The regulatory region of the trp operon of Serratia marcescens

Four RNA families with functional transient structures

Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here.

Determinants of segregational stability of the linear plasmid-prophage N15 of Escherichia coli

N15 is a bacteriophage of Escherichia coli that resembles lambda, but, unlike lambda, it lysogenizes as a linear plasmid. We show that stable maintenance of this unusual plasmid-prophage depends on the parA and parB genes, relatives of the partition genes of F and P1 plasmids. ParB of N15, like its F- and P1-encoded homologues, destabilizes plasmids carrying its target centromere, when present in excess. Within the genome of N15, we identified four unlinked, palindromic sequences that can promote the ParB-mediated destabilization of a moderate-copy vector in cis. They are distant from the parAB operon, unlike the centromeric sites of F and P1. Each of these palindromes could interact in vivo and in vitro with ParB. Each, when cloned separately, had properties characteristic of centromeric sites: exerted incompatibility against the N15 prophage and mini-N15 plasmids, and stabilized a mini-P1 plasmid depleted of its own partition genes when ParA and ParB of N15 were supplied. A pair of sites was more effective than a single site. Two of the centromeric sites are located in the proximity of promoters of phage genes, suggesting that, in addition to their function in partitioning of N15 prophage, they may control expression of N15 lytic functions.

Characterization of the primary immunity region of the Escherichia coli linear plasmid prophage N15

N15 is the only bacteriophage of Escherichia coli known to lysogenize as a linear plasmid. Clear-plaque mutations lie in at least two regions of the 46-kb genome. We have cloned, sequenced, and characterized the primary immunity region, immB. This region contains a gene, cB, whose product shows homology to lambdoid phage repressors. The cB3 mutation confers thermoinducibility on N15 lysogens, consistent with CB being the primary repressor of N15. Downstream of cB lies the locus of N15 plasmid replication. Upstream of cB lies an operon predicted to encode two products: one homologous to the late repressor of P22 (Cro), the other homologous to the late antiterminator of phi 82 (Q). The Q-like protein is essential for phage development. We show that CB protein regulates the expression of genes that flank the cB gene by binding to DNA at symmetric 16-bp sites. Three sites are clustered upstream of cB and overlap a predicted promoter of the cro and Q-like genes as well as two predicted promoters of cB itself. Two sites downstream of cB overlap a predicted promoter of a plasmid replication gene, repA, consistent with the higher copy number of the mutant, N15cB3. The leader region of repA contains terminators in both orientations and a putative promoter. The organization of these regulatory elements suggests that N15 plasmid replication is controlled not only by CB but also by an antisense RNA and by a balance between termination and antitermination.

The tryptophan repressor sequence is highly conserved among the Enterobacteriaceae

Tryptophan biosynthesis in Escherichia coli is regulated by the product of the trpR gene, the tryptophan (Trp) repressor. Trp aporepressor binds the corepressor, L-tryptophan, to form a holorepressor complex, which binds trp operator DNA tightly, and inhibits transcription of the tryptophan biosynthetic operon. The conservation of trp operator sequences among enteric Gram-negative bacteria suggests that trpR genes from other bacterial species can be cloned by complementation in E. coli. To clone trpR homologues, a deletion of the E. coli trpR gene, delta trpR504, was made on a plasmid by site-directed mutagenesis, then crossed onto the E. coli genome. Plasmid clones of the trpR genes of Enterobacter aerogenes and Enterobacter cloacae were isolated by complementation of the delta trpR504 allele, scored as the ability to repress beta-galactosidase synthesis from a prophage-borne trpE-lacZ gene fusion. The predicted amino acid sequences of four enteric TrpR proteins show differences, clustered on the backside of the folded repressor, opposite the DNA-binding helix-turn-helix substructures. These differences are predicted to have little effect on the interactions of the aporepressor with tryptophan, holorepressor with operator DNA, or tandemly bound holorepressor dimers with one another. Although there is some variation observed at the dimer interface, interactions predicted to stabilize the interface are conserved. The phylogenetic relationships revealed by the TrpR amino acid sequence alignment agree with the results of others.

