B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 15
Текст из файла (страница 15)
By this route, or by virus-mediatedtransfer, bacteria and archaea in the wild can acquire genes from neighboringcells relatively easily. Genes that confer resistance to an antibiotic or an abilityto produce a toxin, for example, can be transferred from species to species andMBoC6 m1.27/1.22provide the recipient bacterium with a selective advantage. In this way, new andsometimes dangerous strains of bacteria have been observed to evolve in the bacterial ecosystems that inhabit hospitals or the various niches in the human body.For example, horizontal gene transfer is responsible for the spread, over the past40 years, of penicillin-resistant strains of Neisseria gonorrhoeae, the bacteriumthat causes gonorrhea.
On a longer time scale, the results can be even more profound; it has been estimated that at least 18% of all of the genes in the present-daygenome of E. coli have been acquired by horizontal transfer from another specieswithin the past 100 million years.Sex Results in Horizontal Exchanges of Genetic Information Withina SpeciesHorizontal gene transfer among prokaryotes has a parallel in a phenomenonfamiliar to us all: sex.
In addition to the usual vertical transfer of genetic material from parent to offspring, sexual reproduction causes a large-scale horizontaltransfer of genetic information between two initially separate cell lineages—thoseof the father and the mother. A key feature of sex, of course, is that the geneticexchange normally occurs only between individuals of the same species. But nomatter whether they occur within a species or between species, horizontal geneFigure 1–22 The viral transfer of DNAinto a cell.
(A) An electron micrographof particles of a bacterial virus, the T4bacteriophage. The head of this viruscontains the viral DNA; the tail containsthe apparatus for injecting the DNA into ahost bacterium. (B) A cross section of anE. coli bacterium with a T4 bacteriophagelatched onto its surface. The large darkobjects inside the bacterium are theheads of new T4 particles in the courseof assembly. When they are mature,the bacterium will burst open to releasethem. (C–E) The process of DNA injectioninto the bacterium, as visualized inunstained, frozen samples by cryoelectronmicroscopy. (C) Attachment begins.(D) Attached state during DNA injection.(E) Virus head has emptied all of its DNAinto the bacterium. (A, courtesy of JamesPaulson; B, courtesy of Jonathan Kingand Erika Hartwig from G.
Karp, Cell andMolecular Biology, 2nd ed. New York: JohnWiley & Sons, 1999. With permission fromJohn Wiley & Sons; C–E, courtesy of IanMolineux, University of Texas at Austin andJun Liu, University of Texas Health ScienceCenter, Houston.)20Chapter 1: Cells and Genomestransfers leave a characteristic imprint: they result in individuals who are relatedmore closely to one set of relatives with respect to some genes, and more closely toanother set of relatives with respect to others. By comparing the DNA sequences ofindividual human genomes, an intelligent visitor from outer space could deducethat humans reproduce sexually, even if it knew nothing about human behavior.Sexual reproduction is widespread (although not universal), especiallyamong eukaryotes. Even bacteria indulge from time to time in controlled sexualexchanges of DNA with other members of their own species.
Natural selectionhas clearly favored organisms that can reproduce sexually, although evolutionarytheorists dispute precisely what that selective advantage is.The Function of a Gene Can Often Be Deduced from Its SequenceFamily relationships among genes are important not just for their historical interest, but because they simplify the task of deciphering gene functions. Once thesequence of a newly discovered gene has been determined, a scientist can tap afew keys on a computer to search the entire database of known gene sequencesfor genes related to it. In many cases, the function of one or more of these homologs will have been already determined experimentally.
Since gene sequencedetermines gene function, one can frequently make a good guess at the functionof the new gene: it is likely to be similar to that of the already known homologs.In this way, it is possible to decipher a great deal of the biology of an organismsimply by analyzing the DNA sequence of its genome and using the informationwe already have about the functions of genes in other organisms that have beenmore intensively studied.More Than 200 Gene Families Are Common to All Three PrimaryBranches of the Tree of LifeGiven the complete genome sequences of representative organisms from all threedomains—archaea, bacteria, and eukaryotes—we can search systematically forhomologies that span this enormous evolutionary divide.
In this way we can beginto take stock of the common inheritance of all living things. There are considerable difficulties in this enterprise. For example, individual species have often lostsome of the ancestral genes; other genes have almost certainly been acquired byhorizontal transfer from another species and therefore are not truly ancestral,even though shared. In fact, genome comparisons strongly suggest that both lineage-specific gene loss and horizontal gene transfer, in some cases between evolutionarily distant species, have been major factors of evolution, at least amongprokaryotes. Finally, in the course of 2 or 3 billion years, some genes that wereinitially shared will have changed beyond recognition through mutation.Because of all these vagaries of the evolutionary process, it seems that onlya small proportion of ancestral gene families has been universally retained ina recognizable form.
