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ScienceWeek
GENOME BIOLOGY: ON GENOME INSTABILITY
The following points are made by S.M. Rosenberg and P.J. Hastings (Nature 2004 430:625):
1) DNA carries the coded information that specifies the size, shape, body plan, and many other basic characteristics of most organisms. To transmit these characteristics faithfully, DNA must pass from generation to generation with relatively few mutations. But mutations do happen, and can have profound consequences. These include inherited diseases, cancer, and drug-resistant infections, but also the genetic differences among individuals that, through natural selection, drive evolution.
2) Until now, mutations seemed to be relatively rare and to occur in a characteristic spectrum. But such observations are challenged by recent work[1] that used a particularly powerful way to hunt for mutations in the roundworm Caenorhabditis elegans -- and found at least ten times more mutations, and a different assortment, than anticipated.
3) Traditional ways of estimating mutations are indirect[2], involving either phylogenetic studies of wild organisms or phenotypic methods in the laboratory. Phylogenetic studies involve comparing DNA sequences between species and estimating the number and kinds of changes that have occurred since the species diverged. Phenotypic methods rely on the ability of some mutations to change a trait (phenotype) of an organism. After a defined number of generations, rare mutants carrying the new trait are quantified, and mutation rates are calculated and then extrapolated to predict rates for the whole genome. This extrapolation takes into account the genome's size and the fraction of mutations that has been estimated to produce phenotypic change (about one-third)[2].
4) However, both approaches probably underestimate the inherent mutation rate and skew the variety of mutations found. For instance, some mutations are harmful, and so the organisms that carry them are less likely to contribute to the next generation (they are "selected against"), both in the wild and in large cultures. And the fraction of mutations that produces no phenotypic change might be larger than imagined.
5) Denver et al[1] bypassed the phenotype-bias problem by directly sequencing randomly chosen stretches of DNA in laboratory-grown worms. They also minimized selection against harmful mutations by maintaining many lines of worms, separating a single worm from each progeny and allowing it to produce the next generation by self-fertilization, without competing with other worms. Rapid and severe loss of fitness occurs in these worms because, when their numbers are reduced to one repeatedly, random mutations become fixed -- a phenomenon known as "Muller's ratchet"[3].
6) From these pampered worms, Denver et al[1] sequenced four million base pairs of DNA, and found 30 new mutations compared with the original animals. This equates to a rate of 2.1 mutations per genome per generation. This rate is at least ten times higher than those reported previously in worms and other DNA-based organisms, which curiously maintain constant predicted mutation rates per genome, irrespective of genome size[2]. Moreover, the kinds of mutations differ from those previously seen in many organisms, even worms.[3-5]
References (abridged):
1. Denver, D. R., Morris, K., Lynch, M. & Thomas, W. K. Nature 430, 679-682 (2004)
2. Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Genetics 148, 1667-1686 (1998)
3. Muller, H. J. Mutat. Res. 106, 2-9 (1964)
4. Rutherford, S. L. & Lindquist, S. Nature 396, 336-342 (1998)
5. Caporale, L. H. Annu. Rev. Microbiol. 57, 467-485 (2003)
Nature http://www.nature.com/nature
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Related Material:
MOLECULAR BIOLOGY: A MINIMAL GENOME
Notes by ScienceWeek:
The field of molecular biology is currently engaged in the most extensive project of reverse engineering ever conceived: the elucidation of the molecular components and events that constitute living systems. One central question is simply stated: What is the minimal number of genes necessary to maintain the viability of a living system?
Apart from viruses, the smallest replicating biological systems known are the mycoplasmas (mollicutes). There are over 150 species of this class of cell-wall-free bacteria, some of which are human pathogens. Mycoplasmas apparently evolved from other bacteria by reduction of genome size: the smallest genome of the mycoplasmas is little more than twice the genome size of certain large viruses. Mycoplasmas are the smallest organisms that can be free-living in nature and self-replicating on laboratory media (viruses replicate only in bacteria and other cells). Mycoplasmas range from 125 to 250 nanometers in size. They change shape readily (pleomorphism) because they lack a cell wall, being bounded by a triple-layered lipoprotein membrane that contains a sterol.
The genome of Mycoplasma genitalium (an organism that causes one form of the urinary tract infection urethritis), which has been completely sequenced, consists of 580 kilobases comprising 517 genes (480 protein-coding genes; 37 genes for RNAs), and this is the smallest gene complement for any independently replicating cell so far identified.
