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Changes due to mistakes of thesecond type—selectively neutral changes—may be perpetuated or not: in thecompetition for limited resources, it is a matter of chance whether the alteredcell or its cousins will succeed. But changes that cause serious damage leadnowhere: the cell that suffers them dies, leaving no progeny. Through endlessrepetition of this cycle of error and trial—of mutation and natural selection—THE DIVERSITY OF GENOMES AND THE TREE OF LIFE17organisms evolve: their genetic specifications change, giving them new ways toexploit the environment more effectively, to survive in competition with others,and to reproduce successfully.Clearly, some parts of the genome change more easily than others in thecourse of evolution. A segment of DNA that does not code for protein and has nosignificant regulatory role is free to change at a rate limited only by the frequencyof random errors.
In contrast, a gene that codes for a highly optimized essentialprotein or RNA molecule cannot alter so easily: when mistakes occur, the faultycells are almost always eliminated. Genes of this latter sort are therefore highlyconserved. Through 3.5 billion years or more of evolutionary history, many features of the genome have changed beyond all recognition; but the most highlyconserved genes remain perfectly recognizable in all living species.These latter genes are the ones we must examine if we wish to trace familyrelationships between the most distantly related organisms in the tree of life.The studies that led to the classification of the living world into the threedomains of bacteria, archaea, and eucaryotes were based chiefly on analysis ofone of the two main RNA components of the ribosome—the so-called smallsubunit ribosomal RNA.
Because translation is fundamental to all living cells,this component of the ribosome has been well conserved since early in the history of life on Earth (Figure 1–22).Most Bacteria and Archaea Have 1000–6000 GenesNatural selection has generally favored those procaryotic cells that can reproducethe fastest by taking up raw materials from their environment and replicatingthemselves most efficiently, at the maximal rate permitted by the available foodsupplies. Small size implies a large ratio of surface area to volume, thereby helping to maximize the uptake of nutrients across the plasma membrane andboosting a cell’s reproductive rate.Presumably for these reasons, most procaryotic cells carry very little superfluous baggage; their genomes are small, with genes packed closely together andminimal quantities of regulatory DNA between them.
The small genome sizemakes it relatively easy to determine the complete DNA sequence. We now havethis information for many species of bacteria and archaea, and a few species ofeucaryotes. As shown in Table 1–1, most bacterial and archaeal genomes contain between 106 and 107 nucleotide pairs, encoding 1000–6000 genes.A complete DNA sequence reveals both the genes an organism possessesand the genes it lacks. When we compare the three domains of the living world,we can begin to see which genes are common to all of them and must thereforehave been present in the cell that was ancestral to all present-day living things,and which genes are peculiar to a single branch in the tree of life.
To explain thefindings, however, we need to consider a little more closely how new genes ariseand genomes evolve. humanMethanococcusE. colihumanFigure 1–22 Genetic information conserved since the days of the last common ancestor of all livingthings. A part of the gene for the smaller of the two main RNA components of the ribosome is shown.
(Thecomplete molecule is about 1500–1900 nucleotides long, depending on species.) Corresponding segmentsof nucleotide sequence from an archaean (Methanococcus jannaschii), a bacterium (Escherichia coli) and aeucaryote (Homo sapiens) are aligned. Sites where the nucleotides are identical between species areindicated by a vertical line; the human sequence is repeated at the bottom of the alignment so that allthree two-way comparisons can be seen.
A dot halfway along the E. coli sequence denotes a site where anucleotide has been either deleted from the bacterial lineage in the course of evolution, or inserted in theother two lineages. Note that the sequences from these three organisms, representative of the threedomains of the living world, all differ from one another to a roughly similar degree, while still retainingunmistakable similarities.18Chapter 1: Cells and GenomesTable 1–1 Some Genomes That Have Been Completely SequencedSPECIESSPECIAL FEATURESHABITATGENOME SIZE(1000s OFNUCLEOTIDEPAIRS PERHAPLOID GENOME)ESTIMATEDNUMBEROF GENESCODING FORPROTEINShas one of the smallest of allknown cell genomesphotosynthetic, oxygen-generating(cyanobacterium)laboratory favoritecauses stomach ulcers andpredisposes to stomach cancercauses anthraxlithotrophic; lives at hightemperaturessource of antibiotics; giant genomespirochete; causes syphilisbacterium most closely related tomitochondria; causes typhusorganotrophic; lives at very hightemperatureshuman genital tract580468lakes and streams35733168human guthuman stomach4639166742891590soilhydrothermal vents5227155156341544soilhuman tissueslice and humans(intracellular parasite)hydrothermal vents8667113811117825104183418601877hydrothermal vents16641750hydrothermal vents21782493hydrothermal andvolcanic hot vents491552minimal model eucaryotegrape skins, beer12,069~6300model organism for floweringplantssimple animal with perfectlypredictable developmentkey to the genetics of animaldevelopmentmost intensively studied mammalsoil and air~142,000~26,000soil~97,000~20,000rotting fruit~137,000~14,000houses~3,200,000~24,000BACTERIAMycoplasma genitaliumSynechocystis sp.Escherichia coliHelicobacter pyloriBacillus anthracisAquifex aeolicusStreptomyces coelicolorTreponema pallidumRickettsia prowazekiiThermotoga maritimaARCHAEAMethanococcus jannaschiiArchaeoglobus fulgidusNanoarchaeum equitanslithotrophic, anaerobic,methane-producinglithotrophic or organotrophic,anaerobic, sulfate-reducingsmallest known archaean; anaerobic;parasitic on another, largerarchaeanEUCARYOTESSaccharomyces cerevisiae(budding yeast)Arabidopsis thaliana(Thale cress)Caenorhabditis elegans(nematode worm)Drosophila melanogaster(fruit fly)Homo sapiens (human)Genome size and gene number vary between strains of a single species, especially for bacteria and archaea.