The degA gene product accelerates degradation of Bacillus subtilis phosphoribosylpyrophosphate amidotransferase in Escherichia coli

A search for genes involved in the inactivation and degradation of enzymes in sporulating Bacillus subtilis led to identification of the B. subtilis degA gene, whose product stimulates degradation of B. subtilis glutamine phosphoribosylpyrophosphate amidotransferase in Escherichia coli cells. degA encodes a 36.7-kDa protein that has sequence similarity to several E. coli and B. subtilis regulatory proteins of the LacI class. B. subtilis degA::cat insertional inactivation mutants had no detectable defect in the inactivation or degradation of phosphoribosylpyrophosphate amidotransferase in glucose- or lysine-starved B. subtilis cells, however. We suggest that degA encodes either a novel protease or, more likely, a gene that stimulates production of such a protease.

Transcript elongation and termination are competitive kinetic processes

In this paper, we develop a kinetic approach to predict the efficiency of termination at intrinsic (factor independent) terminators of Escherichia coli and related organisms. In general, our predictions agree well with experimental results. Our analysis also suggests that termination efficiency can readily be modulated by protein factors and environmental variables that shift the kinetic competition toward either elongation or termination. A quantitative framework for the consideration of such regulatory effects is developed and the strengths and limitations of the approach are discussed.

Development of a trpE promoter-strength measuring system and its use in comparison of the trpEDCBA, trpR and aroH promoters

An expression system was developed for measuring in vivo promoter strength at the single copy level and this system was used to compare the trp, aroH and trpR promoters. This system employs trpE enzyme activity as a measure of promoter strength and lacZ expression for internal copy number reference. Promoter-containing fragments are inserted into a cloning vector and subsequently recombined on to phage lambda by genetic exchange. Single lysogens are then prepared and used in promoter-strength analyses. The strength of several promoters was determined using this system. Among the promoters tested, the Escherichia coli trpEDCBA promoter was the strongest; it was four times more active than the lacUV5 promoter and about ten times stronger than the trpR and aroH promoters. To validate measurement of trpE enzyme activity as an indicator of promoter strength, trpE enzyme activity was compared with the level of trpE mRNA. There was excellent correspondence between the two, suggesting that with this system trpE enzyme activity accurately reflects promoter strength. We also examined a homologous promoter-strength measuring system in which the promoter-cloning plasmid lacked a 104 base-pair DNA spacer that was present immediately downstream from the promoter-cloning site in our preferred system. We found that the spacer was essential; the transcribed region accompanying a cloned promoter apparently affected trpE translational efficiency and/or trpE mRNA stability.

Mini-P1 plasmid partitioning: excess ParB protein destabilizes plasmids containing the centromere parS

The partition system of the unit-copy plasmid P1 consists of two proteins, the parA and parB gene products, and a cis-acting site, parS. Production of high levels of the P1 ParB protein, from an external promoter on a high-copy-number vector, inhibits the propagation of lambda-mini-P1 prophages and destabilizes other P1-derived plasmids. The interference by ParB protein depends on the parS site, or centromere, of the P1 partition region; plasmids lacking parS are unaffected. The defect is more severe than the defect due to mutations that simply eliminate par function. In the presence of excess ParB protein, plasmids carrying parS are more unstable than would be predicted from a random distribution at cell division. The destabilization is a segregation defect, as the copy number of parS-bearing plasmids is not decreased under these conditions. Thus, it appears that ParB protein binds to parS; if too much protein is present, it sequesters such plasmids so they cannot be properly, or even randomly, partitioned. This suggests that under normal conditions, ParB protein recognizes and binds to parS and may be the protein responsible for pairing plasmids during the process of partitioning at cell division.

