B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 13
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In the electron microscope,this cell interior appears as a matrix of varying texture without any discernibleorganized internal structure (Figure 1–14).Prokaryotic cells live in an enormous variety of ecological niches, and they areastonishingly varied in their biochemical capabilities—far more so than eukaryotic cells. Organotrophic species can utilize virtually any type of organic moleculeas food, from sugars and amino acids to hydrocarbons and methane gas. Phototrophic species (Figure 1–15) harvest light energy in a variety of ways, some ofthem generating oxygen as a by-product, others not. Lithotrophic species can feedon a plain diet of inorganic nutrients, getting their carbon from CO2, and relyingon H2S to fuel their energy needs (Figure 1–16)—or on H2, or Fe2+, or elementalsulfur, or any of a host of other chemicals that occur in the environment.Figure 1–13 Shapes and sizes of somebacteria.
Although most are small, asshown, measuring a few micrometersin linear dimension, there are also somegiant species. An extreme example (notshown) is the cigar-shaped bacteriumEpulopiscium fishelsoni, which lives in thegut of a surgeonfish and can be up to600 μm long.Figure 1–14 The structure of a bacterium.
(A) The bacterium Vibriocholerae, showing its simple internal organization. Like many other species,Vibrio has a helical appendage at one end—a flagellum—that rotates as apropeller to drive the cell forward. It can infect the human small intestine tocause cholera; the severe diarrhea that accompanies this disease kills morethan 100,000 people a year. (B) An electron micrograph of a longitudinalsection through the widely studied bacterium Escherichia coli (E. coli).
Thecell’s DNA is concentrated in the lightly stained region. Part of our normalintestinal flora, E. coli is related to Vibrio, and it has many flagella distributedover its surface that are not visible in this section. (B, courtesy ofE. Kellenberger.)plasmamembraneDNAcell wallflagellum1 µmribosomes(A)(B)1 µm14Chapter 1: Cells and GenomesFigure 1–15 The phototrophic bacteriumHSAnabaena cylindrica viewed in the lightV10 µmmicroscope. The cells of this species formlong, multicellular filaments.
Most of thecells (labeled V) perform photosynthesis,while others become specialized fornitrogen fixation (labeled H) or develop intoresistant spores (labeled S). (Courtesy ofDave G. Adams.)Much of this world of microscopic organisms is virtually unexplored. Traditional methods of bacteriology have given us an acquaintance with those speciesthat can be isolated and cultured in the laboratory.
But DNA sequence analysis ofthe populations of bacteria and archaea in samples from natural habitats—suchMBoC6 m1.19/1.15as soil or ocean water, or even the humanmouth—has opened our eyes to the factthat most species cannot be cultured by standard laboratory techniques. According to one estimate, at least 99% of prokaryotic species remain to be characterized.Detected only by their DNA, it has not yet been possible to grow the vast majorityof them in laboratories.The Tree of Life Has Three Primary Branches: Bacteria, Archaea,and EukaryotesThe classification of living things has traditionally depended on comparisons oftheir outward appearances: we can see that a fish has eyes, jaws, backbone, brain,and so on, just as we do, and that a worm does not; that a rosebush is cousinto an apple tree, but is less similar to a grass.
As Darwin showed, we can readily interpret such close family resemblances in terms of evolution from commonancestors, and we can find the remains of many of these ancestors preserved inthe fossil record. In this way, it has been possible to begin to draw a family tree ofliving organisms, showing the various lines of descent, as well as branch pointsin the history, where the ancestors of one group of species became different fromthose of another.When the disparities between organisms become very great, however, thesemethods begin to fail.
How do we decide whether a fungus is closer kin to a plantor to an animal? When it comes to prokaryotes, the task becomes harder still: onemicroscopic rod or sphere looks much like another. Microbiologists have therefore sought to classify prokaryotes in terms of their biochemistry and nutritionalrequirements. But this approach also has its pitfalls. Amid the bewildering varietyof biochemical behaviors, it is difficult to know which differences truly reflect differences of evolutionary history.Genome analysis has now given us a simpler, more direct, and much morepowerful way to determine evolutionary relationships.
The complete DNAsequence of an organism defines its nature with almost perfect precision and inexhaustive detail. Moreover, this specification is in a digital form—a string of letters—that can be entered straightforwardly into a computer and compared withthe corresponding information for any other living thing. Because DNA is subjectto random changes that accumulate over long periods of time (as we shall seeshortly), the number of differences between the DNA sequences of two organisms can provide a direct, objective, quantitative indication of the evolutionarydistance between them.This approach has shown that the organisms that were traditionally classedtogether as “bacteria” can be as widely divergent in their evolutionary origins asis any prokaryote from any eukaryote.