The following points are made by C.A. Hutchinson III et al (Science 1999 286:2165):
1) The authors report the use of molecular genetic methods (global transposon mutagenesis) to identify nonessential genes in M. genitalium under laboratory growth conditions. The authors report their analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including approximately 100 genes of unknown function.
2) The authors conclude: "The presence of so many genes of unknown function among the essential genes of the simplest known cell suggests that all the basic molecular mechanisms underlying cellular life may not yet have been described. The essential gene set is not the same as the minimal genome. It is clear that genes that are individually dispensable may not be simultaneously dispensable. The data presented here suggest some specific experiments that could be carried out as a first step in the engineering of a cell with a minimal genome in the laboratory environment."
Science http://www.sciencemag.org
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Related Material:
MOLECULAR BIOLOGY: DNA LOSS AS A DETERMINANT OF GENOME SIZE
Notes by ScienceWeek:
One of the current riddles in molecular biology is the "C-value Paradox", the essential of which are as follows: The total amount of DNA in the (*haploid) genome is a characteristic of each living species and is known as the "C-value". There is enormous variation in the range of C-values, from less than 10^(6) nucleotide base pairs to as much as 10^(11) nucleotide base pairs for certain plants and amphibians. In general, there is an increase in the minimum genome size found in each phylum as the complexity of the phylum increases [*Note #1].
But along with this general increase in the absolute amounts of DNA in the higher phyla, a number of wide variations in genome size within the same phylum occur. Birds, reptiles, and mammals all show little variation of C-value within the phylum, with a range of genome size in each case of approximately 2-fold, but in insects, amphibians, and plants there is wide range of C-values, often more than 10-fold.
For example, the common housefly (Musca domestica) has a genome 6 times larger than the common fruit fly (Drosophila melanogaster). Within protozoa, the genome size variation can be as large as 5800-fold; within arthropods 250-fold; within fish 550-fold; within algae 5000-fold. In amphibians, the smallest genomes are just below 10^(9) nucleotide base pairs, while the largest genomes are almost 10^(11) nucleotide base pairs, and it is difficult to believe this could reflect a 100-fold difference in the number of genes needed to specify different amphibians. Thus the problem: How do we account for these differences within phyla?
The following points are made by D.A. Petrov et al (Science 2000 287:1060):
1) The Drosophila fruit fly species, which have relatively small genomes, spontaneously lose DNA at a much higher rate than mammalian species, which have large genomes. Although many mechanisms can affect genome size, studies of Drosophila suggest that some differences in haploid genome size may result from variation in the rate of spontaneous loss of *nonessential DNA.
2) In connection with this hypothesis, the authors examined the insertion-deletion mutation spectrum in Hawaiian crickets (Laupala), which have a large genome size -- 11-fold larger than that of Drosophila, in order to test the prediction of a lower rate of DNA loss in Laupala than in Drosophila. The basis for the method of the authors is that certain DNA sequences apparently unconstrained by natural selection exhibit patterns of substitution that reflect the underlying spectra of spontaneous mutations. The authors report their results indicate that consistent with their hypothesis, DNA loss is more than 40 times slower in Laupala than in Drosophila, with a higher rate of DNA loss resulting in a lower steady-state number of *pseudogenes in relatively small genomes.
3) The authors suggest that the key question that remains is empirical and quantitative: How much of the variation in genome size can be explained by variation in the insertion-deletion spectra? The authors suggest their method can be used to answer this question in a wide variety of eukaryotes and "thus to test the mutational hypothesis for the C-value paradox in a comprehensive fashion."
Science http://www.sciencemag.org
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Notes by ScienceWeek:
haploid: In general, germ cells (egg cells and sperm cells) and somatic cells (non-germ cells) carry different numbers of chromosomes, with germ cells carrying exactly half the number (haploid number) of somatic cell chromosomes (diploid number).
Note #1: There are important exceptions to the general rule that genome size increases with complexity of the phylum. Many species of plants, for example, have a genome 2 orders of magnitude larger than the human genome.
nonessential DNA: (junk DNA; selfish DNA) In eukaryotes (cells with a nucleus), the bulk of nuclear DNA is apparently noncoding, i.e., it does not get translated into protein polypeptide chains, and it does not code for RNA used in cell function. This sort of DNA, of unknown function, is called "junk DNA", and much of it is highly repetitive and present in many copies scattered or clustered in the chromosomes.
insertion-deletion mutation spectrum: In this context, the insertions and deletions are random insertions and deletions of nucleotide bases in the genome.
pseudogenes: The term "pseudogene" refers to a gene bearing close resemblance to a known gene at a different locus, but rendered nonfunctional by additions or deletions in its structure that prevent normal expression of the gene.
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