3'-terminal polyadenylate sequences of Escherichia coli tryptophan synthetase alpha-subunit messenger RNA

Our earlier studies have shown that the mRNA from many bacterial species, including Escherichia coli and Bacillus subtilis, is extensively polyadenylated, but with shorter poly(A) segments than those associated with eukaryotic mRNA. In this paper, we show that about 40% of the mRNA for the tryptophan synthetase alpha-subunit (TrpA) of E. coli carries a 3'-terminal polyadenylate sequence of 15 to 20 residues. This conclusion was supported by several independent lines of evidence. About 40% of trpA mRNA bound to oligo(dT)-cellulose at high ionic strength and was eluted with water. Treatment with RNase H in the presence of oligo(dT)12-18 destroyed the ability of trpA mRNA to bind to oligo(dT)-cellulose, presumably through the degradation of the poly(A) tract. trpA mRNA could be used as template for complementary DNA synthesis with reverse transcriptase in a reaction that was absolutely dependent on oligo(dT)12-18 as primer. The identity of the cDNA product as a complement to trpA mRNA was established by specific hybridization. In addition, it was possible to synthesize polyadenylated trpA mRNA in toluene-permeabilized cells of E. coli transformed with a recombinant plasmid carrying the trpA gene. In view of the fact that the trpA gene and its 3'-untranslated region contain no continuous deoxyadenylate sequences larger than five nucleotides, one can conclude that the polyadenylate moiety is added post-transcriptionally.

Gene sequence encoding early enzymes of arginine synthesis within a cluster in Bacillus subtilis, as revealed by cloning in Escherichia coli

From a partial Sau3A gene library of Bacillus subtilis chromosomal DNA in the expression plasmid pRK9, four hybrid plasmids were isolated carrying overlapping segments of the argA-argF-cpa cluster. The complementation patterns within Escherichia coli arginine auxotrophs of these hybrids and deletion derivatives provided the gene order argC-argA-argE-argB-argD-cpa-argF.

Theoretical evaluation of transcriptional pausing effect on the attenuation in trp leader sequence

The effect of transcriptional pausing on attenuation is investigated theoretically on the basis of the attenuation control mechanism presented by Oxender et al. (Oxender, D. L., G. Zurawski, and C. Yanofsky, 1979, Proc. Natl. Acad. Sci. USA. 76:5524-5528). An extended stochastic model including the RNA polymerase pausing in the leader region is developed to calculate the probability of relative position between the RNA polymerase transcribing the trp leader sequence and the ribosome translating the transcript. The present study results in a new rationale that the transcriptional pausing site in the leader sequence makes the attenuation control both more sensitive as an on/off switch and less sensitive to variations in the concentration of cellular metabolites not connected with the need for expressing, or not expressing, the particular operon. It is also proposed that the transcriptional pausing diminishes the dependence of attenuation control characteristics on the number of nucleotides in the leader sequence. This result may be useful for understanding the attenuation control efficiencies of other amino acid leader sequences with different lengths of nucleotides.

Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites

The variations in several double helical DNA angular parameters have been calculated along about 60 bacterial and phage sequences, each several hundreds nucleotides long. Regions of large geometric irregularities are found at, or in the vicinity of, regulatory protein recognition sites. Based on these extensive computations I suggest that these structurally "wrinkled" regions facilitate the first stage of the recognition process.

Evolution of glutamine amidotransferase genes. Nucleotide sequences of the pabA genes from Salmonella typhimurium, Klebsiella aerogenes and Serratia marcescens

The amide group of glutamine is a source of nitrogen in the biosynthesis of a variety of compounds. These reactions are catalyzed by a group of enzymes known as glutamine amidotransferases; two of these, the glutamine amidotransferase subunits of p-aminobenzoate synthase and anthranilate synthase have been studied in detail and have been shown to be structurally and functionally related. In some micro-organisms, p-aminobenzoate synthase and anthranilate synthase share a common glutamine amidotransferase subunit. We report here the primary DNA and deduced amino acid sequences of the p-aminobenzoate synthase glutamine amidotransferase subunits from Salmonella typhimurium, Klebsiella aerogenes and Serratia marcescens. A comparison of these glutamine amidotransferase sequences to the sequences of ten others, including some that function specifically in either the p-aminobenzoate synthase or anthranilate synthase complexes and some that are shared by both synthase complexes, has revealed several interesting features of the structure and organization of these genes, and has allowed us to speculate as to the evolutionary history of this family of enzymes. We propose a model for the evolution of the p-aminobenzoate synthase and anthranilate synthase glutamine amidotransferase subunits in which the duplication and subsequent divergence of the genetic information encoding a shared glutamine amidotransferase subunit led to the evolution of two new pathway-specific enzymes.

