New phage-SPO1-induced polypeptides associated with Bacillus subtilis RNA polymerase

What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase

This Reflections article is focused on the 5 years while I was a graduate student (1964-1969). During this period, I made some of the most significant discoveries of my career. I have written this article primarily for a protein biochemistry audience, my colleagues who shared this exciting time in science, and the many scientists over the last 50 years who have contributed to our knowledge of transcriptional machinery and their regulation. It is also written for today's graduate students, postdocs, and scientists who may not know much about the discoveries and technical advances that are now taken for granted, to show that even with methods primitive by today's standards, we were still able to make foundational advances. I also hope to provide a glimpse into how fortunate I was to be a graduate student over 50 years ago in the golden age of molecular biology.

Where to begin? Sigma factors and the selectivity of transcription initiation in bacteria

Transcription is the fundamental process that enables the expression of genetic information. DNA-directed RNA polymerase (RNAP) uses one strand of the DNA duplex as template to produce complementary RNA molecules that serve in translation (rRNA, tRNA), protein synthesis (mRNA) and regulation (sRNA). Although the RNAP core is catalytically competent for RNA synthesis, the selectivity of transcription initiation requires a sigma (σ) factor for promoter recognition and opening. Expression of alternative σ factors provides a powerful mechanism to control the expression of discrete sets of genes (a σ regulon) in response to specific nutritional, developmental or stress-related signals. Here, I review the key insights that led to the original discovery of σ factor 50 years ago and the subsequent discovery of alternative σ factors as a ubiquitous mechanism of bacterial gene regulation. These studies form a prelude to the more recent, genomics-enabled insights into the vast diversity of σ factors in bacteria.

Bacillus subtilis RNA polymerase and its modification in sporulating and phage-infected bacteria

Bacillus subtilis RNA polymerase holoenzyme consists of the subunits beta', beta, sigma, alpha, delta, and omega. In sporulating bacteria and in bacteria infected with phages SP01 and SP82, this enzyme undergoes changes in subunit composition and transcriptional specificity that could play a regulatory role in gene transcription. Sporulating bacteria may contain a specific component that inhibits the activity of the sigma subunit of polymerase probably by interfering with the binding of sigma-polypeptide to core enzyme. The hypothetical inhibitor may be metabolically unstable, since its activity is rapidly depleted from sporulating cells in the presence of chloramphenicol. Inhibition of sigma-polypeptide activity may restrict the transcription of phage DNA an infected sporulating cells. Although lacking the sigma-subunit, RNA polymerase purified from sporulating cells contains sporulation-specific subunits of 85,000 and 27,000 daltons. In SP01-infected bacteria, the sigma-subunit is replaced by phage-induced subunits. Purified enzyme containing the protein product of SP01 regulatory gene 28 directs the transcription of phage middle genes in vitro, while enzyme containing phage-induced polypeptides V and VI preferentially copies late genes. Accurate transcription of middle and late genes in vitro requires the host delta-subunit of polymerase (or high ionic strength) but not sigma-subunit. Phage PBS2 induces an entirely new multisubunit RNA polymerase that specifically transcribes PBS2 DNA in vitro. This enzyme is synthesized de novo after infection and does not arise by modification of the B. subtilis holoenzyme.

Disassociation of sigma subunit from RNA polymerase of Xanthomonas oryzae pv. oryzae by phage Xp10 infection

The sigma subunit of Xanthomonas oryzae pv. oryzae is disassociated from host RNA polymerase after phage Xp10 infection. To clarify the possible mechanism for this observation, sigma subunit was purified and an antiserum against sigma subunit was prepared. Immunoprecipitation of RNA polymerase by the anti-core RNA polymerase antiserum, followed by immunoblotting with anti-sigma subunit antibody, revealed that sigma subunit was lost from RNA polymerase within 10 minutes after Xp10 infection. Loss of sigma subunit was not observed under other stress conditions including heat and cold stress, starvation and growth to stationary phase. Two-dimensional immunoblotting analysis did not reveal any covalent modification of either sigma subunit or RNA polymerase after Xp10 infection. These results suggest that separation of th subunit from RNA polymerase may be due to competition with other binding factors.

