Bacterial Transcription Help
In bacteria, all RNA molecules (mRNAs, rRNAs, and tRNAs) are synthesized by the same enzyme, RNA polymerase. The complete, functional enzyme (holoenzyme) consists of five different polypeptide chains: β, β', α, ω, and σ. Each gene or genes to be transcribed has a region preceding it called the promoter, where the RNA polymerase complex binds to begin transcription. The sigma (σ) subunit is involved in initiation. It recognizes and binds to two different sequences of DNA in the promoter region: at 10 bases upstream (toward the 5' end) of the first base to be copied is the Pribnow box and at 35 bases upstream is the -35 sequence. The first base to be transcribed is generally labeled the +1 base and any sequence in front of or upstream of this base is given a negative number. This is why the sequence located 35 bases upstream is known as the -35 sequence, and the Pribnow box is often referred to as the -10 box. The binding of sigma to this region of DNA helps to align the remainder of the enzyme (called the core enzyme). The most common nucleotide sequence found in Pribnow boxes of various genes, called the consensus sequence, is TATAAT and the consensus of the -35 region is TTGACA. RNA chains usually initiate with 5' adenosine triphosphate (pppA) or guanosine triphosphate (pppG). After transcription has begun, sigma factor dissociates from the core enzyme and may then associate with the same or another core enzyme to get it started on a promoter. "Strong" promoters have Pribnow box and -35 sequences that closely match the consensus sequence, allowing sigma to bind more effectively. This favors the production of many copies of RNA. Promoters that have Pribnow box and -35 sequences that are further from the consensus are "weak" and result in low levels of transcription. The transcriptional activity of RNA polymerase may be blocked or its affinity for a promoter may be increased by the attachment of other specific DNA-binding proteins near the transcription initiation site. Some DNA sequences that precede (leaders) or follow (trailers) the gene may also control transcription, or these sequences may play a role in regulating translation.
During elongation of the RNA molecule, ribonucleoside triphosphates of the bases A, U, G, and C pair with complementary bases in the sense or template strand of DNA and are then connected with 3'–5' phosphodiester bonds by RNA polymerase. Thus, the RNA molecule grows from its 5' end toward its 3' end (5' → 3'). The DNA double helix unwinds ahead of the advancing RNA polymerase to expose more of the sense strand for extending the RNA chain. The DNA reforms its double-helical shape after the enzyme has passed a given region.
RNA polymerase in bacteria stops transcription of an RNA chain at DNA sequences known as terminators [Fig. 10-6(a)], and dissociates from the DNA. To function properly, some terminators require an accessory protein called rho (ρ) factor. The ρ-independent terminators have a diad symmetry in the double-stranded DNA, centered about 15–20 nucleotides before the end of the RNA, and have about six adenines in the sense strand that are transcribed into uracils at the end of the RNA. The RNA transcript of the diad symmetry folds back on itself to form a hairpin structure, ending with approximately 6 uracils [Fig. 10-6(b)]. Because an RNA-DNA hybrid consisting of polyribo-U and polydeoxyribo-A is very unstable, the RNA chain is quickly released from the DNA duplex. The ρ-dependent terminators lack this poly-A region. It is thought that even a weak hairpin structure causes RNA polymerase to pause, allowing ρ factor to attach to the terminator and cause dissociation of the RNA and RNA polymerase.
In bacteria, one single RNA transcript often contains the coding regions for multiple genes. This type of RNA is called polycistronic or polygenic (Fig. 10-7).
The 70S bacterial ribosome consists of two major subunits: a larger 50S subunit and a smaller 30S subunit. The 50S subunit contains two rRNA molecules (23S and 5S); the 30S subunit contains a single 16S rRNA molecule.1 All three rRNAs are transcribed into a single 30S pre-rRNA transcript containing a leader sequence at the 5' end, a trailer sequence at the 3' end, and nonfunctional spacer regions between the three rRNA sequences. Likewise, all tRNAs are derived by nuclease digestion from longer pre-tRNA primary transcripts containing from one to as many as seven different tRNAs. Many bacterial genes with related functions are transcribed into a polycistronic mRNA under the control of one promoter; these genes are said to make up an operon. Genes in operons are either regulatory, producing a protein that plays a role in the regulation of the expression of genes within that operon, such as a repressor, or structural, producing a protein that carries out another function within the cell, such as an enzyme.
Practice problems for these concepts can be found at:
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