Promoter mapping and DNA sequencing of the F plasmid transfer genes traM and traJ

Computational analysis of cancer genome sequencing data

Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.

System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration

Biomedical institutions rely on data evaluation and are turning into data factories. Big-data storage centers, supercomputing systems, and increased algorithmic efficiency allow us to analyze the ever-increasing amount of data generated every day in biomedical research centers. In network science, the principal intrinsic problem is how to integrate the data and information from different experiments on genes or proteins. Data curation is an essential process in annotating new functional data to known genes or proteins, undertaken by a biobank curator, which is then reflected in the calculated networks. We provide an example of how protein-protein networks today have space-time limits. The next step is the integration of data and information from different biobanks. Omics data and networks are essential parts of this step but also have flawed protocols and errors. Consider data from patients with cancer: from biopsy procedures to experimental tests, to archiving methods and computational algorithms, these are continuously handled so require critical and continuous "updates" to obtain reproducible, reliable, and correct results. We show, as a second example, how all this distorts studies in cellular hepatocellular carcinoma. It is not unlikely that these flawed data have been polluting biobanks for some time before stringent conditions for the veracity of data were implemented in Big data. Therefore, all this could contribute to errors in future medical decisions.

The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk

Cancer is driven by genomic mutations in 'cancer driver' genes, which have essential roles in tumor development. These mutations may be caused by exposure to mutagens in the environment or by endogenous DNA-replication errors in tissue stem cells. Recent observations of abundant mutations, including cancer driver mutations, in histologically normal human tissues suggest that mutations alone are not sufficient for tumor development, thus prompting the question of how single mutant cells give rise to neoplasia. In a concept supported by decades-old data from mouse tumor models, non-mutagenic tumor-promoting agents have been posited to activate the proliferation of dormant mutated cells, thus generating actively growing lesions, with the promotion stage as the rate-limiting step in tumor formation. Non-mutagenic promoting agents, either endogenous or environmental, may therefore have a more important role in human cancer etiology than previously thought.

Cancer as a disease of old age: changing mutational and microenvironmental landscapes

Why do we get cancer mostly when we are old? According to current paradigms, the answer is simple: mutations accumulate in our tissues throughout life, and some of these mutations contribute to cancers. Although mutations are necessary for cancer development, a number of studies shed light on roles for ageing and exposure-dependent changes in tissue landscapes that determine the impact of oncogenic mutations on cellular fitness, placing carcinogenesis into an evolutionary framework. Natural selection has invested in somatic maintenance to maximise reproductive success. Tissue maintenance not only ensures functional robustness but also prevents the occurrence of cancer through periods of likely reproduction by limiting selection for oncogenic events in our cells. Indeed, studies in organisms ranging from flies to humans are revealing conserved mechanisms to eliminate damaged or oncogenically initiated cells from tissues. Reports of the existence of striking numbers of oncogenically initiated clones in normal tissues and of how this clonal architecture changes with age or external exposure to noxious substances provide critical insight into the early stages of cancer development. A major challenge for cancer biology will be the integration of these studies with epidemiology data into an evolutionary theory of carcinogenesis, which could have a large impact on addressing cancer risk and treatment.

Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU

Despite decades of research, effective treatments for most cancers remain elusive. One reason is that different instances of cancer result from different combinations of multiple genetic mutations (hits). Therefore, treatments that may be effective in some cases are not effective in others. We previously developed an algorithm for identifying combinations of carcinogenic genes with mutations (multi-hit combinations), which could suggest a likely cause for individual instances of cancer. Most cancers are estimated to require three or more hits. However, the computational complexity of the algorithm scales exponentially with the number of hits, making it impractical for identifying combinations of more than two hits. To identify combinations of greater than two hits, we used a compressed binary matrix representation, and optimized the algorithm for parallel execution on an NVIDIA V100 graphics processing unit (GPU). With these enhancements, the optimized GPU implementation was on average an estimated 12,144 times faster than the original integer matrix based CPU implementation, for the 3-hit algorithm, allowing us to identify 3-hit combinations. The 3-hit combinations identified using a training set were able to differentiate between tumor and normal samples in a separate test set with 90% overall sensitivity and 93% overall specificity. We illustrate how the distribution of mutations in tumor and normal samples in the multi-hit gene combinations can suggest potential driver mutations for further investigation. With experimental validation, these combinations may provide insight into the etiology of cancer and a rational basis for targeted combination therapy.

The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation

Escherichia coli O104:H4 (E. coli O104:H4), which caused a massive outbreak of acute gastroenteritis and hemolytic uremic syndrome in 2011, carries an aggregative adherence fimbriae I (AAF/I) encoding virulence plasmid, pAA. The importance of pAA in host-pathogen interaction and disease severity has been demonstrated, however, not much is known about its transcriptional organization and gene regulation. Here, we analyzed the pAA primary transcriptome using differential RNA sequencing, which allows for the high-throughput mapping of transcription start site (TSS) and non-coding RNA candidates. We identified 248 TSS candidates in the 74-kb pAA and only 21% of them could be assigned as TSS of annotated genes. We detected TSS for the majority of pAA-encoded virulence factors. Interestingly, we mapped TSS, which could allow for the transcriptional uncoupling of the AAF/I operon, and potentially regulatory antisense RNA candidates against the genes encoding dispersin and the serine protease SepA. Moreover, a computational search for transcription factor binding sites suggested for AggR-mediated activation of SepA expression, which was additionally experimentally validated. This work advances our understanding of the molecular basis of E. coli O104:H4 pathogenicity and provides a valuable resource for further characterization of pAA virulence gene regulation.

