Analysis of E. coli promoter sequences

Comparison of the amino acid sequence of the lytic enzyme from broad-host-range bacteriophage PRD1 with sequences of other cell-wall-peptidoglycan lytic enzymes

The gene for the lytic enzyme of the lipid-containing, broad-host-range bacteriophage PRD1 codes for a protein of 149 amino acids (17271 Da). The sequence of the protein is unique when compared to other lytic enzymes sequenced. However, three regions of weak similarity with other phage lytic enzymes were observed. The C-terminal region shared seven amino acids in common with phage P22 lysozyme at a site which is conserved in phage-type lysozymes.

Conjugative transfer of promiscuous IncP plasmids: interaction of plasmid-encoded products with the transfer origin

To characterize protein-DNA interactions involved in the initiation of conjugative transfer replication, we isolated and sequenced the transfer origins (oriT) of the promiscuous IncP plasmids RP4 and R751. The central initiating event at the transfer origin of a conjugative plasmid is the cleavage at a unique site (nic) of the strand to be transferred to a recipient cell. This process can be triggered after the assembly of "relaxosomes" (plasmid DNA-protein relaxation complexes), requiring plasmid-encoded gene products. We analyzed the nicking reaction for plasmid RP4 and demonstrated that one of the plasmid strands is specifically cleaved within oriT. The fully functional oriT of RP4 represents an intergenic DNA region of approximately 350 base pairs. Dissection of oriT revealed that a portion carrying nic and symmetric sequence repeats determines oriT specificity. This part of oriT is contiguous to a region that is essential for efficient mobilization of oriT plasmids. In addition, oriT contains potential promoter sites allowing divergent transcription of two operons flanking oriT. We over-produced gene products and, from analyzing the products of defined deletion mutants, deduced the gene arrangements. Formation of RP4 relaxosomes is likely to depend on the presence of at least two plasmid-encoded components, which act in trans. Corresponding genes map on one side of oriT. Purification of the traJ product revealed it to be an 11-kDa polypeptide that binds to oriT DNA in vitro. The protein recognizes the part of oriT that is responsible for oriT specificity.

A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli

The E. coli minicell locus (minB) was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division spetum. Studies of the phenotypic effects of expression of the three genes, alone and in all possible combinations, indicated the following: cell poles contain potential division sites that will support additional septation events unless specifically inactivated; the minC and minD gene products act in concert to form a nonspecific inhibitor of septation that is capable of blocking cell division at all potential division sites; and the minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites.

Identifying protein-binding sites from unaligned DNA fragments

The ability to determine important features within DNA sequences from the sequences alone is becoming essential as large-scale sequencing projects are being undertaken. We present a method that can be applied to the problem of identifying the recognition pattern for a DNA-binding protein given only a collection of sequenced DNA fragments, each known to contain somewhere within it a binding site for that protein. Information about the position or orientation of the binding sites within those fragments is not needed. The method compares the "information content" of a large number of possible binding site alignments to arrive at a matrix representation of the binding site pattern. The specificity of the protein is represented as a matrix, rather than a consensus sequence, allowing patterns that are typical of regulatory protein-binding sites to be identified. The reliability of the method improves as the number of sequences increases, but the time required increases only linearly with the number of sequences. An example, using known cAMP receptor protein-binding sites, illustrates the method.

Genetic structure, function and regulation of the transposable element IS21

The IncP plasmid R68.45 and other plasmids carrying tandem repeats of the insertion sequence IS21 [= (IS21)2] produce replicon fusions via transposition at high frequencies in Escherichia coli and other gram-negative bacteria, whereas plasmids with a single IS21 copy, e.g. R68, give replicon fusions rarely. The 2131 bp nucleotide sequence of IS21 was determined; at the ends there were 11 bp inverted repeats with one mismatch. Two adjacent open reading frames, istA and istB, were located on one DNA strand of IS21. In E. coli maxicells, polypeptides of 46 kDa (the istA gene product) and 30 kDa (the istB gene product) were expressed by (IS21)2 plasmids, but not by IS21 plasmids. Genetic analysis of (IS21)2 plasmids indicates that the IS21-IS21 junctions form a promoter, which initiates transcription of the istAB operon in one of the two IS21 elements. A single IS21 element fused to an inducible external tac promoter expressed both proteins after induction, but did not promote effective replicon fusion, unless an IS21-IS21 junction (the preferred site for IS21 transposase action) was also present on the plasmid carrying the tac-IS21 construct. The sequences located between the IS21 elements in (IS21)2, 3 bp in R68.45 or 2 bp in pME28, were not recovered in the replicon fusion products. Homologous recombination between the directly oriented IS21 elements in the fusion products led to plasmids with a single IS21 insertion. Analysis of the latter showed that IS21 had a low, but not totally random specificity of insertion and created target duplications of 4 bp (occasionally 5 bp).(ABSTRACT TRUNCATED AT 250 WORDS)

Regulation of transcription in Escherichia coli from the mer and merR promoters in the transposon Tn501

