Bacterial and archaeal genomes have several notable features:
They are relatively small. Prokaryotic genomes range from about 160,000 to 12 million bp and are usually organized into a single chromosome.
They are compact. Typically, more than 85 percent of the DNA is in protein-
Prokaryotic gene sequences usually are not interrupted by introns. An exception is the rRNA and tRNA genes of archaea, which frequently contain introns.
In addition to the main chromosome, prokaryotes often have smaller, circular molecules of DNA called plasmids, which may be transferred between cells (see Key Concept 12.6).
Beyond these similarities, there is great diversity among these single-
FUNCTIONAL GENOMICS As we described in Key Concept 17.1, functional genomics is the biological discipline that assigns functions to the products of gene sequences. You can see the various functions encoded by the genomes of three prokaryotes in Table 17.1. As an example, look at the first bacterial genome sequenced, that of Haemophilus influenzae, which lives in the human respiratory tract and can cause ear infections or, more seriously, meningitis in children. Its single circular chromosome has 1,830,138 bp. In addition to its origin of replication and the genes coding for rRNAs and tRNAs, this bacterial chromosome has 1,727 open reading frames with promoters nearby.
| Category | Number of genes in: | ||
|---|---|---|---|
| E. coli | H. influenzae | M. genitalium | |
| Total protein- |
4,288 | 1,727 | 482 |
| Biosynthesis of amino acids | 131 | 68 | 1 |
| Biosynthesis of cofactors | 103 | 54 | 5 |
| Biosynthesis of nucleotides | 58 | 53 | 19 |
| Cell envelope proteins | 237 | 84 | 17 |
| Energy metabolism | 243 | 112 | 31 |
| Intermediary metabolism | 188 | 30 | 6 |
| Lipid metabolism | 48 | 25 | 6 |
| DNA replication, recombination, and repair | 115 | 87 | 32 |
| Protein folding | 9 | 6 | 7 |
| Regulatory proteins | 178 | 64 | 7 |
| Transcription | 55 | 27 | 12 |
| Translation | 182 | 141 | 101 |
| Uptake of molecules from the environment | 427 | 123 | 34 |
When the H. influenzae sequence was first announced 20 years ago, only 1,007 (58 percent) of the open reading frames coded for proteins with known functions. Since then, scientists have identified the functions of the rest of the encoded proteins. All of the major biochemical pathways and molecular functions are represented. For example, the genes that encode enzymes involved in glycolysis, fermentation, and electron transport have been identified. Gene sequences that code for membrane proteins have been identified as well, including those involved in active transport. An important finding was that highly infective strains of H. influenzae—but not noninfective strains—
COMPARATIVE GENOMICS Soon after the sequence of H. influenzae was announced, smaller (Mycoplasma genitalium: 580,073 bp) and larger (E. coli: 4,639,221 bp) prokaryotic sequences were completed. Thus began the era of comparative genomics. Scientists can identify genes that are present in one bacterium and missing in another, allowing them to relate these genes to bacterial function.
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M. genitalium, for example, lacks enzymes needed to synthesize amino acids, whereas E. coli and H. influenzae both possess such enzymes. This finding reveals that M. genitalium must obtain all its amino acids from its environment (usually the human urogenital tract). Furthermore, E. coli has 55 genes that encode transcriptional activators, whereas M. genitalium has only 12. This relative lack of control over gene expression suggests that the biochemical flexibility of M. genitalium must be limited compared with that of E. coli.