The invertible segment of bacteriophage Mu DNA determines the adsorption properties of Mu particles

Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products

Extracellular vesicles secreted by Gram-negative bacteria have proven to be important in bacterial defense, communication and host–pathogen relationships. They resemble smaller versions of the bacterial mother cell, with similar contents of proteins, LPS, DNA, and RNA. Vesicles can elicit a protective immune response in a range of hosts, and as vaccine candidates, it is of interest to properly characterize their cargo. Genetic sequencing data is already available for vesicles from several bacterial strains, but it is not yet clear how the genetic makeup of vesicles differ from that of their parent cells, and which properties may characterize enriched genetic material. The present study provides evidence for DNA inside vesicles from Vibrio cholerae O395, and key characteristics of their genetic and proteomic content are compared to that of whole cells. DNA analysis reveals enrichment of fragments containing ToxR binding sites, as well as a positive correlation between AT-content and enrichment. Some mRNAs were highly enriched in the vesicle fraction, such as membrane protein genes ompV, ompK, and ompU, DNA-binding protein genes hupA, hupB, ihfB, fis, and ssb, and a negative correlation was found between mRNA enrichment and transcript length, suggesting mRNA inclusion in vesicles may be a size-dependent process. Certain non-coding and functional RNAs were found to be enriched, such as VrrA, GcvB, tmRNA, RNase P, CsrB2, and CsrB3. Mass spectrometry revealed enrichment of outer membrane proteins, known virulence factors, phage components, flagella and extracellular proteins in the vesicle fraction, and a low, negative correlation was found between transcript-, and protein enrichment. This result opposes the hypothesis that a significant degree of protein translation occurs in vesicles after budding. The abundance of viral-, and flagellar proteins in the vesicle fraction underlines the importance of purification during vesicle isolation.

The potential of site-specific recombinases as novel reporters in whole-cell biosensors of pollution

DNA recombinases show some promise as reporters of pollutants providing that appropriate promoters are used and that the apparent dependence of expression on cell density can be solved. Further work is in progress using different recombinases and other promoters to optimize recombinase expression as well as to test these genetic constructs in contaminated environmental samples such as soil and water. It may be that a graded response reflecting pollutant concentration may not be possible. However, they show great promise for providing definitive detection systems for the presence of a pollutant and may be applicable to address the problem of bioavailability of pollutants in complex environments such as soil.

Unusual transcriptional and translational regulation of the bacteriophage Mu mom operon

The bacteriophage Mu mom gene encodes a novel DNA modification that protects the viral genome against a wide variety of restriction endonucleases. Expression of mom is subject to a series of unusual regulatory controls. Transcription requires the action of a phage-encoded protein, C, which binds (probably as a dimer) the mom promoter from -33 to -52 (with respect to the transcription start site) in two adjacent DNA major grooves on one face of the helix. No apparent direct interaction between C and the host RNA polymerase (RNAP) is evident; however, C binding alters mom DNA conformation. In the absence of C, RNAP binds the mom promoter at a site that results in transcription in a direction away from the mom gene. The function of this transcription is unknown. An additional layer of transcriptional regulation complexity is due to the fact that the host Dam DNA-(N6-adenine)methyltransferase is required. Dam methylation of three closely spaced upstream GATC sequences is necessary to prevent binding by the host protein, OxyR, which acts as a repressor. Repression is not mediated by inhibition of C binding, but rather through interference with C-mediated recruitment of RNAP to the correct site. Translation of mom is regulated by the phage Com protein. Com is only 62 amino acids long and contains a zinc finger-like structure (coordinated by four cysteine residues) in the amino terminal domain. Com binds mom mRNA 5' to the mom open reading frame, whose translation start signals are contained in a stem-loop translation-inhibition-structure. Com binding to its target site (5' to and adjacent to the translation-inhibition-structure) results in a stable change in RNA secondary structure that exposes the translation start signals.