The table shows data for particularstrains that have been sequenced. For eucaryotes, many genes can give rise to several alternative variant proteins, so that the total number ofproteins specified by the genome is substantially greater than the number of genes.New Genes Are Generated from Preexisting GenesThe raw material of evolution is the DNA sequence that already exists: there isno natural mechanism for making long stretches of new random sequence. Inthis sense, no gene is ever entirely new. Innovation can, however, occur in several ways (Figure 1–23):1.Intragenic mutation: an existing gene can be modified by changes in itsDNA sequence, through various types of error that occur mainly in the process of DNA replication.2.Gene duplication: an existing gene can be duplicated so as to create a pairof initially identical genes within a single cell; these two genes may thendiverge in the course of evolution.THE DIVERSITY OF GENOMES AND THE TREE OF LIFEORIGINAL GENOME19GENETIC INNOVATIONINTRAGENICMUTATIONmutation1geneGENEDUPLICATION+2gene ADNA SEGMENTSHUFFLING+3+gene Borganism A4+HORIZONTALTRANSFERorganism Borganism B withnew gene3.Segment shuffling: two or more existing genes can be broken and rejoinedto make a hybrid gene consisting of DNA segments that originallybelonged to separate genes.4.Horizontal (intercellular) transfer: a piece of DNA can be transferred fromthe genome of one cell to that of another—even to that of another species.This process is in contrast with the usual vertical transfer of genetic information from parent to progeny.Each of these types of change leaves a characteristic trace in the DNAsequence of the organism, providing clear evidence that all four processes haveoccurred.
In later chapters we discuss the underlying mechanisms, but for thepresent we focus on the consequences.Gene Duplications Give Rise to Families of Related Genes Within aSingle CellA cell duplicates its entire genome each time it divides into two daughter cells.However, accidents occasionally result in the inappropriate duplication of justpart of the genome, with retention of original and duplicate segments in a singlecell. Once a gene has been duplicated in this way, one of the two gene copies isfree to mutate and become specialized to perform a different function within thesame cell. Repeated rounds of this process of duplication and divergence, overmany millions of years, have enabled one gene to give rise to a family of genesthat may all be found within a single genome. Analysis of the DNA sequence ofprocaryotic genomes reveals many examples of such gene families: in Bacillussubtilis, for example, 47% of the genes have one or more obvious relatives (Figure 1–24).When genes duplicate and diverge in this way, the individuals of one speciesbecome endowed with multiple variants of a primordial gene.
This evolutionaryFigure 1–23 Four modes of geneticinnovation and their effects on the DNAsequence of an organism. A special formof horizontal transfer occurs when twodifferent types of cells enter into apermanent symbiotic association. Genesfrom one of the cells then may betransferred to the genome of the other,as we shall see below when we discussmitochondria and chloroplasts.20Chapter 1: Cells and Genomes283 genes in families with38–77 gene members764 genes in families with4–19 gene members2126 genes withno family relationship273 genes in familieswith 3 gene membersFigure 1–24 Families of evolutionarilyrelated genes in the genome of Bacillussubtilis.
The biggest family consists of77 genes coding for varieties of ABCtransporters—a class of membranetransport proteins found in all threedomains of the living world. (Adaptedfrom F. Kunst et al., Nature 390:249–256,1997. With permission from MacmillanPublishers Ltd.)568 genes in familieswith 2 gene membersprocess has to be distinguished from the genetic divergence that occurs whenone species of organism splits into two separate lines of descent at a branchpoint in the family tree—when the human line of descent became separate fromthat of chimpanzees, for example.
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