Reexamination of the genome size of myxobacteria, including the use of a new method for genome size analysis

Genetic Characterization of a Novel Retron Element Isolated from Vibrio mimicus

Bacterial reverse transcriptase coding gene (RT) is essential for the production of a small satellite DNA-RNA complex called multicopy single-stranded DNA (msDNA). In this study, we found a novel retron, retron-Vmi1 (Vm85) from Vibrio mimicus. The retron is comprised of the msr-msd region, orf323, and the ret gene, a genetic organization similar to Salmonella's retron-Sen2 (St85). The protein sequence of the RNA-directed DNA polymerase (RT-Vmi1) is highly homologous to the RTs of Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus. Phylogenetic and protein sequence similarity analysis of retron-Vmi1 ORF323 and RT revealed a close relatedness to retron-Sen2. We found that retron-Vmi1 was inserted in the dusA gene, similar to the insertion of the retron-Vpa1 (Vp96) of V. parahaemolyticus AQ3354, suggesting that retrons can be transferred via the tRNA gene. These results are the first convincing evidence that retron is moving across species. The neighboring genes of retron-Vmi1 shared high homology with the genetic environment of V. parahaemolyticus and V. vulnificus retrons. We also found two junction points within the retron-Vmi1 and the dusA gene suggesting that retron-Vmi1 was inserted into this site in a two-step manner.

A DnaK homolog in Myxococcus xanthus is involved in social motility and fruiting body formation

Myxococcus xanthus is a gram-negative soil bacterium which exhibits a complex life cycle and social behavior. In this study, two developmental mutants of M. xanthus were isolated through Tn5 transposon mutagenesis. The mutants were found to be defective in cellular aggregation as well as in sporulation. Further phenotypic characterization indicated that the mutants were defective in social motility but normal in directed cell movements. Both mutations were cloned by a transposon-tagging method. Sequence analysis indicated that both insertions occurred in the same gene, which encodes a homolog of DnaK. Unlike the dnaK genes in other bacteria, this M. xanthus homolog appears not to be regulated by temperature or heat shock and is constitutively expressed during vegetative growth and under starvation. The defects of the mutants indicate that this DnaK homolog is important for the social motility and development of M. xanthus.

Complementation of sporulation and motility defects in a prokaryote by a eukaryotic GTPase

The complex prokaryote, Myxococcus xanthus, undergoes a program of multicellular development when starved for nutrients, culminating in sporulation. M. xanthus makes MglA, a 22-kDa, soluble protein that is required for both multicellular development and gliding motility. MglA is similar in sequence to the Saccharomyces cerevisiae SAR1 protein, a member of the Ras/Rab/Rho superfamily of small eukaryotic GTPases. The SAR1 gene, when integrated into the M. xanthus genome, complements the sporulation defect of a DeltamglA strain. A forward, second-site mutation on the M. xanthus chromosome, rpm, in combination with SAR1, restores fruiting body morphogenesis and gliding motility to a DeltamglA strain. The result that the rpm mutation suppresses the substitution of SAR1 for mglA suggests that Sar1p interacts with other M. xanthus proteins to control the motility-dependent aggregation of cells during development.

The tgl gene: social motility and stimulation in Myxococcus xanthus

Mutations in the tgl locus inactivate social gliding motility in Myxococcus xanthus and block production of pili. The tgl locus is distinctive among the genes for social motility because social gliding and pili can be restored transiently to tgl mutant cells by mixing them with tgl+ cells, a process known as stimulation. The tgl locus was cloned with a linked insertion of transposon Tn5 by using the kanamycin resistance encoded by that transposon. A 16-kb segment of chromosomal DNA complemented the social motility defect when introduced into tgl mutant cells to form a tandem duplication tgl+/tgl heterozygote. To delimit the autonomous tgl transcription unit, subfragments of this 16-kb piece were integrated at the ectopic Mx8 prophage attachment site. A 1.7-kb DNA fragment was identified which, when integrated at the Mx8 site, simultaneously rescued social motility and pilus production. The ability to stimulate tgl mutants was also rescued by the 1.7-kb fragment. Because rescue of stimulation from an mgl-deficient donor strain which cannot swarm was observed, this demonstrates that a stimulation donor requires a tgl+ allele but does not require the capacity to swarm actively. The nucleotide sequence of the 1.7-kb fragment revealed two protein coding regions, open reading frame A and open reading frame B (ORFB). ORFB is the tgl gene, because a 613-bp DNA fragment which includes 75% of ORFB rescues tgl-1, -2, and -3 mutants and because disruption of ORFB by deletion or insertion of transposon Tn5lac constitutes a tgl mutation.