TraY and integration host factor oriT binding sites and F conjugal transfer: sequence variations, but not altered spacing, are tolerated

Bacterial conjugation is the process by which a single strand of a conjugative plasmid is transferred from donor to recipient. For F plasmid, TraI, a relaxase or nickase, binds a single plasmid DNA strand at its specific origin of transfer (oriT) binding site, sbi, and cleaves at a site called nic. In vitro studies suggest TraI is recruited to sbi by its accessory proteins, TraY and integration host factor (IHF). TraY and IHF bind conserved oriT sites sbyA and ihfA, respectively, and bend DNA. The resulting conformational changes may propagate to nic, generating the single-stranded region that TraI can bind. Previous deletion studies performed by others showed transfer efficiency of a plasmid containing F oriT decreased progressively as increasingly longer segments, ultimately containing both sbyA and ihfA, were deleted. Here we describe our efforts to more precisely define the role of sbyA and ihfA by examining the effects of multiple base substitutions at sbyA and ihfA on binding and plasmid mobilization. While we observed significant decreases in in vitro DNA-binding affinities, we saw little effect on plasmid mobilization even when sbyA and ihfA variants were combined. In contrast, when half or full helical turns were inserted between the relaxosome protein-binding sites, mobilization was dramatically reduced, in some cases below the detectable limit of the assay. These results are consistent with TraY and IHF recognizing sbyA and ihfA with limited sequence specificity and with relaxosome proteins requiring proper spacing and orientation with respect to each other.

The cytoplasmic DNA-binding protein TraM binds to the inner membrane protein TraD in vitro

The cytoplasmic protein TraM is one of four essential gene products of the F factor which are involved in DNA transfer after mating pair formation. TraM binds to three specific sites within the oriT region. Besides regulation of its own synthesis, the precise function of TraM during conjugation is not yet known. In the present work, the affinity of TraM to TraD was studied in vitro by an overlay assay and by affinity chromatography. Whether the interaction between TraM and TraD causes a transient or permanent anchoring of the F factor to the site of transfer is discussed. A 35-kDa host membrane protein of yet unknown function also shows affinity to TraM and may be involved in this anchoring process as well.

Analysis of the sequence and gene products of the transfer region of the F sex factor

Bacterial conjugation results in the transfer of DNA of either plasmid or chromosomal origin between microorganisms. Transfer begins at a defined point in the DNA sequence, usually called the origin of transfer (oriT). The capacity of conjugative DNA transfer is a property of self-transmissible plasmids and conjugative transposons, which will mobilize other plasmids and DNA sequences that include a compatible oriT locus. This review will concentrate on the genes required for bacterial conjugation that are encoded within the transfer region (or regions) of conjugative plasmids. One of the best-defined conjugation systems is that of the F plasmid, which has been the paradigm for conjugation systems since it was discovered nearly 50 years ago. The F transfer region (over 33 kb) contains about 40 genes, arranged contiguously. These are involved in the synthesis of pili, extracellular filaments which establish contact between donor and recipient cells; mating-pair stabilization; prevention of mating between similar donor cells in a process termed surface exclusions; DNA nicking and transfer during conjugation; and the regulation of expression of these functions. This review is a compendium of the products and other features found in the F transfer region as well as a discussion of their role in conjugation. While the genetics of F transfer have been described extensively, the mechanism of conjugation has proved elusive, in large part because of the low levels of expression of the pilus and the numerous envelope components essential for F plasmid transfer. The advent of molecular genetic techniques has, however, resulted in considerable recent progress. This summary of the known properties of the F transfer region is provided in the hope that it will form a useful basis for future comparison with other conjugation systems.

Bioenergetic aspects of the translocation of macromolecules across bacterial membranes

Bacteria are extremely versatile in the sense that they have gained the ability to transport all three major classes of biopolymers through their cell envelope: proteins, nucleic acids, and polysaccharides. These macromolecules are translocated across membranes in a large number of cellular processes by specific translocation systems. Members of the ABC (ATP binding cassette) superfamily of transport ATPases are involved in the translocation of all three classes of macromolecules, in addition to unique transport ATPases. An intriguing aspect of these transport processes is that the barrier function of the membrane is preserved despite the fact the dimensions of the translocated molecules by far surpasses the thickness of the membrane. This raises questions like: How are these polar compounds translocated across the hydrophobic interior of the membrane, through a proteinaceous pore or through the lipid phase; what drives these macromolecules across the membrane; which energy sources are used and how is unidirectionality achieved? It is generally believed that macromolecules are translocated in a more or less extended, most likely linear form. A recurring theme in the bioenergetics of these translocation reactions in bacteria is the joint involvement of free energy input in the form of ATP hydrolysis and via proton sym- or antiport, driven by a proton gradient. Important similarities in the bioenergetic mechanisms of the translocation of these biopolymers therefore may exist.

Nucleotide sequence and characterization of the traABCD region of IncI1 plasmid R64

A 3.6-kb BglII-SmaI segment of the transfer region of IncI1 plasmid R64drd-11 was sequenced and characterized. Analysis of the DNA sequence indicated the presence of four genes, traA, traB, traC, and traD, in this region. The expression of the traB, traC, and traD genes was examined by maxicell experiments and that of the traA gene was examined by constructing the traA-lacZ fusion gene. The introduction of frameshift mutations into the four genes indicated that the traB and traC genes are essential for conjugal transfer in liquid medium and on a solid surface. Both were also required for the formation of the thin pilus, which is the receptor for phages I alpha and PR64FS. Upstream of the traA gene, a promoter sequence for sigma 70 of E. coli RNA polymerase was identified by S1 nuclease mapping and primer extension experiments.

