BIOCHEMISTRY - L. Stryer - 1984

VOLUME 3

Part IV INFORMATION

CHAPTER 29. EUKARYOTIC CHROMOSOMES AND GENE EXPRESSION IN EUKARYOTES

29.15. Most Unique Genes Intersperse with Repetitive Sequences

Approximately 70% of the DNA in A wide variety of eukaryotes consists of unique sequences. How are these unique genes arranged relative to repetitive sequences? Analyses of eukaryotic Chromosomes using various Methods have shown that unique sequences typically alternate with moderately repetitive sequences, which are typically 300 Base Pairs in length. There are several thousand different moderately repetitive sequences. They repeat in The Genome several hundred times and collectively account for 20% of the DNA. The function of these dispersed, moderately repetitive DNA sequences remains unknown. They may serve as binding sites for specific regulatory macromolecules that can control the METABOLISM/31.html">Transcription of neighboring unique structural genes.

29.16 Almost All Protein-Coding Genes in Higher Eukaryotes Have an Interrupted Structure

The existence of repetitive genes in eukaryotes and their alternation with unique genes have no counterparts in prokaryotes. Another striking difference in Genome Organization is the presence of intervening sequences in virtually all protein-coding genes of higher eukaryotes. As discussed previously (Section 26.12), these intervening sequences (introns) are transcribed along with the coding sequences (exons) and are subsequently removed during The formation of mature mRNA. The number of introns in interrupted genes studied to date ranges from 2 to 17 (Table 29.5 and Fig. 29.27)¹. Some introns are very long. For example, the mouse β-globin Gene contains an intron 550 base pairs long, making it longer than its exons. Two fragments of an immunoglobulin gene are separated by an even longer intron—1250 base pairs in length. In some genes, the total length of the introns exceeds that of the exons. For instance, the Ovalbumin gene contains about 7700 base pairs, whereas its mRNA is only 1859 NUCLEOTIDES long. As a rule, the intervening sequences of interrupted genes are longer than the expressed sequences. Interestingly, evolutionary changes occur more rapidly in intron sequences than in exon sequences. The base sequences of the smaller intron in the mouse and rabbit β-globin genes are completely different. However, they are similar in length, and their positions within the gene are identical. Even more significantly, the sequences at the intron-exon junctions where splicing (joining) takes place are conserved.

¹ The Myosin gene contains over 50 introns! — Transl. note.

Class="center">Fig. 29.27. Map of the conalbumin gene. Intervening sequences (introns), which are transcribed but do not form part of the mature mRNA, are shown in yellow.

Table 29.5. Selected eukaryotic genes with an interrupted Structure

Interrupted genes encoding RNA have also been discovered. For example, one of the Yeast Transfer RNA genes contains a 14-base-pair intron adjacent to the anticodon loop of the mature tRNA. The mitochondrial gene encoding ribosomal RNA also has an interrupted structure. At the same time, many rRNAs and tRNAs are continuous. The histone genes of sea urchins and fruit flies likewise appear to lack intervening sequences. To date, such "interrupted" structural genes have been found only in birds and mammals. It will be interesting to determine whether interrupted genes are abundant in lower eukaryotes¹.

¹ A general trend is currently emerging: the higher the evolutionary position of an Organism, the greater the Number and Length of introns its genes generally contain. — Transl. note.

The discovery of interrupted genes came as a complete surprise and gave rise to A number of fascinating problems. Do introns reflect the evolution of new Proteins from fragments of old ones? Do introns play a role in regulating Gene Expression? It is clear that a new and important field of research has emerged. Data concerning the crucial question of how intervening sequences are excised from the primary transcript are rapidly accumulating. We shall examine these findings shortly.

29.17. RNA in Eukaryotic Cells Is Synthesized by Three Distinct RNA Polymerases

Let us now turn to transcription. Eukaryotic Cells possess Three types of RNA polymerases that synthesize RNA. They differ in template Specificity, intracellular localization, and inhibitor sensitivity. Type I polymerase is localized in the nucleolus, where it transcribes the tandem repeats encoding the 18S, 5.8S, and 28S rRNAs. Other RNA molecules—5S rRNA and all tRNAs—are synthesized by another enzyme, type III RNA polymerase, which is located in the nucleoplasm rather than the nucleolus. Large precursor RNA molecules, which give rise to mRNA, are synthesized by RNA polymerase II, also found in the nucleoplasm. In contrast, all classes of cellular RNA in prokaryotes are synthesized by a single RNA polymerase. A common property of eukaryotic RNA polymerases is that they are composed of two large subunits and several small subunits.

29.18. The Fungal Toxin α-Amanitin Is a Potent Inhibitor of RNA Polymerase II

Each year, over 100 people worldwide die from poisoning by toxic mushrooms, specifically Amanitia phalloides (the death cap). One of the toxins found in these

mushrooms—α-amanitin—is a cyclic peptide containing several unusual Amino Acids. α-Amanitin binds very tightly to RNA polymerase II (K = 10^-8 M), thereby blocking the synthesis of mRNA precursors. Polymerase III is inhibited at higher concentrations of α-amanitin (10^-6 M), whereas polymerase I is insensitive to this toxin. α-Amanitin blocks the elongation phase of RNA Synthesis.

29.19. Specific Genes Can Be Activated for Transcription

GENE EXPRESSION IN eukaryotes, as in prokaryotes, is regulated primarily at the transcription level. Some of the most robust evidence for this has come from studies of developing insect chromosomes. Giant polytene chromosomes from the Salivary Glands of Drosophila contain more than a thousand DNA molecules that have failed to separate during Replication and lie side by side. Each polytene chromosome exhibits a series of characteristic bands (discs, or chromomeres) visible under a Light Microscope. As the larva develops into a pupa, certain bands temporarily enlarge (forming puffs) as the DNA in these regions transitions from a condensed to a decondensed state (Fig. 29.29). Puffs correspond to transcriptionally active regions. A striking discovery was made: puffs can be induced in isolated salivary glands in vitro by ecdysone, an insect steroid hormone. This results in the enlargement and subsequent Condensation of specific bands in a precise temporal sequence, accompanied by simultaneous Changes in the population of synthesized mRNAs.

Table 29.6. Eukaryotic RNA Polymerases

Fig. 29.28. The poisonous mushroom Amanita phalloides containing α-amanitin

Fig. 29.29. Formation of a puff in a polytene chromosome at a specific developmental stage. The arrow indicates the largest puff in a Drosophila chromosome