Two recA genes in Myxococcus xanthus

Two recA genes, recA1 and recA2, in Myxococcus xanthus were cloned by using the recA gene of Escherichia coli, and their DNA sequences were determined. On the basis of deduced amino acid sequences, RecA1 and RecA2 have 67.0% identity to each other and 60.5 and 60.9% identities to E. coli RecA, respectively. Expression of recA2 was detected in both vegetative and developmental cells by Northern blot (RNA) analysis, and a threefold induction was observed when cells were treated with nalidixic acid. Repeated attempts to isolate a recA2 disruption mutant have failed, while a recA1 disruption mutant was readily isolated. Both the recA1 and recA2 genes expressed in E. coli complement the UV sensitivity of an E. coli recA strain.

A short introduction to the origin and molecular evolution of viruses

The present review deals with conceptual and experimental approaches to two aspects of the origin and molecular evolution of viruses. In the section "Role of Retrons, Retroelements, and Reverse Transcriptase in the Evolution of Retroviruses and in Eukaryotic Genome Plasticity", Temin's concept that retrons are an ancient genetic element that during evolution of the species gave rise to retroviruses is presented. An opposing view of Xiong and Eickbush that the most probable ancestor of current retroelements is a retrotransposable element with gag- and pol-like genes is presented. Minus-strand RNA viruses are also discussed. The second aspect of this review is the molecular evolution of viruses at the level of the virus genome. Spiegelman's experiment on the evolution of self-replicating nucleic acid molecules outside living cells and Eigen's experimental and conceptual approaches to this subject are presented, along with studies on the evolutionary rates of base substitutions in viral RNA and defective molecules generated during replication.

Clustering and co-ordinated activation of carotenoid genes in Myxococcus xanthus by blue light

Blue light activates carotenoid production in the non-photosynthetic, Gram-negative bacterium Myxococcus xanthus. Light is known to stimulate the expression of two unlinked genes for carotenoid synthesis, carB and carC, through a mechanism in which the regulatory genes carA, carQ and carR take part. Genes carQ and carR are linked together at a separate locus, whereas carA is linked to carB. We have introduced Tn5 at various sites between carA and carB. Chemical analyses of the mutant strains demonstrate the presence in this region of a cluster of genes for carotenoid synthesis. Gene expression analysis strongly argues for most (or all) of the genes in the cluster being transcribed from a single, light-inducible promoter under the control of genes carA, carQ and carR.

A new putative sigma factor of Myxococcus xanthus

A third putative sigma factor gene, sigC, has been isolated from Myxococcus xanthus by using the sigA gene (formerly rpoD of M. xanthus) as a probe. The nucleotide sequence of sigC has been determined, and an open reading frame of 295 residues (M(r) = 33,430) has been identified. The deduced amino acid sequence of sigC exhibits the features which are characteristic of other bacterial sigma factors. The characterization of a sigC-lacZ strain has demonstrated that sigC expression is induced immediately after cells enter into the developmental cycle and is dramatically reduced at the onset of sporulation. A deletion mutant of sigC grows normally in vegetative culture and is able to develop normally. However, in contrast to the wild-type cells, the sigC deletion mutant cells became capable of forming fruiting bodies and myxospores on semirich agar plates. This suggests that sigC may play a role in expression of genes involved in negatively regulating the initiation of fruiting body formation.

Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from two ribosomal protein gene sequences

The families within the class Mollicutes are distinguished by their morphologies, nutritional requirements, and abilities to metabolize certain compounds. Biosystematic classification of the plant-pathogenic mycoplasmalike organisms (MLOs) has been difficult because these organisms have not been cultured in vitro, and hence their nutritional requirements have not been determined nor have physiological characterizations been possible. To investigate the evolutionary relationship of the MLOs to other members of the class Mollicutes, a segment of a ribosomal protein operon was cloned and sequenced from an aster yellows-type MLO which is pathogenic for members of the genus Oenothera and from Acholeplasma laidlawii. The deduced amino acid sequence data from the rpl22 and rps3 genes indicate that the MLOs are more closely related to A. laidlawii than to animal mycoplasmas, confirming previous results from 16S rRNA sequence comparisons. This conclusion is also supported by the finding that the UGA codon is not read as a tryptophan codon in the MLO and A. laidlawii, in contrast to its usage in Mycoplasma capricolum.