FinOP repression of the F plasmid involves extension of the half-life of FinP antisense RNA by FinO

The transfer operon of the F plasmid is positively regulated by the traJ gene product, expression of which, in turn, is regulated by both an antisense RNA, FinP, and the FinO protein (the FinOP system). A finP- F plasmid, pSFL20, was constructed by site-directed mutagenesis and was found to produce wild-type levels of pili encoded by the transfer operon. Transcription of the traJ gene was decreased by a factor of 3-5 fold in the presence of FinOP with no accumulation of a stable RNA duplex between the FinP RNA and the portion of the traJ mRNA which is complementary to finP. Stabilization of FinP RNA by FinO occurs in the absence of traJ transcripts, suggesting that FinO may interact directly with FinP to prevent its degradation.

The TraM protein of the conjugative plasmid F binds to the origin of transfer of the F and ColE1 plasmids

The gene encoding the TraM protein of the conjugative plasmid F was cloned, overexpressed and the gene product was purified. The TraM protein was found in the cytoplasm of cells carrying the F plasmid with a smaller amount in the inner membrane. DNase I footprinting experiments showed that the purified protein protects three regions in the F oriT locus with different affinity for the upper and lower strands of DNA. A 15-nucleotide motif was identified within the protected regions that represented the DNA-binding site. The TraM protein was also found to bind to a sequence in the oriT region of the non-conjugative plasmid ColE1 that resembles the three binding sites in the F oriT region.

Characterization and nucleotide sequence of the oriT-traM-finP region of the IncFVII plasmid pSU233

By hybridizing the IncFVII haemolytic plasmid pSU233 with a probe containing the origin of transfer of the IncFII plasmid R1, we isolated a 1.9 kb BglII fragment containing at least the origin of transfer (oriT), and the genes traM and finP. Functional complementation analysis of deletion derivatives was used to map the origin of transfer. We also determined the nucleotide sequence of traM and finP. Comparison with similar regions of several plasmids, also belonging to the Rep-FIIA family, revelaed that pSU233 resembles the F plasmid by very close. The homology is not evenly distributed along this region, but clustered into homologous regions (TraZb-oriT, TraMb-oriT and traM separated by non-homologous regions (TraYb-oriT, finP). This organization resembles that reported for the replication region and also suggests evolution by exchange of modules. In addition, the nucleotide sequence of finP is different from those previously described for other IncF plasmids and constitutes a new allele, which we have denominated allele VI.

A simple and efficient system for the construction of phoA gene fusions in gram-negative bacteria

We have developed a two-plasmid system for generating gene fusions between phoA and cloned genes encoding envelope proteins. The vector plasmid carries a temperature-sensitive replication system and can be rescued at high temperature by insertion of an IS1-based transposon carrying the ori region of pBR322 and a phoA gene lacking transcription and translation initiation signals. The vector plasmid also carries the transfer origin of the conjugative plasmid, F, permitting transfer into a suitable recipient strain. We have used this system in the analysis of the bla gene cloned from pBR322.

Specific DNA binding of the TraM protein to the oriT region of plasmid R100

The product of the traM gene of plasmid R100 was purified as the TraM-collagen-beta-galactosidase fusion protein (TraM*) by using a beta-galactosidase-specific affinity column, and the TraM portion of TraM* (TraM') was separated by collagenolysis. Both the TraM* and TraM' proteins were found to bind specifically to a broad region preceding the traM gene. This region (designated sbm) was located within the nonconserved region in oriT among conjugative plasmids related to R100. The region seems to contain four core binding sites (designated sbmA, sbmB, sbmC, and sbmD), each consisting of a similar number of nucleotides and including a homologous 15-bp sequence. This result, together with the observation that the TraM* protein was located in the membrane fraction, indicates the possibility that the TraM protein has a function in anchoring the oriT region of R100 at the sbm sites to the membrane pore, through which the single-stranded DNA is transferred to the recipient. sbmC and sbmD, each of which contained a characteristic inverted repeat sequence, overlapped with the promoter region for the traM gene. This suggests that the expression of the traM gene may be regulated by its own product.

Characterization of the oriT region of the IncFV plasmid pED208

DNA sequence analysis of a 2.2kb EcoRI-HindIII fragment from pED208, the derepressed form of the IncFV plasmid Folac, revealed sequences highly homologous to the oriT region, traM, and traJ genes of other IncF plasmids. The TraM protein was purified and immunoblots of fractionated cells containing pED208 or Folac showed that TraM was predominantly in the cytoplasm. Using DNA retardation assays and the DNase I footprinting technique, the TraM protein was found to bind to three large motifs in the oriT region: (I) an inverted repeat, (II) two direct repeats, and (III) the traM promoter region. These three footprint regions contained a Hinfl-like sequence (GANTC) that appeared 16 times, spaced 11-12 bp (or multiples thereof) apart, suggesting that TraM protein binds in a complex manner over this entire region.