The Klebsiella aerogenes glutamate dehydrogenase (gdhA) gene: cloning, high-level expression and hybrid enzyme formation in Escherichia coli

The NADP-dependent glutamate dehydrogenase gene of Klebsiella aerogenes was cloned in E. coli in the expression plasmid pRK9. The cloned gene shows a high level of expression in E. coli in the hybrid plasmid pKG3 and such expression is independent of the vector promoter, as shown by experiments in which the promoter was deleted. Active hybrid GDH hexamers were shown in cell-free extracts of an E. coli strain carrying cloned gdhA genes of both E. coli and K. aerogenes. The nucleotide sequence of the N-terminal coding region of the K. aerogenes gdhA gene was determined and found to be strongly homologous with that of E. coli.

Nucleotide sequence of Escherichia coli pabB indicates a common evolutionary origin of p-aminobenzoate synthetase and anthranilate synthetase

Biochemical and immunological experiments have suggested that the Escherichia coli enzyme p-aminobenzoate synthetase and anthranilate synthetase are structurally related. Both enzymes are composed of two nonidentical subunits. Anthranilate synthetase is composed of proteins encoded by the genes trp(G)D and trpE, whereas p-aminobenzoate synthetase is composed of proteins encoded by pabA and pabB. These two enzymes catalyze similar reactions and produce similar products. The nucleotide sequences of pabA and trp(G)D have been determined and indicate a common evolutionary origin of these two genes. Here we present the nucleotide sequence of pabB and compare it with that of trpE. Similarities are 26% at the amino acid level and 40% at the nucleotide level. We propose that pabB and trpE arose from a common ancestor and hence that there is a common ancestry of genes encoding p-aminobenzoate synthetase and anthranilate synthetase.

RNA1 is sufficient to mediate plasmid ColE1 incompatibility in vivo

The multicopy plasmid ColE1 specifies a small RNA designated RNA1 that has been implicated in copy number control and incompatibility. We have inserted a 148 base-pair ColE1 DNA fragment containing a promoter-less RNA1 gene into a plasmid vector downstream from the tryptophan promoter of Serratia marcesens . The ColE1 RNA1 produced by this plasmid is not functional in vivo due to the presence of 49 nucleotides appended to the 5'-terminus of the wild-type RNA1 sequence. Deletions of these sequences by Bal3l nuclease in vitro and genetic selection for ColE1 incompatibility function in vivo permitted isolation of a plasmid expressing wild-type ColE1 RNA1 initiated properly from the S. marcesens trp promoter. These experiments demonstrate that RNA1 is sufficient to mediate ColE1 incompatibility in vivo. In addition, several plasmids were isolated that contain altered RNA1 genes. These alterations consist of additions or deletions of sequences at the 5'-terminus of RNA1. Analysis of the ability of these altered RNA1 molecules to express incompatibility in vivo suggests that the 5'-terminal region of RNA1 is crucial for its function.

Recombinant nontoxinogenic Vibrio cholerae strains as attenuated cholera vaccine candidates

An ideal vaccine does not yet exist to prevent cholera, a significant health problem in many less developed countries. Vibrio cholerae, the agent of epidemic and endemic cholera, colonizes the small bowel and secretes a potent enterotoxin that consists of a single A subunit, which stimulates adenylate cyclase activity, and five identical B subunits which bind to the ganglioside GM1 receptor of intestinal mucosal cells. Previous studies in man indicate that toxoid-derived antitoxic immunity by itself is insufficient to provide effective, long-lasting protection against cholera. Using recombinant DNA techniques we have now constructed a live, attenuated V. cholerae strain by deleting genes encoding the enterotoxin. Restriction enzyme fragments encoding cholera toxin were deleted in vitro from cloned vibrio chromosomal DNA and the resulting mutations introduced into the chromosome of a vibrio strain of proven immunogenicity. Recently, Mekalanos and coworkers have reported attenuated V. cholerae strains constructed by similar methods. It appears that recombinant DNA techniques offer a promising approach to the development of effective cholera vaccines.