We report studies on deletion mutants of the regulatory region of the mercuric ion resistance (mer) genes of transposon Tn501, isolated from Pseudomonas aeruginosa. Transcription of the mer genes in Escherichia coli from the promoter Pmer is regulated both positively (in the presence of mercuric salts) and negatively (in their absence) by the product of the merR gene. The merR gene is transcribed divergently with respect to the other mer genes, and negatively regulates its own synthesis. The experiments described here suggest that both positive and negative regulation by MerR, as well as its autoregulation, are largely mediated by MerR binding to a single site on DNA. This site contains a hyphenated dyad symmetrical sequence centred 24 base-pairs before the start of the mer transcript. Additional sites may be involved in full repression of the mer and merR promoters. Studies on deletions of the Pmer promoter show that the -35 sequence is not required for constitutive activity. An alternative -10 sequence may be used in the absence of the -35 and normal -10 sequences, but the properties of a point mutation indicate that, in the presence of the -35 sequence, the normal -10 sequence is required for promoter activity. A model for the regulation of expression of the mercury resistance genes by mercuric ions and the MerR protein is discussed.

The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex

Several physical and chemical signals from the extracellular environment are known to be transduced into changes in gene expression through multiple step pathways; however, mechanisms for triggering cellular responses to heavy metal stress have yet to be elucidated. We demonstrate here one such mechanism that employs a single heavy metal receptor protein, MerR, to directly activate transcription of the bacterial mercuric ion resistance operon. The mercuric ion-MerR complex and E. coli RNA polymerase holoenzyme synergistically bind to the metal responsive promoter in an unprecedented spatial relationship to form transcriptionally competent complexes. The activator binds adjacent to and overlaps with the polymerase molecule between the consensus -35 and -10 promoter regions. Our results support a model for transcriptional activation that includes both effector-induced protein-protein interactions and activator-induced alteration in DNA structure.

The 4.5S RNA gene from Pseudomonas aeruginosa

The essential 4.5S RNA of Escherichia coli contains a structural motif, which is also present in RNAs from other organisms, i.e. Bacillus subtilis scRNA, Halobacterium halobium 7S RNA and eukaryotic 7SL RNAs. This suggests a common function in all organisms, which could be related to protein translocation, since 7SL RNA is essential for this process in eukaryotes. We have analysed the structure and expression of the 4.5S RNA gene from another gram-negative eubacterium, Pseudomonas aeruginosa. The single copy gene encodes a 113 nucleotides long RNA, which shares 75% sequence homology to the E. coli 4.5S RNA and also exhibits the completely conserved hairpin structure of the corresponding RNAs of B. subtilis and E. coli. Transcription initiates 24 nucleotides upstream from the mature 5' end and exceeds beyond the 4.5S RNA coding region. A distal open reading frame, similar to that described for E. coli, does not exist downstream from the P. aeruginosa 4.5S RNA gene.

Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes

EcoR124 and EcoR124/3 are type I DNA restriction and modification systems. The EcoR124/3 system arose from the EcoR124 system some 15 years ago and at the electron microscopic DNA heteroduplex level the genes for both systems are still apparently identical. We have shown that the DNA sequences recognized by the two systems are GAA(N6)RTCG for EcoR124 and GAA(N7)RTCG for EcoR124/3. The sequences thus differ only in the length of the non-specific spacer. This difference nevertheless places the two specific domains of the EcoR124/3 recognition sequence 0.34 nm further apart and rotates them 36 degrees with respect to those of EcoR124, which implies major structural differences in the proteins recognizing these sequences. We have now determined the nucleotide sequences of the hsdS and hsdM genes of both systems and of the hsdR gene of EcoR124/3. The hsdS gene products provide DNA sequence specificity in both restriction and modification, the hsdM gene products are necessary for modification and all three hsd gene products are required for restriction. The only difference that we have detected between the two systems is that a 12 base-pair sequence towards the middle of the hsdS gene is repeated twice in the EcoR124 gene and three times in the EcoR124/3 gene. We have deleted one of the repeats in the EcoR124/3 gene and shown that this changes the specificity to that of EcoR124. Thus, the extra four amino acids in the middle of the EcoR124/3 hsdS gene product, which in an alpha-helical configuration would extend 0.6 nm, are sufficient to explain the differences in sequence recognition. We suggest that the EcoR124/3 system was generated by an unequal crossing over and argue that this kind of specificity change should not be rare in Nature.