Regulation of the F plasmid traY promoter in Escherichia coli by host and plasmid factors

F plasmid DNA transfer (tra) gene expression in Escherichia coli is regulated by chromosome- and F-encoded gene products. To study the relationship among these regulatory factors, we constructed low-copy plasmids containing a phi(traY'-'lacZ)hyb gene that couples beta-galactosidase and Lac permease synthesis to the F plasmid traY promoter. Wild-type transformants maintained high levels of beta-galactosidase over a broad range of culture densities. Primer extension analysis of tra mRNA from F'lac and phi(traY'-'lacZ)hyb strains indicated very similar, though not identical, transcription initiation sites. Moreover, phi(traY'-'lacZ)hyb gene expression required both TraJ and SfrA, as does tra gene expression in F+ strains. beta-Galactosidase activity was reduced approximately 30-fold in the absence of TraJ, which could be supplied in cis or in trans. In a two-plasmid system in which TraJ was supplied in trans by a lac-traJ operon fusion, phi(traY'-'lacZ)hyb expression was a linear, saturable function of traJ expression. Enzyme activity was reduced approximately tenfold in sfrA mutants. That reduction could not be attributed to an effect on the TraJ level. Several other cellular or environmental variables had only a modest effect on phi(traY'-'lacZ)hyb expression. Hyperexpression was observed at high cell density (twofold) and in anaerobic cultures (1.2- to 1.5-fold). In contrast, expression was reduced twofold in integration host factor mutants.

traY and traI are required for oriT-dependent enhanced recombination between lac-containing plasmids and lambda plac5

Recombination between F42lac and lambda plac5 is typically 20- to 50-fold more efficient than recombination between chromosomal lac and lambda plac5. This enhancement of recombination requires trans-acting factors located in the promoter-distal and promoter-proximal regions of the main traY-to-traI (traZ) operon. By testing the ability of deletion mutants of tra to support enhanced recombination, we have identified traY as the only product has been ruled out. We also report that traI is the only gene from the promoter-distal end of the traY to traI operon that is required for recombination enhancement. Of the two proposed domains of traI, we conclude that the oriT-nicking activity is essential, whereas the helicase activity is largely dispensable. The possibility of a third traI activity is also discussed.

The TraM protein of plasmid R1 is a DNA-binding protein

The TraM protein of the resistance plasmid R1 was purified to homogeneity and used for DNA-binding studies. Both gel retardation- and footprint experiments showed that TraM specifically binds to DNA of plasmid R1 comprising the region between the origin of transfer and the traM gene. Several TraM molecules bind and, according to the footprint experiments, two distinct sites of specific binding exist. The two sites are separated from each other by 12 nucleotides and each contains an inverted repeat. DNase I protection assays showed that the initial TraM binding occurs at these palindromic sequences. At higher protein concentrations the lengths of the DNA segments protected by TraM were increased towards the traM gene. In one region this extension leads to binding of TraM protein at its own promoters.

The sequences of genes bordering oriT in the enterotoxin plasmid P307: comparison with the sequences of plasmids F and R1

The nucleotide sequences of the enterotoxin plasmid P307 transfer genes traM, finP, traJ, traY, and gene 19 were determined. Gene 19 is highly conserved; its product is very similar to that coded by the F and R1 plasmids. The TraM protein is similar in P307 and in F; the R1 sequence shows differences in the 40 N-terminal amino acids. The traJ product is very different in P307, F, and R1. The traY gene from P307, which in F is almost twice as long, is similar in size to that from R1. The finP RNA shows a high degree of homology with that from R1 and F, except for the two loop regions where base changes were observed. The genes coding for proteins, except traY, could be expressed in minicell- and T7 promoter-driven expression systems, whereas traJ and gene 19 could be expressed only in the latter system.

Nucleotide sequence of the promoter-distal region of the tra operon of plasmid R100, including traI (DNA helicase I) and traD genes

The nucleotide sequence of the promoter-distal region of the tra operon of R100 was determined. There are five open reading frames in the region between traT and finO, and their protein products were identified. Nucleotide sequences of plasmid F corresponding to the junction regions among the open reading frames seen in R100 were also determined. Comparison of these nucleotide sequences revealed strong homology in the regions containing traD, traI and an open reading frame (named orfD). The TraD protein (83,899 Da) contains three hydrophobic regions, of which two are located near the amino-terminal region. This protein also contains a possible ATP-binding consensus sequence at the amino-terminal region and a characteristic repeated peptide sequence (Gln-Gln-Pro)10 at the carboxy-terminal region. The TraI protein (191,679 Da) contains the sequence motif conserved in an ATP-dependent DNA helicase superfamily in its carboxy-terminal region. The protein product of orfD, which is probably a new tra gene (named traX), contains 65% hydrophobic amino acids, especially rich in alanine and leucine. There exist non-homologous regions between R100 and F that could be represented as four I-D (insertion or deletion) loops in heteroduplex molecules. Assignment of each loop to the strand of R100 or F was , however, found to be the reverse from that previously assumed. The three I-D loops that were located between traT and traD, between traD and traI, and between traI and finO had no terminal inverted repeat sequences nor had they any homology with known insertion sequences, while the fourth was IS3, located within the finO gene of F. The sequences in the I-D loops, except IS3, may also code for proteins that are, however, likely to be nonessential for transfer of plasmids.

Integration host factor affects expression of two genes at the conjugal transfer origin of plasmid R100

Integration host factor (IHF) binds to two sites near the origin of transfer of the conjugative antibiotic resistance plasmid, R100. DNase I footprinting shows that one site is immediately adjacent to oriT and the gene X promoter, and another is adjacent to the traM promoter. A third site, known only from retardation gels, is near the traJ promoter. The relative promoter activities of genes X, traJ and traM are reduced in himA mutants (IHF-), as measured by chloramphenicol-resistance assays. Transcript analyses by Northern blots showed a reduction in size of the principal gene X and traJ transcripts in the absence of IHF.

