Stabilization of translationally active mRNA by prokaryotic REP sequences

Nucleotide sequence of the osmoregulatory proU operon of Escherichia coli

The sequence of 4,362 nucleotides encompassing the proU operon of Escherichia coli was determined. Three open reading frames were identified whose orientation, order, location, and sizes were in close accord with genetic evidence for three cistrons (proV, proW, and proX) in this operon. Similarities in primary structure were observed between (i) the deduced sequence of ProV with membrane-associated components of other binding-protein-dependent transport systems, in the nucleotide-binding region of each of the latter proteins, and (ii) that of ProW with integral membrane components of the transport systems above. The DNA sequence data also conclusively established that ProX represents the periplasmic glycine betaine-binding protein. Two copies of repetitive extragenic palindromic sequences were identified beyond the 3' end of the proX gene. The primer extension technique was used to identify the 5' ends of proU mRNA species that are present in cells grown at high osmolarity; the results suggest that at least some of the osmotically induced proU transcripts have a long leader region, extending as much as 250 base pairs upstream of the proV gene. Evidence was also obtained for the existence of a sequence-directed bend in DNA in the upstream regulatory region of the proU operon.

mRNA stabilizing signals encoded in the genome of the bacteriophage phi x174

In Escherichia coli cells infected with bacteriophage phi x174, mRNAs initiated by promoters PB and PD terminate after genes J, F, G, or H (TJ, TF, TG, or TH). These RNAs are relatively stable and contain mRNA-stabilizing signals at their 3' ends. These signals were cloned after gene D of phi x174 in an expression vector plasmid. The cloned signals stabilize mRNA of the upstream gene D and the stabilized mRNA is translationally functional. When these signals are inserted in reverse, no stabilizing effect on mRNA is observed indicating that the correct sequences at the 3' ends of transcripts determine their stability. When a stabilizing signal (+) and a mutated stabilizing signal (-) which has reduced stabilizing activity are tandemly inserted after gene D, two sets of 3' termini of the transcript are observed indicating that both signals also function as terminators. The amount of gpD synthesized from these constructs varies depending upon the relative positions of the (+) or (-) signals after gene D. The stabilizing function seems to act by preventing mRNA degradation from the 3' to 5' direction. Several common features of these stabilizers are described.

Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon

The DNA sequence of a 3.6kb region downstream of the nagB gene (encoding glucosamine-6-PO4-deaminase) in Escherichia coli has been determined. Three open reading frames, which are subsequently referred to as nagA, nagC and nagD, were detected in this sequence. Genetic complementation and enzyme assays have shown that the first of these, nagA, encodes N-acetyl glucosamine-6-phosphate deacetylase. Growth on N-acetyl glucosamine induces the synthesis of a 1900 nucleotide long transcript which covers just nagE, encoding EIINag which is transcribed divergently from nagB, and of a 4200 nucleotide long transcript which covers all four ORFs of the nagB,A,C, D operon. More mRNA corresponding to nagB and nagA is detected than that corresponding to the distal genes, nagC and nagD. Considerable amounts of the induced mRNA are truncated molecules having their 3' ends after nagB and after nagA. Multiple 3' RNA ends have been mapped after nagD and seem to correspond to the ends of transcripts stabilized by mRNA secondary structure (REP sequences) rather than transcription termination sites. A second promoter producing nagD-specific transcripts has been mapped just in front of the nagD gene.

An expression system for trypsin

The eukaryotic serine protease, rat anionic trypsin, and various mutants created by site-directed mutagenesis have been heterologously expressed in Escherichia coli. The bacterial alkaline phosphatase (phoA) promoter was used to control the expression of the enzymes in an induced or constitutive fashion. The DNA coding for the eukaryotic signal peptide of pretrypsinogen was replaced with DNA coding for the phoA signal peptide. The phoA signal peptide successfully directs the secretion of the mammalian trypsinogen to the periplasmic space of E. coli. Active trypsin was expressed in the periplasm of E. coli by deleting the DNA coding for the activation hexapeptide of the zymogen. The activity of trypsin in the periplasm suggests that the enzyme is correctly activated and has folded such that the 12 cysteine residues involved in the six disulfide bonds of rat anionic trypsin have paired correctly. A transcription terminator increased the level of expression by a factor of two. However, increasing the copy number of the plasmid decreased the levels of expression. Localization of the active enzyme in the periplasm allows rapid screening of modified trypsin activities and facilitates the purification of protein to homogeneity and subsequently to crystallinity.

Isolation and characterization of Escherichia coli hag operator mutants whose hag48 expression has become repressible by a Salmonella H1 repressor

The expression of an Escherichia coli K12 flagellin gene, hagA48, is insensitive to the Salmonella H1 repressor (rh1+). By selecting merodiploid cells H2-rh1on-off/F'hag48 for motility in the presence of anti-H48 serum, mutants which had escaped from inhibition by the serum because of repression of their hag48 expression by rh1+ were isolated. Their nucleotide sequences were examined in the region containing the promoter, the position of which was confirmed by S1 nuclease analysis of the transcriptional initiation site. The two independently isolated mutants had the same heptamer insertion AGACGAT at a site overlapping with the promoter sequence, creating a putative operator sequence homologous to Salmonella H1, but not to H2. Other candidates for operator mutants had reduced flagellar synthesis because of mutations between the transcriptional and translational initiation sites or in the structural gene. The sequence analysis also revealed a repetitive extragenic palindrome (REP) consensus sequence and a transcriptional terminator of hag48 in a small, functionally unknown open reading frame (ORF).