Nucleotide sequence analysis of the purEK operon encoding 5'-phosphoribosyl-5-aminoimidazole carboxylase of Escherichia coli K-12

5'-Phosphoribosyl-5-aminoimidazole (AIR) carboxylase (EC 4.1.1.21) catalyzes step 6, the carboxylation of AIR to 5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid, in the de novo biosynthesis of purine nucleotides. As deduced from the DNA sequence of restriction fragments encoding AIR carboxylase and supported by maxicell analyses, AIR carboxylase was found to be composed of two nonidentical subunits. In agreement with established complementation data, the catalytic subunit (deduced Mr, 17,782) was encoded by the purE gene, while the CO2-binding subunit (deduced Mr, 39,385) was encoded by the purK gene. These two genes formed an operon in which the termination codon of the purE gene overlapped the initiation codon of the purK gene. The 5' end of the purEK mRNA was determined by mung bean nuclease mapping and was located 41 nucleotides upstream of the proposed initiation codon. The purEK operon is regulated by the purR gene product, and a purR regulatory-protein-binding site related to the sequences found in other pur loci was identified in the purEK operon control region.

Structure and expression of a split chloroplast gene from mustard (Sinapis alba): ribosomal protein gene rps16 reveals unusual transcriptional features and complex RNA maturation

The mustard chloroplast gene rps16 is split by an 887 bp group II (or III) intron. Three RNA 5' ends upstream of the rps16 coding region define both the transcription start site and two RNA processing sites. The DNA region preceding the start site contains a procaryotic-type "-10" promoter element, but not a typical "-35" element. One single RNA 3' end has been detected downstream from the rps16 coding region, but it is not in close proximity to any inverted repeat that might serve as a termination signal. Northern analysis has revealed several rps16 transcripts ranging in size from 1.6 kb to 0.5 kb. During seedling development, transcript levels show an initial increase and then remain constant without much difference between seedlings grown under light or in the dark.

Homology between virF, the transcriptional activator of the Yersinia virulence regulon, and AraC, the Escherichia coli arabinose operon regulator

Virulent yersiniae (Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica) restrict their growth at 37 degrees C in rich medium deprived of calcium. This property, called calcium dependency, correlates with the secretion of Yersinia outer membrane proteins (Yops) and with pathogenicity. It is mediated by a 70-kilobase plasmid called pYV. The structural genes of the Yops (yop genes), as well as genes involved in the control of their expression (vir genes), have been localized on pYV. In this communication we show that virF encodes a transcriptional activator controlling the yop regulon. This activator is a 30,879-dalton protein related to AraC, the regulator of the Escherichia coli and Salmonella typhimurium arabinose operons. We also show in this paper that transcription of virF is thermodependent and presumably autoregulated. virF is thus responsible for the effect of temperature on the production of the Yops. Finally, we show that virF activates transcription of the yop genes independently of the presence of calcium ions. The role of calcium therefore remains unaccounted for.

Homologous metalloregulatory proteins from both gram-positive and gram-negative bacteria control transcription of mercury resistance operons

We report the overexpression, purification, and properties of the regulatory protein, MerR, for a chromosomally encoded mercury resistance determinant from Bacillus strain RC607. This protein is similar in sequence to the metalloregulatory proteins encoded by gram-negative resistance determinants found on transposons Tn21 and Tn501 and to a predicted gene product of a Staphylococcus aureus resistance determinant. In vitro DNA-binding and transcription experiments were used to demonstrate those purified Bacillus MerR protein controls transcription from a promoter-operator site similar in sequence to that found in the transposon resistance determinants. The Bacillus MerR protein bound in vitro to its promoter-operator region in both the presence and absence of mercuric ion and functioned as a negative and positive regulator of transcription. The MerR protein bound less tightly to its operator region (ca. 50- to 100-fold) in the presence of mercuric ion; this reduced affinity was largely accounted for by an increased rate of dissociation of the MerR protein from the DNA. Despite this reduced DNA-binding affinity, genetic and biochemical evidence support a model in which the MerR protein-mercuric ion complex is a positive regulator of operon transcription. Although the Bacillus MerR protein bound only weakly to the heterologous Tn501 operator region, the Tn501 and Tn21 MerR proteins bound with high affinity to the Bacillus promoter-operator region and exhibited negative, but not positive, transcriptional control.

Sequence analysis of the agrA gene encoding beta-agarase from Pseudomonas atlantica

The nucleotide sequence of the agrA gene encoding an extracellular beta-agarase of Pseudomonas atlantica was determined. An open reading frame of 1,515 nucleotides which corresponded to agrA was found. The nucleotide sequence predicts a primary translation product of 504 amino acids and Mr 57,486. Comparison of the deduced amino acid sequences of beta-agarase from P. atlantica and the extracellular beta-agarase from Streptomyces coelicolor A3(2) suggests that these proteins share several domains in common.

Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816

We have cloned the naphthalene dioxygenase(ND)-coding genes from Pseudomonas putida strain NCIB9816 based on their ability to convert indole to indigo. The region coding for this enzyme activity was sequenced and three successive open reading frames were found. The corresponding gene products were identified using the T7 polymerase/promoter system. All of them are necessary for the ND activity. A comparison of the ND-coding genes with the ones coding for benzene dioxygenase revealed significant homology which was more pronounced at the nucleotide level than at the amino acid level.

Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon

The pathway for glycerol catabolism in Streptomyces coelicolor is determined by the gylABX operon. The sequence of about 1500 base-pairs (bp) preceding the structural genes of the operon has been determined, and related to a detailed transcriptional analysis of this region. The gylABX operon contains two major promoters, gylP1 and gylP2, separated by 50 bp. Both promoters are glycerol-inducible and glucose-repressible. A 900-base transcription unit, gylR, is situated immediately upstream of the gylABX promoter region and contains an open reading frame for a 27,600 Mr protein. The predicted sequence of this protein contains a region that is similar to the helix-turn-helix domains of certain DNA-binding proteins. Transcription of gylR is also glycerol-inducible, but is only weakly glucose-repressible, and initiates predominantly from a single promoter, gylRp. The three promoters, gylRP, gylP1 and gylP2, each resemble the "typical" prokaryotic consensus promoter sequence. The DNA sequence of the gylR and gylABX promoter regions share some striking features. These include almost identical operator-like elements (segments of which are tandemly repeated around gylRP) and tracts of alternating purine-pyrimidine residues.

Cloning and characterization of the gene encoding inorganic pyrophosphatase of Escherichia coli K-12

Escherichia coli K-12 gene ppa encoding inorganic pyrophosphatase (PPase) was cloned and sequenced. The 5' end of the ppa mRNA was identified by primer extension mapping. A typical E. coli sigma 70 promoter was identified immediately upstream of the mRNA 5' end. The structural gene of ppa contains 528 base pairs, from which a 175-amino-acid translation product, Mr 19,572, was deduced. The deduced amino acid composition perfectly fitted with that of PPase as previously determined (P. Burton, D. C. Hall, and J. Josse, J. Biol. Chem. 245:4346-4351, 1970). Furthermore, the partial amino acid sequence (residues 1 to 108) of E. coli PPase determined by S. A. Cohen (Ph.D. thesis, University of Chicago, 1978) was the same as that deduced from the nucleotide sequence. This is the first report of the cloning of a PPase gene.

Nucleotide sequence and transcription analysis of yop51 from Yersinia enterocolitica W22703

Virulent strains of Yersinia enterocolitica, pseudotuberculosis and pestis secrete large amounts of plasmid-encoded proteins involved in virulence and called Yops. A 2 kb fragment of the pYVe227 plasmid from Yersinia enterocolitica 0:9 encoding Yop51 was sequenced. Gene yop51 was found to encode a 50,882 Da protein consisting of 468 amino acids. This protein shows 99% identity with Yop2b, its counterpart from Y. pseudotuberculosis YPIII (pIB1), confirming that the virulence machinery is highly conserved among Yersinia spp. The homology stops abruptly 240 bp upstream and 175 bp downstream of the structural yop51 gene suggesting that all the sequences involved in the regulation of yop51 are located within the conserved region and confirming that the homology between the plasmids of Yersinia enterocolitica and Yersinia pseudotuberculosis is made up of boxes of high homology. Gene yop51 is only transcribed at 37 degrees C from a VirF-regulated promoter. This promoter was tentatively identified by determining the messenger transcriptional startpoint. The putative yop51 promoter resembles E. coli promoters despite the fact that it is not active in that species in the absence of VirF. A transcription terminator was found at the end of the gene while a second terminator was detected within the structural gene leading to premature termination of some of the messenger molecules.

Identification of psiB genes of plasmids F and R6-5. Molecular basis for psiB enhanced expression in plasmid R6-5

PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes share extensive homology the predicted amino acid sequences of the two proteins differing by 5 residues, (ii) the expression of R6-5 psiB is 4 times higher than F psiB gene, (iii) in plasmid R6-5, a Tn10 transposon upstream from the psiB gene enhances psiB expression. Hence, the F sex factor may be unable to prevent SOS induction for two non-exclusive reasons: (i) F PsiB protein, being slightly different from R6-5, may be less active, (ii) the level of synthesis of F PsiB protein may be insufficient to prevent SOS induction.

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.

RSF1010 and a conjugative plasmid contain sulII, one of two known genes for plasmid-borne sulfonamide resistance dihydropteroate synthase

The nucleotide sequence of the type II sulfonamide resistance dihydropteroate synthase (sulII) gene was determined. The molecular weight determined by maxicells was 30,000, and the predicted molecular weight for the polypeptide was 28,469. Comparison with the sulI gene encoded by Tn21 showed 57% DNA similarity. The sulII-encoded polypeptide has 138 of 271 amino acids in common with the polypeptide encoded by sulI. The sulII gene is located on various IncQ (broad-host-range) plasmids and other small nonconjugative resistance plasmids. Detailed restriction maps were constructed to compare the different plasmids in which sulII is found. The large conjugative plasmid pGS05 and the IncQ plasmid RSF1010 contained identical nucleotide sequences for the sulII gene. This type of sulfonamide resistance is very frequently found among gram-negative bacteria because of its efficient spread to various plasmids.