It is now clear that the prokaryotes comprise two distinct groups that diverged early in the history of life on Earth, beforethe eukaryotes diverged as a separate group. The two groups of prokaryotes arecalled the bacteria (or eubacteria) and the archaea (or archaebacteria). Detailedgenome analyses have recently revealed that the first eukayotic cell formed after a6 µmFigure 1–16 A lithotrophic bacterium.Beggiatoa, which lives in sulfurousenvironments, gets its energy by oxidizingH2S and can fix carbon even in the dark.Note the yellow deposits of sulfur inside thecells. (Courtesy of Ralph W. Wolfe.)THE DIVERSITY OF GENOMES AND THE TREE OF LIFE15BACTRIAHaloferaxMethanocyanobacteria thermobacterBacillushumanSulfolobusAeropyrummaizeEUKyeastARYOTEParameciumMethanococcusSEA R CH A E ADictyosteliumEuglenaE. coliThermotogaAquifexcommonancestorcellfirst eukaryoteTrypanosomaGiardiaTrichomonas1 change/10 nucleotidesparticular type of ancient archaeal cell engulfed an ancient bacterium (see Figure12–3).
Thus, the living world today is considered to consist of three major divisionsor domains: bacteria, archaea, and eukaryotes (Figure 1–17).Archaea are often found inhabiting environmentsthatm1.21/1.17we humans avoid, suchMBoC6as bogs, sewage treatment plants, ocean depths, salt brines, and hot acid springs,although they are also widespread in less extreme and more homely environments, from soils and lakes to the stomachs of cattle. In outward appearance theyare not easily distinguished from bacteria. At a molecular level, archaea seem toresemble eukaryotes more closely in their machinery for handling genetic information (replication, transcription, and translation), but bacteria more closely intheir apparatus for metabolism and energy conversion.
We discuss below howthis might be explained.Some Genes Evolve Rapidly; Others Are Highly ConservedBoth in the storage and in the copying of genetic information, random accidentsand errors occur, altering the nucleotide sequence—that is, creating mutations.Therefore, when a cell divides, its two daughters are often not quite identicalto one another or to their parent.
On rare occasions, the error may represent achange for the better; more probably, it will cause no significant difference inthe cell’s prospects. But in many cases, the error will cause serious damage—forexample, by disrupting the coding sequence for a key protein. Changes due tomistakes of the first type will tend to be perpetuated, because the altered cell hasan increased likelihood of reproducing itself. Changes due to mistakes of the second type—selectively neutral changes—may be perpetuated or not: in the competition for limited resources, it is a matter of chance whether the altered cell orits cousins will succeed. But changes that cause serious damage lead nowhere:the cell that suffers them dies, leaving no progeny.
Through endless repetition ofthis cycle of error and trial—of mutation and natural selection—organisms evolve:their genetic specifications change, giving them new ways to exploit the environment more effectively, to survive in competition with others, and to reproducesuccessfully.Some parts of the genome will change more easily than others in the course ofevolution.
A segment of DNA that does not code for protein and has no significantregulatory role is free to change at a rate limited only by the frequency of random errors. In contrast, a gene that codes for a highly optimized essential proteinor RNA molecule cannot alter so easily: when mistakes occur, the faulty cells arealmost always eliminated. Genes of this latter sort are therefore highly conserved.Through 3.5 billion years or more of evolutionary history, many features of thegenome have changed beyond all recognition, but the most highly conservedgenes remain perfectly recognizable in all living species.Figure 1–17 The three major divisions(domains) of the living world. Note thatthe word bacteria was originally used torefer to prokaryotes in general, but morerecently has been redefined to refer toeubacteria specifically. The tree shownhere is based on comparisons of thenucleotide sequence of a ribosomal RNA(rRNA) subunit in the different species, andthe distances in the diagram representestimates of the numbers of evolutionarychanges that have occurred in thismolecule in each lineage (see Figure 1–18).The parts of the tree shrouded in graycloud represent uncertainties about detailsof the true pattern of species divergencein the course of evolution: comparisonsof nucleotide or amino acid sequencesof molecules other than rRNA, as well asother arguments, can lead to somewhatdifferent trees.
As indicated, the nucleus ofthe eukaryotic cell is now thought to haveemerged from a sub-branch within thearchaea, so that in the beginning the treeof life had only two branches—bacteriaand archaea.16Chapter 1: Cells and GenomesGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCChumanGCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTTAAAGGAATTGGCGGGGGAGCACTACAACGGGTGGAGCCTGCGGTTTAATTGGATTCAACGCCGGGCATCTTACCAMethanococcusACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGC.ACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTE.
coliGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCChumanThese latter genes are the ones we must examine if we wish to trace family relationships between the most distantly related organisms in the tree of life. The initial studies that led to the classification of the living world into the three domainsof bacteria, archaea, and eukaryotes were based chiefly on analysis of one of therRNA components of the ribosome. Because the translation of RNA into protein isfundamental to all living cells, this component of the ribosome has been very wellconserved since early in the history of life on Earth (Figure 1–18).MBoC6 m1.22/1.18Most Bacteria and Archaea Have 1000–6000 GenesNatural selection has generally favored those prokaryotic 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.
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