Terminal sequences do not contain the rate-limiting decay determinants of E. coli cat mRNA

The mechanism of E. coli chloramphenicol acetyltransferase (cat) mRNA decay was investigated. Alteration of the 5' untranslated terminus does not appear to have an effect on the turnover rate of the mRNA. Similarly, changes at the 3' terminus of the message, including the addition of a stable stem and loop structure, do not affect the half-life of the message. The data suggest that 5' and 3' terminal untranslated sequences do not contain the rate-limiting determinants for cat message decay. Decay rates for various segments of the cat mRNA were measured and indicate that all regions of the message have similar stabilities. The current model of cat mRNA degradation involves a rate-limiting endonucleolytic decay event that occurs internal to the message followed by degradation of the cleavage products.

Retroregulation of the bacteriophage lambda int gene: limited secondary degradation of the RNase III-processed transcript

Expression of the int gene of bacteriophage lambda from two promoters, pI and pL, is differentially regulated through RNA processing. Efficient Int protein synthesis from the pL RNA is inhibited by the action of sib, a cis-acting retroregulator downstream from the int gene. We have used mapping procedures with nuclease S1 to study the pL transcripts produced in vivo after phage lambda infection. We have found an RNase III-dependent processing site within the Int coding sequence, 387 nucleotides upstream from the site of the primary cleavage by RNase III at Sib. This secondary processing site is located at the most stable region of secondary structure in the sib int region, as predicted by computer analysis. We suggest that RNase III cleavage at the Sib site allows processive exonucleolytic degradation of the RNA to proceed to a region of secondary structure within the Int coding sequence, which protects the upstream region of the transcript from further degradation.

Stability of group I intron RNA in Escherichia coli and its potential application in a novel expression vector

Intron RNA excised from the primary transcript of the phage T4 td gene was found to be unusually stable in vivo. In contrast to the average half-life of about 1.5 min for a typical Escherichia coli mRNA at 37 degrees C, the half-life of the excised group-I td intron ranged from 12 to 19 min for the linear form and from 22 to 33 min for the circular form. A 631-nucleotide region of the intron that is not essential for splicing was replaced by the chloramphenicol acetyltransferase (CAT) structural gene (cat). Although the presence of the foreign sequence reduced intron stability several-fold, the half-life of the resulting intron-cat hybrid RNA was found to be twice that of the normal cat mRNA. The increase in stability was accompanied by a five- to eight-fold increase in CAT production above that seen with transcriptional activation from the strong Ptac promoter alone. The over-production was both temperature-dependent and partially splicing-dependent. This type of intron fusion represents a novel method of transcript stabilization, which is of potential use to augment other means of increasing gene expression for purposes of product amplification.

Coliphage lambda to terminator lowers the stability of messenger RNA in Escherichia coli hosts

The effects of the transcription terminators to and tfd on the overall high-level expression of a human interferon-beta gene (IFN-beta) in Escherichia coli hosts were compared. Deletion mapping shows that mRNA lability is caused by sequences at or near the lambda terminator to stem-loop structure. Extensive RNA secondary structure in this region indicates a potential RNase III cleavage/binding site. In RNase III- E. coli hosts, IFN-beta synthesis is indeed considerably enhanced. The bacteriophage tfd terminator does not confer this mRNA labilization phenomenon. In all cases, RNA level and stability correlate with the level of IFN-beta synthesized in the cell. In the system described, ongoing translation stabilizes mRNA only moderately.

Mechanisms of mRNA decay in bacteria: a perspective

Messenger RNA decay plays an important role in prokaryotic gene expression. The disparate stabilities of bacterial messages in vivo are a consequence of their differential susceptibility to degradation by cellular endoribonucleases and 3' -exoribonucleases, which in turn results from differences in mRNA sequence and structure. RNase II and polynucleotide phosphorylase, the major bacterial exonucleases involved in mRNA turnover, rapidly degrade single-stranded RNA from the 3' end, but are impeded by 3' stem-loop structures. At present, the identify and substrate specificity of the endonucleases that control mRNA decay rates are relatively poorly defined. Ribosomes and antisense RNA also can influence the stability of transcripts with which they associate. Differences in mRNA stability can contribute to differential expression of genes within polycistronic operons and to modulation of gene expression in response to changes in bacterial growth conditions.

The differential stability of the Escherichia coli ompA and bla mRNA at various growth rates is not correlated to the efficiency of translation

Using two monocistronic gene transcripts, bla and ompA, we have studied the relationship between mRNA stability and translational efficiency. It was found that changes in the ompA mRNA stability are not correlated with an alteration in translational efficiency. In addition, at slow bacterial growth rates, the ompA transcript is translated ten times more efficiently than the bla messenger although the stability of the two transcripts is about equal. At rapid bacterial growth rate, chloramphenicol slightly stabilises both the bla and ompA transcripts without affecting their characteristic difference in half-life. Thus, control of mRNA stability seems not necessarily to be mediated either by the efficiency of loading ribosomes on a transcript, or by the arrest or slowing down of translating ribosomes.