The effects of mutations in the ant promoter of phage P22 depend on context

Recombination was used to construct 22 two- or three-way combinations of down- and up-mutations in Pant, a strong, near-consensus promoter of phage P22. The relative strengths of these promoters in vivo were assayed by fusing them to an ant/lacZ gene fusion and measuring beta-galactosidase levels produced by lysogens carrying the fusions on single-copy prophages. The results of these assays show that the magnitude of the effect of a promoter mutation can vary considerably when its context is changed by the presence of another mutation. In addition, as Pant approaches conformity with the consensus promoter sequence, the up-mutations decrease promoter strength, even though the same mutations increase promoter strength in the presence of a down-mutation. These context effects imply that individual consensus base pairs cannot be considered to contribute to promoter strength independently.

Nucleotide sequence of katG, encoding catalase HPI of Escherichia coli

The gene katG, encoding catalase HPI of Escherichia coli, was sequenced, predicting a 726-amino-acid protein. The sequence was confirmed by identification of potential regulatory elements and amino acid sequencing of peptides. HPI shows no homology to other catalases. The distances between katG, metF, and ppc were defined.

Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling

There are four transcriptional promoters present in the 5' control region of the Escherichia coli DNA topoisomerase I (topA) gene. These were identified with Bal31 nuclease-generated deletions and mapping of the 5' ends of the mRNAs with avian reverse transcriptase. Recombinant plasmids with all or some of these promoters fused to the galactokinase (galK) gene-coding region have been constructed and used to study transcription from the promoters both in vitro and in vivo. The promoter (P1) closest to the starting ATG codon has a near consensus -35 sequence (GTTGATA) but unusual -10 (CATATCG) sequence. The other three promoters (P2, P3 and P4) are clustered together 60 base-pairs further upstream. Negative DNA supercoiling is required for efficient transcription from P1, P1 + P2 + P3 + P4, P2 + P3 + P4, P3 + P4 and P4 alone. The combination of all four promoters demonstrates greater supercoiling dependence than does any of the other subsets tested.

Transcription initiation at the tet promoter and effect of mutations

We have identified the startpoint for transcription in vitro of the tetracycline resistance gene (tet) of pBR322 and several deletion and insertion mutations which alter tet promoter structure. Tetracycline resistance in host bacteria correlates qualitatively with the efficiency of DNA fragments from these plasmids to promote tet transcription in vitro. Only in active promoters could we find by computer analysis promoter structures in which the -10 and -35 sequences and the relative spacing of the two regions agree with consensus sequence determinants. These data support the current model of the E. coli promoter sequence. Two promoter mutants gave heterogeneous 5' termini with additional A residues not encoded by the DNA sequence.

Defining the consensus sequences of E.coli promoter elements by random selection

The consensus sequence of E.coli promoter elements was determined by the method of random selection. A large collection of hybrid molecules was produced in which random-sequence oligonucleotides were cloned in place of a wild-type promoter element, and functional -10 and -35 E.coli promoter elements were obtained by a genetic selection involving the expression of a structural gene. The DNA sequences and relative levels of function for -10 and -35 elements were determined. The consensus sequences determined by this approach are very similar to those determined by comparing DNA sequences of naturally occurring E.coli promoters. However, no strong correlation is observed between similarity to the consensus and relative level of function. The results are considered in terms of E.coli promoter function and of the general applicability of the random selection method.

Saturation mutagenesis of the Tn10-encoded tet operator O1. Identification of base-pairs involved in Tet repressor recognition

Saturation mutagenesis of Tn10-encoded tet operator O1 was performed by chemical synthesis of 30 sequence variants yielding all possible point mutations of an operator half side. Their effect on Tet repressor binding was scored by an in-vivo repressor titration system. Tet repressor affinities of selected operator mutants were further characterized in vitro by dissociation rate measurements. The O1 sequence spans 19 base-pairs. Out of these, all 18 palindromic base-pairs are involved in Tet repressor recognition. The central base-pair does not contribute to sequence-specific binding of Tet repressor. At position 1 a pyrimidine residue is sufficient for maximal affinity to the repressor. At positions 2, 3 and 4, each mutation reduces repressor binding at least tenfold. Mutations at positions 5, 6, 7, 8 and 9 result in less drastic reductions of Tet repressor binding. Differential effects of mutations at a given position are used to deduce the chemical functions contacted by Tet repressor. The T.A to A.T transversion at position 9 increases Tet repressor affinity slightly, while all other mutations decrease repressor binding. The increased affinity of the wild-type tet operator O2 compared to wild-type O1 results from the addition of two favorable transversions at positions +/- 9 and an unfavorable T.A to C.G transition at position -7. Deletion or palindromic doubling of the central base-pair of the O1 palindrome reveals that the wild-type spacing of both operator half sides is crucial for efficient Tet repressor binding.

Plasmid pIMI38--the pBR322 derivative with increased stability in E. coli cells

Plasmid pIM138 which had been characterized by the higher resistance of its DNA replication to the action of clorobiocin in comparison with the progenitor plasmid, was tested for its stability in host cells in the absence of the antibiotic. Growing without selective pressure, pIM138 was better maintained in cells than pBR322. The stability in the presence and in the absence of clorobiocin can be unanimously assigned to the plasmid itself, but some influence of host cells cannot be excluded.