Membrane properties of a plant-pathogenic mycoplasmalike organism

In terms of biosystematics, the plant-pathogenic mycoplasmalike organisms (MLOs) have been tentatively placed into the class Mollicutes. Certain physiological tests have been used to distinguish families within this class: the sterol-nonrequiring Acholeplasmataceae differ from the sterol-requiring Mycoplasmataceae in that the former are more resistant to lysis by digitonin and more sensitive to lysis in hypotonic salt solutions. To test MLOs for these membrane properties and thus assist in their definitive classification, a dot-blot microassay procedure was used to detect nucleic acids released from lysed cells. The results show that MLOs resemble acholeplasmas grown in the absence of sterols in that they are resistant to digitonin and sensitive to hypotonic salt solutions. The MLOs can be differentiated from acholeplasmas grown without sterols by their greater resistance to lysis in hypotonic sucrose solutions.

Nucleotide sequence and characterization of the gene for secreted alkaline phosphatase from Lysobacter enzymogenes

Lysobacter enzymogenes produces an alkaline phosphatase which is secreted into the medium. The gene for the enzyme (phoA) was isolated from a recombinant lambda library. It was identified within a 4.4-kb EcoRI-BamH1 fragment, and its sequence was determined by the chain termination method. The structural gene consists of an open reading frame which encodes a 539-amino-acid protein with a 29-residue signal sequence, followed by a 119-residue propeptide, the 281-residue mature phosphatase, and a 110-residue carboxy-terminal domain. The roles of the propeptide and the carboxy-terminal peptide remain to be determined. A molecular weight of 30,000 was determined for the mature enzyme from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amino acid sequence was compared with sequences available in the current protein data base, and a region of the sequence was found to show considerable homology with sequences in mammalian type 5 iron-containing purple acid phosphatases.

The genome size of a plant-pathogenic mycoplasmalike organism resembles those of animal mycoplasmas

The genome size of a mycoplasmalike organism was determined by comparing fluorescence intensities of restriction fragments. Its genome size was similar to that of Mycoplasma gallisepticum and much smaller than that of Acholeplasma laidlawii. Although the genome size is "mycoplasmalike," other molecular data indicate a closer evolutionary relationship to A. laidlawii.

Mutations affecting germination in Myxococcus xanthus

Myxococcus xanthus mutants defective in myxospore germination have been isolated both by a selective and by a non-selective method after UV or Tn5-lac-induced mutagenesis. The ability of these mutants to germinate in germinant solutions other than those used for their isolation has been tested. Six of seven mutants isolated behaved as germination-defective in all germinants. Germination of the seventh mutant was conditional on the germinant used, being normal in Casamino acids but defective in a Casitone-based medium. Genetic analysis of the four mutant strains carrying Tn5-lac insertions revealed that the transposon had disrupted a different locus in each mutant, so that the four mutants defined four unlinked loci involved in the germination process (gerA, gerB, gerC, gerD). Strain MR307 was studied in more detail. Cloning of the gene affected in this mutant, gerC, and construction of merodiploids revealed that the wild-type allele is dominant over the mutated one. In vitro construction of lacZ fusions allowed study of gerC expression throughout the M. xanthus life cycle, revealing that the gene affected by insertion at ΩMR307 is developmentally regulated.

Retroelements in bacteria

A peculiar type of satellite DNA, called msDNA, has been discovered in myxobacteria and some natural isolates of E. coli. These molecules are characterized by the presence of single-stranded DNA branching out from an internal guanosine residue of an RNA molecule by a unique 2',5'-phosphodiester linkage. Reverse transcriptase is required for the synthesis of msDNA. The discovery of retroelements in bacterial populations raises many intriguing questions concerning the evolutionary origin of reverse transcriptase, the function and the biosynthesis of msDNA, and the nature of the mechanisms generating the extensive diversity found in msDNA and reverse transcriptase genes among different bacterial strains.