Antisense RNA: its functions and applications in gene regulation--a review

All known antisense RNAs existing in nature are described. Of 11 natural antisense RNAs, nine function at the level of transcription and two at the level of DNA replication. On the basis of their inhibitory mechanisms they can be separated into three classes. From what can be found in the naturally occurring antisense RNAs, strategies in designing artificial antisense RNAs for gene expression are proposed, and applications and potential problems discussed.

Mechanism of puf mRNA degradation: the role of an intercistronic stem-loop structure

The puf photosynthesis operon of Rhodobacter capsulatus encodes two major classes of mRNA: operon-length pufBALMX transcripts and short pufBA messages. The pufBA messages, which end in a large intercistronic stem-loop structure, are long-lived processing products of the puf operon transcripts. Decay of the labile pufLMX segment of the operon-length transcripts begins with non-random endonucleolytic cleavage well downstream of the intercistronic hairpin structure. This hairpin, which is necessary but insufficient for the stability of the RNA segment upstream of it, appears to function as an mRNA decay terminator that protects the upstream pufBA segment from 3' exonucleolytic propagation of the initial degradative event. The comparative stability of the pufBA mRNA segment depends not only on the presence of this stem-loop structure, but also on the relative resistance of the pufBA segment to endonuclease attack.

Post-transcriptional control in Escherichia coli: translation and degradation of the atp operon mRNA

An attractive subject for investigations of post-transcriptional control is the atp operon, whose nine genes are differentially expressed. The primary mode of control of atp gene expression is exercised at the translational level. It has been clearly demonstrated for almost all of the atp genes that the primary and secondary structures of their respective translational initiation regions direct translational initiation rates that correspond well to the requirements for these subunits in the cell. The relationship between the structure of the translational initiation region, including bases upstream from the Shine-Dalgarno region and downstream from the start codon, and the rates of initiation that it determines, has been investigated in more detail using various polycistronic and monocistronic systems. No evidence could be found for a role of codon usage bias in controlling overall translation rates. The functional half-lives of atpE and of the other six cistrons downstream from it are similar. The chemical stabilities of the first two cistrons of the polycistronic atp mRNA may, however, be lower, and we are investigating the possibility that there may also be control of atp gene expression exercised at the level of mRNA stability. The effects of manipulations of the intercistronic regions of at least the plasmid borne atp operon are consistent with a model of mRNA decay in which rate control is associated with endonucleolytic cleavages within individual cistrons. The experimental data are discussed in relation to the possible ways in which primary and secondary structures of the mRNA might control translational efficiency and stability.

Messenger RNA degradation in Saccharomyces cerevisiae

The analysis of 17 functional mRNAs and two recombinant mRNAs in the yeast Saccharomyces cerevisiae suggests that the length of an mRNA influences its half-life in this organism. The mRNAs are clearly divisible into two populations when their lengths and half-lives are compared. Differences in ribosome loading amongst the mRNAs cannot account for this division into relatively stable and unstable populations. Also, specific mRNAs seem to be destabilized to differing extents when their translation is disrupted by N-terminus-proximal stop codons. The analysis of a mutant mRNA, generated by the fusion of the yeast PYK1 and URA3 genes, suggests that a destabilizing element exists within the URA3 sequence. The presence of such elements within relatively unstable mRNAs might account for the division between the yeast mRNA populations. On the basis of these, and other previously published observations, a model is proposed for a general pathway of mRNA degradation in yeast. This model may be relevant to other eukaryotic systems. Also, only a minor extension to the model is required to explain how the stability of some eukaryotic mRNAs might be regulated.

Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review

Repetitive extragenic palindromic (REP) sequences are highly conserved inverted repeats present in up to 1000 copies on the Escherichia coli chromosome. We have shown both in vivo and in vitro that REP sequences can stabilize upstream mRNA by blocking the processive action of 3'----5' exonucleases. In a number of operons, mRNA stabilization by REP sequences plays an important role in the control of gene expression. Furthermore, differential mRNA stability mediated by the REP sequences can be responsible for differential gene expression within polycistronic operons. Despite the key role of REP sequences in mRNA stability and gene expression in a number of operons, several lines of evidence suggest that this is unlikely to be the primary reason for the exceptionally high degree of sequence conservation between REP sequences. Other possible functions for REP sequences are discussed. We propose that REP sequences may be a prokaryotic equivalent of 'selfish DNA' and that gene conversion may play a role in the evolution and maintenance of REP sequences.

DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences

A family of repetitive extragenic palindromic (REP) sequences is composed of hundreds of copies distributed throughout the chromosome. Their palindromic nature and conservation suggested that they are specifically recognized by a protein(s). We have identified DNA gyrase [DNA topoisomerase (ATP-hydrolysing), EC 5.99.1.3] as one of the REP-binding proteins. Gyrase has at least a 10-fold higher affinity for DNA containing REP sequences than for DNA not containing REP sequences. Binding effectiveness correlates directly with the number of REP sequences in the DNA. DNase I footprinting shows that gyrase protects 205 base pairs on a REP-containing DNA fragment enclosing the REP sequences. In agreement with the above results, a comparison of the REP consensus sequence with the sequence of previously identified pBR322 "strong" gyrase cleavage sites reveals a high degree of homology. Because REP sequences are numerous and found throughout the genome, we suggest they have physiological functions mediated through their interaction with gyrase, such as being sites of action for the maintenance of DNA supercoiling. In addition, we speculate that these interactions may be of a structural nature, such as involvement in the higher-order structure of the bacterial chromosome.