Bidirectional transcription in the mom promoter region of bacteriophage Mu

Transcription of the Mu mom operon requires activation by the phage gene product, C, a site-specific DNA binding protein. Previous in vivo and in vitro footprinting studies showed that Escherichia coli RNA polymerase (Esigma70=RNAP) bound the wild-type (wt) mom promoter (Pmom) region in the absence of C; this site, now designated momP2 (-11 to -64), is slightly upstream of, but overlapping with, momP1 (+16 to -49), the functional binding site for mom operon (rightward) transcription. The location/distribution of KMnO4-sensitive sites on the two DNA strands suggested that RNAP bound at momP2 was in an open-complex, but that transcription was in the opposite direction. Here, we used both runoff transcription and reverse transcriptase-primer extension sequencing to provide direct evidence that in the absence of C protein, RNAP carries out leftward transcription from momP2 both in vitro and in vivo. In addition, the 5' ends of these transcripts were mapped to the same upstream initiation site, -58G, relative to the initiation site of C-activated rightward transcription. We also present evidence that leftward transcription from momP2 requires RNAP recognition of an UP-element by the carboxyl-terminal domain of the alpha subunit.

Escherichia coli OxyR protein represses the unmethylated bacteriophage Mu mom operon without blocking binding of the transcriptional activator C

Transcription of the bacteriophage Mu mom operon requires transactivation by the phage-encoded C protein. DNase I footprinting showed that in the absence of C, Escherichia coli RNA polymerase E(sigma)70 (RNAP) binds to the mom promoter (Pmom) region at a site, P2 (from -64 to -11 with respect to the transcription start site), on the top (non-transcribed) strand. This is slightly upstream from, but overlapping P1 (-49 to +16), the functional binding site for rightward transcription. Host DNA-[N6-adenine] methyltransferase (Dam) methylation of three GATCs immediately upstream of the C binding site is required to prevent binding of the E.coli OxyR protein, which represses mom transcription in dam- strains. OxyR, known to induce DNA bending, is normally in a reduced conformation in vivo, but is converted to an oxidized state under standard in vitro conditions. Using DNase I footprinting, we provide evidence supporting the proposal that the oxidized and reduced forms of OxyR interact differently with their target DNA sequences in vitro. A mutant form, OxyR-C199S, was shown to be able to repress mom expression in vivo in a dam- host. In vitro DNase I footprinting showed that OxyR-C199S protected Pmom from -104 to -46 on the top strand and produced a protection pattern characteristic of reduced wild-type OxyR. Prebinding of OxyR-C199S completely blocked RNAP binding to P2 (in the absence of C), whereas it only slightly decreased binding of C to its target site (-55 to -28, as defined by DNase I footprinting). In contrast, OxyR-C199S strongly inhibited C-activated recruitment of RNAP to P1. These results indicate that OxyR repression is mediated subsequent to binding by C. Mutations have been isolated that relieve the dependence on C activation and have the same transcription start site as the C-activated wild-type promoter. One such mutant, tin7, has a single base change at -14, which changes a T6 run to T3GT2. OxyR-C199S partially inhibited RNAP binding to the tin7 promoter in vitro, even though the OxyR and RNAP-P1 binding sites probably do not overlap, and in vivo expression of tin7 was reduced 5- to 10-fold in dam- cells. These results suggest that OxyR can repress tin7.

Integration of bacteriophage Mx8 into the Myxococcus xanthus chromosome causes a structural alteration at the C-terminal region of the IntP protein

Mx8 is a generalized transducing phage that infects Myxococcus xanthus cells. This phage is lysogenized in M. xanthus cells by the integration of its DNA into the host chromosome through site-specific recombination. Here, we characterize the mechanism of Mx8 integration into the M. xanthus chromosome. The Mx8 attachment site, attP, the M. xanthus chromosome attachment site, attB, and two phage-host junctions, attL and attR, were cloned and sequenced. Sequence alignments of attP, attB, attL, and attR sites revealed a 29-bp segment that is absolutely conserved in all four sequences. The intP gene of Mx8 was found to encode a basic protein that has 533 amino acids and that carries two domains conserved in site-specific recombinases of the integrase family. Surprisingly, the attP site was located within the coding sequence of the intP gene. Hence, the integration of Mx8 into the M. xanthus chromosome results in the conversion of the intP gene to a new gene designated intR. As a result of this conversion, the 112-residue C-terminal sequence of the intP protein is replaced with a 13-residue sequence. A 3-base deletion within the C-terminal region had no effect on Mx8 integration into the chromosome, while a frameshift mutation with the addition of 1 base at the same site blocked integration activity. This result indicates that the C-terminal region is required for the enzymatic function of the intP product.