msDNA of bacteria

The msDNA-retron element represents the first prokaryotic member of the large and diverse retroelement family found in many eukaryotic genomes (Table II). This prokaryotic retroelement exists as a single copy element in the chromosome of two different bacterial groups: the common soil microbe M. xanthus and the enteric bacterium E. coli. It encodes an RT similar to the polymerases found in retroviruses, containing most of the strictly conserved amino acids found in all RTs. The RT is responsible for the production of an unusual extrachromosomal RNA-DNA molecule known as msDNA. Each composed of a short single strand of RNA and a short single strand of DNA, msDNAs vary considerably in their primary nucleotide sequences, but all share certain secondary structural features, including the unique 2',5' branch linkage that joins the 5' end of the DNA chain to the 2' position of an internal guanosine residue of the RNA strand. It is proposed that msDNA is synthesized by reverse transcription of a precursor RNA transcribed from a region of the retron containing the genes msr (encoding the RNA portion) and msd (encoding the DNA portion) and the ORF (encoding the RT). The precursor RNA transcript folds into a stable secondary structure that serves as both the primer and the template for the synthesis of msDNA. The msDNA-retron elements of E. coli are found in less than 10% of all strains observed, are heterogeneous in nature, and have an atypical aminoacid codon usage for this species, suggesting that this element was transmitted to E. coli by some other source. The presence of directly repeated 26-base-pair sequences flanking the junctions of the Ec67-retron of E. coli also suggests that it may be a mobile element. However, the msDNA-retrons of M. xanthus appear to be as old as other genes native to this species, based on codon-usage data for the RT genes and the fact that every strain of M. xanthus appears to have the same type of msDNA. If the msDNA-retron element originated with the myxobacteria, it would place the existence of retrons before the appearance of eukaryotic cells, suggesting that the bacterial element is perhaps the ancestral gene from which eukaryotic retroviruses and other retroelements evolved.(ABSTRACT TRUNCATED AT 400 WORDS)

Social and developmental biology of the myxobacteria

Myxobacteria are soil bacteria whose unusually social behavior distinguishes them from other groups of procaryotes. Perhaps the most remarkable aspect of their social behavior occurs during development, when tens of thousands of cells aggregate and form a colorful fruiting body. Inside the fruiting body the vegetative cells convert into dormant, resistant myxospores. However, myxobacterial social behavior is not restricted to the developmental cycle, and three other social behaviors have been described. Vegetative cells have a multigene social motility system in which cell-cell contact is essential for gliding in multicellular swarms. Cell growth on protein is cooperative in that the growth rate increases with the cell density. Rippling is a periodic behavior in which the cells align themselves in ridges and move in waves. These social behaviors indicate that myxobacterial colonies are not merely collections of individual cells but are societies in which cell behavior is synchronized by cell-cell interactions. The molecular basis of these social behaviors is becoming clear through the use of a combination of behavioral, biochemical, and genetic experimental approaches.

Social and developmental biology of the myxobacteria

Myxobacteria are soil bacteria whose unusually social behavior distinguishes them from other groups of procaryotes. Perhaps the most remarkable aspect of their social behavior occurs during development, when tens of thousands of cells aggregate and form a colorful fruiting body. Inside the fruiting body the vegetative cells convert into dormant, resistant myxospores. However, myxobacterial social behavior is not restricted to the developmental cycle, and three other social behaviors have been described. Vegetative cells have a multigene social motility system in which cell-cell contact is essential for gliding in multicellular swarms. Cell growth on protein is cooperative in that the growth rate increases with the cell density. Rippling is a periodic behavior in which the cells align themselves in ridges and move in waves. These social behaviors indicate that myxobacterial colonies are not merely collections of individual cells but are societies in which cell behavior is synchronized by cell-cell interactions. The molecular basis of these social behaviors is becoming clear through the use of a combination of behavioral, biochemical, and genetic experimental approaches.

Development-specific sigma-factor essential for late-stage differentiation of Myxococcus xanthus

The gene for a developmentally expressed sigma-factor, sigB, has been isolated from Myxococcus xanthus by use of the sigA gene (formerly rpoD) of the vegetative sigma-factor as a probe. The sequence of sigB has been determined, and an open reading frame of 193 amino acid residues (Mr = 21,551) was identified. The amino-terminal region of SigB contains 69 residues, of which 35 are identical (50% identity) to the region of SigA required for core RNA polymerase binding and initiation of RNA polymerization. SigB also possesses many features commonly found in other prokaryotic sigma-factors. Analysis of an M. xanthus strain carrying a sigB-lacZ fusion gene revealed that sigB is expressed from a middle to late stage of differentiation corresponding to the period from the onset of sporulation to late development. A sigB deletion mutant displayed normal mound formation and sporulation; however, production of the ops gene product in myxospores of the delta sigB strain was shown to be blocked. Myxospores from the sigB deletion strain also exhibited severe defects in stability and viability during late development. Our data indicate that sigB encodes a sigma-factor essential for the maturation of myxospores at a late stage of M. xanthus differentiation. Our results also suggest that differentiation of M. xanthus is regulated by development-specific sigma-factors.