Purified Escherichia coli F-factor TraY protein binds oriT

The traY gene of the Escherichia coli F plasmid has been shown by genetic studies (R. Everett and N. Willetts, J. Mol. Biol. 136:129-150, 1980) to be involved in the site-specific nicking reaction at oriT required for the initiation of DNA transfer during bacterial conjugation. In order to assign a biochemical function to TraY protein, the traY gene was cloned in a plasmid vector which utilizes the strong T7 phi 10 promoter to overproduce the protein. The plasmid-encoded TraY protein was specifically labeled with [35S]methionine, and purification of the polypeptide was accomplished by monitoring the radioactive label. Purified TraY protein had a relative molecular mass of approximately 17,000, as determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The amino terminus of the purified protein was sequenced to confirm that the protein was encoded by the traY gene. The protein sequence revealed that the start codon for the TraY protein was a UUG codon 36 base pairs upstream of the AUG start site originally deduced from the DNA sequence (T. Fowler, L. Taylor, and R. Thompson, Gene 26:79-89, 1983). This start sequence confirmed the premise of Inamoto et al. that the F-plasmid TraY polypeptide-coding sequence would begin with UUG, creating a reading frame which renders a large degree of amino acid sequence identity with the TraY polypeptide from R100 (S. Inamoto, Y. Yoshioka, and E. Ohtsubo, J. Bacteriol. 170:2749-2757, 1988). The purified TraY protein from F bound specifically to the origin of transfer region of the F plasmid. However, no nicking activity was detected at oriT by using TraY protein or TraY protein in conjunction with helicase I.

Nucleotide sequence of the traD region in the Escherichia coli F sex factor

The complete nucleotide sequence has been determined of a 3635-bp region, extending from the HpaI site in traT, at F coordinate 90.3 kb, to beyond the end of traD, of the F sex factor plasmid of Escherichia coli K-12. This region contains the C-terminal coding part of traT and the entire traD gene. An open reading frame (ORF) of 2148 bp within the sequence confirms that traD encodes an 81.4-kDa cytoplasmic membrane protein. The TraD protein has several regions with an unusually high pI (greater than 10), suggesting that they may correspond to the DNA-binding domains. Several other ORFs were detected within the region including the gene (ORF1) for a 26.3-kDa protein and ORF2, probably corresponding to traI, which continues to the end of the sequence. An ORF for an 8.5-kDa protein preceded by an excellent promoter and ribosome-binding site is present in the region following traD but on the opposite strand. This promoter is thought to correspond to the major RNA polymerase binding site in this region, implying that traI does not have its own promoter. The lack of a typical terminator following traD and ORF1 and the translational coupling provided by overlapping stop and start codons is consistent with this conclusion.

finP and fisO mutations in FinP anti-sense RNA suggest a model for FinOP action in the repression of bacterial conjugation by the Flac plasmid JCFL0

Expression of the transfer operon in the F plasmids is negatively regulated by FinOP which has two components, the finP and finO gene products. Mutations in either gene result in increased expression of the positive regulator of transcription, traJ, leading to derepressed levels of conjugal transfer. Five mutations in the finP gene have been previously characterised by Finnegan and Willetts (1971). Three were complementable in trans and were named finP mutations and two were complementable at low levels (fisO) presumably because they affected the site of action of the finO gene product. In this study, DNA sequence analysis revealed three different mutations shared by the five mutants which were located in the stems of the predicted stem-and-loop structures in the finP anti-sense RNA. The properties of three mutants created by site-specific mutagenesis suggested that the stability of the stem structure was important in FinP action and that a small region in one of the stems appears to be the target of the finO gene product. Analysis of wild-type and fisO FinP RNA showed that FinO increased the amount of an 80 nuceotide FinP RNA, probably by stabilizing this transcript or preventing its degradation. The fisO mutation decreased the amount of 80 nucleotide RNA substantially. FinP transcripts from either the finP promoter of the lac promoter appeared to be stabilized by FinO.

Derepression of conjugal transfer of the antibiotic resistance plasmid R100 by antisense RNA

Conjugal transfer of the normally repressed antibiotic resistance plasmid R100 was derepressed by fragments of R100 that carried the traJ promoter and the traJ leader but lacked the finP promoter.

Sense and antisense transcripts of traM, a conjugal transfer gene of the antibiotic resistance plasmid R100

The region of the antibiotic resistance plasmid R100 that encodes the plasmid-specific transfer gene traM has two tandemly aligned promoters separated by 145 nucleotides. The principal transcripts are 705 and 562 nucleotides long. Minor transcripts are 1550 and 1700 nucleotides long. The 705-base transcript appears to encode an 11 kD traM protein. The 562-base transcript does not encode a detectable protein. When subcloned on short fragments, the promoter for the 562-base transcript initiates efficiently but that for the 705 site does not. The 3' ends of the 705 and 562 base transcripts end inside the traJ ORF. Thus they provide additional sense RNA to compete with traJ for finP, the antisense translational regulator of traJ. A model is proposed for the participation of these sense and antisense transcripts in the control of expression of the traJ gene.

Nucleotide sequence of traQ and adjacent loci in the Escherichia coli K-12 F-plasmid transfer operon

The F tra operon region that includes genes trbA, traQ, and trbB was analyzed. Determination of the DNA sequence showed that on the tra operon strand, the trbA gene begins 19 nucleotides (nt) distal to traF and encodes a 115-amino-acid, Mr-12,946 protein. The traQ gene begins 399 nt distal to trbA and encodes a 94-amino-acid, Mr-10,867 protein. The trbB gene, which encodes a 179-amino-acid, Mr-19,507 protein, was found to overlap slightly with traQ; its start codon begins 11 nt before the traQ stop codon. Protein analysis and subcellular fractionation of the products expressed by these genes indicated that the trbB product was processed and that the mature form of this protein accumulated in the periplasm. In contrast, the protein products of trbA and traQ appeared to be unprocessed, membrane-associated proteins. The DNA sequence also revealed the presence of a previously unsuspected locus, artA, in the region between trbA and traQ. The artA open reading frame was found to lie on the DNA strand complementary to that of the F tra operon and could encode a 104-amino-acid, 12,132-dalton polypeptide. Since this sequence would not be expressed as part of the tra operon, the activity of a potential artA promoter region was assessed in a galK fusion vector system. In vivo utilization of the artA promoter and translational start sites was also examined by testing expression of an artA-beta-galactosidase fusion protein. These results indicated that the artA gene is expressed from its own promoter.