Regulatory factors acting at the bacteriophage Mu middle promoter

Lytic development of bacteriophage Mu proceeds through three phases of transcription: early, middle, and late. Initiation of middle transcription from Pm requires the phage-encoded activator, Mor. An examination of the sequences surrounding the promoter revealed possible binding sites for Mu proteins A and c, as well as for Escherichia coli integration host factor. Promoter fragments containing 5' and 3' deletions were fused to the lacZ reporter gene and assayed for activity after induction of a Mu prophage or a plasmid-borne mor gene. Sequences upstream of position -62 and downstream of +10 were dispensable for promoter activity. In DNase I footprinting with both crude extract and purified protein, Mor protected Pm sequences from position -56 to -33. Mutations disrupting the dyad symmetry of the terminator of early transcription overlapping the Mor binding site did not reduce promoter activity, suggesting that the symmetry per se is not required for Mor binding or Pm activation. Purified Mu lysogenic repressor (c) also bound to Pm, overlapping the Mor binding site. Production of large amounts of repressor in vivo reduced Mor-dependent promoter activity nearly 10-fold. Promoters with mutations in the repressor binding site showed a reduction in this repressor-mediated inhibition of Pm activity.

Mating variation by DNA inversions of shufflon in plasmid R64

Gene organization of the 54-kb transfer region of IncI1 plasmid R64 was deduced from the DNA sequence. Forty-eight ORFs were found in this region. A unique DNA rearrangement designated shufflon is located at the downstream region of an operon responsible for synthesis of thin pilus. The shufflon of R64 consists of four DNA segments, designated as A, B, C, and D, which are flanked and separated by seven 19-bp repeat sequences. Site-specific recombination mediated by the product of the rci gene between any two inverted repeats results in a complex DNA rearrangement. An analysis of open reading frames revealed that the shufflon is a biological switch to select one of seven C-terminal segments of the pilV genes. The products of pilV genes were shown to be components of thin pilus which was required for liquid mating. Seven R64 derivatives where the pilV genes were fixed in the seven C-terminal segments were constructed and their transfer frequencies in liquid mating were measured using various bacterial strains as recipients. Transfer frequencies of R64 in liquid mating strongly depended on the combination of C-terminal segments of the pilV genes in donor cells and bacterial strains of recipient cells, suggesting that the shufflon determines the recipient specificity in liquid mating of plasmid R64.

DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages

We have determined the DNA sequence of the bacteriophage P2 tail genes G and H, which code for polypeptides of 175 and 669 residues, respectively. Gene H probably codes for the distal part of the P2 tail fiber, since the deduced sequence of its product contains regions similar to tail fiber proteins from phages Mu, P1, lambda, K3, and T2. The similarities of the carboxy-terminal portions of the P2, Mu, ann P1 tail fiber proteins may explain the observation that these phages in general have the same host range. The P2 H gene product is similar to the products of both lambda open reading frame (ORF) 401 (stf, side tail fiber) and its downstream ORF, ORF 314. If 1 bp is inserted near the end of ORF 401, this reading frame becomes fused with ORF 314, creating an ORF that may represent the complete stf gene that encodes a 774-amino-acid-long side tail fiber protein. Thus, a frameshift mutation seems to be present in the common laboratory strain of lambda. Gene G of P2 probably codes for a protein required for assembly of the tail fibers of the virion. The entire G gene product is very similar to the products of genes U and U' of phage Mu; a region of these proteins is also found in the tail fiber assembly proteins of phages TuIa, TuIb, T4, and lambda. The similarities in the tail fiber genes of phages of different families provide evidence that illegitimate recombination occurs at previously unappreciated levels and that phages are taking advantage of the gene pool available to them to alter their host ranges under selective pressures.

A site-specific DNA inversion in Bacteroides plasmid pBF4 is influenced by the presence of the conjugal tetracycline resistance element

pBF4 is a 42-kb R plasmid from Bacteroides fragilis which transfers clindamycin resistance (Clr) independently of the chromosomal tetracycline resistance (Tcr) transfer element. We have found that this plasmid exists in two nonequimolar conformations, A and B. These forms differ by an inversion of approximately 11.5 kb which does not involve the repeated DNA sequences previously mapped on the plasmid. The presence of chromosomal tetracycline resistance conjugal elements influences the relative amounts of the two conformations: induction with tetracycline shifts the dominant form from B to A.