Erythromycin-induced stabilization of ermA messenger RNA in Staphylococcus aureus and Bacillus subtilis

Erythromycin-induced stabilization of ermA mRNA was studied in Staphylococcus aureus, its original host background, and in Bacillus subtilis, subcloned on plasmid vectors. By RNA blot analysis it was shown that 40 nM-erythromycin specifically increased the chemical half-life of ermA mRNA from 2.5 to 17.5 minutes whereas the half-life of cat-86 mRNA was not increased by erythromycin. While expression of ermA has been shown to be induced by erythromycin at the level of translation, our studies with three ermA constitutive mutants demonstrated that mRNA stabilization in growing cells occurred independently of induced gene expression, suggesting that the stabilized mRNA was not functional for protein synthesis. Studies of ermA/lacZ fusions demonstrated that the 5' end of the mRNA was sufficient to confer stabilization. Translation of specific amino acid codons in a leader peptide located at the extreme 5' end of the mRNA was required for the erythromycin-induced stabilization as a frameshift mutation introduced into the leader peptide determinant abolished stabilization. By S1 mapping, no differences were detected in the length of the 5' or 3' end of ermA mRNA with the addition of erythromycin, indicating that the stabilized transcript was not processed at its ends.

Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons

We have determined the complete nucleotide sequence of the histidine operons of Escherichia coli and of Salmonella typhimurium. This structural information enabled us to investigate the expression and organization of the histidine operon. The proteins coded by each of the putative histidine cistrons were identified by subcloning appropriate DNA fragments and by analyzing the polypeptides synthesized in minicells. A structural comparison of the gene products was performed. The histidine messenger RNA molecules produced in vivo and the internal transcription initiation sites were identified by Northern blot analysis and S1 nuclease mapping. A comparative analysis of the different transcriptional and translational control elements within the two operons reveals a remarkable preservation for most of them except for the intercistronic region between the first (hisG) and second (hisD) structural genes and for the rho-independent terminator of transcription at the end of the operon. Overall, the operon structure is very compact and its expression appears to be regulated at several levels.

Positive and negative regulators for glucitol (gut) operon expression in Escherichia coli

Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). The activator and repressor are predicted to possess 119 (Mr = 12,955) and 257 (Mr = 28,240) aminoacyl residues, respectively, as deduced from the nucleotide sequences of their structural genes. Both of the genes encoding the two regulators are located downstream from the other known gut structural genes. Reverse transcriptase mapping revealed that the gutM gene is a promoter-distal constituent of the gut operon. The gutR gene has its own promoter, but expression of this gene is primarily due to readthrough from the gut operon operator-promoter. Thus, the gut operon consists of at least five structural genes and has the following gene order: gutOPABDMR. Interestingly, synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes. An additional cistron of the gut operon, of unknown function, may follow the gutR gene.

Molecular characterization of a gene encoding a 72-kilodalton mosquito-toxic crystal protein from Bacillus thuringiensis subsp. israelensis

A gene encoding a 72,357-dalton (Da) crystal protein of Bacillus thuringiensis var. israelensis was isolated from a native 75-MDa plasmid by the use of a gene-specific oligonucleotide probe. Bacillus megaterium cells harboring the cloned gene (cryD) produced significant amounts of the 72-kDa protein (CryD), and the cells were highly toxic to mosquito larvae. In contrast, cryD-containing Escherichia coli cells did not produce detectable levels of the 72-kDa CryD protein. The sequence of the CryD protein, as deduced from the sequence of the cryD gene, was found to contain regions of homology with two previously described B. thuringiensis crystal proteins: a 73-kDa coleopteran-toxic protein and a 66-kDa lepidopteran- and dipteran-toxic protein of B. thuringiensis subsp. kurstaki. A second gene encoding the B. thuringiensis subsp. israelensis 28-kDa crystal protein was located approximately 1.5 kilobases upstream from and in the opposite orientation to the cryD gene.

Photoregulation of gene expression in the filamentous cyanobacterium Calothrix sp. PCC 7601: light-harvesting complexes and cell differentiation

Light plays a major role in many physiological processes in cyanobacteria. In Calothrix sp. PCC 7601, these include the biosynthesis of the components of the light-harvesting antenna (phycobilisomes) and the differentiation of the vegetative trichomes into hormogonia (short chains of smaller cells). In order to study the molecular basis for the photoregulation of gene expression, physiological studies have been coupled with the characterization of genes involved either in the formation of phycobilisomes or in the synthesis of gas vesicles, which are only present at the hormogonial stage.In each system, a number of genes have been isolated and sequenced. This demonstrated the existence of multigene families, as well as of gene products which have not yet been identified biochemically. Further studies have also established the occurrence of both transcriptional and post-transcriptional regulation. The transcription of genes encoding components of the phycobilisome rods is light-wavelength dependent, while translation of the phycocyanin genes may require the synthesis of another gene product irrespective of the light regime. In this report, we propose two hypothetical models which might be part of the complex regulatory mechanisms involved in the formation of functional phycobilisomes. On the other hand, transcription of genes involved in the gas vesicles formation (gvp genes) is turned on during hormogonia differentiation, while that of phycobiliprotein genes is simultaneously turned off. In addition, and antisense RNA which might modulate the translation of the gvp mRNAs is synthezised.

Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12

The degradation of mRNA in Escherichia coli is thought to occur through a series of endonucleolytic and exonucleolytic steps. By constructing a series of multiple mutants containing the pnp-7 (polynucleotide phosphorylase), rnb-500 (RNase II), and ams-1 (altered message stability) alleles, it was possible to study general mRNA turnover as well as the degradation of specific mRNAs. Of most interest was the ams-1 pnp-7 rnb-500 triple mutant in which the half-life of total pulse-labeled RNA increased three- to fourfold at the nonpermissive temperature. RNA-DNA hybridization analysis of several specific mRNAs such as trxA (thioredoxin), ssb (single-stranded-DNA-binding protein), uvrD (DNA helicase II), cat (chloramphenicol acetyltransferase), nusA (N utilization substance), and pnp (polynucleotide phosphorylase) demonstrated two- to fourfold increases in their chemical half-lives. A new method for high-resolution Northern (RNA) analysis showed that the trxA and cat mRNAs are degraded into discrete fragments which are significantly stabilized only in the triple mutant. A model for mRNA turnover is discussed.

In vivo analysis of puf operon expression in Rhodobacter sphaeroides after deletion of a putative intercistronic transcription terminator

The intercistronic region of the mRNA derived from the puf operon of Rhodobacter sphaeroides is capable of forming two stable stem-loop structures, the first of which resembles a factor-independent transcription terminator. A puf operon construction lacking the putative transcription terminator was made in vitro and crossed into the chromosome of R. sphaeroides PUFB1 to yield a single chromosomal copy in the terminator-deleted strain. The mutant strain, designated PUF delta 348-420 which was otherwise isogenic with the wild-type strain 2.4.1, showed a normal growth rate at high light intensity compared with the wild type, with the levels of the B875 and reaction center spectral complexes being approximately 7% and 25%, respectively, of those found in the wild type. The deletion mutation correlated with a reduction in the size of the fixed photosynthetic unit from 15:1 in the wild type to 4:1 in the mutant. The level of the B800-850 complex was increased approximately twofold in the mutant strain. However, substantial amounts of the B875 and reaction center polypeptides were not incorporated into spectrally active complexes, suggesting the importance of other factors in the assembly of these complexes. Removal of the intercistronic stem-loops resulted in increased readthrough of the puf operon terminator to regions downstream, as well as altering the stability of the resulting puf operon-specific transcripts. A model is proposed which links ribosome stalling within the open reading frame K leader region of the puf operon transcript with chain termination.

Differential stability of c-myc mRNAS in a cell-free system

We have developed a simple cell-free system for studying the stability of different mRNAs in vitro. We demonstrate that the threefold greater stability in vivo of truncated c-myc mRNA (lacking exon 1) compared with that of full-length c-myc mRNA is maintained in our in vitro system. Chimeric mRNAs in which the first exon of c-myc was fused to immunoglobulin C alpha heavy chain or glyceraldehyde-3-phosphate dehydrogenase mRNAs were not rapidly degraded, demonstrating that c-myc exon 1 alone is not sufficient to tag mRNAs for rapid degradation. Competition experiments show that full-length c-myc mRNA is specifically recognized by a factor(s) responsible for its rapid degradation. This system will allow further characterization and purification of these factors.

Rat pulmonary surfactant protein A is expressed as two differently sized mRNA species which arise from differential polyadenylation of one transcript

In rat, the surfactant-associated glycoprotein A, SP-A, is encoded by two mRNA species of 0.9 and 1.6 kb. Each transcript is polyadenylated and is found in approximately the same ratio in total cellular RNA isolated from either alveolar type II cells or from whole lung. The two mRNA species have identical coding regions and differ only in the length of the 3' untranslated sequences. Restriction analysis and partial sequence analysis of rat genomic clones indicate that each mRNA species arises from one gene, with the difference in size most easily accounted for by differential polyadenylation. During fetal development, the accumulation of mRNA encoding SP-A is detectable by day 18 but increases many-fold on day 19. However, there are no apparent alterations in the prevalence of either mRNA species during fetal development or in the early postnatal period.

Cloning and sequencing of the Escherichia coli chlEN operon involved in molybdopterin biosynthesis

The nucleotide sequence of a HinPI-HpaII restriction nuclease fragment which complemented a delta chlE strain of Escherichia coli was determined. Two open reading frames were deduced to be the structural genes for ChlE and ChlN proteins, which have molecular weights of 44,067 and 26,719, respectively. Both proteins were required for complementing a chromosomal deletion of the chlE locus. The chlE and chlN genes were transcribed from a common promoter, chlEp, located upstream of chlE. Transcriptional and translational signal sequences were recognized in this region.