Identification and characterization of the products from the traJ and traY genes of plasmid R100

The nucleotide sequence of part of the tra region of R100 including traJ and traY was determined, and the products of several tra genes were identified. The nucleotide sequence of traJ, encoding a protein of 223 amino acids, showed poor homology with the corresponding segments of other plasmids related to R100, but the deduced amino acid sequences showed low but significant homology. The first four amino acids at the N-terminal region of the TraJ protein were not essential for positive regulation of expression of traY, the first gene of the traYZ operon. The nucleotide sequence of traY shows that this gene may use TTG as the initiation codon and that it encodes a protein of 75 amino acids. Analysis of the traY gene product, which was obtained as the fusion protein with beta-galactosidase, showed that the N-terminal region of the product has an amino acid sequence identical to that deduced from the assigned frame but lacks formylmethionine. traY of plasmid F, which encodes a larger protein than the TraY protein of R100, is thought to use ATG as an initiation codon. However, a TTG initiation codon was found in the preceding region of the previously assigned traY coding frame of F. Interestingly, when translation of traY of F was initiated from TTG, the amino acid sequence homologous to the TraY protein of R100 appeared in tandem in the TraY protein of F. This may suggest that traY of F has undergone duplication of a gene like the traY gene of R100.

Transcript analysis of the plasmid R100 traJ and finP genes

Single-stranded RNA probes were used to study the regulation of plasmid transfer in the infectious antibiotic resistance plasmid R100. Transcription of the positive transfer control gene traJ of R100 appears to be initiated continuously. In the presence of finO, the traJ transcript is 235 bases long, and in the absence of finO it is 1050. These sizes are strain specific. finO increases four-to tenfold the amount of the transcript from the finP gene that is detectable in cells containing R100, R136, or the sex factor F. The size of the principal finP transcript from R100 as determined on Northern blots is 105 bases. A secondary transcript with a size of 180 bases was detected in small amounts in R100 extracts. The finP transcript size was also determined by nuclease protection experiments. In this case the size was 74 bases. The 5' ends of the finP and traJ transcripts were located by primer extension experiments. A new model of FinO/P control is proposed.

Analysis of transfer genes and gene products within the traB-traC region of the Escherichia coli fertility factor, F

A series of plasmids that carry overlapping segments of F DNA encoding the genes in the traB-traC interval was constructed, and a restriction enzyme map of the region was derived. Plasmids carrying deletions that had been introduced at an HpaI site within this interval were also isolated. The ability of these plasmids to complement transfer of F lac plasmids carrying mutations in traB, traV, and traW, and traC was analyzed. The protein products of the plasmids were labeled in UV-irradiated cells and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. These analyses showed that the product of traV is a polypeptide that migrates with an apparent molecular weight of 21,000. It was not detected when [35S]methionine was used to label plasmid products, but was readily detected in 14C-amino acid labeling experiments. A 21,500-dalton product appeared to stem from the region assigned to traP. A 9,000-dalton product was found to stem from a locus, named traR, that is located between traV and traC. No traW activity could be detected from the region of tra DNA examined. Our data also indicated that traC is located in a more promoter-proximal position than suggested on earlier maps. The plasmids constructed are expected to be useful in studies designed to identify the specific functions of the traB, -P, -V, -R, and -C products.

Fertility inhibition gene of plasmid R100

The fin0 gene of R100 was isolated from the Fin0+ transducing phage VA lambda 57. The limits of the gene were determined by BAL31 digestions and by analysis of deletion mutations derived from an internal restriction site. The DNA sequence contained an open reading frame of 558 nucleotides that would encode a protein of 21,268 daltons. Synthesis of such a protein was observed only when the fragment was cloned in front of the TAC promoter. Deletions entering the large open reading frame from either end were Fin0-, while internal frame shift mutations retained high Fin0 activity. One such strain had a 13 bp internal deletion that would produce a protein of 63 amino acid residues of which 21 were basic. We were consequently unable to rigorously establish that the 558 base orf encoded a fin0 product. The strand opposite the large open reading frame contained several transcription termination signals, and it is possible that the active gene product is one or two small RNAs from this strand.

Artificial transposable elements in the study of the ends of IS1

We have constructed artificial IS1-based transposons by attaching synthetic oligodeoxynucleotides, corresponding to the sequence of the ends of IS1, to a selectable DNA segment ['omega' fragment; Prentki and Krisch, Gene 29 (1984) 303-313]. These transposons were used to examine the sequence requirements at the ends for IS1 transposition. We show here that a 24- to 28-bp sequence from the left or right ends of IS1 is capable of transposition when present at both ends of the omega fragment in the correct orientation. Transposition activity requires the presence of an intact IS1 in cis on the same plasmid molecule. In trans, however, neither resident genomic copies of IS1, nor copies carried by a compatible, high-copy-number plasmid present in the same cell, complement the artificial transposons efficiently. Transposition frequencies in the presence of a cis-complementing IS1 are, however, similar to those of the naturally occurring IS1-based transposon, Tn9. In addition, transposition results in a 9-bp duplication in the target DNA molecule as is usually the case for insertion of the intact IS1. Using this system, we have obtained evidence indicating that the activity of a synthetic IS1 end is not determined exclusively by its sequence, but can be strongly enhanced by a second, wild-type end used in the transposition event. The data also show that single base pair mutations can exhibit a cumulative effect in reducing transposition activity.

