B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 14
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Small size implies a large ratio of surface area to volume, thereby helpingto maximize the uptake of nutrients across the plasma membrane and boosting acell’s reproductive rate.Presumably for these reasons, most prokaryotic 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 size hasmade it easy to use modern DNA sequencing techniques to determine completegenome sequences. We now have this information for thousands of species ofbacteria and archaea, as well as for hundreds of species of eukaryotes. 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 possesses andthe genes it lacks. When we compare the three domains of the living world, wecan begin to see which genes are common to all of them and must therefore havebeen present in the cell that was ancestral to all present-day living things, andwhich genes are peculiar to a single branch in the tree of life. To explain the findings, however, we need to consider a little more closely how new genes arise andgenomes evolve.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 severalways (Figure 1–19):1. Intragenic mutation: an existing gene can be randomly modified by changesin its DNA sequence, through various types of error that occur mainly in theprocess of DNA replication.2. Gene duplication: an existing gene can be accidentally duplicated so as tocreate a pair of initially identical genes within a single cell; these two genesmay then diverge in the course of evolution.3. DNA segment shuffling: two or more existing genes can break and rejoin tomake a hybrid gene consisting of DNA segments that originally belonged toseparate 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 DNA sequenceof the organism, and there is clear evidence that all four processes have frequentlyFigure 1–18 Genetic informationconserved since the days of the lastcommon ancestor of all living things.A part of the gene for the smaller of the twomain rRNA components of the ribosome isshown.
(The complete molecule is about1500–1900 nucleotides long, dependingon species.) Corresponding segments ofnucleotide sequence from an archaean(Methanococcus jannaschii), a bacterium(Escherichia coli), and a eukaryote (Homosapiens) are aligned. Sites where thenucleotides are identical between speciesare indicated by a vertical line; the humansequence is repeated at the bottom ofthe alignment so that all three two-waycomparisons can be seen. A dot halfwayalong the E.
coli sequence denotes a sitewhere a nucleotide has been either deletedfrom the bacterial lineage in the courseof evolution or inserted in the other twolineages. Note that the sequences fromthese three organisms, representative ofthe three domains of the living world, stillretain unmistakable similarities.THE DIVERSITY OF GENOMES AND THE TREE OF LIFEORIGINAL GENOME17GENETIC INNOVATIONINTRAGENICMUTATIONmutation1geneGENEDUPLICATION+2gene A+3DNA SEGMENTSHUFFLING+gene Borganism A4+HORIZONTALTRANSFERorganism Borganism B withnew geneoccurred.
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.MBoC6 m1.23/1.19However, accidents occasionallyresult 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 genes thatmay all be found within a single genome.
Analysis of the DNA sequence of prokaryotic genomes reveals many examples of such gene families: in the bacteriumBacillus subtilis, for example, 47% of the genes have one or more obvious relatives(Figure 1–20).When genes duplicate and diverge in this way, the individuals of one speciesbecome endowed with multiple variants of a primordial gene. This evolutionaryprocess has to be distinguished from the genetic divergence that occurs when onespecies of organism splits into two separate lines of descent at a branch point inthe family tree—when the human line of descent became separate from that ofchimpanzees, for example. There, the genes gradually become different in thecourse of evolution, but they are likely to continue to have corresponding functions in the two sister species.
Genes that are related by descent in this way—thatis, genes in two separate species that derive from the same ancestral gene in thelast common ancestor of those two species—are called orthologs. Related genesthat have resulted from a gene duplication event within a single genome—andFigure 1–19 Four modes of geneticinnovation and their effects on the DNAsequence of an organism.
A specialform of horizontal transfer occurs whentwo different types of cells enter intoa permanent symbiotic association.Genes from one of the cells then may betransferred to the genome of the other,as we shall see below when we discussmitochondria and chloroplasts.Chapter 1: Cells and Genomes18283 genes in families with38–77 gene members764 genes in families with4–19 gene members2126 genes withno family relationship273 genes in familieswith 3 gene membersFigure 1–20 Families of evolutionarilyrelated genes in the genome of Bacillussubtilis.
The largest gene family in thisbacterium consists of 77 genes coding forvarieties of ABC transporters—a class ofmembrane transport proteins found in allthree domains 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 membersare likely to have diverged in their function—are called paralogs. Genes that arerelated by descent in either way are called homologs, a general term used to coverboth types of relationship (Figure 1–21).Genes Can Be Transferred Between Organisms, Both in theLaboratory and in Nature MBoC6 m1.24/1.20Prokaryotes provide good examples of the horizontal transfer of genes from onespecies of cell to another.
The most obvious tell-tale signs are sequences recognizable as being derived from viruses, those infecting bacteria being called bacteriophages (Figure 1–22). Viruses are small packets of genetic material that haveevolved as parasites on the reproductive and biosynthetic machinery of host cells.Although not themselves living cells, they often serve as vectors for gene transfer.A virus will replicate in one cell, emerge from it with a protective wrapping, andthen enter and infect another cell, which may be of the same or a different species.Often, the infected cell will be killed by the massive proliferation of virus particlesinside it; but sometimes, the viral DNA, instead of directly generating these particles, may persist in its host for many cell generations as a relatively innocuouspassenger, either as a separate intracellular fragment of DNA, known as a plasmid,or as a sequence inserted into the cell’s regular genome.
In their travels, virusescan accidentally pick up fragments of DNA from the genome of one host cell andferry them into another cell. Such transfers of genetic material are very commonin prokaryotes.Horizontal transfers of genes between eukaryotic cells of different speciesare very rare, and they do not seem to have played a significant part in eukaryoteevolution (although massive transfers from bacterial to eukaryotic genomes haveoccurred in the evolution of mitochondria and chloroplasts, as we discuss below).ancestral organismancestral organismgene Ggene GSPECIATION TO GIVE TWOSEPARATE SPECIESspecies Aspecies Bgene GAgene GBGENE DUPLICATIONAND DIVERGENCElater organismgene G1gene G2genes GA and GB are orthologs(A)genes G1 and G2 are paralogs(B)Figure 1–21 Paralogous genes andorthologous genes: two types ofgene homology based on differentevolutionary pathways.
(A) Orthologs.(B) Paralogs.THE DIVERSITY OF GENOMES AND THE TREE OF LIFE(A)(C)100 nm(D)(B)19100 nm(E)100 nmIn contrast, horizontal gene transfers occur much more frequently between different species of prokaryotes. Many prokaryotes have a remarkable capacity to takeup even nonviral DNA molecules from their surroundings and thereby capturethe genetic information these molecules carry.
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