Prokaryotic ribosome binding sites

Expressing Cloned Genes for Protein Production, Purification, and Analysis

Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.

Use of natural mRNAs in the cell-free protein-synthesizing systems of the moderate halophile Vibrio costicola

In vitro protein synthesis was studied in extracts of the moderate halophile Vibrio costicola by using as mRNAs the endogenous mRNA of V. costicola and the RNA of the R17 bacteriophage of Escherichia coli. Protein synthesis (amino acid incorporation) was dependent on the messenger, ribosomes, soluble cytoplasmic factors, energy source, and tRNA(FMet) (in the R17 RNA system) and was inhibited by certain antibiotics. These properties indicated de novo protein synthesis. In the V. costicola system directed by R17 RNA, a protein of the same electrophoretic mobility as the major coat protein of the R17 phage was synthesized. Antibiotic action and the response to added tRNA(FMet) showed that protein synthesis in the R17 RNA system, but not in the endogenous messenger system, absolutely depended on initiation. Optimal activity of both systems was observed in 250 to 300 mM NH4+ (as glutamate). Higher salt concentrations, especially those with Cl- as anion, were generally inhibitory. The R17 RNA-directed system was more sensitive to Cl- ions than the endogenous system was. Glycine betaine stimulated both systems and partly overcame the toxic effects of Cl- ions. Both systems required Mg2+, but in lower concentrations than the polyuridylic acid-directed system previously studied. Initiation factors were removed from ribosomes by washing with 3.0 to 3.5 M NH4Cl, concentrations about three times as high as that needed to remove initiation factors from E. coli ribosomes. Washing with 4.0 M NH4Cl damaged V. costicola ribosomes, although the initiation factors still functioned. Cl- ions inhibited the attachment of initiation factors to tRNA(FMet) but had little effect on binding of initiation factors to R17 RNA.

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts

Heterogeneous nuclear ribonucleic acid (hnRNA) molecules in eucaryotic cell nuclei associate with a well-defined group of abundant, highly conserved proteins to form heterogeneous nuclear ribonucleoproteins (hnRNP). The exact manner in which these 30S complexes assemble on nuclear transcripts, however, has not been well documented. To determine whether any site selectivity in the formation of hnRNP can be detected (e.g., preferential recognition of intervening sequences or of premessage regions), we investigated the distribution of 30S hnRNP on a particular nuclear RNA, the polyoma virus late transcript. Hybridization studies showed not only that the majority of polyoma late nuclear RNA sequences can be isolated in the form of 30S complexes, but that the RNP were located equally on intervening sequences and premessage portions of the transcript. The latter conclusion was confirmed by ribonuclease T1 oligonucleotide fingerprint analysis of polyoma virus-specific RNA recovered from native 30S complexes. However, fingerprint analysis of the small segments of viral RNA in the 30S fraction that survived extensive ribonuclease treatment revealed that oligonucleotides corresponding to intervening sequences were preferentially lost. We discuss these findings in relation to the structure of 30S hnRNP and their function in RNA biogenesis.

Translational control of phage f1 gene expression by differential activities of the gene V, VII, IX and VIII initiation sites

Phage-specific transcription and subsequent RNA processing in Escherichia coli infected with the filamentous phage (f1, M13, fd) generate a pool of abundant and relatively long-lived phage mRNA species encoding the four adjacent genes V, VII, IX and VIII. Yet the products of gene V and gene VIII are synthesized at much higher levels than the gene VII and gene IX proteins. To ask if the translational initiation sites heading these genes show corresponding differences in activity and/or functional properties, we have purified a number of the phage mRNAs from cells infected with f1 and examined them in in vitro initiation reactions. The ribosome binding patterns obtained for the phage mRNA species and for smaller defined RNA fragments containing selected initiator regions reveal a large range in apparent ribosome binding strengths. The gene V and gene VIII sites are recognized efficiently in each mRNA species in which they are present. Gene IX site activity appears to be limited by local mRNA structure: the site has undetectable or low ribosome binding activity in all of the phage mRNA species, but is at least tenfold more active if the RNA sequences required to form a potential hairpin stem-and-loop 15 nucleotides upstream from the initiator AUG have been removed. The gene VII site shows no evidence of interaction with ribosomes in any phage mRNA or RNA fragment tested. The same striking differences in initiation activity were observed in vivo by cloning small f1 DNA fragments containing gene V or gene VII initiation site sequences to drive beta-galactosidase synthesis. High levels of a gene V-beta-galactosidase fusion protein are initiated at the V site, but no detectable synthesis occurs from the VII site. If the VII site is preceded by all of the information encoding the upstream gene V, however, modest amounts of a fusion protein initiated at the VII site are produced. The overall results, in accord with the observed yields of proteins in the phage-infected cell, provide strong evidence that the properties of these translational initiation sites determine in a significant way the differential expression of phage f1 genes V, VII, IX and VIII.

