Promoter prokaryotic structure

Busby S, Ebright RH Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 1994 79 ... 

There is a single prokaryotic RNA polymerase that synthesizes all types of RNA in the cell. The core polymerase responsible for making the RNA molecule has the subunit structure Ojpp. A protein factor called sigma (a) is required for the initiation of transcription at a promoter. Sigma factor is released immediately after initiation of transcription. Termination of transcription sometimes requires a protein called rho (p) faaor. This enzyme is inhibited by rifampin. Actinomycin D binds to the DNA preventing transcription. 

In E. coli, all genes are transcribed by a single large RNA polymerase with the subunit structure a2pp a. This complete enzyme, called the holoenzyme, is needed to initiate transcription since the a factor is essential for recognition of the promoter it decreases the affinity of the core enzyme for nonspecific DNA binding sites and increases its affinity for the promoter. It is common for prokaryotes to have several a factors that recognize different types of promoter (in E. coli, the most common a factor is a70). 

Copper ion homeostasis in prokaryotes involves Cu ion efflux and sequestration. The proteins involved in these processes are regulated in their biosynthesis by the cellular Cu ion status. The best studied bacterial Cu metalloregulation system is found in the gram-positive bacterium Enterococcus hirae. Cellular Cu levels in this bacterium control the expression of two P-type ATPases critical for Cu homeostasis (Odermatt and Solioz, 1995). The CopA ATPase functions in Cu ion uptake, whereas the CopB ATPase is a Cu(I) efflux pump (Solioz and Odermatt, 1995). The biosynthesis of both ATPases is regulated by a Cu-responsive transcription factor, CopY (Harrison et al., 2000). In low ambient Cu levels Cop Y represses transcription of the two ATPase genes. On exposure to Cu(I), CopY dissociates from promoter/operator sites on DNA with a for Cu of 20 jlM (Strausak and Solioz, 1997). Transcription of copA and copB proceeds after dissociation of CuCopY. The only other metal ions that induce CopY dissociation from DNA in vitro are Ag(I) and Cd(II), although the in vivo activation of copA and copB is specihc to Cu salts. The CuCopY complex is dimeric with two Cu(I) ions binding per monomer (C. T. Dameron, personal communication). The structural basis for the Cu-induced dissociation of CopY is unknown. Curiously, CopY is also activated in Cu-dehcient cells, but the mechanism is distinct from the described Cu-induced dissociation from DNA (Wunderh-Ye and Solioz, 1999). 

The structure resembles that of a tRNA by molecular mimicry. The sequence Gly-Gly-Gln, present in both eukaryotes and prokaryotes, occurs at the end of the structure corresponding to the acceptor stem of a tRNA. This region binds a water molecule. Disguised as an aminoacyl-tRNA, the release factor may carry this water molecule into the peptidyl transferase center and, assisted by the catalytic apparatus of the ribosome, promote this water molecule s attack on the ester linkage, freeing the polypeptide chain. The detached polypeptide leaves the ribosome. Transfer RNA and messenger RNA remain briefly attached to the 70S ribosome until the entire complex is dissociated in a GTP-dependent fashion by ribosome release factor (RRF) and EF-G. Ribosome release factor is an essential factor for prokaryotic translation. 

The chemistry of transcription in eukaryotes is the same as in prokaryotes. However, the promoter structure and the mechanism for initiation are strikingly different. 

The structure of eukaryotic promoters is more complex than that of prokaryotic promoters. DNA sequences, hundreds of base pairs (bp) upstream from the transcription start site, control the rate of initiation. Furthermore, initiation requires numerous specific proteins (transcription factors) that bind to particular DNA sequences. Without the transcription factors, RNA polymerase II cannot bind to a promoter. However, KNH polymerase II itself is not a transcription factor. The complexity of initiation may derive, in part, from the fact that eukaryotic DNA is in the form of chromatin, which is inaccessible to RNA polymerases. Many RNA polymerase II promoters have the following features ... 

In prokaryotes, many genes are clustered into operons, which are units of coordinated genetic expression. An operon consists of control sites (an operator and a promoter) and a set of structural genes. In addition,... 

Cells are the fundamental units of life. They are functional entities, each of which is enclosed in a semipermeable membrane that varies in composition and function both over a single cell surface and between different cell types. There are two basic forms of cell prokaryotic and eukaryotic. Prokaryotes are most noted for their small sizes and relatively simple structures. Presumably because of these traits, in addition to their remarkably rapid reproduction rates and biochemical diversity, various prokaryotic species occupy virtually every ecological niche in the biosphere. In contrast, the most conspicuous feature of the eukaryotes is their extraordinarily complex internal structure. Because eukaryotes carry out their various metabolic functions in a variety of membrane-bound organelles, they are capable of a more sophisticated intracellular metabolism. The diverse metabolic regulatory mechanisms made possible by this complexity promote two important lifestyle features required by multicellular organisms cell specialization and intercellular cooperation. Consequently, it is not surprising that the majority of eukaryotes are multicellular organisms composed of numerous types of specialized cells. 

EF-Tu (Figure 19A), the protein factor that positions aminoacyl-tRNA complexes in the A site of prokaryotic ribosomes, is a well-researched example of a GTP-binding motor protein. Recall that motor proteins (Section 2.1) use nucleotide hydrolysis to drive changes in their own conformations that are often used to promote ordered conformational changes in adjacent molecules or subunits. In other words, motor proteins, often called NTPases, function as mechanochemical transducers. These NTP-hydrolysis driven conformational changes, which principally occur in localized structural units called switches, alter the affinity of the NTPase for other molecules. 

See also The Genetic Code, Structure of tRNAs, Initiation of Translation, Prokaryotic Translation Regulation, Lactose Operon Regulation (from Chapter 26), Promoter Organization... 

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