2IntroductionThe two types of transcription regulation control in prokaryotic cellsThe lac operon an inducible regulatory feedback systemThe tryp operon a repressible regulatory feedback system.The role of bioinformatics analysis in such systems
3Gene RegulationAll “genes” must have some way of regulating their expression (converting the DNA to amino acids) in order to allow them to adopt appropriately to the environment.In prokaryotic cells the process, owing to the simple nature of the genomic material, is basically controlled “mainly” at the transcription level…Essentially the molecule “RNA polymerase” must bind to an “exposed“ part of DNA strand called a promoter; it must then move, in the 5’ to 3’ direction, “transcribing” the DNA sequence of “the gene” to RNA.The transcribed sequence begins at the Transcription start site (TSS) and finishes at the Transcription Termination site (TES) ;The sequence of DNA that is translated into the amino acid sequences is knows as the CDS (coding sequence)
4Types of Transcription control The transcription is controlled/ regulated at two stages:RNA polymerase binds to the DNA strand;If it binds to DNA transcription beginsElse if it is prevented from binding; DNA is not transcribed: gene not expressed.RNA polymerase moves in the 5’ to 3’ direction:If the movement of RNA polymerase is [physically] blocked transcription is stopped and gene is not expressedOtherwise transcription is completed and the gene is expressed.
5Transcriptional control systems Inducible: gene is expressed (DNA is converted to RNA) only if the molecule (inducer) is present.Repressible: if molecule is present gene expression is turned offIn both cases the molecule works via a feedback loop.
6“gene expression” regulatory loops Feedback loop: product of the gene expression loops back (directly/indirectly) and alter the expression of the same gene.The effect can be either :positive : “turns on” transcription via an inducer; e.g. [lactose ]Negative: “turns off” transcription via a repressor e.g. [tryptophan]Gene product
7Inducible Prokaryotic regulation Lactose, a complex sugar (glucose)In order for E. Coli to use (metabolise) the sugar a gene system referred to as the “lac operon” must produce three enzyme(s) that allow lactose to be utilised by the bacteria. For simplicity we will refer to the combined system as: lactose dehydrogenise (a more detailed description of the enzymes and their functions can be found in Klug p. 310).The function of this enzyme is to break convert lactose to glucose and increase its absorption into the bacterial cell.Basically In order to ensure efficient functionality of the “lac operon” system it must have the following properties:will not be expressed if there is no lactosewill be expressed if there is lactose.Note a more complete description of the system, involving glucose, can be found in the supplementary notes.
8Function of Lac operonKlug chapter 15The term operon is the common “gene regulatory system” used in prokaryotic cells and generally a number of genes are regulated as a one.In the E Coli Lac operon DNA there are:1 repressor gene (A promoter (where RNA polymerase binds)A Cis–acting regulatory region (operator)A leader region (where transcription starts but leader is an UTR)3 structural genes: LacZ, LacY and LacA (refer to here as lactose dehydrogenase); actually 3 different genes with different functionality in the utilisation of lactose.
9Function of Lac operon Repressor protein RNA polymerase RNA polymerase binds to the promoter regionThe repressor gene produces a product “a repressor protein”This binds to the DNA at the operator region and blocks RNA polymerase moving down the DNA strand.If lactose is present it alters the repressor protein.The alter repressor protein is unable to bind to the DNARNA polymerase binds to the promoter region and begins transcribing the 3 structural genes.When lactose levels drop to zero: what happens?RNA polymeraseKlug chapter 15
10Glucose and the lac operon Lactose is metabolised into glucose so what happens if glucose is present.Catabolite-activation protein (CAP): CAP must be present to make RNA polymerase binding efficientlyIn the presence of glucose the CAP is altered and prevents RNA polymerase binding to the promoter region and so prevents transcription.Klug chapter 15
11A repressible operonTryptophan is an essential AA and is normally made (biosynthesised) by E Coli.If tryptophan is present externally [in sufficient levels] then the biosynthesis stops;The DNA strand has the same elements as the lactose operon: repressor gene, promoter, operator, leader and genesIn this system the repressor protein is altered by tryptophan and the modified repressor protein now binds to the operator region and blocks RNA polymerase transcribing the genes required to make tryptophan.Klug chapter 15
12The tryptophan operonIn addition in the presence of tryptophan there is an additional control mechanism called:The attenuation regulatory mechanism:In the sequence prior to structural genes is the attenuator region:If tryptophan and its gene expression is repressed they still found that transcription was initiated… ; there was “RNA” fragments of leader [L]sequence: this shows that transcription begins at a transcription start site (TSS) upstream of AUG (start codon)Thus altering the repressor protein is not enough to prevent expression.It seems that tryptophan also binds to the attenuator [A]region and prevents transcription beyond the leader region.Attenuator regionLeader regionKlug chapter 15
13Importance of bioinformatics Bioinformatics can help with improving our understanding of such regulation by:Finding potential gene regions and promoter regions since a gene will be in close proximity to a promoter regions.The prokaryotic sequence normally has specific sequences associated with it and so do genes [begin with AUG/ATG]. [This will be covered in more detail in the lecture “finding genes/promoters”Prokaryotic systems usually have polycistronic mRNA ; multiple gene sequences in very close proximity (contiguous) or in some cases the may even slightly overlap. (understanding bioinformatics section 9.2)The gene sequence can be converted into amino acid sequence via universal codeFinally the promoter sequences and gene sequences can be analysed using advanced computational techniques to help understand or suggest how the “operon” works
14Exam questionDistinguish, using suitable examples, the difference between inducible and repressible transcription control in prokaryotic organisms. (20 marks)Discuss, using examples, how analysis of DNA sequences can help improve our understanding of genome in prokaryotic cells. (10 marks)