GENETIC TRANSCRIPTION DURING MORPHOGENESIS

CONSERVATION OF RIBOSOMAL AND MESSENGER RIBONUCLEIC ACID CISTRONS IN BACILLUS SPECIES

Doi, Roy H. (Syracuse University, Syracuse, N.Y.), and Richard T. Igarashi. Conservation of ribosomal and messenger ribonucleic acid cistrons in Bacillus species. J. Bacteriol. 90:384-390. 1965.-Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) fractions from various Bacillus species were tested for interspecies DNA-RNA hybrid formation. DNA preparations from B. subtilis, B. cereus, B. megaterium, B. stearothermophilus, and B. macerans, whose base composition varied from 33 to 50% guanylate + cytidylate content, were used in the hybrid annealing mixtures with pulse-labeled RNA from sporulating cells and from log-phase cells of B. subtilis and B. cereus. Efficient hybridization in these cases was obtained only in homologous annealing situations. When heterologous DNA and RNA preparations were tested for hybrid formation, only 1 to 6% of the homologous hybridization was obtained. Although the efficiency of hybrid formation was low, the results were reproducible. No difference in efficiency of hybrid formation was observed between the messenger RNA from sporulating cells and that from log-phase cells. When B. subtilis ribosomal RNA was placed in annealing mixtures with heterologous DNA, 47.5 to 62.9% of the homologous hybridization was obtained. These results suggest that a small number of identical sequences are present among the Bacillus species. Furthermore, the ribosomal RNA cistrons appear to be more highly conserved relative to other genetic sequences.

Two polypeptides associated with the ribonucleic acid polymerase core of Bacillus subtilis during sporulation

The ribonucleic acid (RNA) polymerase from log-phase and sporulating cells of Bacillus subtilis was analyzed to determine whether any structural changes occurred during sporulation. The elution pattern of RNA polymerase from a deoxyribonucleic acid (DNA)-cellulose column revealed that sporulating cells at stages III and IV contained a new RNA polymerase fraction in addition to the vegetative holoenzyme (alpha2betabeta'sigma). Stage III cells contained the vegetative holoenzyme and a new enzyme with the composition alpha2betabeta'delta1; the molecular weight of delta1 was 28,000. Stage IV cells contained the vegetative holoenzyme, the delta1-containing enzyme, and another enzyme with the composition alpha2betabeta'delta2. The delta2 factor had a molecular weight of around 20,000. The delta-containing enzymes have a higher affinity for the DNA-cellulose column and a higher specific activity on various templates than vegetative holoenzyme. The simultaneous appearance of these enzymes with vegetative holoenzymes in sporulating cells is consistent with the data found previously with DNA-RNA hybridization studies, which showed that sporulating cells contained both vegetative and sporulation messenger RNAs.

Genetic aspects of bacterial endospore formation

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Encystment and germination in Azotobacter vinelandii

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Chloramphenicol restores sigma factor activity to sporulating Bacillus subtilis

The sigma subunit of RNA polymerase from sporulating Bacillus subtilis is markedly inhibited in its ability to direct active transcription of phage varphie DNA in vitro. Treatment of sporulating bacteria with chloramphenicol rapidly restores sigma activity, suggesting that sporulating cells contain an inhibitor of sigma that is physiologically unstable or that becomes unstable after drug treatment. The hypothetical inhibitor is depleted exponentially with an apparent half-life of 11 min at 37 degrees .

Transcription from the complementary deoxyribonucleic acid strands of Bacillus subtilis during various stages of sporulation

The messenger ribonucleic acid (mRNA) pattern of log-phase and sporulating cells of Bacillus subtilis has been analyzed by deoxyribonucleic acid (DNA)-RNA hybrid studies with the complementary-strand fragments of DNA. Approximately 80% of the mRNA of log-phase and sporulating cells from stages I, III, and IV hybridizes with the heavy DNA fragments, and 20% hybridizes with the light DNA fragments. Hybrid competition studies indicated that there was either a greatly reduced rate of transcription or a turn-off of some log-phase genes during the sporulation stages. However, a significant amount of log-phase gene transcription occurred even at late stages of sporulation. Similar studies indicate a significantly increased rate of transcription or a turn-on of sporulation phase genes during the latter stages of sproulation. There is a sequential increase in the amount of sporulation-specific transcription from both complementary-strand fragments of DNA. These results indicate that the RNA polymerase population in sporulating cells can transcribe both log-phase and sporulation-phase genes.