Molecular biology of pyridine nucleotide biosynthesis in Escherichia coli. Cloning and characterization of quinolinate synthesis genes nadA and nadB

The two genes, nadA and nadB, responsible for quinolinate biosynthesis from aspartate and dihydroxyacetone phosphate in Escherichia coli were cloned and characterized. Quinolinate (pyridine-2,3-dicarboxylate) is the biosynthetic precursor of the pyridine ring of NAD. Gene nadA was identified by complementation in three different nadA mutant strains. Sequence analysis provided an 840-bp open reading frame coding for a 31,555-Da protein. Gene nadB was identified by complementation in a nadB mutant strain and by the L-aspartate oxidase activity of its gene product. Sequence analysis showed a 1620-bp open reading frame coding for a 60,306-Da protein. For both genes, promoter regions and ribosomal binding sites were assigned by comparison to consensus sequences. The nadB gene product, L-aspartate oxidase, was purified to homogeneity and the N-terminal sequence of 19 amino acids was determined. The enzyme was shown to be specific for L-aspartate. High-copy-number vectors, carrying either gene nadA, nadB or nadA + nadB, increased quinolinate production 1.5-fold, 2.0-fold and 15-fold respectively. Both gene products seem to be equally rate-limiting in quinolinate synthesis.

Organization and characterization of the virCD genes from Agrobacterium rhizogenes

We have precisely localized virulent (vir) genes of the hairy root-inducing plasmid pRiA4b on the basis of sequence similarity with the tumor-inducing plasmid pTiA6NC, and shown that the overall organizations of vir genes in both plasmids are fairly analogous, although sizes and spacer lengths in some genes differ from each other. Among the vir genes thus mapped, the virC and virD loci were characterized in detail. Transposon insertions in virD led to loss of tumorigenicity on Kalanchoe stems and carrot discs, and one within virC exhibited an attenuated pathogenicity. The avirulent phenotype of the virD2 strain among these mutants was due to the lack of ability to recombine T-DNA border repeats in Agrobacterium cells. The nucleotide sequence of most parts of the virCD loci were similar in both plasmids. The virCD genes of these two plasmids, therefore, seem comparable both functionally and structurally. Phylogeny of pRi and pTi has also been discussed from the sequence data.

Site-specific recombination promotes linkage between trimethoprim- and sulfonamide resistance genes. Sequence characterization of dhfrV and sulI and a recombination active locus of Tn21

A new gene for trimethoprim resistance, dhfrV, found in several plasmid isolates with different characteristics, was sequenced and found to correspond to a peptide of 157 amino acids showing 75% similarity with the previously characterized, drug resistant dihydrofolate reductase of type I. The sequenced surroundings of dhfrV in plasmid pLMO20, were found to be almost identical with genetic areas surrounding resistance genes in transposon Tn21 and in R plasmid R388. The trimethoprim resistance genes of pLMO20 and R388 and the spectinomycin resistance gene of Tn21 could be regarded as having been inserted, by recombination, into an evolutionary older structure containing the sulfonamide resistance gene, sulI. The latter gene was sequenced and found to correspond to a peptide of 279 amino acids and with a molecular weight of 30,126 daltons. The inserted genes were found to be governed by a promoter situated in the highly conserved structure and also controlling expression of sulI. The insertion points of the different resistance genes were precisely defined, and at the 3' ends of the inserted genes inverted repeats allowing the formation of stem and loop structures were found. Similar structures were found at the 3' ends of the antibiotic resistance genes in Tn7, which could indicate similar recombination mechanisms to be effective in the evolutionary construction of all these different resistance elements.

Regulation of in vitro expression of the Escherichia coli frd operon: alanine and Fnr represent positive and negative control elements

The frdABCD operon of Escherichia coli encodes the anaerobically expressed terminal electron transport enzyme, fumarate reductase. Two mutually exclusive hairpin loop structures can occur in frdmRNA just downstream of the start of the frdA cistron. The mRNA sequence involved encodes a stretch of sequence rich in Ala and uses all four of the codons for this amino acid. In vitro expression of the frdABCD operon showed that as the level of plasmid DNA was increased from 150 fmol to 225 fmol, transcription of mRNA was suddenly elevated 6.5-fold, consistent with the concept of titrating out a repressor protein. Further studies showed that the concomitant 10.9-fold increase in translation of protein was heavily biased towards the proximal end of the operon, with little or no expression of FrdC or FrdD and a ratio of FrdA:FrdB of 2.6:1. Addition of Ala to the S-30 extract caused a 6.1-fold amplification of frd messenger transcription, a 17.6-fold increase in Frd protein translation, and a balancing of the subunit ratios to 1:1:1:1. The expression of the bla gene carried on the plasmid was not affected by DNA titration or the addition of Ala. When fnr DNA was added in equimolar ratio to frdDNA the amplification of fumarate reductase expression by Ala was abolished and the ratio of subunits produced showed a high degree of polarity with or without Ala.