Nucleotide sequence of the tra YALE region from IncFV plasmid pED208

The pED208 plasmid is a 90-kilobase conjugative plasmid which is the derepressed form of Fo lac plasmid (IncFV). A 3.3-kilobase HindIII-PstI fragment from the pED208 plasmid was cloned and sequenced and was found to contain four open reading frames which were highly homologous to the traA, traL, traE, and traY gene products of the F plasmid. The pED208 traA propilin protein was 119 amino acids in length, consisting of a leader sequence of 55 amino acids and a mature pilin subunit of 64 residues. The leader sequence contained a hydrophobic region followed by a classic signal peptidase cleavage site (Ala-Ser-Ala-55). F and pED208 pilin proteins shared 27 conserved residues and had similar predicted secondary structures. The pED208 traA and traL genes were separated by a single base pair, and no ribosome binding site preceded the traL gene. The pED208 traY gene contained an IS2 insertion element in orientation II 180 nucleotides (60 residues) upstream of the traY stop codon. This insertion of IS2 resulted in a predicted fusion peptide of 69 residues for traY which may provide the observed traY activity. Since IS2 is absent in the wild-type plasmid, Fo lac, derepression and concomitant multipiliation may be due to the insertion of IS2 providing constitutive expression of the pED208 tra operon.

Origin of transfer of IncF plasmids and nucleotide sequences of the type II oriT, traM, and traY alleles from ColB4-K98 and the type IV traY allele from R100-1

The complete nucleotide sequences of the ColB4-K98 (ColB4) plasmid transfer genes oriT, traM, and traY as well as the traY gene of R100-1 are presented and compared with the corresponding regions from the conjugative plasmids F, R1, and R100. The sequence encoding the oriT nick sites and surrounding inverted repeats identified in F was conserved in ColB4. The adenine-thymine-rich sequence following these nick sites was conserved in R1 and ColB4 but differed in F and R100, indicating that this region may serve as the recognition site for the traY protein. A series of direct repeats unique to the ColB4 plasmid was found in the region of dyad symmetry following this AT-rich region. This area also encodes 21-base-pair direct repeats which are homologous to those in F and R100. The traM gene product may bind in this region. Overlapping and following these repeats is the promoter(s) for the traM protein. The traM protein from ColB4 is similar to the equivalent products from F, R1, and R100. The traY protein from ColB4 is highly homologous to the R1 traY gene product, while the predicted R100-1 traY product differs at several positions. These differences presumably define the different alleles of traM and traY previously identified for IncF plasmids by genetic criteria. The translational start codons of the ColB4 and R100-1 traY genes are GUG and UUG, respectively, two examples of rare initiator codon usage.

Nucleotide sequences of five IncF plasmid finP alleles

The nucleotide sequences of five finP alleles from various IncF plasmids (finP types I to V) as well as of three finP mutations were determined and compared. The finP gene specificity could be attributed to a variable, six-to-seven-nucleotide loop located between inverted repeats, and the sequence data were consistent with the product of finP being an RNA molecule rather than a protein. The finP mutations interrupted a proposed finP promoter or destabilized a predicted stem-and-loop structure in the finP RNA molecule.

Cloning, mapping, and sequencing of plasmid R100 traM and finP genes

The fertility control gene finP, the transfer gene traM, and the transfer origin, oriT, of plasmid R100 were isolated on a single 1.2-kilobase EcoRV fragment and were then subcloned as HaeIII fragments. The sequence of the 754-base-pair finP-containing fragment is reported here. In addition to the finP gene, the sequence includes all but two bases of the R100 traM open reading frame and apparently all of the leader mRNA sequence and amino end of the traJ gene of R100. The sequence contains two open reading frames which encode small proteins on the opposite strand from the traM and traJ genes. It also shows two sets of inverted repeats that have the characteristics of transcription terminators. One set is positioned as if it was the traM terminator, and the other set, which is downstream from the first, sits in the middle of the leader mRNA sequence for traJ. On the bottom strand, this inverted repeat has the structure of a rho-independent terminator. Other less-stable inverted repeats overlap this second terminator in the same way as is seen in attenuation sequences, and the two separate small open reading frames on the bottom strand also totally overlap the stem of the rho-independent terminator, suggesting that their translation would cause shifting of termination to the bottom strand homolog of the putative traM terminator. The finP gene product was not identified, but the gene was mapped to the sequence which contains the traJ gene. It either overlaps traJ or is antisense to it.

Nucleotide sequences of the R1-19 plasmid transfer genes traM, finP, traJ, and traY and the traYZ promoter

The complete nucleotide sequences of the R1 drd-19 (R1-19) plasmid transfer genes traM, finP, traJ, and traY and the region encoding the traYZ promoter were determined. The traM protein from R1-19 was similar to the 127-amino-acid traM product from the conjugative plasmid F; only 28 residues were not identical. finP, a negative regulatory element of the traJ gene, contained a 12-base-pair inverted repeat identical to that found in the F plasmid, but differed in the 7 base pairs found between the repeats. The traJ gene and the traYZ promoter (the site of transcriptional stimulation by the traJ product) were completely different from the equivalent sequences in plasmid F. Galactokinase fusion studies of the traYZ promoter indicated that the R1-19 and F plasmids have analogous but not homologous traYZ promoter strengths and regulation. The traY protein from R1-19 was 44 residues shorter than the traY product from plasmid F, but there was some homology within the C-terminal halves of the traY gene products. The predicted translational start codon for the traY gene is GUG.