Bacterial differentiation

The foregoing studies are intended to define a differentiation process and to permit genetic access to the mechanisms that control this process. In order to elucidate the basic mechanisms whereby a cell dictates its own defined morphogenic changes, we have found it helpful to study an organism that can be manipulated both biochemically and genetically. We have attempted to develop the studies initiated by Poindexter,Stove and Stanier, and Schmidt and Stanier (16, 17, 20) with the Caulobacter genus so that these bacteria can serve as a model system for prokaryotic differentiation. The Caulobacter life cycle, defined in synchronously growing cultures, includes a sequential series of morphological changes that occur at specific times in the cycle and at specific locations in the cell. Six distinct cellular characteristics, which are peculiar to these bacteria, have been defined and include (i) the synthesis of a polar organelle which may be membranous (21-23), (ii) a satellite DNA in the stalked cell (26), (iii) pili to which RNA bacteriophage specifically adsorb (16, 33), (iv) a single polar flagellum(17), (v) a lipopolysaccharide phage receptor site (27), and (vi) new cell wall material at the flagellated pole of the cell giving rise to a stalk (19, 20). Cell division, essential for the viability of the organism, is dependent on the irreversible differentiation of a flagellated swarmer cell to a mature stalked cell. The specific features of the Caulobacter system which make it a system of choice for studies of the control of sequential events resulting in cellular differentiation can be summarized as follows. 1) Cell populations can be synchronized, and homogeneous populations at each stage in the differentiation cycle can thus be obtained. 2) A specific technique has been developed whereby the progress of the differentiation cycle can be accurately measured by adsorption of labeled RNA phage or penetration of labeled phage DNA into specific cell forms. This technique can be used to select for mutants blocked in the various stages of morphogenesis. 3) Temperature-sensitive mutants of Caulobacter that are restricted in macromolecular synthesis and development at elevated temperatures have been isolated. 4) Genetic exchange in the Calflobacter genus has been demonstrated and is now being defined. Two questions related to control processes can now readily be approached experimentally. (i) Is the temporal progression of events occurring during bacterial differentiation controlled by regulator gene products? (ii) Is the differentiation cycle like a biosynthetic pathway where one event must follow another? The availability of temperature-sensitive mutants blocked at various stages of development permits access to both questions. An interesting feature of the differentiation cycle is that the polar organelle may represent a special segregated unit which is operative in the control of the differentiation process. Perhaps the sequential morphogenic changes exhibited by Caulobacter are dependent on the initial synthesis of this organelle. Because the ultimate expression of cell changes are dependent on selective protein synthesis, specific messenger RNA production-either from DNA present in an organelle or from the chromosome-may prove to be a controlling factor in cell differentiation. We have begun studies with RNA polymerase purified from Caulobacter crescentus to determine whether cell factors or alterations in the enzyme structure serve to change the specificity of transcription during the cell cycle. Control of sequential cell changes at the level of transcription has long been postulated and has recently been substantiated in the case of Bacillus sporulation (6). The Caulobacter bacteria now present another system in which direct analysis of these control mechanisms is feasible.

Asymmetric template function of microbial deoxyribonucleic acids: transcription of messenger ribonucleic acid

In Bacillus subtilis and Escherichia coli, pulse-labeled ribonucleic acid (RNA) synthesized during step-down growth hybridized preferentially with the heavy (H) strand of methylated albumin-Kieselguhr-fractionated deoxyribonucleic acid (DNA). At high RNA inputs, the ratio of RNA hybridized with the H strand to that hybridized with the light (L) strand was 8.7 for B. subtilis and 2.0 for E. coli. At high DNA inputs, the H/L hybridization ratio increased by a factor of two. This change in the hybridization ratio was attributable to the fraction of the pulse-labeled RNA which is in stable RNA components. The hybridization peak of pulse-labeled RNA was specifically located in the late-eluting region of the absorbance profile of the H strand. This region was considered to represent the most actively transcribing H strand templates.