Differential stability of c-myc mRNAS in a cell-free system

We have developed a simple cell-free system for studying the stability of different mRNAs in vitro. We demonstrate that the threefold greater stability in vivo of truncated c-myc mRNA (lacking exon 1) compared with that of full-length c-myc mRNA is maintained in our in vitro system. Chimeric mRNAs in which the first exon of c-myc was fused to immunoglobulin C alpha heavy chain or glyceraldehyde-3-phosphate dehydrogenase mRNAs were not rapidly degraded, demonstrating that c-myc exon 1 alone is not sufficient to tag mRNAs for rapid degradation. Competition experiments show that full-length c-myc mRNA is specifically recognized by a factor(s) responsible for its rapid degradation. This system will allow further characterization and purification of these factors.

Molecular characterization of malQ, the structural gene for the Escherichia coli enzyme amylomaltase

The structural gene for the Escherichia coli enzyme amylomaltase, malQ, is the second gene in the malPQ operon. The nucleotide sequence of malQ shows that the gene encodes an Mr 78360 protein close to the experimentally determined Mr of purified amylomaltase (72000-74000). The malQ initiation codon was identified by sequence analysis of clustered deletions around the 5' end of the gene. One of these deletions removed the first 5 bases from the malQ coding sequence. Strains carrying a plasmid with this truncated malQ gene under lacZ promoter control and out-of-frame with the first four codons of lacZ were Mal-. The Mal+ phenotype could be restored by inserting small, random fragments of E. coli chromosomal DNA into the unique EcoRI site. Nucleotide sequencing showed that the inserts either joined the lacZ and malQ sequences in frame, or contained a new translation start signal and coding sequence in frame with malQ. These results indicate that amylomaltase could be useful as a reporter protein in gene fusion studies.

Expression of the E.coli hemolysin secretion gene hlyB involves transcript anti-termination within the hly operon

The genes hly A and hly B dictating synthesis and secretion of hemolytic toxin by Escherichia coli are transcribed as part of an operon hly C, hly A, hly B but are separated by an inverted repeat and poly-T sequence characteristic of a rho-independent terminator. The hly A-hly B intergenic sequence caused a reduction of in vivo transcriptional read-through from the gal promotor into gal K when inserted in the pKG1900 terminator-probe vector and also in vitro 3' to the bacteriophage T7 luminal diameter 10 promotor. Hybridisation of mRNA generated by the hly determinant of recombinant DNA pBR202-312 to an antisense RNA probe spanning the hly intergenic sequence revealed specific termination of 80% of in vivo hly transcripts within the poly-T sequence, immediately preceding the hly B translation start. Extension of the hly determinant with 3.5kbp of hly promotor-proximal DNA sequence raised intracellular and cell-free hemolytic activity 3-fold and 20-fold respectively and increased markedly the secretion of the 107Kd hemolysin protein (HlyA). Parallel hybridisation of in vivo mRNA to hly A and hly B antisense probes revealed that levels of hly A and hly B mRNA were increased by approximately 3-fold and 90-fold. The dramatically enhanced level of hly B mRNA resulted primarily from specific suppression of transcription termination at the intergenic rho-independent terminator from 80% to 1%, thus allowing virtually all hly A transcripts to elongate into hly B.

Evidence for endonucleolytic cleavages in decay of lacZ and lacI mRNAs

S1 nuclease mapping revealed lacZ mRNA molecules whose 5' and 3' ends were internal to the transcription start and consistent with cleavages at pyrimidine-adenosine bonds 20 to 50 nucleotides apart. With the net 5'-to-3' direction known, lacZ mRNA is probably degraded by sequential cleavages of naked mRNA at vulnerable sites exposed by transit of the last translating ribosome.

Nucleotide sequence of the mannitol (mtl) operon in Escherichia coli

The nucleotide sequence of the known portions of the mannitol operon in Escherichia coli (mtlOPAD) has been determined. Both the operator-promoter region and the intercistronic region between the mtlA and mtlD genes (encoding the mannitol-specific Enzyme II of the phosphotransferase system and mannitol-1-phosphate dehydrogenase, respectively) show parallels with corresponding regions of the glucitol (gut) operon, but neither the mtlA nor the mtlD gene products show obvious homology with the corresponding gene products of the glucitol operon. Five potential cyclic AMP receptor protein binding sites were identified in the mtlOP region, all showing near identity with the consensus sequence. Four regions of dyad symmetry (four to seven bases in length), serving as potential repressor binding sites, overlap with the potential cyclic AMP receptor protein binding sites. Repetitive extragenic palindromic (REP) sequences, forming stem-loop structures in the intercistronic region between mtlA and mtlD and following the mtlD gene were identified. Probable terminator sequences were not found in any of these three regulatory regions. Mannitol-1-phosphate dehydrogenase exhibits two overlapping, potential NAD+ binding sites near the N-terminus of the protein. Computer techniques were used to analyse the mtlD gene and its product.