Genome size of Myxococcus xanthus determined by pulsed-field gel electrophoresis

Genomic DNA of the myxobacterium Myxococcus xanthus was digested with the rare cutting restriction endonuclease AseI or SpeI, and the restriction products were separated by pulsed-field gel electrophoresis. Transposons Tn5-132 and Tn5 lac, which contain AseI restriction sites, were used to determine the number of restriction fragments in each band. The size of the genome was determined by adding the molecular sizes of the restriction products. The genomes of strains DK101, MD2, and DZF1 have identical restriction patterns and were estimated to be 9,454 +/- 101 kilobase pairs from the AseI digestions and 9,453 +/- 106 kilobase pairs from the SpeI digestions. DK1622, which was derived from DK101 by treatment with UV light, has suffered a 220- to 222-kilobase-pair deletion that removed an AseI and an SpeI restriction site. The deleted DNA may consist exclusively of Mx alpha-associated sequences.

Cloning and DNA sequence of the gene coding for the major sigma factor from Myxococcus xanthus

The gene for a sigma factor (rpoD) was cloned from Myxococcus xanthus, a soil bacterium which differentiates to form fruiting bodies upon starvation for nutrients. The DNA sequence of the gene was determined, and an open reading frame encoding a polypeptide of 708 amino acid residues (Mr = 80,391) was identified. Except for the amino-terminal sequence consisting of 100 residues, the M. xanthus sigma factor (sigma-80) showed extensive similarity with Escherichia coli sigma-70 as well as Bacillus subtilis sigma-43. In particular, the carboxy-terminal sequence of 242 residues that is known to be required for promoter recognition and core recognition showed 78 and 72% amino acid sequence identity with the E. coli and B. subtilis sigma factors, respectively. The putative RpoD protein was detected at the position of an apparent molecular weight of 86,000 by Western blot (immunoblot) analysis by using antiserum against B. subtilis sigma-43, which agreed well with the position of a vegetative sigma factor of M. xanthus previously identified by Rudd and Zusman (K. Rudd and D. R. Zusman, J. Bacteriol. 151:89-105, 1982).

Major cold shock protein of Escherichia coli

When exponentially growing Escherichia coli cell cultures were transferred from 37 degrees C to 10 degrees C or 15 degrees C, the production of a 7.4-kDa cytoplasmic protein (CS7.4) was prominently induced. The rate of CS7.4 production reached 13% of total protein synthesis within 1-1.5 hr after a shift to 10 degrees C and subsequently dropped to a lower basal level. Regulation of CS7.4 expression was very strict, such that synthesis of the protein was undetectable at 37 degrees C. We have cloned the gene encoding this protein and have completed the nucleotide sequence analysis, which revealed that the gene encodes a hydrophilic protein of 70 amino acid residues.

asgB, a gene required early for developmental signalling, aggregation, and sporulation of Myxococcus xanthus

The asgB genetic locus of Myxococcus xanthus specifies a function which is required early in the developmental pathway leading to aggregation and sporulation in fruiting bodies. The developmental defect of asgB mutants can be compensated by extracellular complementation using either intact wild-type cells or cell-free supernatants conditioned by developing wild-type cells. A Tn5 insertion was isolated closely linked to asgB480 and facilitated the cloning of both the wild-type (asgB+) and the mutant (asgB480) alleles in Escherichia coli plasmid. Tandem duplications of the asgB locus were constructed in M. xanthus; the completely wild-type phenotype of asgB+/asgB480 partial diploids implies that the asgB480 allele is recessive. This finding, along with extracellular complementation by wild-type cells, is consistent with the hypothesis that the asgB+ locus is required to produce a substance with an intercellular signalling function. At least part of the asgB gene was found to lie within a 1.2 kb SmaI DNA fragment. This 1.2 kb fragment, as well as smaller fragments derived from it, were used as DNA probes in RNA/DNA hybrid analyses of transcription in the asgB region. Two small mRNA species were detected, one about 650 bp long, and the other about 500 bp; the two species of mRNAs apparently overlap. Both mRNAs are present in low, but approximately equal amounts, in vegetatively growing cells. This is consistent with the observation that asg mutants display a mutant vegetative phenotype (a change in colony color and spreading behavior) as well as defective development.

