Single protein nrß/i

Several proteins

In eukaryotes, each mRNA carries only a single gene. In prokaryotes, several genes may be carried on the same mRNA.

is any sequence of bases (in DNA or RNA) that could, in theory, encode a protein. The ORF is "open" in the sense that it does not contain any stop codons that would interrupt its translation into a polypeptide chain (although, of course, every ORF ends in a stop codon). (Any cistron that encodes a protein must also be an ORF, whereas a cistron that encodes an untranslated RNA is not an ORF.)

In eukaryotes, each gene is transcribed to give a separate mRNA and each mRNA molecule therefore encodes the information for only a single protein and is known as monocistronic mRNA (Fig. 6.03). In bacteria, clusters of related genes, known as operons, are often found next to each other on the chromosome and are transcribed together to give a single mRNA, which is therefore called polycistronic mRNA. Thus, a single bacterial mRNA molecule may encode several proteins, usually with related functions, such as the enzymes that oversee the successive steps in a metabolic pathway.

Before starting transcription, RNA polymerase binds to the promoter, a recognition sequence in front of the gene.

How Is the Beginning of a Gene Recognized?

Transcription will first be described in bacteria because it is simpler. The principles of transcription are similar in higher organisms, but the details are more complicated, as will be shown below.The major differences between prokaryotes and eukaryotes occur in the initiation and regulation of transcription, rather than in the actual synthesis of RNA. In front of each gene is a region of regulatory DNA that is not itself transcribed. This contains the promoter, the sequence to which RNA polymerase binds (Fig. 6.04), together with other sequences involved in the control of gene expression. This stretch of DNA in front of a gene (i.e., at the 5'-end) is often referred to as the upstream region. Note also that the first base of the mRNA of a protein-encoding gene is not the first base of the protein coding sequence. Between these two points there is a short stretch known as the 5'-untranslated region, or 5'-UTR, meaning it will not be translated to form protein (Fig. 6.04). At the far end of the mRNA there is another short

5'-untranslated region (5'-UTR) Region of an mRNA between the 5'-end and the translation start site monocistronic mRNA mRNA carrying the information of a single cistron, that is a coding sequence for only a single protein operon A cluster of prokaryotic genes that are transcribed together to give a single mRNA (i.e. polycistronic mRNA) polycistronic mRNA mRNA carrying the information of multiple cistrons, that is coding sequences for several proteins promoter Region of DNA in front of a gene that binds RNA polymerase and so promotes gene expression upstream region Region of DNA in front (i.e. beyond the 5'-end) of a structural gene;its bases are numbered negatively counting backwards from the start of transcription

Upstream region Downstream region

Upstream region Downstream region

Start and end of protein coding sequence t t

Start and end of protein coding sequence

Start of transcript End of transcript

FIGURE 6.04 Upstream and Downstream Regions

Genes and their regulatory regions are divided into upstream and downstream portions. The upstream portion contains the promoter. The downstream region begins with the information for the 5'-untranslated component, then the structural gene. The messenger RNA begins with the 5'-untranslated region (5'-UTR), then the coding sequence for the protein. Transcription begins by definition at the first base after the promoter. The upstream region, including the promoter, is given negative numbers counting backward from the beginning of transcription.

The sigma subunit of bacterial RNA polymerase recognizes the promoter. The core enzyme makes RNA.

Strong promoters usually have sequences close to consensus.

Promoter sequences vary in different organisms.

region, beyond the end of the protein coding sequence, that is not translated. This is the 3'-untranslated region, or 3'-UTR.

Bacterial RNA polymerase consists of two major components, the core enzyme (itself made of four subunits) and the sigma subunit. The core enzyme is responsible for RNA synthesis whereas the sigma subunit is largely responsible for recognizing the promoter. The sigma subunit, recognizes two special sequences of bases in the promoter region of the coding (non-template) strand of the DNA (Fig. 6.05). These are known as the -10 sequence and the -35 sequence because they are found by counting backward approximately 10 and 35 bases, respectively, from the first base that is transcribed into mRNA. [Previously, the -10 sequence was known as the Pribnow box, after its discoverer. This name is rarely used nowadays.]

The consensus sequence for the -10 sequence is TATAA and the consensus sequence at -35 is TTGACA. (Consensus sequences are found by comparing many sequences and taking the average.) Although a few highly expressed genes do have the exact consensus sequences in their promoters, the -10 and -35 region sequences are rarely perfect. However, as long as they are wrong by only up to three or four bases, the sigma subunit will still recognize them. The strength of a promoter depends partly on how closely it matches the ideal consensus sequence. Strong promoters are highly expressed and are often close to consensus. Promoters further away from the consensus sequence will be expressed only weakly (in the absence of other factors— but see below).

In practice, consensus sequences for regulatory sites on DNA such as promoters will vary from one group of organisms to another. Thus, the -10 and -35 consensus sequences given above are for Escherichia coli and related bacteria. Both the consensus sequences and the proteins that recognize them will diverge in more distantly related organisms. This is of practical importance when genes from one organism are expressed in another as a result of biotechnological manipulations. Consequently, it is

-10 region Region of bacterial promoter 10 bases back from the start of transcription that is recognized by RNA polymerase 3'-untranslated region (3'-UTR) Sequence at the 3'-end of mRNA, downstream of the final stop codon, that is not translated into protein -35 region Region of bacterial promoter 35 bases back from the start of transcription that is recognized by RNA polymerase core enzyme Bacterial RNA polymerase without the sigma (recognition) subunit Pribnow box Another name for the -10 region of the bacterial promoter sigma subunit Subunit of bacterial RNA polymerase that recognizes and binds to the promoter sequence

Manufacturing the Message 137

FIGURE 6.05 Sigma Recognizes the -10 and -35 Sequences

The sigma protein binds to both the -10 and -35 sequences of the promoter, thereby establishing a constant position with respect to the start of transcription.


Coding strand of

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