Transcription of the target is required for IS102 mediated deletions

We have constructed several plasmids to test the specificity of target selection for IS102 associated deletions. We had previously shown that the cIII region of phage lambda is a target for IS102 mediated deletions and this region was therefore introduced in pSC101, where IS102 resides, in such a way that it was silent, transcribed or fully expressed. The deletion selection was provided by the galactokinase system. The results we have obtained show that transcription of the target region is required for deletion formation. The frequency of deletions in this target depends on its position along the transcript and is also influenced by translation. Implications of these results on the regional specificity of transposition are discussed.

Nucleotide sequence and regulation of a gene involved in bile acid 7-dehydroxylation by Eubacterium sp. strain VPI 12708

Eubacterium sp. strain VPI 12708 is an anaerobic intestinal bacterium that has inducible bile acid 7-dehydroxylation activity. At least four new polypeptides were synthesized after addition of primary bile acids to the growth medium. One of these, of molecular weight 27,000 (P-27), was shown to be involved in the 7-dehydroxylation reaction sequence. The gene coding for P-27 was cloned, and the entire DNA sequence for the protein-coding region was determined. In addition, sequence information was obtained for 294 bases upstream from the translational start codon and 329 bases downstream from the stop codon. Induction studies with a synthetic oligonucleotide probe (16-mer) revealed the presence of a cholic acid-inducible mRNA species approximately 900 bases long. A 5' terminus of this mRNA was detected by primer extension analysis, and the location of the 3' terminus of the mRNA was estimated by using S1 nuclease mapping. The 3' terminus of the mRNA contained a large element with dyad symmetry of unknown function. The open reading frame contained 249 codons, and the corresponding polypeptide had a calculated molecular weight of 26,745. The amino acid sequence of P-27 showed significant homology to several previously described alcohol-polyol dehydrogenases ("nonzinc" dehydrogenases), especially in the region believed to contain a pyridine nucleotide-binding domain. The implications of this homology and the possible function of P-27 in bile acid 7-dehydroxylation are discussed.

Transcriptional organization of the Escherichia coli hemolysin genes

The transcriptional organization of the Escherichia coli hemolysin genes (hlyCABD) encoded by pSF4000 was examined. The use of different hemolysin gene-specific radiolabeled probes in blots containing isolated in vivo RNA revealed 4.0-kilobase hlyCA and 8.0-kilobase hlyCABD transcripts. The treatment of cells with rifampin just before RNA isolation showed the half-lives of these mRNAs to be 10.2 and 4.4 min, respectively. The 5' ends of the hly transcripts were 462 and 464 nucleotides from the putative initiation codon of hlyC based on a primer extension method of RNA mapping. Deletion analysis of pSF4000 combined with quantification of the hemolysin structural protein HlyA by immunoblotting confirmed that major control of HlyA expression occurs within a 168-base-pair PstI fragment located 433 base pairs upstream of the start of hlyC. A second recombinant plasmid, pANN202-312, encoding an E. coli hemolysin of different origin expressed 6-fold less total HlyA and 50-fold less extracellular HlyA than pSF4000 in identical cell backgrounds. The pANN202-312 recombinant had a different hly promoter, with the hly mRNA beginning 264 nucleotides upstream from the start of hlyC. We showed by RNA blotting that cells harboring pANN202-312 compared with pSF4000 have similar steady-state levels of the hlyCA transcript but they lack a consistently detectable hlyCABD transcript. We propose that one reason for the disparate levels of extracellular hemolysin produced by hemolytic E. coli is dissimilar levels of mRNA encoding in part the transport genes hlyB and hlyD.

Site-specific endonucleolytic cleavages and the regulation of stability of E. coli ompA mRNA

The stability of ompA mRNA is growth-rate dependent. We show that the 5' noncoding region of this mRNA provides a target for site-specific endonucleases. The rate of degradation of ompA mRNA parallels the rate of these endonucleolytic cleavages, implying that endonucleolytic rather than exonucleolytic attack is the initial step in ompA mRNA degradation. Thus the 5' noncoding region appears to be a determinant of mRNA stability, and endonucleolytic cleavages in the 5' noncoding region may well regulate expression of the ompA gene.

Recombination among protein II genes of Neisseria gonorrhoeae generates new coding sequences and increases structural variability in the protein II family

Expression of Neisseria gonorrhoeae Protein II (P.II) is subject to phase variation and antigenic variation. The P.II proteins made by one strain possess both unique and conserved antigenic determinants. To study the mechanism of antigenic variation, we cloned several P.II genes, using as probes a panel of monoclonal antibodies (MAbs) specific for unique determinants. The DNA sequences of three P.II genes showed that they shared a conserved framework, with two short hypervariable (HV) regions being responsible for most of the differences among them. We demonstrated that unique epitopes recognized by the MAbs were at least partially encoded by one of the HV regions. Moreover, we found that reassortment of the two HV regions among P.II genes occurs, generating increased structural and antigenic variability in the P.II protein family.

