Effects of the transciption inhibitory protein, TF1, on phage SP01 promoter complex formation and stability

Some properties of HU are modified after the infection of Escherichia coli by bacteriophage T4

Escherichia coli HU, an abundant, nucleoid-associated, DNA-binding protein, plays a role in several biological processes including DNA replication. Many other bacteria have well-conserved HU homologs, and there are several more-distantly related members of the family, including TF1, encoded by Bacillus subtilis phage SPO1. We have asked whether coliphage T4, like SPO1, encodes an HU homolog or whether it alters the properties of host HU. We have been unable to detect a T4-specified HU homolog, but we have shown that E. coli HU extracted from phage-infected cells differs in some properties from that extracted from uninfected cells. First, HU from uninfected cells inhibits a reconstituted T4 DNA replication system, whereas HU from infected cells does not. Second, HU from infected cells appears to bind a T4-encoded polypeptide, as shown by coimmunoprecipitation. We propose that such binding alters HU function in T4-infected cells.

Effects of mutations at amino acid 61 in the arm of TF1 on its DNA-binding properties

Transcription factor 1 (TF1) is the Bacillus subtilis phage SPO1-encoded member of the family of bacterial DNA-binding proteins that includes Escherichia coli HU and integration host factor (IHF). We have initiated a mutational analysis of the TF1 molecule to understand better its unique DNA-binding properties and to investigate its physiological function. We report here the consequences of mutating the putative DNA-binding "arms" of TF1. At position 61 in its primary sequence, TF1 contains a Phe residue in place of the Arg residue found in all other known members of the HU family. Substituting polar, uncharged residues for Phe61 substantially reduced the DNA-binding affinity and site-selectivity of TF1 in vitro, whereas the substitution of Tyr had no effect. Substituting Trp or Arg for Phe61 had little effect on the affinity of TF1 for SPO1 DNA, but altered the electrophoretic mobilities of protein-DNA complexes in non-denaturing gels. The Arg61 substitution increased the affinity of the protein for non-specific sites on thymine-containing DNA, thus reducing the natural preference of TF1 for (5-hydroxymethyluracil)-containing DNA. The Phe61-to-Arg mutation was also correlated with decreased phage yield and aberrant regulation of viral protein synthesis in vivo.

Construction and properties of a temperature-sensitive mutation in the gene for the bacteriophage SPO1 DNA-binding protein TF1

The Bacillus subtilis bacteriophage SPO1 encodes the DNA-binding protein TF1, a homolog of the ubiquitous type II DNA-binding proteins that are components of bacterial chromatin. The known three-dimensional structure of a related protein was used in devising a scheme of site-directed mutagenesis that led to the creation of a temperature-sensitive mutation in the TF1 gene. At the nonpermissive temperature, this mutation disrupted the temporal regulation of viral protein synthesis and processing, altered the kinetics of accumulation of at least one viral transcript, and prohibited the production of infective progeny phage. We suggest that TF1 function is required to shut off the expression of several early-middle and middle viral genes and that TF1 plays a role in phage head morphogenesis. Spontaneous second-site mutations of the temperature-sensitive mutant TF1 allele that suppressed its associated phenotypes were analyzed. These suppressor mutations conferred greater amino acid sequence homology with the type II DNA-binding protein from the thermophile Bacillus stearothermophilus.

TF1, the bacteriophage SPO1-encoded type II DNA-binding protein, is essential for viral multiplication

The lytic Bacillus subtilis bacteriophage SPO1 encodes an abundant, 99-amino-acid type II DNA-binding protein, transcription factor 1 (TF1). TF1 is special in this family of procaryotic chromatin-forming proteins in its preference for hydroxymethyluracil-containing DNA, such as SPO1 DNA, and in binding with high affinity to specific sites in the SPO1 chromosome. We constructed recessive null alleles of the TF1 gene and introduced them into SPO1 chromosomes. Segregation analysis with partially diploid phage heterozygous for TF1 showed that phage bearing only these null alleles was inviable. Deletion of the nine C-proximal amino acids of TF1 prohibited phage multiplication in vivo and abolished its site-specific DNA-binding activity in vitro.

