Regulation of Gene Expression Chapter 18

How do Organisms Control the Level of Gene Expression? Cells must only express genes when needed Gene expression (transcription, translation) takes up large amounts of cellular energy and resources Cells live frugal lifestyles – they conserve energy and resources So genes will only be expressed when their products are needed.

How Prokaryotes Control Gene Expression Bacteria control genes at the transcriptional level In other words, the gene is either transcribed or not, based on certain external stimuli

The Operon An operon is a segment of DNA that consists of the following: A gene or group of genes A promoter of the gene/group of genes A region upstream of the gene called the an operator

Operons 5

Lac Operon – Inducible operon The lac operon is always off and is turned on by an inducer molecule (allolactose). This is why it is called an inducible operon 6

The trp Operon - repressible operon The trp operon is always on and is turned off only by end product – tryptophan. This is why it is called a repressible operon.                                                      7

trp Operon – repressible operon 8

How do Eukaryotes Control the Level of Gene Expression? Cells of more complex organisms turn on and turn off genes based on the functions of the cells – hence cells differentiate Eukaryotes control genes at almost every level: Regulation of Chromatin Structure Regulation at the transcriptional level Regulation at a post-transcriptional level Regulation at a translational level Regulation at a post-translational level

Regulation of Chromatin Structure Histone acetylation prevents DNA from winding tightly around histones, allowing easy access to promoter sites (Deacetylation does the opposite) DNA methylation causes DNA to wind tightly around histones, preventing easy access to gene promoters (Demethylation does the opposite)

Bacteria lack histones, although some archea have them Histone subunits are: 2 units of H2A 2 units of H2B 2 units of H3 2 units of H4 Histone H1 is not in the core, but acts as a clamp and keeps the linker DNA in place Histones are positively charged, so DNA which is negatively charged, wraps around them Linker DNA links one nucleosome to the next Bacteria lack histones, although some archea have them

Histones have tails that get actylated by HAT enzymes (Histone Acetyl Transferases) Histone acetylation makes their (+) charge more neutral, so DNA interaction is reduced Histone Acetyl group

DNA Methylation in conjunction with Histone deacetylation

Epigenetic Inheritance Modification of chromatin does not change the DNA, only its expression. However, this modification pattern IS inherited (remember genomic imprinting?) Scientists now believe that certain environmental factors may play a part in promoting chromatin modification that causes expression or suppression of certain genes – e.g. one twin gets schizophrenia and another doesn’t. Certain cancers may also be caused that way

Regulation at the transcriptional level Enhancers (proximal and distal) Silencers Transcription factors at promoters General transcription factors Specific transcription factors All these play a role in regulating gene expression. Enhancers increase the rate of a gene’s expression and silencers decrease it. Transcription factors are needed if the gene is to be expressed at all.

Organization of a typical Eukaryotic Gene

Regulation at a post-transcriptional level RNA processing – alternative splicing allows certain proteins to be made instead of others (all from the same gene) mRNA Degradation – cytoplasmic nucleases degrade mRNAs so polypeptide synthesis stops. More mRNA is made later, if necessary 5’ caps and 3’ tails can be removed or changed and this will prevent translation

Pre-translational Regulation Certain proteins in the cytoplasm can bind to the mRNA’s 5’ UTR and prevent ribosomes from binding Any change in mRNA shape will prevent ribosome binding Decreased length of poly-A tail will prevent translation

Ribosome stalls due to hairpin loop in mRNA mRNA is then degraded by a cluster of exonucleases (exosomes)

Post-translational Regulation Proteins can be ubiquitinzed and degraded in a proteasome

Non-protein-coding RNAs and Gene Regulation MicroRNAs or miRNAs are small non-coding RNAs that were Transcribed from DNA Complexed with a number of proteins These miRNAs have several bases that are complementary to some protein-coding mRNAs The miRNA-protein complex can bind to these protein-coding mRNAs and prevent them from being translated Nucleases eventually degrade the dsRNA

RNA Interference A relatively new technology uses the concept of miRNAs to stop the expression of certain genes This is done by creating small RNAs that have a corresponding sequence (antisense RNA) to mRNAs that will give rise to unwanted proteins The small interfering RNAs (siRNAs) then bind to these mRNAs and block their translation

Sense and Antisense RNA Messenger RNA (mRNA) is single-stranded. Its sequence of nucleotides is called "sense" because it results in a gene product (protein). Normally, its unpaired nucleotides are "read" by transfer RNA anticodons as the ribosome proceeds to translate the message.

RNAi However, RNA can form duplexes just as DNA does. All that is needed is a second strand of RNA whose sequence of bases is complementary to the first strand; e.g. 5´   C A U G   3´     mRNA 3´   G U A C   5´     Antisense RNA The second strand is called the antisense strand because its sequence of nucleotides is the complement of message sense. When mRNA forms a duplex with a complementary antisense RNA sequence, translation is blocked. This may occur because the ribosome cannot gain access to the nucleotides in the mRNA or duplex RNA is quickly degraded by ribonucleases in the cell synthetic genes (DNA) encoding antisense RNA molecules can be introduced into the organism.

Flavr Savr tomato Most tomatoes that have to be shipped to market are harvested before they are ripe. Otherwise, ethylene synthesized by the tomato causes them to ripen and spoil before they reach the customer. Transgenic tomatoes have been constructed that carry in their genome an artificial gene (DNA) that is transcribed into an antisense RNA complementary to the mRNA for an enzyme involved in ethylene production. These tomatoes make only 10% of the normal amount of the enzyme. The goal of this work was to provide supermarket tomatoes with something closer to the appearance and taste of tomatoes harvested when ripe. However, these tomatoes often became damaged during shipment and handling and have been taken off the market.

Zygote  Embryo  Adult organism How does a single egg or zygote become a complete organism with many different tissues and differentiated cells? How can this happen, when the zygote undergoes many rounds of mitosis – mitosis is supposed to produce identical daughter cells?

Cytoplasmic Determinants Certain molecules such as maternal mRNAs, transcription factors and other proteins are localized in specific cytoplasmic regions of the unfertilized egg or zygote These molecules affect cell fate decisions by segregating into different embryonic cells and controlling distinct gene activities in these cells (specialized transcription factors will only turn on certain genes). Cytoplasmic determinants are also found in some post-embryonic cells, where they produce cytoplasmic asymmetry. In dividing cells, this leads to asymmetric cell division in which each of the daughter cells differentiates into a different cell type. Also called localized cytoplasmic determinants or morphogenetic determinants.

Cytoplasmic Determinants and Cell Fate

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