Messenger RNA conformation and ribosome selection of translational reinitiation sites in the lac repressor mRNA

In the early region of the Escherichia coli lac repressor mRNA, the pattern of cleavage by nucleases specific for single or double-stranded RNA confirms the presence of secondary structures previously proposed to influence the pattern of translational reinitiation. These are positioned so as to mask a potential restart site centered on an in-phase GUG triplet corresponding to repressor amino acid position Val38. Our finding that a restart polypeptide initiated at the Val38 GUG codon is observed only in situations that that preclude base-pairing of adjacent mRNA sequences establishes a functional role for these structures in vivo. This evidence for structure, considered with the overall pattern of reinitiation events, suggests that local mRNA conformation is the major determinant that dictates ribosomal selection of restart sites within the early region of the repressor cistron.

Functional analysis of lac repressor restart sites in translational initiation and reinitiation

To define some of the features that influence ribosomal recognition of translational restart sites in the lac repressor mRNA, recombinant DNA methods have been used to construct lacI-Z fusions in which lacZ gene expression is dependent upon initiation or reinitiation within lacI mRNA sequences. Reinitiation efficiencies, as assessed by beta-galactosidase levels in strains bearing such plasmids, appear to be determined by at least three features of the RNA between the termination codon and reinitiation codon: the presence of competing out-of-frame AUG or GUG triplets, the distance between termination and reinitiation points, and the extent to which restart sequences remain accessible to ribosomes. While some of the restart sites are used with substantial efficiency for reinitiation, they do not function detectably as primary initiators if placed at the 5' end of the lacZ mRNA. This finding concurs with our observation that relative to the wild-type initiator region, which is recovered in quantitative yield from in vitro initiation reactions, ribosome protection of the four restart sites occurs at more than 100-fold lower efficiencies. In part, the lack of initiation activity is rationalized by the striking potential these sequences have for forming stable secondary structures that sequester elements essential for ribosome binding. However, the differential functioning of the restart sites in primary initiation versus reinitiation must also reflect real differences in the mechanisms operative in the two events.

Cloning and characterization of a ribosomal RNA gene from Plasmodium berghei

The ribosomal RNA (rRNA) of Plasmodium berghei strain NYU2 was characterized with respect to size and used to identify molecular clones of ribosomal RNA genes (rDNA) from this organism. The intact large rRNA species (Mr 1.40 X 10(6] is intermediate in size between prokaryotic and eukaryotic large rRNAs. It is specifically cleaved in vivo near the 5'-end yielding one large component (Mr 1.10 X 10(6] and one small component (Mr 0.30 X 10(6]. The small rRNA species (Mr 0.75 X 10(6] is larger than in higher eukaryotic organisms, but is similar in size to some other protozoa. Using 5'-end labeled rRNA as a probe, clones of rDNA were selected from genomic DNA libraries prepared in lambda phage Charon 4A and plasmid pBR322. The clones prepared in lambda were prone to recombination. The 14.7 kilobase (kb) insert in phage lambda PbR27 contains the complete coding sequences for both the small and larger rRNA species. A complete set of small plasmid clones were isolated which hybridize to the different segments of the rRNA transcription unit. A restriction map of the genes cloned in lambda PbR27 with the approximate position of the coding region is presented. The polarity of transcription of the rDNA was determined by hybridizing 3'-OH end labeled rRNA to Southern blots of genomic and cloned rDNA. The results indicate that a transcription unit of P. berghei rDNA is arranged as in other organisms with the small rRNA at the 5' end and the large rRNA at the 3' end.

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts

Heterogeneous nuclear ribonucleic acid (hnRNA) molecules in eucaryotic cell nuclei associate with a well-defined group of abundant, highly conserved proteins to form heterogeneous nuclear ribonucleoproteins (hnRNP). The exact manner in which these 30S complexes assemble on nuclear transcripts, however, has not been well documented. To determine whether any site selectivity in the formation of hnRNP can be detected (e.g., preferential recognition of intervening sequences or of premessage regions), we investigated the distribution of 30S hnRNP on a particular nuclear RNA, the polyoma virus late transcript. Hybridization studies showed not only that the majority of polyoma late nuclear RNA sequences can be isolated in the form of 30S complexes, but that the RNP were located equally on intervening sequences and premessage portions of the transcript. The latter conclusion was confirmed by ribonuclease T1 oligonucleotide fingerprint analysis of polyoma virus-specific RNA recovered from native 30S complexes. However, fingerprint analysis of the small segments of viral RNA in the 30S fraction that survived extensive ribonuclease treatment revealed that oligonucleotides corresponding to intervening sequences were preferentially lost. We discuss these findings in relation to the structure of 30S hnRNP and their function in RNA biogenesis.