In vitro synthesis of the tryptophan operon leader peptides of Escherichia coli, Serratia marcescens, and Salmonella typhimurium

We used an in vitro DNA-dependent protein-synthesizing system to demonstrate de novo synthesis of the leader peptide specified by the tryptophan (trp) operons of several bacterial species. Peptide synthesis was directed by self-ligated short restriction fragments containing the trp promoter and leader regions. Synthesis of leader peptides was established by demonstrating that they were labeled in vitro only by those amino acids predicted to be present in the peptides. Leader peptide synthesis was abolished by the addition of the Escherichia coli trp repressor. The E. coli trp leader peptide was found to be extremely labile in vitro; it had a half-life of 3-4 min. In a highly purified DNA-dependent peptide-synthesizing system, synthesis of the di- and tripeptides predicted from the Salmonella typhimurium trp operon leader sequence, fMet-Ala and fMet-Ala-Ala, also was observed. Using this dipeptide synthesis system, we demonstrated that translation initiation at the ribosome binding site used for trp leader peptide synthesis was reduced 10-fold when the transcript contained a segment complementary to the ribosome binding site.

Transcription termination in vitro at the tryptophan operon attenuator is controlled by secondary structures in the leader transcript

The role of alternative RNA secondary structures in regulating transcription termination at the attenuator of the tryptophan (trp) operon of Serratia marcescens was examined in vitro by transcribing mutant DNA templates having deletions of different segments of the trp leader region. Deletions that removed sequences corresponding to successive segments of postulated RNA secondary structures either increased or decreased transcription termination at the attenuator. The results obtained are consistent with the hypothesis that transcription termination results from RNA polymerase recognition of a particular RNA secondary structure, the terminator. This structure forms only in the absence of an alternative, preceding, RNA secondary structure, the antiterminator.

Construction of expression plasmids producing high levels of human leukocyte-type interferon in Escherichia coli

An expression plasmid was constructed, consisting of the promoter/operator region of the tryptophan operon from Serratia marcescens and a synthetic ribosome-binding site ligated into pBR322. Leukocyte-type interferon gene fragments (IFN-alpha A and IFN-alpha C) isolated from a cDNA library from human lymphoblastoid (Namalwa) cells were inserted into the unique HindIII site of the expression plasmid, and the resulting recombinant plasmids directed the synthesis of up to 5 X 10(5) units of A-type preinterferon, 2 X 10(7) units of A-type mature interferon and 8 X 10(5) units of C-type mature interferon per liter culture.

Gene expression in Streptomyces: construction and application of promoter-probe plasmid vectors in Streptomyces lividans

Promoter-probe plasmid vectors were constructed for Streptomyces lividans using expression of the Escherichia coli chloramphenicol acetyltransferase gene as an indicator of promoter activity. These vectors have been used to isolate and to study the activity of DNA sequences that contain transcriptional control signals from Streptomyces, Bacillus licheniformis, E. coli, and Serratia marcescens. Studies of these promoter regions in heterospecific hosts indicate that genus or species-specific factors may present barriers to the expression of bacterial genetic material in certain heterologous cellular environments. While promoter regions isolated from E. coli, S. marcescens and B. licheniformis all appear to be recognized by the RNA polymerase of S. lividans, the Streptomyces transcriptional control signals isolated do not appear to function normally in E. coli.

