membrane components involved in the translocation process namely the signal recognition particle and the SRP receptor as well as the way the vectorial transport mechanism of nascent secretory proteins occurs are also discussed.

Amino Acid Sequence↗