From genes to genomes. Concepts and applications of DNA technology

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With the advent of We also have to be careful as we may want to refer to the whole transcribed re- gion, which will be longer than the translated open reading frame, or indeed we may want to include the control regions that are necessary for the start of transcription. Other DNA re- gions are important in gene regulation because they act as binding sites for regulatory proteins. There is relatively little DNA to which we can ascribe no likely function, compared to eukaryotic cells, and especially animal and plant cells with much larger genomes, where there is a much higher proportion of non-coding DNA.

Increasingly, much of it is recognized as having important functions within the cell. These include enabling the DNA to be folded correctly and in ensuring that the coding regions are available for expression under the appropriate conditions, as well as coding for small non-translated RNA molecules that play a major role in modulating gene expression. However, this is rarely a serious prob- lem. We just have to be careful how we use it depending on whether we are discussing only the coding region ORF , or the length of sequence that is transcribed into mRNA including untranslated regions , or whether we wish to include DNA regions with regulatory functions as well as coding se- quences.

In this context, we will also encounter the words allele and locus. An allele is one version of that locus. So variation of a genetic characteristic between individuals would be due to different alleles at one locus or several loci. The basic dogma Figure 1. A typical bacterial promoter carries two consensus sequences i.

It is important to understand the nature of a consensus: few bac- terial promoters have exactly the sequences shown, but if you line up a large number of promoters you will see that at any one position a large number of them have the same base Box 1. The nature and regulation of bacterial promoters, in- cluding the existence of alternative types of promoters, is considered further in Chapter 5.

In eukaryotes, by contrast, the promoter is a considerably larger area around the transcription start site, where a number of trans-acting transcrip- tion factors i. Nonetheless, the promoter region, however simple or complex, gives rise to different lev- els of transcription of various genes. A further complexity in eukaryotes is that there are commonly additional regulatory elements known as enhancers, Spaces are inserted to optimise the alignment.

Note that the consensus is derived from a much larger collection of characterized promoters. Position 1 is the transcription start site. Eukaryotes have three different RNA polymerases. Only one of these, RNA polymerase II, is involved in the transcription of protein-coding tran- scripts, plus the transcription of a group of small non-coding RNAs called micro-RNAs, which we will encounter in Chapter It is very short-lived as such, being rapidly processed in a number of steps called maturation.

Essentials of Genomics and Bioinformatics

A specialized nucleotide cap is added to the 5 end; this is the site recognized by the ribosomes in protein synthesis see below. This transcript contains intervening sequences introns between the exons that carry the coding information see below.

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In bacteria, the processes of transcription and translation take place in the same compartment and simultaneously. In eukaryotes, by contrast, the mature mRNA molecule is transported out of the nucleus to the cytoplasm, where translation takes place. The level of an mRNA species will be affected by its rate of degradation as well as by its rate of synthesis. In bacteria, most mRNA molecules are degraded quite quickly with a half-life of only a few minutes , although some are much more stable.

From Genes to Genomes: Concepts and Applications of DNA Technology

By contrast, the lifespans of most eukary- otic mRNA molecules are measured in hours rather than minutes, although Consequently, mRNA molecules tend to be more stable in multicellular organisms than in, for ex- ample, yeast. Nonetheless, the principle remains — the level of an mRNA in a cell is a function of its production and degradation rates. We will discuss how to study and disentangle these parameters in Chapter The se- quence of the ribosome binding site also known as the Shine—Dalgarno se- quence has been recognized as being complementary to the 3 end of the 16S rRNA Figure 1.

This concept is explored more fully in Chapter 7. In bacterial systems, where transcription and translation occur in the same compartment of the cell, ribosomes will bind to the mRNA, a process known as initiation, as soon as the RBS has been synthesized. Thus, there will be a procession of ribosomes following close behind the RNA polymerase, trans- lating the mRNA in the process of elongation as and when it is being pro- duced.

So, although the mRNA may be very short-lived, the bacteria are ca- pable of producing substantial amounts of the corresponding polypeptide in a short time. Translation stops when a termination codon is reached. In eukaryotes, the mechanism is much more complicated. Sometimes, translation may be initiated at an internal ribosome entry site IRES ; the best studied of these occur in some viruses, but they also occur in some transcripts encoded naturally by the cell. If we are considering protein-coding genes, the transcription product, messenger RNA mRNA , is then translated into a number of separate polypeptides.

This can occur by the ribosomes reaching the stop codon at the end of one polypeptide-coding sequence, terminating translation and releasing the product before reinitiating without dissociation from the mRNA.

