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| .and are then crossed with wild-type females.

EMS-treated male

Wild-type female J

Variant fish may posses a dominant mutation (M1).

Wild-type female J

Variant fish may posses a dominant mutation (M1).

.and backcrossed to reveal recessive mutations.

.and backcrossed to reveal recessive mutations.

Some fish homozygous for recessive mutations are produced.

Some fish homozygous for recessive mutations are produced.

Further breeding and positional cloning

119.21 Genes affecting a particular characteristic or function can be identified by a genomewide mutagenesis screen. In this illustration, M1 represents a dominant mutation and m2 represents a recessive mutation.

ping clones from the area of interest. A physical map of these overlapping clones that includes information about the molecular markers allows the identification of one or more clones that contain the gene of interest. These clones are then sequenced to find potential candidate genes that might encode the mutant phenotype. Candidate genes are evaluated by studying their expression patterns, protein products, and homology to genes of known function. This information might suggest that one or more of the candidate genes is likely to be the cause of the phenotype. The candidate genes can be examined for the presence of mutations in the gene sequences carried by those individuals having a mutant phenotype. Further proof that a particular gene causes the phenotype can be obtained by mutating a specific gene and observing the phenotype in the offspring. __

Concepts 9

Genomewide mutagenesis screening coupled with positional cloning can be used to identify genes that affect a specific characteristic or function.

Comparative Genomics

Genome-sequencing projects provide detailed information about gene content and organization in different species and even in different members of the same species, allowing inferences about how genes function and genomes evolve. They also provide important information about evolutionary relationships among organisms and about factors that influence the speed and direction of evolution.

Prokaryotic Genomes

A large number of bacterial genomes have now been sequenced (Table 19.2). Most prokaryotic genomes consist of a single circular chromosome, but there are exceptions, such as Vibrio cholerae (the bacterium that causes cholera; see introduction to Chapter 8), which has two circular chromosomes, and Borrelia burgdorferi, which has one large linear chromosome and 21 smaller chromosomes.

The total amount of DNA in prokaryotic genomes ranges from more than 7 million base pairs in Mesorhizo-

Characteristics of some completely sequenced representative prokaryotic genomes



Archaeoglobus fulgidus Methanobacterium thermoautotrophicum Methanococcus jannaschii Thermoplasma acidophilum

Eubacteria Bacillus subtilis Bordetella parapertussis Buchnera species Campylobacter jejuni Escherichia coli Haemophilus influenzae Mesorhizobium loti Mycobacterium tuberculosis Mycoplasma genitalium Staphylococcus aureus Treponema pallidum Ureaplasma urealyticum Vibrio cholerae

Size Number of

(Millions of Predicted

2.18 2407 49

1.75 1869 50

1.66 1715 32

1.56 1478 46

4.21 4100 44

0.64 564 27

1.64 1654 31

4.64 4289 51

1.83 1709 39

7.04 6752 63

4.41 3918 66

0.58 480 32

2.88 2697 33

1.14 1031 53

0.75 611 26

4.03 3828 48

Source: Data from the Genome Atlas of the Center for Biological Sequence Analysis,

* Data not available.

bium loti to only 580,000 bp in Mycoplasma genitalium. Escherichia coli, the most widely used bacterium for genetic studies, has 4.6 million base pairs (I Figure 19.22a). The number of genes is usually from 1000 to 2000, but some species have as many as 6700, and others as few as 480. The density of genes is rather constant across all species, with about 1 gene for every 1000 bp. Thus bacteria with larger genomes usually have more genes.

Only about half of the genes identified in prokaryotic genomes can be assigned a function. Almost a quarter of the genes have no significant sequence similarity to any other known genes in bacteria, suggesting that there is considerable genetic diversity among bacteria. The number of genes that encode biological functions such as transcription and translation tends to be similar among species, even when their genomes differ greatly in size. This similarity suggests that these functions are encoded by a basic set of proteins that does not vary among species. On the other hand, the number of genes taking part in biosynthesis, energy metabolism, transport, and regulatory functions varies greatly among species and tends to be higher in larger genomes. The functions of predicted genes (i.e., genes identified by computer programs) and known genes in E. coli are presented in I Figure 19.22b. A substantial part of the "extra" DNA found in the larger bacterial genomes is made up of paralogous genes that have arisen by duplication.

The G + C content (percentage of bases that consist of guanine or cytosine) of prokaryotic genomes varies widely, from 26% to 69%. This more-than-twofold difference in G + C content affects the frequency of particular amino acids in the proteins produced by different bacterial species. For example, glycine, alanine, proline, and argi-

nine are encoded by codons that have G and C nu-cleotides; so these amino acids are incorporated into proteins with higher frequency in organisms whose genomes have a high G + C content. On the other hand, isoleucine, phenylalanine, tyrosine, and methionine are encoded by codons that tend to have A and T (U in RNA) nucleotides; so these amino acids are found more frequently in proteins encoded by species whose genome has a low G + C content. Which synonymous codons are used is also affected by the G + C content; some synonymous codons have more G and C nucleotides than do others, and these codons tend to be used more frequently in those species with high G + C content.

The results of genomic studies of prokaryotic species support the conclusion that archaea and eubacteria are evolutionarily unique (see Chapter 2). The results also reveal that both closely and distantly related bacterial species periodically exchange genetic information over evolutionary time, a process called horizontal gene exchange. Such exchange may take place through bacterial uptake of DNA in the environment (transformation), through the exchange of plasmids, and through viral vectors (see Chapter 8). Horizontal gene exchange has been recognized for some time, but analyses of many microbial genomes now indicate that it is more extensive than was previously recognized. For example, an analysis of two eubacteria species demonstrated that from 20% to 25% of their genes were more similar to genes from archaea than to those from other eubacterial species.

and other genomes

Information on prokaryotic

1. Fatty acids, phospholipid metabolism

2. Transcription, RNA metabolism

3. Nucleotide metabolism

4. Phage, transposon, plasmid functions

5. DNA replication, recombination, repair

6. Carbon compounds metabolism

7. Amino acid metabolism

8. Other genes with known functions

9. Regulatory functions

10. Translation, protein metabolism

11. Central intermediary metabolism

12. Adaptation, protection functions

13. Cell, wall, membrane structural components

14. Energy metabolism

15. Putative enzymes

16. Transport proteins

17. Genes with unknown functions

119.22 Genomic characteristics of the bacterium E. coli. (a)

Genome size, number of genes, and G + C content. (b) Percentages of genes affecting various known and unknown functions.

[Table 19.3 Characteristics of Some Eukaryotic Genomes That Have Been 1

Completely Sequenced

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