Identification of phage SP01 proteins coded by regulatory genes 33 and 34

Phage_UniR_LGBM: Phage Virion Proteins Classification with UniRep Features and LightGBM Model

Phage, the most prevalent creature on the planet, serves a variety of critical roles. Phage's primary role is to facilitate gene-to-gene communication. The phage proteins can be defined as the virion proteins and the nonvirion ones. Nowadays, experimental identification is a difficult process that necessitates a significant amount of laboratory time and expense. Considering such situation, it is critical to design practical calculating techniques and develop well-performance tools. In this work, the Phage_UniR_LGBM has been proposed to classify the virion proteins. In detailed, such model utilizes the UniRep as the feature and the LightGBM algorithm as the classification model. And then, the training data train the model, and the testing data test the model with the cross-validation. The Phage_UniR_LGBM was compared with the several state-of-the-art features and classification algorithms. The performances of the Phage_UniR_LGBM are 88.51% in Sp,89.89% in Sn, 89.18% in Acc, 0.7873 in MCC, and 0.8925 in F1 score.

Small things considered: the small accessory subunits of RNA polymerase in Gram-positive bacteria

The DNA-dependent RNA polymerase core enzyme in Gram-positive bacteria consists of seven subunits. Whilst four of them (α2ββ(')) are essential, three smaller subunits, δ, ε and ω (∼9-21.5 kDa), are considered accessory. Both δ and ω have been viewed as integral components of RNAP for several decades; however, ε has only recently been described. Functionally these three small subunits carry out a variety of tasks, imparting important, supportive effects on the transcriptional process of Gram-positive bacteria. While ω is thought to have a wide range of roles, reaching from maintaining structural integrity of RNAP to σ factor recruitment, the only suggested function for ε thus far is in protecting cells from phage infection. The third subunit, δ, has been shown to have distinct influences in maintaining transcriptional specificity, and thus has a key role in cellular fitness. Collectively, all three accessory subunits, although dispensable under laboratory conditions, are often thought to be crucial for proper RNAP function. Herein we provide an overview of the available literature on each subunit, summarizing landmark findings that have deepened our understanding of these proteins and their function, and outline future challenges in understanding the role of these small subunits in the transcriptional process.

Without a license, or accidents waiting to happen

This is a memoir of circumstances that have shaped my life as a scientist, some of the questions that have excited my interest, and some of the people with whom I have shared that pursuit. I was introduced to transcription soon after the discovery of RNA polymerase and have been fascinated by questions relating to gene regulation since that time. My account touches on early experiments dealing with the ability of RNA polymerase to selectively transcribe its DNA template. Temporal programs of transcription that control the multiplication cycles of viruses (phages) and the precise mechanisms generating this regulation have been a continuing source of fascination and new challenges. A longtime interest in eukaryotic RNA polymerase III has centered on yeast and on the enumeration and properties of its transcription initiation factors, the architecture of its promoter complexes, and the mechanism of transcriptional initiation. These areas of research are widely regarded as separate, but to my thinking they have posed similar questions, and I have been unwilling or unable to abandon either one for the other. An additional interest in archaeal transcription can be seen as stemming naturally from this point of view.

Genetic analysis of nonhistone chromosomal protein inheritance in recombinant inbred mouse strains using two-dimensional electrophoresis

Analysis of hepatic nonhistone chromosomal protein (NHCP) expression in male mice from progenitor strains (C3H/HeN, C57BL/6N), their F1 hybrid (B6C3), and seven recombinant inbred strains (RIs) (B6N x C3N) by high-resolution two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) detected 16 NHCPs whose expression in RIs could be correlated to each other and with strain distribution patterns (SDP) of 20 genetic markers differing in the progenitors. Of the 400+ NHCP spots detected in RI 2D-PAGE maps, 172 were common to progenitors and all RIs. There was a characteristic absence of five NHCPs in one RI, Y. Ten C3H-specific and six C57-specific NHCP inherited in B6C3 also appeared in RIs. The SDP of C3H-specific NHCP 2 matched the SDP of beta-glucuronidase on chromosome 5 and carbonic anhydrase on chromosome 3, and C57-specific NHCP 5 SDP corresponded to that for nonagouti trait on chromosome 2. These 16 NHCP genetic marker inheritance differences detected in RIs add to the 23 previously established genetic marker differences between the progenitors.

Bacillus subtilis mutant allele sup-3 causes lysine insertion at ochre codons: use of sup-3 in studies of translational attenuation

The mutation sup-3 in Bacillus subtilis suppresses ochre (TAA) mutations at each of three codons in the 5' end of the cat-86 coding sequence. The suppressor is shown to insert lysine at ochre codons. The efficiency of suppression by sup-3 is about 15%, as determined by changing a cat-86 Lys codon (codon 12) to an ochre codon and measuring the level of CAT in the suppressor-containing strain. The results obtained are discussed in light of previous observations that ochre mutations at cat leader codons 2 and 3 can be phenotypically suppressed by sup-3, whereas ochre mutations at leader codons 4 and 5 cannot. Translation of the cat leader is essential to inducible expression of cat. Our data support the interpretation that the nature of amino acids 2 through 5 of the leader peptide contributes to determining whether chloramphenicol can stall a ribosome in the leader, which in turn leads to induction of cat expression.