Preferential transcription of Bacillus subtilis light deoxyribonucleic acid strands during sporulation

Messenger ribonucleic acid (RNA) from log and sporulation stages of growth were transcribed mainly from the heavy strand of the complementary strands of Bacillus subtilis deoxyribonucleic acid (DNA). During sporulation a slight transcription shift from heavy to light DNA strands was observed. RNA-DNA hybrid competition experiments revealed that this shift was due to sporulation-specific transcription from light-DNA strands.

Ribonucleic acid synthesis during microcyst formation in Myxococcus xanthus: characterization by deoxyribonucleic acid-ribonucleic acid hybridization

The technique of deoxyribonucleic acid-ribonucleic acid (RNA) hybridization was used to compare the RNA synthesized during vegetative growth and microcyst formation in Myxococcus xanthus. All classes of RNA, including ribosomal RNA, were synthesized during microcyst formation. The results indicate that the ribosomal RNA synthesized during microcyst formation was indistinguishable from that made during vegetative growth. Hybridization competition experiments demonstrated that certain messenger RNA species are synthesized only during vegetative growth, whereas others are synthesized only during microcyst formation. The synthesis of a new species of RNA polymerase does not appear to be responsible for differential transcription during morphogenesis in M. xanthus since the rifampicin sensitivity of transcription was conserved during microcyst formation.

Replacement sporulation of Bacillus subtilis 168 in a chemically defined medium

A replacement sporulation technique (i.e., the sporulation of vegetative cells upon suspension in an appropriate medium) has been developed for Bacillus subtilis 168 (a transformable Marburg strain of B. subtilis). The replacement sporulation medium used is composed of inorganic salts and 10 mm ammonium lactate or glutamate. The requirement for ammonium lactate or glutamate could also be satisfied by other compounds that are metabolized via the tricarboxylic acid cycle. Sporulation of the suspended vegetative cells was completed by 8 to 10 hr after suspension, and the resulting spores were indistinguishable from spores produced in a conventional growth and sporulation medium. Various physiological changes previously reported to be associated with sporulation (e.g., increase in the level of tricarboxylic acid cycle enzymes and changes in the rates of synthesis of deoxyribonucleic acid, ribonucleic acid, and protein) could also be demonstrated during replacement sporulation.

Relationship between protein and ribonucleic acid synthesis during outgrowth of spores of Bacillus cereus

The rate of protein and ribonucleic acid (RNA) synthesis was examined during the outgrowth of spores of Bacillus cereus T in a chemically defined medium. RNA synthesis started 2.5 min after the initiation of germination, and protein synthesis after 4 min. Addition of a complete amino acid supplement and uracil supported high rates of RNA and protein synthesis throughout outgrowth. To determine the relationship between the rate of protein (k) and RNA synthesis, the kinetics of formation of various classes of RNA were followed during outgrowth. Ribosomal RNA (rRNA) comprised a relatively constant fraction of the total RNA throughout outgrowth (71 to 78%). The classes of RNA synthesized during this period were determined by germinating spores in radioactive uracil and then at intervals following their stability to actinomycin D. Initially, labile RNA comprised the largest fraction of newly formed RNA (DeltaRNA), and this proportion decreased during outgrowth. The ratio of k/rRNA or k/Delta stable RNA varied considerably during outgrowth, whereas the ratio of k/labile RNA remained constant. The data suggest that the rate of protein synthesis is not rigidly coupled to either total or newly synthesized rRNA (ribosomes) during the early stages of outgrowth.