Mutations that affect production of branched RNA-linked msDNA in Myxococcus xanthus

A deletion mutation of the gene (msd-msr) for the branched RNA-linked msDNA of Myxococcus xanthus was constructed by replacing the chromosomal 0.7-kilobase (kb) SmaI-XhoI fragment encompassing msd-msr with a 1.4-kb fragment carrying a gene for kanamycin resistance. It was found that this deletion strain (delta msSX) could not produce msDNA, although it still contained another species of msDNA, mrDNA (msDNA, reduced size). No apparent differences between delta msSX and the wild-type strain were observed in terms of cell growth, morphogenesis, fruiting-body formation, or motility. Both a deletion mutation at the region 100 base pairs upstream of msd and an insertion mutation at a site 500 base pairs upstream of msd showed a significant reduction of msDNA production, indicating that there is a cis- or trans-acting positive element in this region. When the 3.5-kb BamHI fragment carrying msd-msr from Stigmatella aurantiaca was inserted into the M. xanthus chromosome, the S. aurantiaca msDNA was found to be produced in M. xanthus.

Cloning of the gene for myxobacterial hemagglutinin and isolation and analysis of structural gene mutations

Myxobacterial hemagglutinin (MBHA) is a major developmentally induced protein that accumulates during the period of cellular aggregation in the bacterium Myxococcus xanthus. It has been shown that this lectin is targeted to the cell surface and periplasmic space of developmental cells, suggesting that it may play a role in cell-cell recognition or agglutination. We have cloned the structural gene for MBHA by using synthetic deoxyoligonucleotides containing sequences deduced from the amino acid sequence of MBHA and have used the cloned gene to construct strains of M. xanthus that cannot synthesize MBHA. We found that although the MBHA-deficient strains are delayed in their developmental time course, they are otherwise able to aggregate and sporulate normally. Our results suggest that MBHA may function to increase the efficiency of fruiting-body formation but is not a critical component of cellular aggregation.

Branched RNA covalently linked to the 5' end of a single-stranded DNA in Stigmatella aurantiaca: structure of msDNA

Stigmatella aurantiaca is a gliding, gram-negative bacterium that shows a spectacular fruiting body formation upon starvation of nutrient. This bacterium was found to contain approximately 500 copies per cell of a short single-stranded linear DNA (multicopy single-stranded DNA: msDNA). The primary structure of msDNA was determined and found to consist of 162 or 163 deoxyribonucleotides. Its unique chromosomal gene was cloned and sequenced. The msDNA was found to be attached to a branched RNA by its 5' end. Structural analysis of the branched RNA revealed that it consists of a triribonucleotide, 5'A-G-(C or U)3', and that msDNA is branched out from the 2' position of the rG residue forming a 2', 5' phosphodiester linkage with the dC residue at the 5' end of msDNA.

Control of morphogenesis in myxobacteria

The myxobacteria are Gram-negative soil bacteria that live in large communities known as swarms. The most remarkable characteristic of myxobacteria is their ability to form fruiting bodies that have a species-specific shape and color. Fruiting body formation requires the concerted effort of hundreds of thousands of cells. Development is initiated only when two conditions are satisfied. The cells must be nutritionally deprived (environmental signal) and there must be many other cells in the vicinity (intercellular signal). The development of one species, Myxococcus xanthus, has been studied in the most detail. M. xanthus uses amino acids as its primary carbon, nitrogen, and energy source. Starvation for a single amino acid, or for inorganic phosphate, serves as the environmental signal. A variety of intercellular signals appear to control the initiation of development and the timing of subsequent developmental events.

A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA

Two-dimensional heteroduplex mapping of Neisseria gonorrhoeae genomic DNA revealed a number of spots, indicating the existence of repetitive sequences. When one of the spots was extracted and used as a probe for Southern blot analysis, two HindIII bands (11.0 and 3.6 kilobases [kb]) of the genomic digest hybridized with approximately equal intensity. The 3.6-kb fragment was cloned and found to contain two different types of repeated sequence. One type was approximately 1.1 kb in length and was found at least twice in the entire genome. The other consisted of a 26-base-pair family GT(C/A)C(Py)G(Pu)TTTTTGTTAAT(Py)C(Pu)CTATA (Py, pyrimidine; Pu, purine) that was repeated at least 20 times in the entire genome. This repetitive sequence was found also in Neisseria meningitidis but not in various other gram-negative bacteria.

Cell interactions in myxobacterial growth and development

During their complex life cycle, myxobacteria manifest a number of cell interactions. These include contact-mediated interactions as well as those mediated by soluble extracellular signals. Some of these interactions are well-defined; in addition, the tools for molecular and genetic analysis of these interactions in Myxococcus xanthus are now available.

