Category: 2. Gene Regulation

Many genes play specialized roles and are expressed only under certain conditions, as described above. However, there are also genes whose products are constantly needed by the cell to maintain essential functions. These housekeeping genes are constantly expressed under normal growth conditions (“constitutively active”). Housekeeping genes have promoters and other regulatory DNA sequences that ensure constant expression.

Some operons are usually “off,” but can be turned “on” by a small molecule. The molecule is called an inducer, and the operon is said to be inducible.

• For example, the lac operon is an inducible operon that encodes enzymes for metabolism of the sugar lactose. It turns on only when the sugar lactose is present (and other, preferred sugars are absent). The inducer in this case is allolactose, a modified form of lactose.

Other operons are usually “on,” but can be turned “off” by a small molecule. The molecule is called a corepressor, and the operon is said to be repressible.

• For example, the trp operon is a repressible operon that encodes enzymes for synthesis of the amino acid tryptophan. This operon is expressed by default, but can be repressed when high levels of the amino acid tryptophan are present. The corepressor in this case is tryptophan.

These examples illustrate an important point: that gene regulation allows bacteria to respond to changes in their environment by altering gene expression (and thus, changing the set of proteins present in the cell).

Operons aren’t just made up of the coding sequences of genes. Instead, they also contain regulatory DNA sequences that control transcription of the operon. Typically, these sequences are binding sites for regulatory proteins, which control how much the operon is transcribed. The promoter, or site where RNA polymerase binds, is one example of a regulatory DNA sequence.

Diagram illustrating that the promoter is the site where RNA polymerase binds. The promoter is found in the DNA of the operon, upstream of (before) the genes. When the RNA polymerase binds to the promoter, it transcribes the operon and makes some mRNAs.Most operons have other regulatory DNA sequences in addition to the promoter. These sequences are binding sites for regulatory proteins that turn expression of the operon “up” or “down.”

• Some regulatory proteins are repressors that bind to pieces of DNA called operators. When bound to its operator, a repressor reduces transcription (e.g., by blocking RNA polymerase from moving forward on the DNA).

Diagram illustrating how a repressor works. A repressor protein binds to a site called on the operator. In this case (and many other cases), the operator is a region of DNA that overlaps with or lies just downstream of the RNA polymerase binding site (promoter). That is, it is in between the promoter and the genes of the operon. When the repressor binds to the operator, it prevents RNA polymerase from binding to the promoter and/or transcribing the operon. When the repressor is bound to the operator, no transcription occurs and no mRNA is made.

• Some regulatory proteins are activators. When an activator is bound to its DNA binding site, it increases transcription of the operon (e.g., by helping RNA polymerase bind to the promoter).

Diagram illustrating how an activator works. The activator protein binds to a specific sequence of DNA, in this case immediately upstream of (before) the promoter where RNA polymerase binds. When the activator binds, it helps the polymerase attach to the promoter (makes promoter binding more energetically favorable). This causes the RNA polymerase to bind firmly to the promoter and transcribe the genes of the operon much more frequently, leading to the production of many molecules of mRNA.Where do the regulatory proteins come from? Like any other protein produced in an organism, they are encoded by genes in the bacterium’s genome. The genes that encode regulatory proteins are sometimes called regulatory genes.

Many regulatory proteins can themselves be turned “on” or “off” by specific small molecules. The small molecule binds to the protein, changing its shape and altering its ability to bind DNA. For instance, an activator may only become active (able to bind DNA) when it’s attached to a certain small molecule.

In bacteria, related genes are often found in a cluster on the chromosome, where they are transcribed from one promoter (RNA polymerase binding site) as a single unit. Such a cluster of genes under control of a single promoter is known as an operon. Operons are common in bacteria, but they are rare in eukaryotes such as humans.

Diagram illustrating what an operon is. At the top of the diagram, we see a bacterial cell with a circular bacterial chromosome inside it. We zoom in on a small segment of the chromosome and see that it is an operon. The DNA of the operon contains three genes, Gene 1, Gene 2, and Gene 3, which are found in a row in the DNA. They are under control of a single promoter (site where RNA polymerase binds) and they are transcribed together to make a single mRNA that has contains sequences coding for all three genes. When the mRNA is translated, the three different coding sequences of the mRNA are read separately, making three different proteins (Protein 1, Protein 2, and Protein 3).