Analysis of sporulation mutants. I. Response of uracil incorporation to carbon sources, and other mutant properties

Mutants deficient in sporulation were isolated and characterized with respect to antibiotic and protease activity, transformability, growth, and sporulation. All but two mutants could grow on minimal medium containing glucose. The inability of most mutants to incorporate uracil into trichloroacetic acid-precipitable material (ribonucleic acid) during the developmental period, and their response to a number of carbon sources, were used to characterize their biochemical blocks. Reproducible measurements of these responses were possible when the pH of the culture, which changed during growth and greatly influenced the rate of uracil uptake, was adjusted to 6.5. By their response to ribose and glutamate, the sporulation mutants could then be divided into four groups. All mutants of the first three groups produced antibiotic activity against Staphylococcus aureus, whereas all mutants, except one, of the fourth group produced none or very little of this activity. Mutants which did not respond to glutamate belonged to the first three groups; they also grew slowly or not at all on glutamate as sole carbon source. One of these mutants lacked succinic dehydrogenase activity. The results indicate that most of our sporulation mutants are unable to produce or utilize a natural carbon precursor, which is normally used as a slowly available carbon and energy source via the Krebs cycle when other carbon sources are used up. It enters the Krebs cycle as a precursor of alpha-ketoglutarate, probably via acetylcoenzyme A. All mutants of group four are blocked in this pathway before alpha-ketoglutarate.

Satellite deoxyribonucleic acid from Bacillus cereus strain T

DNA isolated from exponentially growing cultures of Bacillus cereus T has a single component (density 1.696 g cm(-3)) in a cesium chloride density gradient whereas DNA isolated from spores shortly after the initiation of germination has two components: a major one (density 1.696 g cm(-3)) and a satellite (density, 1.725 g cm(-3)). The DNA of both components is doublestranded. By the first cell division there is no satellite DNA.

Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis

Doi, Roy H. (University of California, Davis), and Richard T. Igarashi. Heterogeneity of the conserved ribosomal ribonucleic acid sequences of Bacillus subtilis. J. Bacteriol. 92:88-96. 1966.-Hybrid formation was demonstrated between Bacillus subtilis ribosomal ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) from various bacterial species. The high degree of complementarity between B. subtilis ribosomal RNA and the DNA from B. cereus and B. stearothermophilus suggested a method to test whether the same RNA sequences were hybridizing with the DNA from these two species. Saturation studies with 16S and 23S RNA preparations from B. subtilis showed that a definite number of complementary sites was present in each DNA. Base composition analyses of the RNA in the hybrid demonstrated that ribosomal RNA sequences were involved. Hybrid competition studies revealed that B. stearothermophilus ribosomal RNA could compete totally against B. subtilis ribosomal RNA for B. stearothermophilus DNA, although it could compete only partially against the B. subtilis ribosomal RNA hybridizing with B. cereus DNA. These observations were made independently with both 16S and 23S ribosomal RNA preparations. These results revealed that different nucleotide sequences of B. subtilis ribosomal RNA were hybridizing with the DNA from B. cereus and B. stearothermophilus. Two possible interpretations of these results are: (i) different nucleotide sequences from a homogeneous ribosomal RNA population are hybridizing with heterologous DNA preparations, and (ii) ribosomal RNA cistrons are heterogeneous.

Morphogenesis in Trichoderma: suppression of photoinduction by 5-fluorouracil

Sporulation in the fungus Trichoderma viride is inducible with a short light pulse. 5-Fluorouracil applied prior to photoinduction and removed thereafter suppressed sporulation without greatly aflecting growth. This compound also halved the rate of incorporation of uracil-C(14) into RNA but did not change the ratio of uridylic to cytidylic acid. The effect of 5-fluorouracil was counteracted by uracil but not by thymidine. This supports the hypothesis that 5-fluorouracil affects RNA rather than DNA.

Isolation and characterization of ribosomes from Bacillus subtilis spores

Bishop, Helen L. (Syracuse University, Syracuse, N.Y.), and Roy H. Doi. Isolation and characterization of ribosomes from Bacillus subtilis spores. J. Bacteriol. 91:695-701. 1966.-The isolation of ribosomes from Bacillus subtilis spores was accomplished by freezing the spores in liquid nitrogen and grinding the spore pellet with an equal weight of levigated alumina. The ribosomes, which were adsorbed to the alumina, were freed by the addition of vegetative-cell ribosomes or bulk ribonucleic acid (RNA) to the crude alumina-ground extract. The spore ribosomes had sedimentation properties and RNA and protein compositions similar to those of vegetative-cell ribosomes. The difficulty encountered in obtaining spore ribosomes by ordinary extraction methods may be the result of nuclease and protease activities which were demonstrated in spore extracts.