An intercistronic stem-loop structure functions as an mRNA decay terminator necessary but insufficient for puf mRNA stability

Segmental differences in stability within the polycistronic transcripts of the puf operon contribute to differential expression of photosynthesis genes in R. capsulatus. The comparatively stable 5' segment of these transcripts ends in a large intercistronic stem-loop structure. We show here that deletion of this RNA hairpin destabilizes the 5' puf mRNA segment but that its insertion at the 3' end of the puf operon transcripts fails to stabilize the labile 3' puf mRNA segment. Evidence is presented that decay of the 3' segment begins with endonucleolytic cleavage in which the intercistronic stem-loop structure does not participate. We conclude that this RNA hairpin is necessary but insufficient for the stability of mRNA upstream of it, and that it functions in message degradation solely as an mRNA decay terminator that protects upstream mRNA segments from degradation by 3' exoribonucleases.

Molecular characterization and evolution of sequences encoding light-harvesting components in the chromatically adapting cyanobacterium Fremyella diplosiphon

The major light-harvesting complex in eukaryotic red algae and prokaryotic cyanobacteria is the phycobilisome, a water-soluble complex located on the outer surface of the photosynthetic membranes and composed of both pigmented phycobiliproteins (85%) and non-pigmented linker (15%) polypeptides. The phycobiliproteins are encoded by a gene family and exhibit varying degrees of sequence homology (25 to 55%). Some cyanobacteria can maximize the absorption of prevalent wavelengths of light by adjusting the phycobiliprotein composition of the phycobilisome, a process called complementary chromatic adaptation. In the chromatically adapting species Fremyella displosiphon, there are at least two sets of phycocyanin genes; one is transcribed as two red light-induced transcripts and the other is encoded on a single transcript present in both red and green light. We have determined the complete nucleotide sequences of both sets of phycocyanin subunit genes and their associated 5' and 3' regulatory regions. Based on S1 nuclease protection experiments, the transcripts (1600 and 3800 bases) encoding the inducible phycocyanin subunits have the same 5' end, and possible mechanisms for their synthesis are presented. The 5' end of the 1500-base transcript encoding the constitutive phycocyanin subunits was determined and revealed an Escherichia coli-like "-10" and "-35" region, and sequences near the transcription initiation site homologous to the analogous region of the phycocyanin gene set of Anabaena sp. 7120. Determination of the 3' ends of the transcripts encoding both F. diplosiphon phycocyanin gene sets revealed regions of potential secondary structure that may be important for transcription termination and/or transcript stability. In addition, the sequence of an open reading frame (encoding a 30 kDa polypeptide), located 3' to the constitutive phycocyanin gene set in F. diplosiphon and highly conserved in at least three cyanobacterial species, is presented. The same high degree of sequence homology between the two F. diplosiphon PC alpha and PC beta sequences (85 and 77%, respectively) was found at both the nucleotide and amino acid levels, and similar results were obtained for interspecies comparisons. Implications of these homologies with regard to the evolution of phycobiliprotein subunits are discussed.

Expression of the unc genes in Escherichia coli

The unc (or atp) operon of Escherichia coli comprises eight genes encoding the known subunits of the proton-translocating ATP synthase (H+-ATPase) plus a ninth gene (uncI) of unknown function. The subunit stoichiometry of the H+-ATPase (alpha 3 beta 3 gamma 1 delta 1 epsilon 1 a1b2c10-15) requires that the respective unc genes be expressed at different rates. This review discusses the experimental methods applied to determining how differential synthesis is achieved, and evaluates the results obtained. It has been found that the primary level of control is translational initiation. The translational efficiencies of the unc genes are determined by primary and secondary mRNA structures within their respective translational initiation regions. The respective rates of translation are matched to the subunit requirements of H+-ATPase assembly. Finally, points of uncertainty remain and experimental strategies which will be important in future work are discussed.

Complex RNA maturation in chloroplasts. The psbB operon from spinach

The psbB operon of the spinach plastid chromosome encodes the genes for the 51-kDa chlorophyll a apoprotein (psbB), the 10-kDa phosphoprotein (psbH), both associated with photosystem II, as well as cytochrome b6 (petB) and subunit IV (petD) of the cytochrome b/f complex in the order given. These genes are not expressed coordinately. The RNA pattern of this DNA region is complex and resolves into eighteen major RNA species. Using northern and S1 protection analysis we demonstrate (a) that all RNA species derive from one DNA strand and hybridize in an overlapping fashion; and (b) that they arise by processing rather than by multiple transcription initiation/termination. (c) The operon is bordered by a single prokaryote-like promotor in front of psbB, and by a putative factor-independent terminator with characteristic sequence elements following petD. The terminator appears to function bidirectionally. (d) At least four distinct modification activities operate on the putative primary transcript of 5650 nucleotides and on the processing intermediates, including a novel endonucleolytic activity cleaving within a characteristic hexanucleotide motif, 3'-exonucleolytic activity at discrete RNA ends, 5' shortage of mRNA (psbB), and excision of class II intervening sequences (petB and petD). (e) Kinetically, maturation of the primary transcript is largely a stochastic process. (f) Processing results ultimately in the formation of monocistronic mRNAs for each of the two photosystem II polypeptides and a bicistronic mRNA encoding both subunits of the cytochrome b/f complex. We postulate that these RNA species represent the translationally active components in the non-coordinate dark/light expression of these genes. (g) Light is without any noticeable effect on posttranscriptional modification. Under our conditions it appears to operate at a translational rather than a transcriptional or posttranscriptional level indicating that the biogenesis of thylakoid membranes is regulated at various levels.