Novel one-step cloning vector with a transposable element: application to the Myxococcus xanthus genome

A new strategy was developed for rapid cloning of genes with a transposon mutation library. We constructed a transposon designated TnV that was derived from Tn5 and consists of the gene coding for neomycin phosphotransferase II as well as the replication origin of an Escherichia coli plasmid, pSC101, flanked by Tn5 inverted repeats (IS50L and IS50R). TnV can transpose to many different sites of DNA in E. coli and Myxococcus xanthus and confers kanamycin resistance (Kmr) to the cells. From the Kmr cells, one-step cloning of a gene which is mutated as a result of TnV insertion can be achieved as follows. Chromosomal DNA isolated from TnV-mutagenized cells is digested with an appropriate restriction enzyme, ligated, and transformed into E. coli cells with selection for Kmr. The plasmids isolated contain TnV in the target gene. The plasmid DNA can then be used as a probe for characterization of the gene and screening of clones from a genomic library. We used this vector to clone DNA fragments containing genes involved in the development of M. xanthus.

Determination of the molecular mass of bacterial genomic DNA and plasmid copy number by high-pressure liquid chromatography

Relatively rapid methods for the determination of relative genome molecular mass (Mr) and the estimation of plasmid copy number have been developed. These methods are based on the ability of the Bio-Rad high-pressure liquid chromatography hydroxylapatite column to separate and quantify single-stranded DNA, double-stranded DNA, and plasmid DNA. Genome Mr values were calculated from reassociation kinetics of single-stranded DNA as measured with the hydroxylapatite column. Bacteriophage T4 DNA was used to establish a C0t (moles of nucleotides times seconds per liter), or standard reassociation value. From this C0t value, C0t values for Escherichia coli B, Beggiatoa alba B18LD, and Streptomyces coelicolor were determined by comparative calculations. From those calculated C0t values, the Mr values of 1.96 X 10(9) for E. coli, 2.02 X 10(9) for B. alba, and 3.28 X 10(9) for S. coelicolor were estimated. Plasmid concentration was determined from cleared lysates by comparing the integrated area under the phosphate buffer-eluted plasmid peak to values obtained with known amounts of plasmid. The plasmid copy number was estimated by multiplying the ratio between the amounts of plasmid and chromosomal DNA by the ratio between the Mr values of the chromosome and the plasmid. A copy number of 29 was obtained from a culture of E. coli HB101 harboring pBR322 grown to a culture density of 1.6 X 10(9) CFU . ml-1.

Physical mapping of a 330 X 10(3)-base-pair region of the Myxococcus xanthus chromosome that is preferentially labeled during spore germination

Myxococcus xanthus was pulse-labeled with [3H]thymidine immediately after germination of dimethyl sulfoxide-induced spores. The restriction enzyme digests of the total chromosomal DNA from the pulse-labeled cells were analyzed by one-dimensional as well as two-dimensional agarose gel electrophoresis. Four PstI fragments preferentially labeled at a very early stage of germination were cloned into the unique PstI site of pBR322. By using these clones as probes, a restriction enzyme map was established covering approximately 6% of the total M. xanthus genome (330 X 10(3) base pairs). The distribution of the specific activities of the restriction fragments pulse-labeled after germination suggests a bidirectional mode of DNA replication from a fixed origin.

Cloning and complementation analysis of the "Frizzy" genes of Myxococcus xanthus

Fruiting-body formation in Myxococcus xanthus involves the aggregation of cells into raised mounds, where they sporulate. "Frizzy" mutants fail to aggregate into mounds, but rather aggregate into "frizzy" filaments (D.R. Zusman 1982). The frizzy mutations (frz) were found to be genetically linked. The region of DNA carrying the frz genes was cloned in Escherichia coli by selecting for the kanamycin resistance element present on a transposon Tn5 insertion linked to the frz genes. Phage P1 mediated transduction of the cloned DNA into M. xanthus frizzy mutants showed that the cloned DNA could complement the frz mutations. The cloned DNA was analyzed by isolating and characterizing new Tn5 insertions at short intervals within the M. xanthus DNA and by constructing in vitro deletions. The mutated DNA was then transduced into M. xanthus where the cloned DNA became integrated into the bacterial chromosome as gene replacements or as merodiploids. The gene replacement strains allowed us to define the limits of the frz region, since Tn5 insertions in the frz genes resulted in the frizzy phenotype. The merodiploid strains allowed us to perform complementation analyses. Using appropriate crosses, we were able to identify 5-6 frz complementation groups on 7.5 kb of cloned DNA. One of the complementation groups was separated from the others by 1.4 kb of DNA, whereas the others were contiguous. The different frz loci behave as separate transcriptional groups although interactions between some of the gene products are indicated.