Evolutionary divergence of the Citrobacter freundii tryptophan operon regulatory region: comparison with other enteric bacteria

The regulatory region of the trp operon of Citrobacter freundii was sequenced and compared with the corresponding regions of other enteric bacteria. Significant differences were noted in the promoter region. These differences are presumably responsible for the weak expression of the cloned trp operon in Escherichia coli. The presumed operator region, although nonfunctional in E. coli, has dyad symmetry, but the sequence of the symmetrical region differs appreciably from those of operators that can be regulated by the E. coli trp repressor. The sequence of the trp leader region of C. freundii resembles that of other enteric bacteria, suggesting that the C. freundii operon is also regulated by attenuation. Comparison of the sequence of the initial portion of trpE with the homologous regions of E. coli and Salmonella typhimurium indicates that the three organisms probably are evolutionary equidistant.

Regulatory region of the Klebsiella aerogenes tryptophan operon

The trp operon of Klebsiella aerogenes was cloned, and its regulatory region was sequenced. Comparison with previously reported trp regulatory sequences of other enteric bacteria indicates that the K. aerogenes trp promoter-operator region is most similar to the corresponding region of Salmonella typhimurium. The trp leader regions of K. aerogenes and other enteric bacteria are organized similarly, but there are significant differences in the stabilities of the predicted secondary structures in their leader transcripts. These differences should make the K. aerogenes attenuator a weaker transcription termination site than any of the other attenuator regions studied; this was confirmed in in vitro transcription experiments. The sequence of the leader transcript and the precise site of in vitro termination were determined.

Superattenuation in the tryptophan operon of Serratia marcescens

Deletions were generated in vitro in the leader region of the tryptophan operon of Serratia marcescens and subsequently incorporated into the Escherichia coli chromosome in single copy form. Deletions which removed the translation start codon for the leader peptide or which ended in the ribosome recognition region preceding the leader peptide coding segment, caused superattenuation, that is, increased transcription termination at the attenuator. Apparently, the capacity to initiate translation of this coding region modulates expression of the operon.

Transcript secondary structures regulate transcription termination at the attenuator of S. marcescens tryptophan operon

We have analysed the regulatory behaviour of deletion mutants lacking different segments of the leader region of the tryptophan operon of Serratia marcescens. Our results support the model in which a particular RNA structure, the terminator, is recognized during transcription as a transcription termination signal, and an alternative RNA structure, the anti-terminator, prevents formation of the terminator. It appears that the role of translation, ribosome stalling and shifts between alternative RNA secondary structures, is simply to regulate formation of the terminator.

Transcription termination at the tryptophan operon attenuator is decreased in vitro by an oligomer complementary to a segment of the leader transcript

A DNA oligomer 15 nucleotides long was used to probe the involvement of RNA secondary structure in the control of transcription termination at the attenuator of the tryptophan (trp) operon of Escherichia coli. This 15-mer is perfectly complementary to a segment of trp RNA that is thought to play a role in regulation of attenuation. When added to an in vitro transcription reaction mixture containing wild-type E. coli or Salmonella typhimurium trp operon templates, the complementary 15-mer caused a 4-fold increase in read-through transcription. By contrast, the 15-mer did not affect attenuation when a mutant E. coli template was used that does not allow formation of a crucial RNA secondary structure. Control experiments established that oligomers that were not complementary to E. coli trp leader RNA did not affect attenuation and that the 15-mer did not reduce termination when the transcript lacked a complementary region. Other experiments established that the 15-mer did not increase read-through transcription by allowing RNA polymerase molecules that might have already stopped at the attenuator to resume transcription. These findings provide direct support for the view that alternate base-paired structures control transcription termination at the trp attenuator.

Iron-related modification of bacterial transfer RNA

Transfer RNAs isolated from E. coli grown in media where ferric iron is not freely available show well characterized chromatographic changes due to the absence of the methylthio moiety of ms2i6A. The altered tRNA molecules include tRNA trp tRNA tyr, tRNA phe and two minor tRNA ser species. It has been suggested that methylthiolation of tRNA affects its function in regulation. We now show iron-related changes in tRNA trp from S. typhimurium, Ps. aeruginosa and K. pneumoniae. tRNA trp from S. typhimurium contains ms2i6A and it seems probable that the availability of iron affects the synthesis of ms2i6A-tRNA trp from i6A-tRNA trp in this organism. An iron-related methylthiolating system may also be operative in K. pneumoniae. S. marcescens tRNA trp, however was not affected by the availability of iron. Neither ms2i6A nor i6A was found in S. marcescens tRNA, although an, as yet unidentified, hydrophobic nucleoside was present.