The sigma factors of Bacillus subtilis

The specificity of DNA-dependent RNA polymerase for target promotes is largely due to the replaceable sigma subunit that it carries. Multiple sigma proteins, each conferring a unique promoter preference on RNA polymerase, are likely to be present in all bacteria; however, their abundance and diversity have been best characterized in Bacillus subtilis, the bacterium in which multiple sigma factors were first discovered. The 10 sigma factors thus far identified in B. subtilis directly contribute to the bacterium's ability to control gene expression. These proteins are not merely necessary for the expression of those operons whose promoters they recognize; in many instances, their appearance within the cell is sufficient to activate these operons. This review describes the discovery of each of the known B. subtilis sigma factors, their characteristics, the regulons they direct, and the complex restrictions placed on their synthesis and activities. These controls include the anticipated transcriptional regulation that modulates the expression of the sigma factor structural genes but, in the case of several of the B. subtilis sigma factors, go beyond this, adding novel posttranslational restraints on sigma factor activity. Two of the sigma factors (sigma E and sigma K) are, for example, synthesized as inactive precursor proteins. Their activities are kept in check by "pro-protein" sequences which are cleaved from the precursor molecules in response to intercellular cues. Other sigma factors (sigma B, sigma F, and sigma G) are inhibited by "anti-sigma factor" proteins that sequester them into complexes which block their ability to form RNA polymerase holoenzymes. The anti-sigma factors are, in turn, opposed by additional proteins which participate in the sigma factors' release. The devices used to control sigma factor activity in B, subtilis may prove to be as widespread as multiple sigma factors themselves, providing ways of coupling sigma factor activation to environmental or physiological signals that cannot be readily joined to other regulatory mechanisms.

Kinetic study of alterations in the host RNA polymerase and protein synthesis during phage Xp 10 infection

We monitored the compositional change of host RNA polymerase in Xp 10 infected cells by one-step immunoprecipitation with core enzyme-specific antiserum. Results showed a rapid loss of sigma subunit from the RNA polymerase complex by 3 min after infection. In addition, some putative binding proteins were reduced to various extents. In contrast, increasing levels of several other polypeptides were detected. The de novo host protein synthesis was inhibited within 1 min after Xp 10 infection. On the other hand, a sequential expression of phage specific proteins was found and can be categorized as early, middle, and late stage. The alteration of host RNA polymerase and the shutdown of early class proteins took place in parallel.

In vitro synthesis of late bacteriophage phi 29 RNA

A crude P-100 fraction prepared from Bacillus subtilis 21 min after infection with wild-type phage phi 29 supported the in vitro synthesis of late phi 29 RNA by added RNA polymerase. Synthesis of late RNA was also detected when purified phi 29 DNA was transcribed by RNA polymerase in the presence of an S-150 fraction obtained by lysis of phi 29-infected cells in the presence of 1 M NaCl. Late phi 29 RNA was not synthesized when either the P-100 or the S-150 fraction was prepared from cultures infected with phi 29 having a mutation in gene 4.

Purification and DNA-binding properties of RNA polymerase from Bacillus subtilis

Four RNA-polymerizing activities having different subunit composition can be purified from uninfected and from SPO1-infected Bacillus subtilis. Lysozyme and sodium deoxycholate are used for lysing the cells. Polymin P is used for precipitating nucleic acids and DEAE-cellulose chromatography allows separation of enzymatic activity from the residual Polymin P. After these common steps, one can purify core + sigma + delta by chromatography on single-stranded DNA-agarose followed by gel filtration while pure core + sigma can be obtained by chromatography on double-stranded DNA cellulose. Core + delta is obtained by high-salt sucrose/glycerol gradient centrifugation. The host enzyme modified by the product of gene 28 of phage SPO1 can be purified from SPO1 infected cells by chromatography on DNA cellulose (or CNA agarose) followed by chromatography on phosphocellulose. The pH and salt dependance of the initial rate of RNA synthesis of core + sigma has been investigated using SPO1 and SPP1 DNA as templates. The optimum pH for the initial rate of transcription is 8.2 at 30 degrees C in 50 mM N,N-bis(2-hydroxyethyl)glycine buffer, and the optimum Na+ concentration is between 0.1 and 0.15 M. The kinetics of formation and of dissociation of non-filterable complexes between SPP1 DNA and core + sigma have been analyzed at different cationic concentrations. The value of the rate constant of dissociation in 0.1 M NaCl at 30 degrees C is kd = 2.16 x 10(-4) S-1. The value of the rate constant of association, under the same conditions, is ka = 5.5 x 10(8) M-1 S-1; this value is compatible with a diffusion-controlled reaction for promoter selection.