Note: The operon does not consist of just the three genes. Instead, it also includes the promoter and other regulatory sequences that regulate expression of the genes.In general, an operon will contain genes that function in the same process. For instance, a well-studied operon called the lac operon contains genes that encode proteins involved in uptake and metabolism of a particular sugar, lactose. Operons allow the cell to efficiently express sets of genes whose products are needed at the same time.

There are various forms of gene regulation, that is, mechanisms for controlling which genes get expressed and at what levels. However, a lot of gene regulation occurs at the level of transcription.Bacteria have specific regulatory molecules that control whether a particular gene will be transcribed into mRNA.

Often, these molecules act by binding to DNA near the gene and helping or blocking the transcription enzyme, RNA polymerase. Let’s take a closer look at how genes are regulated in bacteria.

Key points:

• Bacterial genes are often found in operons. Genes in an operon are transcribed as a group and have a single promoter.
• Each operon contains regulatory DNA sequences, which act as binding sites for regulatory proteins that promote or inhibit transcription.
• Regulatory proteins often bind to small molecules, which can make the protein active or inactive by changing its ability to bind DNA.
• Some operons are inducible, meaning that they can be turned on by the presence of a particular small molecule. Others are repressible, meaning that they are on by default but can be turned off by a small molecule.

Introduction

We tend to think of bacteria as simple. But even the simplest bacterium has a complex task when it comes to gene regulation! The bacteria in your gut or between your teeth have genomes that contain thousands of different genes. Most of these genes encode proteins, each with its own role in a process such as fuel metabolism, maintenance of cell structure, and defense against viruses.Some of these proteins are needed routinely, while others are needed only under certain circumstances. Thus, cells don’t express all the genes in their genome all the time. You can think of the genome as being like a cookbook with many different recipes in it. The cell will only use the recipes (express the genes) that fit its current needs.

Differences in gene regulation makes the different cell types in a multicellular organism (such as yourself) unique in structure and function. If we zoom out a step, gene regulation can also help us explain some of the differences in form and function between different species with relatively similar gene sequences.For instance, humans and chimpanzees have genomes that are about 98.8\%98.8%98, point, 8, percent identical at the DNA level.

The protein-coding sequences of some genes are different between humans and chimpanzees, contributing to the differences between the species. However, researchers also think that changes in gene regulation play a major role in making humans and chimps different from one another. For instance, some DNA regions that are present in the chimpanzee genome but missing in the human genome contain known gene-regulatory sequences that control when, where, or how strongly a gene is expressed.

In the articles that follow, we’ll examine different forms of eukaryotic gene regulation. That is, we’ll see how the expression of genes in eukaryotes (like us!) can be controlled at various stages, from the availability of DNA to the production of mRNAs to the translation and processing of proteins.Eukaryotic gene expression involves many steps, and almost all of them can be regulated. Different genes are regulated at different points, and it’s not uncommon for a gene (particularly an important or powerful one) to be regulated at multiple steps.

• Chromatin accessibility. The structure of chromatin (DNA and its organizing proteins) can be regulated. More open or “relaxed” chromatin makes a gene more available for transcription.
• Transcription. Transcription is a key regulatory point for many genes. Sets of transcription factor proteins bind to specific DNA sequences in or near a gene and promote or repress its transcription into an RNA.
• RNA processing. Splicing, capping, and addition of a poly-A tail to an RNA molecule can be regulated, and so can exit from the nucleus. Different mRNAs may be made from the same pre-mRNA by alternative splicing.

Stages of eukaryotic gene expression (any of which can be potentially regulated).

1. Chromatin structure. Chromatin may be tightly compacted or loose and open.
2. Transcription. An available gene (with sufficiently open chromatin) is transcribed to make a primary transcript.
3. Processing and export. The primary transcript is processed (spliced, capped, given a poly-A tail) and shipped out of the nucleus.
4. mRNA stability. In the cytosol, the mRNA may be stable for long periods of time or may be quickly degraded (broken down).
5. Translation. The mRNA may be translated more or less readily/frequently by ribosomes to make a polypeptide.
6. Protein processing. The polypeptide may undergo various types of processing, including proteolytic cleavage (snipping off of amino acids) and addition of chemical modifications, such as phosphate groups.

