Transcription in Bacteria PDF

Transcription in Bacteria Transcription (DNA to RNA) is carried out by RNA polymerase. (Figure 4.19) RNA polymerase uses DNA as template. RNA precursors are ATP, GTP, CTP, and UTP. chain growth 5′ to 3′, just as in DNA replication only one strand transcribed no...

Transcription in Bacteria Transcription (DNA to RNA) is carried out by RNA polymerase. (Figure 4.19) RNA polymerase uses DNA as template. RNA precursors are ATP, GTP, CTP, and UTP. chain growth 5′ to 3′, just as in DNA replication only one strand transcribed no priming needed  DNA-dependent RNA polymerase In most eukaryotes e.g. yeast, mammals, there are 3 different multiple subunit (more than 10 subunits) RNA polymerases, with each transcribing different types of genes. – Pol I: rRNAs – Pol II: mRNA – Pol III: 5S rRNA, tRNA and other small RNAs In plants, two additional multiple subunit RNA polymerases. – Pol IV: Generation of small interfering RNAs from transposon, repetitive sequences and epigenetic – Pol V: silencing (DNA and histone methylation) of those elements.  Prokaryotic Eukaryotic Bacteria and Archaea have only a single RNA Bacteria Yeast polymerase. RNA polymerase from E. coli is composed of five subunits: two α (αI and αII), β, β’ and ω (forming a complex called a holoenzyme or the “core” enzyme). RNA polymerase itself does not have a proof- reading mechanism, a major difference from DNA polymerase which can have 3’ to 5’ exonuclease activity. http://reasonandscience.heavenforum.org/t2036-the-complexity-of-transcription-through-rna-polymerase-enzymes-and-general-transcription-factors-in- eukaryotes  Overall structures of RNA polymerases from eukaryotes and prokaryotes are remarkably similar  Structure of bacterial RNA polymerase Bacterial RNA polymerase contains 5 subunits: two α (αI and αII), β, β’ and ω (forming a complex called a holoenzyme or the “core” enzyme). The groove for template DNA binding is positively charged while DNA is negatively charged DNA and RNA are negatively charged The groove (channel) for template DNA because of negatively charged binding/entry in the RNA polymerase is phosphate group (on the positively charged – to facilitate binding phosphodiester bond). with DNA. Mg2+ is required for RNA polymerase activity. Mg2+ www.learner.org www.quora.com Overview of RNA transcription process Initiation Chain elongation Termination  Transcription initiation in bacteria Initiation is sequence specific and takes place at the promoter sequence, a piece of DNA sequence upstream the RNA transcription start site. In bacteria, the core enzyme can catalyze RNA transcription by itself, but the sigma factor (bacterial transcription factors) is required for the recognition of the promoter. Sigma factor is not tightly bound and can dissociate easily from the core enzyme. Consensus sequences recognized by sigma factor “+1” is the transcription initiation site (the first ribonucleotide). All other DNA elements on the left (5’ side) is “upstream” and on the right (3’ side) is “downstream” of the start site. A consensus sequence that is about 10 base-pair (bp) is the -10 region, which is called the Pribnow box. There is another consensus region further upstream that is about 35 bp from the start site, -35 region. Sigma factor recognizes and binds both regions.  Multiple sigma factors in bacteria In E. coli, there are 7 distinct sigma factors. The number of sigma factors varies among bacterial species e.g., Bacillus subtilis has more than 10 sigma factors. The presence of various sigma factors can allow the RNA polymerase to recognize many different promoter sequences.  In E. coli, the major sigma factor (“housekeeping" or primary sigma factor), σ70 refers to the sigma factor with a molecular weight of 70 kDa. Each sigma factor seems to bind to the promoter of genes that have a similar function (enable transcription of a particular set of genes of related functions); for example, sporulation sigma factor in Bacillus subtilis is responsible for the transcription of genes involved in sporulation of the bacteria under adverse conditions. The number of genes that each sigma factor can transcribe varies. Three-dimensional crystal structure of the E. coli RNAP σ70 holoenzyme. a and b, surface representation of the E. coli RNAP holoenzyme. Sigma factor (orange part in the picture on the right) is attached to the core RNA polymerase complex. It will dissociate from the core enzyme after transcription initiation. Katsuhiko S. Murakami J. Biol. Chem. 2013;288:9126-9134  Regulation of gene expression through sigma factors Regulation of gene expression is controlled by the changing amounts or activity of the sigma factors. The key to controlling transcription with multiple sigma factors comes down to the control of synthesis and activity of each sigma factor. The concentration of each sigma factor is modulated by the transcriptional control or the rate of degradation of the factor in the cell by specific proteases. Sigma factor can be activated by certain signals like stresses. E.g., σs activity is induced under various stress conditions such as osmotic shock, heat and low pH. The activity of sigma factor can be controlled by the presence of proteins called anti-sigma factor, which can temporarily inactivate the sigma factor.