Multicopy single-stranded DNA isolated from a gram-negative bacterium, Myxococcus xanthus

A gram-negative bacterium, Myxococcus xanthus, was found to contain 500 to 700 copies per chromosome of a short single-stranded linear DNA fragment. When this DNA (multicopy single-stranded DNA; msDNA) labeled at the 5' end with kinase was used as a probe against total chromosomal blots, it hybridized to unique high molecular weight bands, which were cloned and sequenced. Labeling of msDNA was also possible using the Klenow fragment of DNA polymerase I as well as terminal deoxynucleotidyl transferase, permitting direct sequencing. The 5' end of msDNA was found to be primed by a short RNA segment. The DNA portion of msDNA consisted of 163 bases. Exact correspondence was seen between the msDNA sequence and the sequence of a chromosomal clone. An elaborate secondary structure is postulated for the msDNA sequence. A similar satellite DNA was also found in another myxobacterium, Stigmatella aurantiaca.

Effects of deletion of the gene for the development-specific protein S on differentiation in Myxococcus xanthus

A deletion mutation of the gene for protein S (tps), a development-specific protein of Myxococcus xanthus, was constructed. No significant differences in the process of fruiting body formation or the yield of myxospores were observed between mutant and wild-type cells. On the other hand, when the tps gene was deleted together with a 2.0-kilobase sequence including the ops gene immediately upstream of the tps gene, fruiting body formation was substantially delayed, and the yield of myxospores was reduced. These results indicate that protein S is not essential for differentiation of M. xanthus, whereas a gene product(s) coded from the sequence upstream of the tps gene appears to be required for normal fruiting body formation.

In situ transposon replacement and isolation of a spontaneous tandem genetic duplication

Using a specialized transducing P1 phage carrying an insertion of Tn5-132, an insertion of Tn5-wt in the chromosome of Myxococcus xanthus, which codes for resistance to kanamycin, can be replaced with one of Tn5-132, which codes for resistance to tetracycline. That Tn5-132 in the daughter is inserted at the same location in the chromosome as Tn5-wt was in the parent was shown by a variety of physical and genetic tests. Southern blot hybridizations of restriction digests of daughter and parent DNAs probed for sequences homologous to Tn5 show that the physical location is the same. When KmR was transduced from the parent to the TcR daughter by the generalized transducing myxophage Mx4 or Mx8, all the transductants were TcS. Likewise, when the daughter was used as donor, TcR transductants of its KmR parent were KmS. Flanking markers that were linked to KmR in the parent were linked to TcR in the daughter. Spontaneous tandem genetic duplications of portions of bacterial chromosomes can be trapped by transducing a selectable marker from a donor to a recipient that has a different selectable marker at the same genetic location and selecting transductants with both markers. Using Tc-replacement, this technique can be applied to any region of the chromosome. We used it to isolate a spontaneous tandem duplication of part of the M. xanthus chromosome. The duplication was characterized by Southern blot hybridizations probed for Tn5-homologous DNA. It was also shown to be unstable by quantitation of loss of drug resistance. Transduction of the novel joint led to reconstruction of the duplication in the recipient strain. All these tests gave results consistent with the proposed structure. The methods described here are applicable to any bacterium into which transposons can be introduced, and for which some means of genetic exchange is available.

Coliphage P1-mediated transduction of cloned DNA from Escherichia coli to Myxococcus xanthus: use for complementation and recombinational analyses

We have found that coliphage P1 can be used to transduce cloned DNA from Escherichia coli to Myxococcus xanthus. Transduction occurred at a high efficiency, and no evidence for DNA restriction was observed. The analysis of the transductants showed that they fall into three general categories: (i) haploid cells which contain portions of the cloned DNA substituted for homologous chromosomal DNA; (ii) heterozygous merodiploids which contain the recombinant plasmid integrated into the chromosome at a region of homology; and (iii) homozygous merodiploids which contain two copies of a portion of the cloned DNA with the loss of the chromosomal copy of the genes. The merodiploids, once formed, are relatively stable. They were used to analyze two genes necessary for aggregation and thus fruiting body formation. P1 transduction also permits the reintroduction and substitution of mutated regions of cloned DNA into M. xanthus for the analysis of the role of the DNA in cellular physiology and development.