regA protein of bacteriophage T4D: identification, schedule of synthesis, and autogenous regulation

Proteins labeled with 14C-amino acids after infection of Escherichia coli B by T4 phage were examined by electrophoresis in the presence of sodium dodecyl sulfate. Four regA mutants (regA1, regA8, regA11, and regA15) failed to make a protein having a molecular weight of about 12,000, whereas mutant regA9 did make such a protein; regA15 produced a new, apparently smaller protein that was presumably a nonsense fragment, whereas regA11 produced a new, apparently larger protein. We conclude that the 12,000-dalton protein was the product of the regA gene. The molecular weight assignment rested primarily on our finding that the regA protein had the same mobility as the T4 gene 33 protein, which we identified by electrophoresis of whole-cell extracts of E. coli B infected with a gene 33 mutant, amE1120. Synthesis of wild-type regA protein occurred from about 3 to 11 min after infection at 37 degrees C in the DNA+ state and extended to about 20 min in the DNA- state. However, synthesis of the altered regA proteins of regA9, regA11, and regA15 occurred at a higher rate and for a much longer period in both the DNA+ and DNA- states; thus, the regA gene is autogenously regulated. At 30 degrees C, both regA9 and regA11 exhibited partial regA function by eventually shutting off the synthesis of many T4 early proteins; the specificity of this shutoff differed between these two mutants. We also obtained evidence that the regA protein is not Stevens's "polypeptide 3." As a technical point, we found that, when quantitating acid-precipitable radioactivity in protein samples containing sodium dodecyl sulfate, it was necessary to use 15 to 20% trichloroacetic acid; use of 5% acid, e.g., resulted in loss of over half of the labeled protein.

Bacillus subtilis bacteriophages SP82, SPO1, and phie: a comparison of DNAs and of peptides synthesized during infection

The genomes of Bacillus subtilis phages phie, SPO1, and SP82 were compared by DNA-DNA hybridization, analysis of DNA fragments produced by digestion with restriction endonucleases, comparison of the arrays of peptides synthesized during infection, and phage neutralization. DNA-DNA hybridization experiments indicated that about 78% of the SP82 DNA was homologous with SPO1 DNA, whereas 40% of the phie DNA was homologous to either SPO1 or SP82 DNA. Agarose gel electrophoresis was used to compare the molecular weights of DNA fragments produced by cleavage of SP82, SPO1, and phie DNAs with the restriction endonucleases Hae III, Sal I, Hpa II, and Hha I. Digestion of the DNAs with Hae III and Sal I produced only a few fragments, whereas digestion with Hpa II and Hha I yielded 29 to 40 fragments, depending on the DNA and the enzyme. Comparing the Hpa II fragments, 51% of the SP82 fragments had mobilities which matched those of SPO1 fragments, 32% of the SP82 fragments matched the phie fragments, and 34% of the SPO1 fragments matched the phie fragments. Comparing the Hha I digestion products, 62% of the SP82 fragments had mobilities matching the SPO1 fragments, 24% of the SP82 fragments matched the phie fragments, and 22% of the SPO1 fragments matched the phie fragments. Analysis of peptides by electrophoresis on one-dimensional sodium dodecyl sulfate-polyacrylamide slab gels showed that approximately 70 phage-specific peptides were synthesized in the first 24 min of each infection. With mobility and the intervals of synthesis as criteria, 66% of the different SP82 peptides matched the SPO1 peptides, 34% of the SP82 peptides matched the phie peptides, and 37% of the SPO1 peptides matched the phie peptides. Phage neutralization assays using antiserum to SP82 yielded K values of 510 for SP82, 240 for SPO1, and 120 for phie.

Bacteriophage SPO1 development: defects in a gene 31 mutant

SPO1 temperature-sensitive mutant ts14-1, located in cistron 31, has a DD (DNA synthesis-delayed) phenotype at 37 degrees C and produces progeny in a stretched program. At 44 degrees C it behaves as a DO (DNA synthesis-defective) mutant and shuts off the viral RNA synthesis about 10 min after infection. The thermal sensitivity of this mutant is due to the inactivity of gp-31 (the product of gene 31) at 44 degrees C. However, gp-31 is synthesized at that temperature and partly recovers its activity at 37 degrees C. Only 5 min at the permissive temperature is enough to trigger the continuation of the phage program and to produce progeny. The partial defect at 37 degrees C and the expansion of the middle program together with the pleiotropic defects at the nonpermissive temperature could be suitable for the study of the controls involved in bacteriophage development.