The sequences of the traJ gene and the 5' end of the traY gene of the resistance plasmid R1

The traJ gene and the 5' end of the neighbouring traY gene of the resistance plasmid R1 were sequenced. Both structural genes show relatively little homology with the corresponding sequences of the related F plasmid. At the amino acid level sufficient homology is detected to allow an assignment of the two genes in R1. In traJ two methionine codons have to be regarded as potential chain initiation signals. Because of the analogy with the F plasmid sequence the second ATG is believed to be the main translational start site. The traJ gene codes for 228 amino acids. The 5' untranslated region of the traJ gene of R1 is highly homologous to the corresponding sequence in F indicating that it fulfills an important role in regulation. The transcription of the traY-Z operon starts in the structural gene of traJ. The amino terminal part of the TraY protein shows only limited homology with the F factor counterpart. However, the few conserved amino acids are a strong indication that our sequence contains the traY gene of R1.

Shadow promoters in the F plasmid transfer operon

The in vivo transcription start site for PYZ, the promoter of the F plasmid transfer operon, has been located. When transcription start sites for PYZ are deleted, two additional shadow promoters, upstream of PYZ, are activated in vivo. The shadow promoters correspond to those previously identified by in vitro run-off transcription experiments. The activated shadow promoters are stimulated by TraJ protein, a positive regulator of the transfer operon.

Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them

We present here a compilation of prokaryotic transcription terminator sequences (ref. 1-152). The compilation includes 49 independent terminators, 52 speculated independent terminators, 27 sites shown to function in vivo, and some 20 proven or speculated rho-dependent terminators. In addition to the well-known features of independent terminators (dyad symmetry and T-run), two consensus are found: CGGG(C/G) upstream and TCTG downstream of the termination point. A subset of the collection of sequence has been used to construct a computer algorithm to locate independent terminators by sequence analysis.

The traM gene of the resistance plasmid R1: comparison with the corresponding sequence of the Escherichia coli F factor

The 7.7-kb EcoRI fragment of the resistance plasmid R1 contains the gene for the TraM protein. The sequence was identified by the presence of an open reading frame (ORF) which is preceded upstream by two promoter sequences. Both these promoters were found to be active, although the more distant one predominates, as was judged by the relative abundance of mRNA of the expected length. The TraM protein could be synthesized in an in vitro DNA-dependent protein synthesis system if the DNA of the corresponding region was supplied as template. Comparison of the traM genes of R1 and the F factor showed a high degree of similarity, although a number of mutations, especially near the 5' terminus, introduce specific amino acid (aa) changes. Two-thirds of the 3' sequences differ mainly in silent mutations; hence the aa sequence of the corresponding carboxy-terminal portion of the protein is highly conserved. The 5' and 3' untranslated regions of the mRNAs show little homology. One of the promoter regions, the ribosome-binding sequences, and the transcription termination sites are located at comparable positions but differ in details.

Enhanced recombination between lambda plac5 and F42lac: identification of cis- and trans-acting factors

Enhanced transductional recombination between specialized transducing phage lambda plac5 and plasmid F42lac depends on cis- and trans-acting factors. By constructing a series of recombinant molecules, the cis-acting site required for enhanced recombination has been identified as oriT, the origin of conjugational transfer of the F sex factor of Escherichia coli. The trans-acting factors are located in the promoter-proximal and the promoter-distal regions of the traY-to-traZ operon.

Anomalous expression of the E. coli lac operon in Proteus mirabilis. II. Effects of lacI and lacP mutations

The lac operon introduced into Proteus mirabilis shows two anomalies of expression: the maximal induced level is reduced by about an order of magnitude, and the basal level becomes about 100 times higher than in E. coli, as a result of which the induction ratio appears very small, around 2-5 in contrast to as much as 1000 in E. coli. It was suggested by Baumberg and Dennison (1975) that the two anomalies might be manifestations of a single effect whereby some exogenous promoters give poor expression in this host, since they could result from poor expression of the lacZYA and lacI promoters respectively. We show here that when the lacP class II promoter mutation L305 was transferred on an F-prime into P. mirabilis, its effect on lac expression was much as in E. coli. However, when Flac bearing the IQ1 up-promoter mutation was introduced into P. mirabilis, the basal level decreased by three orders of magnitude, in accord with poor expression of lacI+ being responsible for the usual low induction ratio. These results are consistent with the hypothesis of Baumberg and Dennison (1975) but do not prove it: poor expression of lacI and/or lacZYA could also result from weak translation initiation, problems of continuation of transcription or translation (e.g. due to pause sequences or differences in codon use), or diminished mRNA stability.

DNA sequence of the F traALE region that includes the gene for F pilin

The complete sequence of a 1.4-kilobase PstI fragment containing the F transfer genes traA, -L, and -E is presented. The traA reading frame has been located both genetically and by comparing the primary structure of F pilin (the traA product) predicted by the DNA sequence to the amino acid composition and sequence of N- and C-terminal peptides isolated from purified F pilin. Taken together, these data show that there is a leader peptide of 51 amino acids and that F pilin contains 70 amino acids, giving molecular weights of 13,200 for F propilin and 7,200 for mature F pilin. Secondary structure predictions for F pilin revealed a reverse turn that precedes the sequence Ala-Met-Ala51, a classic signal peptidase cleavage site. The N-terminal alanine residue is blocked by an acetyl group as determined by 1H-nuclear magnetic resonance spectroscopy. The traL and traE genes encode proteins of molecular weights 10,350 and 21,200, respectively. According to DNA sequence predictions, these proteins do not contain signal peptide leader sequences. Secondary structure predictions for these proteins are in accord with traLp and traEp being membrane proteins in which hydrophobic regions capable of spanning the membrane are linked by sequences that form turns and carry positively charged residues capable of interacting with the membrane surface.