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Alternatively, the ribosomes may attach independently to internal ribosome binding sites within the mRNA sequence. Generally, the genes involved are responsible for different steps in the same pathway, and this arrangement facilitates the coordinate regulation of those genes, i. In eukaryotes, by contrast, the way in which ribosomes initiate transla- tion is different, which means that they cannot usually produce separate proteins from a single mRNA in this way.

Although there are some exam- ples where polygenic transcripts analogous to bacterial operons are produced, these are very much the exception rather than the rule. Generally, when a sin- gle mRNA gives rise to different proteins, this is due to alternative processing of the mRNA see below or by producing one long polyprotein or precur- sor, which is then cleaved into different proteins as occurs in some viruses. We will consider this in more detail in Chapter Introns do occur in bacteria, but quite infrequently.

This is partly due to the need for economy in a bacterial cell. A further factor arises from the nature of transcription and translation in a bacterial cell. Since the ribosomes translate the mRNA while it is being made, there is less opportunity for sections of the RNA to be removed before translation. These properties are manifested by transcription of the DNA into RNA, which in eukaryotes is processed by removal of introns to produce a messenger RNA that is then translated into protein.

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We now know that several aspects of this model are inadequate. Firstly, there can be differences between cells that have identical DNA sequences, and these differences can be passed on from one cell to its progeny. This phe- nomenon is known as epigenetic inheritance. The ex- tent and position of this methylation can be passed on from one cell to its progeny, hence it is inherited, but you will not see that difference by conven- tional DNA sequencing. Later on in Chapter 10 we will consider ways in which this can be investigated, together with other differences such as varia- tion in the number of copies of regions of the DNA copy number variation.

Secondly, we now know that much of the DNA that does not code for proteins is not actually junk at all. It plays an important role in the regulation of the activity of the cell through the action of small RNA molecules. It may also be exploited as a way of silencing gene expression in the laboratory, one that demands much less resources and is much more amenable to high-throughput screening than other methods see Chapters 8 and Thirdly, sequencing of eukaryotic genomes see Chapter 8 , especially those of humans and other mammals, showed that the genome appeared to code for far fewer proteins than expected.

Human DNA is thought to contain only about 21 distinct protein-coding genes, which can be com- pared to a bacterium such as Mycobacterium tuberculosis, with over such genes. However, the number of potential protein species in a human cell is much larger than 21 The main reason for this is that the splicing mechanism, by which introns are removed to produce the mRNA, is capable This con- trasts with sexual reproduction, where the offspring are not usually geneti- cally identical.

This applies to all organisms, from bacteria to humans. In particular, anyone with an interest in gardening will know that it is possible to propagate plants by taking cuttings. These are clones. Similarly, the routine bacteriological procedure of purifying a bacte- rial strain by picking a single colony for inoculating a series of fresh cultures is also a form of cloning. The term cloning is applied to genes, by extension of the concept. If you introduce a foreign gene into a bacterium, or into any other type of cell, in such a way that it will be copied when the cell replicates, then you will pro- duce a large number of cells all with identical copies of that piece of DNA — you have cloned the gene Figure 2.

By producing numerous copies in this way, you can sequence it or label it as a probe to study its expression in the organism it came from. You can express its protein product in bacterial or eukaryotic cells. You can mutate it and study what difference that mutation makes to the properties of the gene, its protein product, or the cell that car- ries it.

You can even purify the gene from the bacterial clone and inject it into a mouse egg, and produce a line of transgenic mice that express it. Behind all these applications lies a cloning process with the same basic steps. We will start with an overview of the process, before considering the vari- ous steps in more detail. In this chapter, we will focus on using bacterial cells mainly E.

Later in the book Chapter 7 we will extend the discussion to alternative host cells, as well as looking at vectors that are designed for optimising expression of cloned genes. However, most bacteria have to be subjected to chemical or phys- ical treatments before DNA will enter the cells.

In all cases, the DNA will not be replicated by the host cell unless it either recombines with i. For most pur- poses the latter strategy is the relevant one. We use vectors to carry the DNA and allow it to be replicated. There are many types of vectors for use with bacteria, but, to start with, we will consider plasmids, which are naturally oc- curring pieces of DNA that are replicated independently of the chromosome, and are inherited by the two daughter cells when the cell divides. In later The DNA that we want to clone is inserted into a suitable vector, produc- ing a recombinant molecule consisting of vector plus insert Figure 2.

This recombinant molecule will be replicated by the bacterial cell, so that all the cells descended from that initial transformant will contain a copy of this piece of recombinant DNA.

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