IS150: distribution, nucleotide sequence and phylogenetic relationships of a new E. coli insertion element

Recently we identified the new insertion (IS) sequence IS150 in various strains of Escherichia coli K-12. We have screened other strains of E. coli and Salmonella typhimurium for the presence of homologous sequences. The strains of E. coli K-12 and W tested contain one or more copies of homology to IS150. We have also determined the complete nucleotide sequence of a copy of IS150 inserted into IS1. Comparison of nucleotide and deduced amino acid sequences of IS150, IS2, IS3, IS51, IS600 and IS629 reveals significant homologies suggesting that these elements are members of a family of phylogenetically related insertion sequences.

Nucleotide sequence of the rci gene encoding shufflon-specific DNA recombinase in the IncI1 plasmid R64: homology to the site-specific recombinases of integrase family

Shufflon is a novel type of DNA rearrangement in which four DNA segments are flanked by seven 19-bp repeat sequences. The site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. The recombination is mediated by a gene designated rci. We have determined the nucleotide sequence of the rci gene and found that it encodes a basic protein with 384 amino acid residues. The rci gene was fused with lacZ and its gene product was identified by Western blot analysis. The Rci protein shows regional homologies to the site-specific recombinases encoded by the bacteriophage genomes, including those of lambda, phi 80, P22, P2, 186, P4 and P1.

Transcriptional organization of the phycocyanin subunit gene clusters of the cyanobacterium Anacystis nidulans UTEX 625

The phycocyanin subunit gene cluster is duplicated on the chromosome of the cyanobacterium Anacystis nidulans UTEX 625. The two gene clusters cpcB1A1 (left) and cpcB2A2 (right) are separated by about 2,500 base pairs, and in each cluster the beta-subunit gene is located upstream from the alpha-subunit gene. Filter hybridizations with phycocyanin-specific probes to total RNA detected at least two major transcripts that were 1,300 to 1,400 nucleotides long. Besides these major mRNA species, two minor transcripts of 3,400 and 3,700 nucleotides covering one of the gene clusters and the region between the clusters were found. No additional minor transcripts were found in the intergenic region between the two phycocyanin gene clusters. The lengths of the major mRNAs indicated that the beta- and alpha-subunit genes were cotranscribed. No apparent homologies were found when the DNA sequences located upstream from the proposed ribosome-binding site of the two phycocyanin beta-subunit genes were compared. Northern hybridizations with gene cluster-specific probes from the regions 5' of the beta-subunit genes, as well as S1 nuclease mapping and mRNA primer extension experiments, showed that both gene clusters were transcribed. The minor transcripts were found to initiate upstream from the left gene cluster. Two mRNA 5' ends were mapped upstream from the cpcB1A1 gene cluster, while only one 5' end was mapped in front of the cpcB2A2 gene cluster. All transcripts were present in RNA preparations from cultures grown under high levels of white light as well as under low levels of red light. The level of phycocyanin-specific mRNA, measured as part of the total RNA, was lower under low levels of red light compared with that under high levels of white light. Conserved sequence motifs were found when the promoter region of the cpcB1A1 gene cluster and promoter regions from other cyanobacterial photosynthesis genes were compared. The DNA sequences covering the proposed transcriptional attenuators and transcriptional stop signals contained several potential hairpin structures. One potential hairpin structure was located immediately downstream of the left phycocyanin gene cluster and was concluded to limit the level of transcription for the minor transcripts initiating upstream of the cpcB1A1 gene cluster.

Nucleotide sequence and organization of copper resistance genes from Pseudomonas syringae pv. tomato

The nucleotide sequence of a 4.5-kilobase copper resistance determinant from Pseudomonas syringae pv. tomato revealed four open reading frames (ORFs) in the same orientation. Deletion and site-specific mutational analyses indicated that the first two ORFs were essential for copper resistance; the last two ORFs were required for full resistance, but low-level resistance could be conferred in their absence. Five highly conserved, direct 24-base repeats were found near the beginning of the second ORF, and a similar, but less conserved, repeated region was found in the middle of the first ORF.

Analysis of transcription and processing signals in the 5' regions of the two Mycoplasma capricolum rRNA operons

The transcription and RNA processing signals of the rRNA operons (rrnA and rrnB) of Mycoplasma capricolum were analyzed by mapping the 5' ends of in vivo and in vitro synthesized RNAs. The results of both in vitro and in vivo analyses point to the rrnA operon being transcribed from two promoters (P1 and P2) into large precursor RNAs. Transcripts initiating at P1 contain two tRNAs, and probably 16 S, 23 S, and 5 S rRNAs, whereas the transcripts starting from P2 consist only of the three rRNAs. The precursor RNAs are processed via distinct intermediates into mature tRNAs and rRNAs. In vivo experiments indicated that the rrnB operon is transcribed only from one promoter, although a second promoter could be identified using cell free extracts. The rrnB operon does not contain tRNA genes, but the precursor is still processed in the same way as the rrnA precursor that is synthesized from P2.

