Prokaryotic Gene Structure
Note: All the required diagrams are posted on the topic of prokaryotic gene expression.
Genes, based on their activity, can be grouped as housekeeping genes and others are classed as induced to express or express in a stage-specific or tissue-specific manner.
• Housekeeping genes express all the time under all normal conditions.
Most of the gene products of housekeeping genes are involved in day-to-day metabolic activities responsible for the maintenance of the cell.
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• But when cell confers with other signals such as, change in the temperature, change in the pH, and other environmental features such as exposure to toxic chemicals, or chemical inducers, light, non availability of nutrients, and any other factor that is not ambient to cells and not conducive to cells, specific genes respond to such changes or inductions and express to overcome such hostile or unfavorable situations.
Structural features of promoters of these genes, though basically have common features, individually they vary from one to the other.
• Most of the housekeeping genes have the following generalized structural features.
The coding region starts with an initiator codon and the reading frame ends in a terminator codon.
Typical Prokaryotic Gene structural elements
The coding region of structural genes is not split, but rRNA genes have spacers within them.
• The upstream elements from the start of the coding region include promoter elements.
Nearly 50 to 100 ntds upstream of the start codon, is the first nucleotide at which transcription initiates, it means, it is at this site the first nucleotide is incorporated into the transcribed RNA.
• The site is called transcriptional initiation site or START.
Nearly 10 nucleotides upstream of the start, there is a sequence called TATAAT or Pribnow box.
• Any nucleotide present on the left of the start is denoted by (-) symbol and the region is called upstream element. The numbers are written as -10, -20, -35 etc.
The start site is the first ends and symbolized by +1, any sequence to the right of the start is called downstream elements and numbered as +10, +35 and so on.
At –35 there is another consensus sequence TTGACA. These two sequences are the most important promoter elements, for if there is any change in their sequence and position, transcriptional initiation suffers.
Recombinant DNA technology
• The meaning of a promoter essentially is a distinct sequence module recognized by RNA polymerase (as a holoenzyme), bind to the sequence tightly and initiate transcription by unwinding the helically coiled DNA into the transcriptional bubble.
The said sequences not only facilitate the binding of the enzyme and also provide sequence information for the site at which the enzyme to initiate transcription. If anyone of the consensus sequences is deleted or changed drastically, the enzyme won’t bind, even if it binds, it initiates transcription at different positions.
-200 -65 -60 -35 -10 +1
Enhancers Activator TTGACA TATAT
-RNA polymerase binding region-
-35 –10 +1—–>
TTGACA——-TATAAT—-C A T—–
The prokaryotic RNA-pol Holoenzyme, when it binds properly in a sequence context, it covers a length from –60 to +20 or little more. It is this segment of the gene that is called Promoter. Whether it is a housekeeping gene or special gene, either from prokaryote or eukaryote, the meaning and the function of the promoter are the same.
• So promoters act as defining a set of sequence structural elements, which positions the transcriptional apparatus to initiate the transcriptional process. Whether transcription is successfully initiated or not the criteria, but positioning and potentiality for initiating, is an important criterion, then only such sequence modules are called promoters.
For the RNA pol to recognize different genes, the promoter elements have recognition sequences (signature sequences), which are recognized by specific sigma factors that associate the RNA-Pol.
• In prokaryotes, there are other sequences in the upstream of the promoter, beyond –35 sequences. Such sequences may present at –65 to –60 or they may be present at –200 or they may be present at—1000 bp upstream or they may present in downstream regions.
The –65 to –60 sequences, position certain factors, whose binding leads to the activation of the polymerase, which was hitherto remained inactive even though it is bound to correct promoter elements. This process is termed as activation and the element as activator elements.
• The other sequence at –200 or —1000, is called enhancer, for it enhances the rate of transcription by 100 to 200 fold. This is achieved through certain proteins bind to enhancer elements, and then contacts RNA Holoenzyme by protein-protein interactions, by way of DNA bending or looping, and enhances the efficiency of the enzyme.
Some proteins, after binding to their DNA sequences, interact with the transcriptional apparatus and activate the enzyme.
• The kind of sequences, however, and the position of the sequences vary from one gene to another.
It is important to realize, that the proteins that bind have specific motifs called DNA binding motifs, and also possess protein-protein interacting domains.
• The DNA also provides a structural motif in the form of sequence.
Understanding of DNA sequence context and 3-D structural organization of DNA binding protein is of great importance to appreciate the regulatory processes.
• Genes that are regulated in response to the needs, basically have the promoter components. In addition, they have operators, activators and enhancers in different positions, which require specific regulator proteins for operation.
Terminal Region of the Gene:
At the end of the coding region that is the terminal region beyond the terminator codon or codons, there are certain sequences positioned from the TER codon which provide a sequence for the transcript to generate a secondary structure that facilitates the termination of transcription.
• One of the structural motifs that the sequence provides is the formation of the stem with GC rich sequence and open loop and terminates in 2 to 4 U sequences.
In some of the transcriptional terminator sequences, there are specific sequences rich in Cs; they are a little longer and far away from the TER codon.
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