In vitro maturation and encapsidation of the DNA of transposable Mu-like phage D108

Mu and D108 are related, temperate, transposable coliphages with unusual modes of DNA replication (transposition) and virion DNA maturation. These double-stranded DNA genomes replicate intrachromosomally and are matured and encapsidated linked to DNA sequences flanking the dispersed, integrated phage genomes. We have developed an in vitro system that employs crude lysates prepared from cells late in the Mu lytic cycle and that is proficient for both maturation and encapsidation of D108 DNA. Different forms of phage DNA were packaged at different efficiencies, with a circular pSC101::D108cts10 plasmid being most efficient, linearized plasmid less so, and mature virion DNA a poor substrate. The addition of purified D108 Ner protein to the reaction had no effect, whereas D108 repressor (c protein) inhibited the reaction. Escherichia coli integration host factor and D108 transposase proteins exerted an inhibitory effect on circular DNA substrates but had little effect on linear DNA packaging. This in vitro system, coupled with that developed for transposition, can now be used to biochemically dissect the protein and substrate requirements of these phages' DNA maturation pathway and the nature of the molecular switch between DNA transposition and encapsidation.

Minute amounts of RNA are synthesized from several regions of the bacteriophage Mu DNA during the lysogenic state

The transcription of phage Mu DNA during the lysogenic state has been quantitatively analysed. For this purpose pulse-labelled RNA from two lysogens and from their nonlysogenic parental strains were hybridized to non-overlapping Mu DNA restriction fragments covering the whole phage genome. The data revealed that all regions of the prophage are transcribed at low rates and that phage promoters are involved in this transcription. For this study an improved assay for quantitative filter hybridization was employed. The high sensitivity and reproducibility that can be obtained with the assay make it suitable for the quantitative analysis of minute amounts of mRNA.

Localization and regulation of bacteriophage Mu promoters

Mu promoters active during the lytic cycle were located by isolating RNA at various times after induction of Mu prophages, radiolabeling it by capping in vitro, and hybridizing it to Mu DNA fragments on Southern blots. Signals were detected from four new promoters in addition to the previously characterized Pe (early), PcM (repressor), and Pmom (late) promoters. A major signal upstream of C was first observed at 12 min and intensified thereafter with RNA from cts and C amber but not replication-defective prophages; these characteristics indicate that this signal arises from a middle promoter, which we designate Pm. With 20- and 40-min RNA, four additional major signals originated in the C-lys, F-G-I, N-P, and com-mom regions. These signals were missing with RNA from C amber and replication-defective prophages and therefore reflected the activity of late promoters, one of which we presume was Pmom. Uninduced lysogens showed weak signals from five regions, one from the early regulatory region, three between genes B and lys, and one near the late genes K, L, and M. The first of these probably resulted from PcM activity; the others remain to be identified.

The terminal a sequence of the herpes simplex virus genome contains the promoter of a gene located in the repeat sequences of the L component

The herpes simplex virus DNA genome consists of two covalently linked components, L and S. The unique sequences of the L component are flanked by 9-kilobase-pair inverted repeat sequences ab and b'a', whereas those of the S component are flanked by 6.5-kilobase-pair inverted repeat sequences c'a' and ca. We report that the 500-base-pair a sequence contains the promoter-regulatory domain and the transcription initiation site of a diploid gene, the coding sequences of which are located in the b sequences of the inverted repeats of the L component. The chimeric gene constructed by fusion of the a sequence to the coding sequences of the thymidine kinase gene and recombined into the viral genome was regulated as a gamma 1 gene. The size of the protein predicted from its sequence is 358 amino acids; it was designated as infected cell protein (ICP) 34.5. Thus, the inverted repeats flanking the unique sequences of the L component contain two genes specifying ICP0 and ICP34.5, respectively. Moreover, in addition to the cis-acting sites for the inversion of L and S components relative to each other, for cleavage of unit length DNA molecules from head-to-tail concatemers, and for packaging of the DNA into capsids, the a sequence also contains the promoter-regulatory domain and transcription initiation sites of a gene.