Nucleotide sequence of the genes encoding cytochrome b-559 from the cyanelle genome of Cyanophora paradoxa

Cyanophora paradoxa is a flagellated protozoan which possesses unusual, chloroplast-like organelles referred to as cyanelles. The psbE and psbF genes, which encode the two apoprotein subunits of cytochrome b-559, have been cloned from the cyanelle genome of C. paradoxa. The complete nucleotide sequences of these genes and their flanking sequences were determined by the chain-termination, dideoxy method. The psbE gene is composed of 75 codons and predicts a polypeptide of 8462 Da that is seven to nine residues smaller than most other psbE gene products. The psbF gene consists of 43 codons and predicts a polypeptide of 4761 Da. Two open reading frames, whose sequences are highly conserved among cyanobacteria and numerous higher plants, were located in the nucleotide sequence downstream from the psbF gene. The first open reading frame, denoted psbI, is composed of 39 codons, while the second open reading frame, denoted psbJ, is composed of 41 codons. The predicted amino acid sequences of the psbI and psbJ gene products predict proteins of 5473 and 3973 Da respectively. These proteins are probably integral membrane proteins anchored in the membrane by a single, transmembrane alpha helix. The psbEFIJ genes are probably co-transcribed and constitute an operon as found for other organisms. Each of the four genes is preceded by a polypurine sequence which resembles the consensus ribsosome binding sequences for Escherichia coli.

Expression and DNA sequence of the cloned bacteriophage T4 dCMP hydroxymethylase gene

A plasmid expressing the cloned bacteriophage T4 gene 42 gave the same levels of complementation of gene 42 mutants in a polarity-suppressing rho mutant as in a rho+ host. A reading frame likely corresponding to gene 42 and putative promoter and terminator sequences were identified in the partial sequence of the cloned fragment.

Neisseria meningitidis C114 contains silent, truncated pilin genes that are homologous to Neisseria gonorrhoeae pil sequences

Neisseria meningitidis pili can be classified into two groups: those (referred to here as class I pili) which are similar to gonococcal pili in that they react with monoclonal antibody SM1 and those that are dissimilar to gonococcal pili in that they lack the SM1-reactive epitope (class II pili). Pilus expression in N. meningitidis C114, a class II pilus-producing isolate, was investigated. The sole genomic segment of this strain that bore extensive homology with the pilE locus of Neisseria gonorrhoeae P9 was cloned in Escherichia coli. The production of the pilus structural subunit (pilin) from this meningococcal segment could not be detected by immunological and coupled in vitro transcription-translation analyses. Nucleotide sequence analysis revealed the presence in the C114 genome of two variant, tandemly arranged pilin genes (copies 1 and 2). Copies 1 and 2 are partial pilin genes that constitute part of a silent meningococcal pilin gene (pil gene) region, designated pilS. Both copies are truncated, corresponding to variable domains of the gonococcal pilE gene but lacking homologous N-terminal coding sequences. Located within sequences surrounding copies 1 and 2 were several classes of repeated elements that are associated with pil loci in N. gonorrhoeae.

Lipoamide dehydrogenase from Azotobacter vinelandii. Molecular cloning, organization and sequence analysis of the gene

The gene encoding lipoamide dehydrogenase from Azotobacter vinelandii has been cloned in Escherichia coli. Fragments of 9-23 kb from Azotobacter vinelandii chromosomal DNA obtained by partial digestion with Sau3A were ligated into the BamHI site of plasmid pUC9. E. coli TG2 cells were transformed with the resulting recombinant plasmids. Screening for clones which produced A. vinelandii lipoamide dehydrogenase was performed with antibodies raised against the purified enzyme. A positive colony was found which produced complete chains of lipoamide dehydrogenase as concluded form SDS gel electrophoresis of the cell-free extract, stained for protein or used for Western blotting. After subcloning of the 14.7-kb insert of this plasmid the structural gene could be located on a 3.2-kb DNA fragment. The nucleotide sequence of this subcloned fragment (3134 bp) has been determined. The protein-coding sequence of the gene consists of 1434 bp (478 codons, including the AUG start codon and the UAA stop codon). It is preceded by an intracistronic region of 85 bp and the structural gene for succinyltransferase. A putative ribosome-binding site and promoter sequence are given. The derived amino acid composition is in excellent agreement with that previously published for the isolated enzyme. The predicted relative molecular mass is 50223, including the FAD. The overall homology with the E. coli enzyme is high with 40% conserved amino acid residues. From a comparison with the three-dimensional structure of the related enzyme glutathione reductase [Rice, D. W., Schultz, G. E. & Guest, J. R. (1984) J. Mol. Biol. 174, 483-496], it appears that essential residues in all four domains have been conserved. The enzyme is strongly expressed, although expression does not depend on the vector-encoded lacZ promoter. The cloned enzyme is, in all the respects tested, identical with the native enzyme.