Gene encoding the sigma 37 species of RNA polymerase sigma factor from Bacillus subtilis

sigma 37 is a minor species of RNA polymerase sigma factor found in the Gram-positive bacterium Bacillus subtilis. sigma 37 governs the transcription in vitro of genes that are turned on at an early stage in spore formation, as well as other genes that are switched on at the end of the exponential phase of growth but that are not under sporulation control. To study the role of sigma 37 in B. subtilis gene expression, we have cloned the gene for this minor species of sigma factor in Escherichia coli by using as a hybridization probe a synthetic oligonucleotide that was designed on the basis of the NH2-terminal amino acid sequence of sigma 37 protein. We determined the nucleotide sequence of the entire sigma 37 gene, which was found to encode a 262-amino acid residue polypeptide of 29.9 kDa. The predicted amino acid sequence of sigma 37 showed significant homology to that of other sigma proteins in a region that has been proposed to be the site of binding of these factors to core RNA polymerase. Genetic mapping experiments placed the gene for sigma 37, herein designated sigB, at 40 degrees on the genetic map of Piggot and Hoch [Piggot, P. & Hoch, J. A. (1985) Microbiol. Rev. 49, 158-179]. An insertion mutation was constructed in sigB and found not to impair growth or sporulation.

Transcription of Bacillis subtilis plasmid pBD64 and expression of bacteriophage SPO1 genes cloned therein

Plasmid pBD64, a vector which is useful for cloning in Bacillis subtilis (T. J. Gryczan, A. G. Shivakumar, and D. Dubnau (1980), J. Bacteriol. 141, 246-253), has at least three substantial transcription units. Two of these include the single EcoRI, XbaI, and BamHI sites, while the other includes the single BglII site. Each of these transcripts was synthesized in the counterclockwise direction, relative to the pBD64 restriction map. No transcripts were detected in the opposite direction. Infection by bacteriophage SPO1 caused a substantial decrease in each of these transcripts. No new pBD64 transcripts were detected during SPO1 infection. Various SPO1 genes, cloned at several of these pBD64 sites, were tested for expression by observing their capacity to complement SPO1 mutants. Several middle and late genes were expressed substantially, regardless of the orientation in which the fragments were inserted. Since transcription from the vector could cause expression only in one orientation, this argues that the necessary transcription originated at SPO1 promoters, and, thus, that SPO1 middle and late promoters can be active in thymine-containing DNA.

Bacteriophage SPO1 genes 33 and 34. Location and primary structure of genes encoding regulatory subunits of Bacillus subtilis RNA polymerase

Bacteriophage SPO1 gene 33 and 34 products are required for SPO1 late gene transcription. Both proteins bind to the core RNA polymerase of the Bacillus subtilis host to direct the recognition of SPO1 late gene promoters, whose sequences differ from those of SPO1 early and middle gene promoters. We have located and cloned the genes for these two regulatory proteins, and have engineered their expression in Escherichia coli by placing them under the control of the bacteriophage lambda PL promoter. Nucleotide sequence analysis indicated that genes 33 and 34 overlap by 4 base-pairs and encode highly charged, slightly basic proteins of molecular weight 11,902 and 23,677, respectively.

Defining a bacteriophage T4 late promoter: bacteriophage T4 gene 55 protein suffices for directing late promoter recognition

The RNA polymerase from bacteriophage T4-infected Escherichia coli, which specifically initiates transcription at phage T4 late promoters, is extensively modified by ADP-ribosylation of core subunits and by binding several virus-encoded subunits. We show here that one of these subunits, the phage T4 gene 55 protein, designated gp55, alone endows unmodified RNA polymerase core enzyme from uninfected E. coli with the ability to selectively initiate transcription at the phage T4 late promoters, without participation by E. coli RNA polymerase o- subunit.

Bacteriophage SPO1 gene 27: location and nucleotide sequence

Bacteriophage SPO1 gene 27, whose product is required for late gene transcription and DNA replication, has been cloned in Escherichia coli, and its complete nucleotide sequence has been determined. We infer that the product of gene 27 is a highly basic 17,518-dalton protein of 155 amino acids. The gene for this regulatory protein is transcribed from two promoters: an early promoter situated before the adjacent upstream gene 28 and a middle promoter located between genes 28 and 27.

Transcriptional regulation of bacteriophage SPO1 protein synthesis in vivo and in vitro

There are six classes of SPO1 transcripts which are, at least partially, regulated independently of each other. Analysis of proteins made in infections by phage mutants defective in DNA synthesis, or in genes which positively control transcription, permitted each protein to be assigned to one transcription class. Most of the late proteins belong to transcription class m2l. There seem to be few, if any, phage proteins in the l class whose mRNA synthesis depends absolutely on phage DNA synthesis, UV irradiation of host cells allowed the detection of many additional early proteins. The early proteins detected in vivo were compared with proteins synthesized in vitro, using bacterial or gp28 phage-modified RNA polymerase in an Escherichia coli cell-free system. Proteins characterized in vivo as belonging to the e transcription class could be made efficiently in vitro only when transcription was performed by bacterial RNA polymerase. em proteins could be elicited through the use of either bacterial or gp28 polymerase, indicating that their genes can be transcribed in either the early or the middle mode.