Highly mobile DNA segment of IncI alpha plasmid R64: a clustered inversion region

When R64 DNA was digested with EcoRI, two DNA fragments not equimolar to the plasmid DNA were produced. A DNA region including these fragments was cloned (pKK009), and the pKK009 DNA sample was found to be a mixture of six or more DNA species with EcoRI, PstI, and AvaI cleavage sites at different positions, suggesting a complex rearrangement of DNA. When a part of the pKK009 DNA was removed by HindIII digestion, 33 different types of plasmids (pKK010-series plasmids) were obtained out of 58 clones tested, but no DNA rearrangement could be observed. On the basis of a comparison of the detailed restriction maps of these pKK010-series plasmids, we propose a model in which four DNA segments invert independently or in groups within the 1.95-kilobase region of R64, so that the arrangements of these four segments change randomly. The fixed pKK010-series plasmid DNA was again rearranged in the presence of R64, indicating that trans-acting gene function may be present to mediate the DNA rearrangement. The gene (tentatively designated as rci) was located on a 4.5-kilobase E9' fragment of R64.

Plasmid rearrangements in the photosynthetic bacterium Rhodopseudomonas sphaeroides

Mu d1(Ap lac) was introduced into the photosynthetic bacterium Rhodopseudomonas sphaeroides 2.4.1. via the R-plasmid R751 in an attempt to isolate fusion derivatives involving photosynthetic operons. The selection system is potentially very powerful since R. sphaeroides is normally Lac negative. Among the exconjugants, photosynthesis-deficient mutants were recovered, some of which had elevated beta-galactosidase levels. Among the mutants examined, beta-galactosidase expression was linked exclusively to R751 . Many of the photosynthesis-deficient mutants were found to have alterations in their indigenous plasmids which apparently involved the exchange of DNA from one plasmid to another. Southern blot analysis revealed that there are extensive DNA sequences which are shared by the two plasmids that are involved in the rearrangements and that no exogenous DNA sequences appear to be involved. It was further discovered that plasmid rearrangement is a general phenomenon which can occur spontaneously in R. sphaeroides 2.4.1 and shows a high correlation with a photosynthesis minus phenotype.

Involvement of the invertible G segment in bacteriophage mu tail fiber biosynthesis

The orientation [G(+) or G(-)] of the invertible G segment of bacteriophage Mu DNA determines the host range specificity of the phage particles. In this study the hypothesis that the G segment genes are involved in synthesis of Mu tail fibers has been tested. Serum blocking power (SBP) assays demonstrated that among Mu late gene mutants only those defective in genes S or U encoded by the G segment were defective in G(+) SBP and that they lacked the same antigens. Electron microscopy of lysates produced by inversion-defective gin mutants (isolated by their inability to complement a hin inversion-defective mutant of the Salmonella phase variation segment) showed that G(+) phages with amber mutations in S or U made tail-fiberless particles with contracted tail sheaths. Inversion of G to the G(-) orientation or suppression of the amber mutations restored the normal phage particle morphology. These experiments demonstrate that genes S and U are required for Mu G(+) tail fiber biosynthesis and/or attachment.

Bacteriophage P1 carries two related sets of genes determining its host range in the invertible C segment of its genome

The bacteriophage P1 genome carries an invertible C segment consisting of 3-kb unique sequences flanked by 0.6-kb inverted repeats. Host range mutations of P1 have been mapped in the C segment region. P1 derivatives carrying insertions and deletions in the left half of the C segment in one of two orientations termed C(+) do not affect the plaque-forming ability on Escherichia coli K12 and E coli C, whereas those having insertions in the right half of the C segment fail to form plaques on these hosts. An E. coli C mutant which allows the latter insertion mutants with the C segment in the C(-) configuration to form plaques has been isolated. Not only P1 C(-) but also P1 C(+) phages gave plaques on this E. coli C mutant. The results are consistent with the notion that the C segment of P1 carries two sets of genes for host specificity, and that C inversion alters the P1 host range through activation of one set of the genes. Furthermore, extended host range mutants can be isolated by point mutation in either set of the P1 genes. C inversion is a slow process, but it occurs on the phage genome upon its vegetative growth as well as on the prophage in the lysogenic state. The 3-kb invertible G segment of the phage Mu genome is known to be homologous with the central 3-kb part of the C segment of P1 and to carry also two sets of genes for Mu host specificity. While only Mu G(-) grows on E. coli C, both Mu G(+) and Mu G(-) phages form plaques on the E. coli C mutant sensitive to P1 C(-). In the discussion the gene organization of the P1 C segment is compared with that of the Mu G segment.

