1. Control of Protein expression
Transcription is most regulated step in gene expression in prokaryotes
Successful survival requires adaptability and economy:
In prokaryotes mRNA is generally very short lived (a few minutes)
Much of the regulation of what proteins are expressed is at the transcriptional level in prokaryotes

2. Points of transcriptional control
Accessibility of chromatin
Promotor sequence and how conserved it is (affects RNA polymerase binding)
-10 and –35 sequences and how conserved
Sigma factors
Whether or not a repressor protein is present
Enhancer/activator sequences
Once the transcript has been produced there is the opportunity for anti sense RNAs to get involved in control e.g. by binding to sense message and preventing it from being translated
mRNA processing and turnover
large transcripts are processed into smaller units as a means of regulating the expression of specific genes within each operon.

3. Chromatin
DNA in the bacterial chromosome is condensed through part of the cell cycle. This can affect its availability for transcription.
Promoters
The nucleotide sequence of promoters is similar but not identical. The more similar the sequence is to a consensus sequence, the more likely that RNA polymerase will attach and produce mRNA from the associated genes.
Sigma factors
Different sigma factors recognize different promoters thus, the availability of sigma factors can regulate the transcription of genes associated with these promoters.
The availability of sigma factors can be used to regulate sets of genes.
E.g., a group of genes whose product is rarely needed might have a different promoter sequence than other genes and thus require different sigma factors. These genes would only be transcribed when the correct sigma factor became available.
Repressors and activators
See Lac and tryp examples.
Some activators in particular can act on a sequence a long way away from gene and promoter.

4. Activation at a distance

5. Synthesis of antisense RNA
mRNA is synthesized off the template (antisense) strand of DNA. Antisense RNA is synthesized from the noncoding (sense) strand of DNA. The two mRNA molecules bond together, inactivating the mRNA

6. mRNA Processing and turnover 1. RNA polyadenylation
Post transcriptional additions of As to 3’ end of RNA strand
Growth rate dependent
20-50 nucleotides added
Not all RNA types are adenylated
Results in decreased transcript stability
Enzymes involved include
polyA polymerase 1 (PAP 1)
polyA polymerase 2 (PAP 2)
PAP1 is responsible for 90% of polyadenylation
RNA molecules are adenylated with different degrees of efficiency
Presence of specific ss segments at either 5’ or 3’ end thought to be important
How polyadenylation effects/facilitates degradation
In proks most messages end with a hairpin (due to transcription termination)
3’ end would not normally be accessible to ribonucleases as they act on ss RNA
Addition of 3’ tail makes ss piece and allows nucleases access
RNA degradation is performed by multicomponent complex called an RNA degradosome

7. Proteins
involved in degradosome include
PNPase (an exonuclease)
RNase E
Enolase and an RNA helicase
Catalytic RNA
PAP 1 is thought to be an accessory factor
As a result of getting the poly A tail the RNA molecule becomes accessible to the exonucleases which munches it up to ultimately mononucleotides. The enolase and helicase are involved in unwinding the stem loops

8. 2. mRNA stability
Affected by presence of hairpin loops and stem loops
More secondary structure more stability
Seems to be because degrading enzymes can not easily access