Translation of RNAs synthesized in vivo and in vitro from bacteriophage SP82 DNA

The synthesis of 69 phage-specific polypeptides during the infection of Bacillus subtilis with bacteriophage SP82 was detected by pulse-labeling, one-dimensional electrophoresis, and autoradiography. SP82 virions were found to contain approximately 22 polypeptides, most of which were synthesized late in infection; evidence was obtained for the processing of the major virion protein. RNAs extracted at different times during infection were translated by using an Escherichia coli cell-free extract. Only smaller-molecular-weight peptides were produced efficiently in vitro; in the 9,000- to 60,000-molecular-weight range, 50 to 60% of the peptides synthesized in vivo were produced by translation of RNAs extracted from infected cells. Eight of the virion peptides were produced by in vitro translation of RNAs extracted from infected cells. RNAs were synthesized under defined conditions by RNA polymerase extracted from uninfected B. subtilis and by polymerases isolated from cells 8 and 20 min after infection with SP82. Translation of these RNAs yielded characteristic and different patterns of polypeptides. Nine of the 12 polypeptides produced by translation of RNAs synthesized by the host polymerase corresponded in mobility to peptides appearing in vivo in the 0 to 3 and 3 to 6 min intervals of pulse-labeling after infection; 12 of the 25 peptides synthesized from RNAs produced by polymerase extracted 8 min after infection corresponded in mobility to peptides detected in vivo 8 min after infection, and 15 of the 22 peptides directed by RNAs made by the polymerase isolated 20 min after infection corresponded to peptides present in vivo late in infection. Five of the peptides produced in vitro from the latter RNA corresponded to virion peptides.

Lipiarmycin-resistant ribonucleic acid polymerase mutants of Bacillus subtilis

Lipiarmycin inhibited the activity of deoxyribonucleic acid-dependent ribonucleic acid (RNA) polymerase in vitro. We showed that inhibition was due to interference by lipiarmycin with the activity of sigma-containing molecules of RNA polymerase. Transcription by core enzyme was relatively resistant to the drug, but addition of sigma led to highly drug-sensitive RNA synthesis. We isolated lipiarmycin-resistant mutants of Bacillus subtilis and characterized them genetically and biochemically. Drug-resistant mutants contained an altered RNA polymerase that was resistant to the drug in vitro. By separation and mixed reconstitution of core and sigma fractions of mutant and wild-type RNA polymerase, we showed that lipiarmycin resistance in one mutant strain was a property of the core fraction. Genetic mapping experiments indicated that at least two lpm mutants are located between loci determining rifampin resistance and streptolydigin resistance.

Transcription of the genome of bacteriophage phi 29: isolation and mapping of the major early mRNA synthesized in vivo and in vitro

The phi29 early mRNA's synthesized in infected Bacillus subtilis were studied by using sedimentation velocity analysis, polyacrylamide gel electrophoresis, and hybridization of phi29 DNA fragments generated by the restriction endonuclease Eco RI. Viral RNAs synthesized in vivo in the resence of chloramphenicol were found to hybridize to Eco RI-A, -C, and -D fragments, but not to Eco RI-B and -E fragments, of the viral genome. Major early mRNA sedimenting as 16S material in neutral sucrose gradients was examined in detail. Radioactive phi29 RNA, purified by sucrose gradient centrifugation, was hybridized to either the Eco RI-A or Eco RI-C DNA fragment. The RNA was eluted from the hybrids and then tested for complementary hybrid formation with Eco RI-A and -C fragments. RNA eluted from the Eco RI-A fragment annealed only to the Eco RI-A fragment and not to the Eco RI-C fragment. Similarly, RNA eluted from the Eco RI-C fragment hybridized to the Eco RI-C and -D fragments. Viral RNAs synthesized in vitro using B. subtilis RNA polymerase hybridized to both Eco RI-A and -C DNA fragments. Furthermore, RNA initiated with [gamma-(32)P]GTP also hybridized to both Eco RI-A and -C fragments. These results indicate that there are at least two efficient promotors for early transcription on the phi29 chromosome. In addition, a low-molecular-weight RNA initiated with [gamma-(32)P]ATP was found to hybridize exclusively with the Eco RI-A fragment. Kinetic studies of phi29 mRNA synthesis during the lytic cycle have shown that viral RNAs hybridizable to the Eco RI-A and -C fragments are synthesized immediately after phage infection. On the other hand, mRNA specific for the Eco RI-B fragment was not synthesized for several minutes after phage infection. Based on the results of the in vivo and in vitro transcription studies, a transcription map of the phi29 chromosome is proposed.