Thus, out of 4873 protein-coding gene families defined bycomparing the genomes of 50 species of bacteria, 13 archaea, and 3 unicellulareukaryotes, only 63 are truly ubiquitous (that is, represented in all the genomesanalyzed). The great majority of these universal families include components ofthe translation and transcription systems. This is not likely to be a realistic approximation of an ancestral gene set. A better—though still crude—idea of the latter canbe obtained by tallying the gene families that have representatives in multiple, butnot necessarily all, species from all three major domains. Such an analysis reveals264 ancient conserved families.
Each family can be assigned a function (at least interms of general biochemical activity, but usually with more precision). As shownin Table 1–1, the largest number of shared gene families are involved in translation and in amino acid metabolism and transport. However, this set of highly conserved gene families represents only a very rough sketch of the common inheritance of all modern life. A more precise reconstruction of the gene complementof the last universal common ancestor will hopefully become feasible with furthergenome sequencing and more sophisticated forms of comparative analysis.THE DIVERSITY OF GENOMES AND THE TREE OF LIFE21TABLE 1–1 The Number of Gene Families, Classified by Function, Common to All Three Domains of the Living WorldInformation processingTranslationTranscriptionReplication, recombination, and repairMetabolism63713Cellular processes and signalingEnergy production and conversion19Carbohydrate transport and metabolism16Amino acid transport and metabolism43Nucleotide transport and metabolism1522Cell-cycle control, mitosis, and meiosis2Coenzyme transport and metabolismDefense mechanisms3Lipid transport and metabolism9Signal transduction mechanisms1Inorganic ion transport and metabolism8Cell wall/membrane biogenesis2Secondary metabolite biosynthesis,transport, and catabolism5Intracellular trafficking and secretion4Poorly characterizedPost-translational modification, proteinturnover, chaperones8General biochemical function predicted;specific biological role unknown24For the purpose of this analysis, gene families are defined as “universal” if they are represented in the genomes of at least two diverse archaea(Archaeoglobus fulgidus and Aeropyrum pernix), two evolutionarily distant bacteria (Escherichia coli and Bacillus subtilis), and one eukaryote(yeast, Saccharomyces cerevisiae).
(Data from R.L. Tatusov, E.V. Koonin and D.J. Lipman, Science 278:631–637, 1997; R.L. Tatusov et al., BMCBioinformatics 4:41, 2003; and the COGs database at the US National Library of Medicine.)Mutations Reveal the Functions of GenesWithout additional information, no amount of gazing at genome sequences willreveal the functions of genes. We may recognize that gene B is like gene A, buthow do we discover the function of gene A in the first place? And even if we knowthe function of gene A, how do we test whether the function of gene B is trulythe same as the sequence similarity suggests? How do we connect the world ofabstract genetic information with the world of real living organisms?The analysis of gene functions depends on two complementary approaches:genetics and biochemistry.
Genetics starts with the study of mutants: we eitherfind or make an organism in which a gene is altered, and then examine the effectson the organism’s structure and performance (Figure 1–23). Biochemistry moredirectly examines the functions of molecules: here we extract molecules from anorganism and then study their chemical activities. By combining genetics andbiochemistry, it is possible to find those molecules whose production depends ona given gene. At the same time, careful studies of the performance of the mutantorganism show us what role those molecules have in the operation of the organism as a whole. Thus, genetics and biochemistry used in combination with cellbiology provide the best way to relate genes and molecules to the structure andfunction of an organism.In recent years, DNA sequence information and the powerful tools of molecular biology have accelerated progress.
From sequence comparisons, we can oftenidentify particular subregions within a gene that have been preserved nearlyunchanged over the course of evolution. These conserved subregions are likelyto be the most important parts of the gene in terms of function. We can test theirindividual contributions to the activity of the gene product by creating in the laboratory mutations of specific sites within the gene, or by constructing artificialhybrid genes that combine part of one gene with part of another.
Organisms canbe engineered to make either the RNA or the protein specified by the gene in largequantities to facilitate biochemical analysis. Specialists in molecular structure candetermine the three-dimensional conformation of the gene product, revealingthe exact position of every atom in it. Biochemists can determine how each of the5 µmFigure 1–23 A mutant phenotypereflecting the function of a gene. A normalyeast (of the species Schizosaccharomycespombe) is compared with a mutant in whicha change in a single gene has converted thecell from a cigar shape (left) to a T shapeMBoC6 m1.28/1.23(right). The mutant gene therefore has afunction in the control of cell shape. Buthow, in molecular terms, does the geneproduct perform that function? That is aharder question, and it needs biochemicalanalysis to answer it.
(Courtesy of KennethSawin and Paul Nurse.)22Chapter 1: Cells and Genomesparts of the genetically specified molecule contributes to its chemical behavior.Cell biologists can analyze the behavior of cells that are engineered to express amutant version of the gene.There is, however, no one simple recipe for discovering a gene’s function, andno simple standard universal format for describing it. We may discover, for example, that the product of a given gene catalyzes a certain chemical reaction, andyet have no idea how or why that reaction is important to the organism.
![](https://s.studizba.com/z.php?f=/templates/si/i/noavatar.png&w=100&h=100&t=1"){kind=avatar}