Suppressor of yeast mitochondrial ochre mutations that maps in or near the 15S ribosomal RNA gene of mtDNA

A polypeptide chain-terminating mutation in the yeast mitochondrial oxi 1 gene has been shown to be an ochre (TAA) mutation by DNA sequence analysis. Mitochondrially inherited revertants of this mutation include two types: In the first, the ochre codon has been changed to a sense codon by further mutation in the oxi 1 gene while, in the second, the ochre codon is still present, indicating the occurrence of an extrageneic ochre suppressor mutation. This mitochondrial ochre suppressor, termed MSU1, has been "cloned" in rho- strains of yeast and tested against other oxi 1 mutations. Several additional mutations are also suppressible, and those examined so far are also ochre mutations. MSU1 does not suppress known frameshift or missense mutations at oxi 1. Isoelectric focusing of the gene product (cytochrome oxidase subunit II) from a suppressed-mutant strain indicates that suppression does not involve insertion of charged amino acids. Physical mapping of the mtDNA retained in the MSU1-carrying rho- clones localizes the suppressor mutation to the gene coding the 15S rRNA or a site not more than 300 base pairs from it. No known tRNA genes occur this close to the 15S rRNA gene, and mtDNA from a suppressor-carrying rho- does not hybridize detectably to mitochondrial tRNAs. These results suggest that MSU1 may be an alteration in the 15S rRNA.

SP01 gene 27 is required for viral late transcription

The SP01 mutant sus HA20 (gene 27) was found to be defective for synthesis of viral late RNA. It is known that gene 27 is also required for viral DNA replication. The SP01 gene 27 product resembles the T4 gene 45 product, which also has a dual role in viral DNA replication and late transcription.

Regulation of polypeptide synthesis during Caulobacter development: two-dimensional gel analysis

The gram-negative bacterium Caulobacter crescentus progresses through three distinct morphological transitions, including both motile and nonmotile cell types, during its cell cycle. Assessment of the extent of regulation of polypeptide synthesis during these transitions was carried out with two-dimensional gel electrophoresis of whole-cell extracts. Synchronous cells were pulse-labeled with 14C-amino acids for 10-min intervals throughout the entire 2-h cell cycle. The radioactively labeled polypeptides were analyzed by two-dimensional polyacrylamide gel electrophoresis. Autoradiograms resulting from fluorography of the second dimension provided the detection of approximately 1,000 unique spots. The 600 predominant polypeptide spots, representing approximately 40% of the coding capacity of Caulobacter deoxyribonucleic acid, were analyzed for major changes in their synthetic rates. Quantitation by densitometric scanning of individual polypeptide spots represented on the sequential fluorograms demonstrated significant changes in the temporal synthesis of 6% of the polypeptides. Extracts from asynchronous cells were fractionated to obtain total-membrane and deoxyribonucleic acid-binding polypeptide fractions. Subsequent electrophoresis of these cellular fractions revealed approximately 100 membrane polypeptides and 25 deoxyribonucleic acid-binding polypeptides. Eight of the regulated polypeptides were identified as membrane or deoxyribonucleic acid-binding proteins. The regulated polypeptides can be grouped into three main categories based on their interval of synthesis. The three categories are in direct correlation with the three distinct cell cycle stages. This analysis has also revealed a unique transition period in the cell cycle in which a significant proportion of gene expression is regulated.

Novel RNA polymerase sigma factor from Bacillus subtilis

A modified form of Bacillus subtilis RNA polymerase (RNA nucleotidyltransferase) has been isolated that exhibits distinctive transcriptional specificity. This modified enzyme transcribes two cloned genes from the purA-cysA region of the B. subtilis chromosome whose expression in vivo is associated with the process of sporulation. Neither of these genes is transcribed by the usual form of B. subtilis RNA polymerase holoenzyme containing a sigma factor of 55,000 daltons (sigma 55). The modified RNA polymerase lacks sigma 55 but contains a newly identified subunit of 37,000 daltons termed sigma 37. A reconstitution experiment in which sigma 37 was added to core RNA polymerase strongly suggests that sigma 37 is responsible for the transcriptional specificity of the modified RNA polymerase. Sigma 37 apparently acts at the level of promoter recognition; this transcriptional determinant enabled core RNA polymerase to form stable binary and ternary ("initiation") complexes with endonuclease restriction fragments containing promoters for the cloned B. subtilis genes.

Purification of a positive regulatory subunit from phage SP01-modified RNA polymerase

A phage-induced subunit has been purified from phage SP01-modified Bacillus subtilis RNA polymerase. This subunit binds in vitro to RNA polymerase core from uninfected B. subtilis thereby template-selective transcription and asymmetric synthesis of SP01 middle RNA.