Escherichia coli deoxyribonucleic acid dependent ribonucleic acid polymerase transcriptional pause sites on SV40 DNA F1

We have studied elongation of SV40 DNA F1 by E. coli RNA polymerase looking specifically at the length of the transcript as a function of time. By running the transcription reactions at 18 degrees C with limited enzyme and adding heparin or rifampicin after elongation has started, we have achieved almost exclusive initiation from the SV40 DNA preferred promotor size [Zain, B. S., Weissmann, S. M., Lebowitz, P., & Lewis, A. M., Jr. (1973) J. Virol. 11, 682-693]. In the region within 1500 nucleotides of the initiation we observe nine prominent sites and a number of minor site where hesitation during elongation occurs. The positions of these hesitation points or pause sites are not effected by changes in the salt concentration, the simultaneous lowering of the concentrations of all the NTPs, or by increases in the RNA polymerase concentration, implying that the pause sites are a consequence of the RNA, DNA, and RNA polymerase ternary complex. The pause sites are not an artifact of the lowered temperature (18 degrees C) used in the experiments since they are also observed at 37 degrees C. The first four of these sites have been sequenced by using the 3'-O-methyl analogues of the ribonucleotide triphosphates. We have found no sequence homology between the pause sites. The kinetics of the pause reactions do not fit a first-order model but do correspond to a scheme were continuation through a pause site and termination at a pause site are both represented. For one of the pause sites, the relaxation time for continuation through the pause site was determined to be approximately 2.5 min and for the termination approximately 50 min at 18 degrees C. If the concentration of one of the NTPs is lowered to 10 muM, the strength of a pause site can be increased if that NTP is contained in the pause. Also, minor pause sites are observed at regions in the RNA sequence which are rich in the NTP that has the lowered concentration. When GTP is replaced by ITP during transcription, a new set of pause site quite different from the normal sites of hesitation are observed. The major new pause sites occur at or near sequences in the RNA which are rich in I-U residues preceded by a region rich in C residues. This indicates, as has been previously noted, that sequences where the DNA.RNA hybrid is quite stable followed by a region that is very unstable may cause termination. When BrUTP replaced UTP, very little effect was observed on the pause sites. The addition of p termination factor causes termintion to increase in all the pause sites with a length greater than 300 nucleotides. In the type of experiments performed here, those pause sites had continuation relaxation times greater than 45 s at 37 degrees C. This implies that regardless of the nature of a pause, p will cause at least some termination at all hesitation sites with a relaxation time greater than 45 s. All the results are discussed in terms of a kinetic model for the termination of elongation.

Attenuation in the control of expression of bacterial operons

Bacterial operons concerned with the biosynthesis of amino acids are often controlled by a process of attenuation. The translation product of the initial segment of the transcript of each operon is a peptide rich in the amino acid that the particular operon controls. If the amino acid is in short supply translation is stalled at the relevant codons of the transcript long enough for the succeeding segment of the transcript to form secondary structures that allow the transcribing RNA polymerase molecule to proceed through a site that otherwise dictates termination of transcription. This site is the attenuator; the process is attenuation.

Conservation and variation of nucleotide sequences within related bacterial genomes: enterobacteria

We have assessed the degree of relatedness of several portions of the Escherichia coli genome to the corresponding portions of the genomes of representative enteric bacteria, using the Southern transfer and hybridization technique (E. Southern, J. Mol. Biol. 98:503-517, 1975). The degree of relatedness varied among the regions examined. Judging both by the relative amounts of deoxyribonucleic acid in the various enteric genomes that are highly homologous and by the conservation of positions of restriction enzyme cleavage sites in these regions, the enteric genomes have diverged to greater extents in some parts of the genomes than in others. Portions of the genomes (including the tnaA and thyA genes, the trp operon, and one other unassigned segment) appear to have evolved in concert with the genome as a whole. By contrast, the lacZ gene and portions of the genome that are homologous to phage lambda vary more widely, perhaps reflecting a separate evolutionary origin for these segments of deoxyribonucleic acid.