Bacteriophages of Bacillus subtilis

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Conversion of Bacillus subtilis RNA polymerase activity in vitro by a protein induced by phage SP01

A protein fraction from B. subtilis infected with phage SP01 (fraction LGG) stimulates the activity of RNA polymerase (EC 2.7.7.6; nucleosidetriphosphate:RNA nucleotidyltransferase) core from uninfected bacteria. Fraction LGG contains a protein (P-28, molecular weight 28,000) that is labeled after phage infection and binds tightly to RNA polymerase core at a relatively high ionic strength. B. subtilis RNA polymerase core with bound P-28 has the transcription specificity of the previously purified, phage-modified B-P RNA polymerase; the latter contains two subunits, v-28 and v-13 (molecular weights 28,000 and 13,000, respectively) that are synthesized after phage infection. Both enzymes transcribe SP01 DNA preferentially and direct the asymmetric synthesis of viral middle RNA. P-28, like v-28, binds more tightly to B. subtilis RNA polymerase core than the B. subtilis initiation factor, sigma, at higher ionic strength. We propose that P-28 and v-28 are the same protein. P-28 and, by implication, v-28 suffice to endow the bacterial RNA polymerase core with a novel transcription specificity.

Bacteriophage SPO1-induced macromolecular synthesis in minicells of Bacillus subtilis

SPO1 bacteriophage injects its DNA into minicells produced by Bacillus subtilis CU403 divIVB1. The injected DNA is partially degraded to small trichloracetic acid-precipitable material and trichloroacetic acid-soluble material. The injected DNA is not replicated; however, it serves as a template for RNA and protein synthesis. The RNA produced specifically hybridizes to SPO1 DNA, and the amount of RNA hybridized can be reduced by competition with RNA isolated at all stages of the phage cycle from infected nucleate cells of the B. subtilis CU403 divIVB1. An unrelated phage, SPP1, also induces phage-specific RNA in infected minicells. Translation occurs in SPO1-infected minicells resulting in at least eight proteins which have been separated by gel electrophoresis, and two of these proteins have mobilities similar to proteins found only in infected B. subtilis CU403 divIVB1 nucleate cells. A large proportion of the polypeptide material synthesized in infected minicells is very small and heterogeneous in size.

DNA strand specificity of transcripts produced in vivo and in vitro by RNA polymerase from SP82-infected Bacillus subtilis

Phage-specific RNA synthesized early in the infection of Bacillus subtilis with SP82 hybridizes to both heavy (H) and light (L) strands of SP82 DNA nearly equally. Phage RNA synthesized during the middle of the infection hybridizes preferentially to the H strand. The ratio of H/L strand binding of RNAs synthesized in vitro by RNA polymerases isolated from uninfected and infected cells resembles the ratios of early and middle phage RNA classes, respectively. This supports the conclusion that a modified RNA polymerase is required for the transcription of middle RNA classes.

Highly asymmetric transcription by RNA polymerase containing phage-SP01-induced polypeptides and a new host protein

An RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) has been purified from phage-SP01-infected Bacillus subtilis that copies RNA almost exclusively from the heavy strand of native SP01 DNA, the DNA strand from which "middle" and "late" classes of RNA are copied in vivo. Hybridization-competition established that this RNA polymerase termed enzyme A, preferentially synthesizes middle RNA in vitro. Enzyme A contains beta',beta, alpha, and two newly identified host polypeptides, variation of (21,500 daltons) and omega (11,000 daltons). All of these polypeptides are associated with highly purified RNA polymerase from uninfected bacteria. In addition, enzyme A contains phage-induced subunits of 26,000, 24,000, and 13,500 daltons. Enzyme A lacks sigma polypeptide, and strand-selective transcription by this enzyme is resistant to anti-sigma antibody. A reconstitution experiment strongly suggests that the host variation of protein is required in addition to a phage-induced subunit(s) (or an unidentified phage-induced modification) for strand-selective transcription of SP01 middle genes in vitro.

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 .