All these steps (if applicable) need to be executed for a given gene for an active protein to be present in the cell.Image based on similar diagrams from Reece et al. ^11start superscript, 1, end superscript and Purves et al. ^22squared

• RNA stability. The lifetime of an mRNA molecule in the cytosol affects how many proteins can be made from it. Small regulatory RNAs called miRNAs can bind to target mRNAs and cause them to be chopped up.
• Translation. Translation of an mRNA may be increased or inhibited by regulators. For instance, miRNAs sometimes block translation of their target mRNAs (rather than causing them to be chopped up).
• Protein activity. Proteins can undergo a variety of modifications, such as being chopped up or tagged with chemical groups. These modifications can be regulated and may affect the activity or behavior of the protein.

Although all stages of gene expression can be regulated, the main control point for many genes is transcription. Later stages of regulation often refine the gene expression patterns that are “roughed out” during transcription.

Now there’s a tricky question! Many factors can affect which genes a cell expresses. Different cell types express different sets of genes, as we saw above. However, two different cells of the same type may also have different gene expression patterns depending on their environment and internal state.Broadly speaking, we can say that a cell’s gene expression pattern is determined by information from both inside and outside the cell.

• Examples of information from inside the cell: the proteins it inherited from its mother cell, whether its DNA is damaged, and how much ATP it has.
• Examples of information from outside the cell: chemical signals from other cells, mechanical signals from the extracellular matrix, and nutrient levels.

How do these cues help a cell “decide” what genes to express? Cells don’t make decisions in the sense that you or I would. Instead, they have molecular pathways that convert information – such as the binding of a chemical signal to its receptor – into a change in gene expression.As an example, let’s consider how cells respond to growth factors. A growth factor is a chemical signal from a neighboring cell that instructs a target cell to grow and divide. We could say that the cell “notices” the growth factor and “decides” to divide, but how do these processes actually occur?

Growth factors bind to their receptors on the cell surface and activate a signaling pathway in the cell. The signaling pathway activates transcription factors in the nucleus, which bind to DNA near division-promoting and growth-promoting genes and cause them to be transcribed into RNA. The RNA is processed and exported from the nucleus, then translated to make proteins that drive growth and division.

• The cell detects the growth factor through physical binding of the growth factor to a receptor protein on the cell surface.
• Binding of the growth factor causes the receptor to change shape, triggering a series of chemical events in the cell that activate proteins called transcription factors.
• The transcription factors bind to certain sequences of DNA in the nucleus and cause transcription of cell division-related genes.
• The products of these genes are various types of proteins that make the cell divide (drive cell growth and/or push the cell forward in the cell cycle).

This is just one example of how a cell can convert a source of information into a change in gene expression. There are many others, and understanding the logic of gene regulation is an area of ongoing research in biology today.Growth factor signaling is complex and involves the activation of a variety of targets, including both transcription factors and non-transcription factor proteins.

Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes – despite the fact that almost all the cells of your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell type uniquely specialized to do its job.For example, one of the jobs of the liver is to remove toxic substances like alcohol from the bloodstream. To do this, liver cells express genes encoding subunits (pieces) of an enzyme called alcohol dehydrogenase. This enzyme breaks alcohol down into a non-toxic molecule. The neurons in a person’s brain don’t remove toxins from the body, so they keep these genes unexpressed, or “turned off.” Similarly, the cells of the liver don’t send signals using neurotransmitters, so they keep neurotransmitter genes turned off.

Left panel: liver cell. The liver cell contains alcohol dehydrogenase proteins. If we look in the nucleus, we see that an alcohol dehydrogenase gene is expressed to make RNA, while a neurotransmitter gene is not. The RNA is processed and translated, which is why the alcohol dehydrogenase proteins are found in the cell.Right panel: neuron. The neuron contains neurotransmitter proteins. If we look in the nucleus, we see that the alcohol dehydrogenase gene is not expressed to make RNA, while the neurotransmitter gene is. The RNA is processed and translated, which is why the neurotransmitter proteins are found in the cell.There are many other genes that are expressed differently between liver cells and neurons (or any two cell types in a multicellular organism like yourself).