Immunochemical localization of myosin heavy chain isoforms and paramyosin in developmentally and structurally diverse muscle cell types of the nematode Caenorhabditis elegans

The nematode Caenorhabditis elegans contains two major groups of muscle cells that exhibit organized sarcomeres: the body wall and pharyngeal muscles. Several additional groups of muscle cells of more limited mass and spatial distribution include the vulval muscles of hermaphrodites, the male sex muscles, the anal-intestinal muscles, and the gonadal sheath of the hermaphrodite. These muscle groups do not exhibit sarcomeres and therefore may be considered smooth. Each muscle cell has been shown to have a specific origin in embryonic cell lineages and differentiation, either embryonically or postembryonically (Sulston, J. E., and H. R. Horvitz. 1977. Dev. Biol. 56:110-156; Sulston, J. E., E. Schierenberg, J. White, and J. N. Thomson. 1983. Dev. Biol. 100:64-119). Each muscle type exhibits a unique combination of lineage and onset of differentiation at the cellular level. Biochemically characterized monoclonal antibodies to myosin heavy chains A, B, C, and D and to paramyosin have been used in immunochemical localization experiments. Paramyosin is detected by immunofluorescence in all muscle cells. Myosin heavy chains C and D are limited to the pharyngeal muscle cells, whereas myosin heavy chains A and B are localized not only within the sarcomeres of body wall muscle cells, as reported previously, but to the smooth muscle cells of the minor groups as well. Myosin heavy chains A and B and paramyosin proteins appear to be compatible with functionally and structurally distinct muscle cell types that arise by multiple developmental pathways.

Cloning and mapping of the SPO1 genome

Many of the XbaI, EcoRI, KpnI, and BglII fragments of bacteriophage SPO1, accounting for about 65% of the genomic sequences, were cloned in Bacillus subtilis. Four of the EcoRI fragments were specifically refractory to cloning in both Escherichia coli and B. subtilis, probably because of expression of deleterious genes carried on the SPO1 fragments. To permit complete identification of the regions cloned, the SPO1 restriction map has been extended to include the XbaI fragments and the previously unmapped KpnI fragments. Markers for 26 of the 39 known genes have been located on specific cloned fragments, permitting more precise determination of the positions of most of the genes. One cloned SPO1 fragment was inhibitory to SPO1 development.

Autorepressor properties of the pi-initiation protein encoded by plasmid R6K

A DNA fusion containing the promoter of the pir gene of plasmid R6K that encodes for the pi-initiation protein and the beta-galactosidase gene of Escherichia coli (lacZ) is described. The synthesis of beta-galactosidase promoted by this pir-lac fusion was almost completely inhibited when an R6K sequence containing the pir gene was provided in trans in E. coli. Transcription in vitro from the pir promoter but not the trp promoter of E. coli, was inhibited by purified pi protein indicating that the pi protein alone is responsible for repression of its own gene and that the effect is promoter specific. The DNA-protein interaction sites in the pir regulatory region have been determined for the pi protein and E. coli RNA polymerase using the DNase I protection method. The binding sites for these two proteins overlap for three helical turns. Competition DNA binding experiments show that the pi protein will displace bound RNA polymerase. From these studies we conclude that repression of the pir gene is accomplished by binding of the pi protein and this association blocks access of RNA polymerase to the pir promoter region.

Sequence of the bacteriophage SP01 gene coding for transcription factor 1, a viral homologue of the bacterial type II DNA-binding proteins

The Bacillus subtilis phage SP01, whose DNA contains 5-hydroxymethyluracil (hmUra) in place of thymine, codes for an abundant, small, basic protein called TF1. TF1 binds preferentially to hydroxymethyluracil-containing DNA and thereby selectively inhibits transcription of such DNA in vitro. The gene for TF1 has been sequenced. We find that this viral protein is a homologue of the ubiquitous bacterial type II DNA-binding proteins. The three-dimensional structure of one of these bacterial proteins has recently been determined. We are able to discern common as well as distinctive features in the amino acid sequence and the three-dimensional structure of the homologous viral protein.

Gel electrophoretic separation of transcription complexes: an assay for RNA polymerase selectivity and a method for promoter mapping

We describe a method for analyzing ternary transcription complexes, of RNA polymerase, DNA and nascent RNA32 chains, by agarose gel electrophoresis. When the RNA of such complexes is 32P-labelled, a simple comparison of the DNA fluorogram with an autoradiogram identifies transcriptionally active DNA molecules and restriction fragments in any mixture. Two limitations on the method are described: 1) retardation during electrophoresis of polymerase-DNA complexes relative to their conjugate bare NA fragments; 2) failure of very large ternary complexes to enter gels. The following potential applications of the method are surveyed: transcription unit (elongation) mapping, separation of RNA molecules in a mixture of transcripts, dinucleotide primer mapping and identification of preferred template conformations.