IS200: a Salmonella-specific insertion sequence

A new IS element (IS200) has been identified in Salmonella. The sequence was identified as an IS element by the following criteria: its insertion caused the mutation hisD984; six copies of the sequence are present in strain LT2 of S. typhimurium; and transposition of the sequence has been observed on several occasions. IS200 is found in almost all Salmonella species examined but is absent from most other enteric bacteria. The specificity of this element for Salmonella (and the absence of IS1-IS4 from Salmonella) suggest that transfer of insertion sequences between bacterial groups may be less extensive than is commonly believed. Alternatively, the distribution may suggest that these elements play a selectively important role in bacteria.

Recombination within the yeast plasmid 2mu circle is site-specific

The multicopy yeast plasmid, 2mu circle, encodes a specialized recombination system. It contains two regions, each 599 bp in length, that are precise inverted repeats of each other and between which recombination occurs readily. In addition, this recombination requires the product of a 2mu circle gene, designated FLP. By examining the products of FLP-mediated recombination of plasmids containing single insertions within one of the repeated regions, we show that this recombination occurs only at a specific site within the repeat. This result was confirmed from analysis of the ability of plasmids containing various deletions within one of the repeated regions to serve as substrates for FLP-mediated recombination. These experiments limit the recombination site to a sequence of less than 65 bp. In addition, by mutational analysis of the recombination potential of a hybrid plasmid containing the entire 2mu circle genome, we have shown that FLP is only the 2mu circle gene necessary for this site-specific recombination. Finally, we describe a sensitive assay for recombination between the repeated sequences of 2mu circle; using it, we demonstrate that even in the absence of FLP gene product, recombination between the repeats occurs at a low but detectable level during meiosis.

Homology between the invertible deoxyribonucleic acid sequence that controls flagellar-phase variation in Salmonella sp. and deoxyribonucleic acid sequences in other organisms

The invertible deoxyribonucleic acid (DNA) segment cloned from Salmonella sp. was radioactively labeled and used as a probe to search for homologous sequences by Southern hybridization. Only one copy of the invertible segment could be found on the Salmonella sp. genome. Partial sequence homology with the invertible region was detected in bacteriophage Mu and P1 DNA by low-stringency hybridization. Under these conditions, no homology was detected with Escherichia coli DNA. A strain of Salmonella sp. defective in phase variation carrying the vH2- allele was also analyzed by DNA-DNA hybridization. The results show that there is sequence divergence between diphasic and vH2- strains within the invertible sequence.

The relationship of two invertible segments in bacteriophage Mu and Salmonella typhimurium DNA

A Mu gin- mutant which lacks the function required for inversion of the G segment can be complemented by hybrid plasmids and phages carrying the invertible segment that controls flagellar phase variation in Salmonella typhimurium. This suggests that the same kind of site-specific recombination mechanism is responsible for these inversions. Based on the different features of the two invertible segments we propose a model for their evolutionary relationship.

Inversions of specific DNA segments in flagellar phase variation of Salmonella and inversion systems of bacteriophages P1 and Mu

Prophages P1 and Mu produces a trans-acting factor possessing the din+ activity which catalyzes the inversion of the specific DNA segment responsible for flagellar phase variation of Salmonella, din mutants were isolated from PICMclr100 phage by selecting phages that did not suppress the yh2 mutation of Salmonella in prophage state. No inversion loop structure was detected among DNA forms arising after denaturation and rehybridization of DNAs extracted from the din mutants. The DNA fragment containing C region of P1 was cloned on a plasmid vector, pCR1. The resulting hybrid plasmid, pKK2, was shown to possess the din+ activity: the vh2 mutant of Salmonella harboring the plasmid changed the flagellar phase. From analysis of the plasmid by use of BamHI and Bgl II, the din gene specifying the din+ activity was located near or within the C region of P1. It is highly plausible that the din gene of P1 was also involved in the inversion of the C region. Similarly, the DNA fragment containing the G and beta segments of Mu was cloned on pCR1. The resulting hybrid plasmid, pII101, also possessed the din+ activity.