DNA sequence of the Serratia marcescens lipoprotein gene

The Serratia marcescens gene for the outer membrane lipoprotein (lpp) was cloned in lambda phage vector Charon 14. The recombinant phage was very unstable, and the lpp gene with a 300-base-pair deletion at the transcription termination site was further cloned in pBR322. The DNA sequence of 834 base pairs encompassing the lpp gene was determined and compared with that of the Escherichia coli lpp gene. The sequence comparisons exhibit several unique features. (i) The promoter region is highly conserved (84% homology) and has an extremely high A+T content (78%) as in E. coli (80%). (ii) The 5' nontranslated region of the lipoprotein mRNA is also highly conserved (95% homology). (iii) In the DNA sequence corresponding to the signal peptide of this secretory protein, there are three drastic changes, including addition of one base pair and deletion of four base pairs in S. marcescens as compared to E. coli. The resultant alterations in the amino acid sequence, however, do not change the basic properties of the signal peptide, which are assumed to be essential for its function in the secretory mechanism. (iv) The DNA sequence from the amino terminus to the 51st residue of the mature lipoprotein is highly conserved (95% homology) and there is no amino acid substitution. (v) The DNA sequence corresponding to the seven amino acid residues at the carboxyl terminus has only 42% homology, resulting in four amino acid substitutions. (vi) Within the section of 40 base pairs beginning with the termination codon (UAA) and ending immediately before the oligo(T) transcription termination site in the E. coli lpp gene, there is about 60% homology. However, after this section, there is no obvious homology between the two sequences, probably because of a deletion of 300 base pairs at this region. (vii) Seven stable stem-and-loop structures could be formed in the mRNA region. (viii) Alterations in the third position of codons used in the lpp gene suggest that the gene has evolved somewhat differently from other genes in S. marcescens.

Interspecies homology of nitrogenase genes

Cloned nitrogen fixation (nif) genes from Klebsiella pneumoniae hybridize to DNA from 19 out of 19 widely divergent nitrogen-fixing bacterial strains but do not hybridize to DNA from 10 different non-nitrogen-fixing species. K. pneumoniae nif DNA fragments that hybridize to DNA from other species contain part of the three structural genes that code for nitrogenase polypeptides. We have utilized this homology to clone an EcoRI restriction endonuclease fragment from Rhizobium meliloti that hybridizes to the K. pneumoniae nif structural genes. Some of the species whose DNA hybridizes with K. pneumoniae nif DNA have been postulated to have diverged from K. pneumoniae 3 x 10(9) years ago. Nitrogenase genes are the only known example of such highly conserved prokaryotic translated genes. Nitrogenase genes are either extraordinarily conserved in evolution or have been exchanged between different nitrogen-fixing species relatively recently in evolutionary time.

Hybrid tryptophan synthase beta 2 proteins: apparent conservation of the beta-beta binding region of the beta monomer among enteric bacteria

Purified borohydride-reduced tryptophan synthase beta 2 protein (EC 4.2.1.20) from Escherichia coli and purified native beta 2 protein from Serratia marcescens were mixed and dissociated in urea. Removal of the urea resulted in random reassociation of the reduced and native beta monomers, forming interspecies hybrid beta 2 molecules. Interspecies hybrid beta 2 protein molecules of the reciprocal composition were also formed. Interspecies hybrid reconstituted molecules were formed with approximately the same efficiency as intraspecies reconstituted molecules (reduced and native monomers from the same species) indicating no particular preference for reassembly. The data provide evidence that the structural region of interaction between the beta monomers necessary for dimerization is highly conserved in the enzymes from the two organisms examined.