Replication and recombination functions associated with the yeast plasmid, 2 mu circle

By examining both the transformation efficiency of yeast of various plasmids containing defined regions of the 2 mu circle genome and the characteristics of the resultant transformants, we have identified several regions of the 2 mu circle genome which are involved in 2 mu circle replication or recombination. First, by identifying those DNA fragments from the molecule which promote high frequency transformation of yeast, we have localized the origin of replication to a sequence partially within the large unique region, which, as determined by subsequent deletion analysis, extends from the middle of the inverted repeat region into the contiguous unique region. Second, by examining the relative efficiency of replication in yeast of hybrid plasmids containing either the entire 2 mu circle genome or a fragment of 2 mu circle encompassing the origin of replication, we have determined that efficient use of the 2 mu circle origin requires some function or functions encoded in the molecule at a site away from the origin. Third, by examining the ability of a mutant 2 mu circle molecule to undergo intramolecular recombination in yeast, we have identified a 2 mu circle gene which codes for a product required for this process.

Binary developmental commitments in normal and abnormal human morphogenesis

An hypothesis is presented to account for the occurrence of overlapping patterns of anomalies in various malformation syndromes. According to this proposal, normal human morphogenesis occurs by means of a series of sequential commitments by neighboring groups of cells to alternative developmental programs.

Perturbance analysis of nuclear determination in Tetrahymena: effects of nutrition, cell extracts, and CaCl2 on A/B hybrids

Mating type frequencies were ascertained among the progeny of crosses of strains A x B, Tetrahymena thermophila under a number of different circumstances. The frequencies are different if the parents are severely starved than if they are well-fed at the time of conjugation; severe starvation of the progeny before the first post-zygotic division has an effect similar to that of starving the parents. Mating type frequencies may also be modified by isolating conjugating pairs into cell extracts before the new macronuclei begin to develop; the changes do not appear to be related in a meaningful way to the mating type of the cells used as a source of the cell extracts. A third means of changing the mating type frequencies involves the exposure of conjugating pairs to CaCl2 solutions. Finally, changed frequency patterns may appear "spontaneously", and reflect either some as yet unsuspected environmental variable, or else an intrinsic metastable state that conditions the probabilities of mating type fixation. With the exception of the starvation effects, the pattern variations seem to fall into two groups. No satisfactory mechanism to account for these results is yet available.

Physical mapping of Staphylococcus aureus penicillinase plasmid pI524: characterization of an invertible region

The staphylococcal penicillinase plasmid pI524 and a series of derivatives have been extensively mapped by restriction endonuclease digestion and by heteroduplex analysis. We report here the identification of a 2.2 kb region that undergoes a reversible, rec-independent inversion. This sequence is bounded by a pair of inverted repeats 650 base pairs in length, and has asymmetrically located recognition sites for at least three restriction endonucleases. A series of deleted derivatives and one naturally occurring, closely related plasmid, were studied. Two of these retain the inversion; the remainder are incapable of inverting and were all found to be locked in the same orientation of the inversion. The invertible sequence is adjacent to the region of the plasmid encoding beta-lactamase (bla); this entire region appears to be transposable and the inversion may be involved in the regulation of beta-lactamase expression or in translocation.

Chromosomal rearrangements by an IS2 insertion in phage Mu-1

We have isolated and characterized a mutant of temperate phage Mu-1 carrying an IS2 insertion in the middle of its beta region. This mutant gives rise spontaneously to secondary mutants which have deletions of different sizes adjacent to IS2. One particular derivative however, was found to have acquired an additional insertion sequence adjacent to IS2. This derivative gave rise to tertiary mutants carrying a deletion next to the tandem insertion. The tandem insertion was located at the same place in the Mu beta region as another 2.6 kb insertion independently isolated by Chow et al. (1977) and was found to be homologous to that insertion. The properties of this particular secondary mutant show that Mu phage particles lacking their S end are defective for growth and lysogenisation.