Forcing evolution: Molecular Evolution and Diversity (BBSRC), University of Warwick, UK, 10-11 May 1999. British Biotechnology and Biological Sciences Research Council.
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Animals↗
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On the generation of information as motive power for molecular evolution.
Molecular evolution can be described as a learning process during which previously inanimate matter developed the ability to organize all the reaction pathways that establish a living system. Common to all natural self-organizing procedures is the ability of matter to store, process and evaluate the information achieved by learning. Genetic information which is stored in RNA or DNA is the object of natural evolution. With the recognition of nature's concepts, evolutionary optimization was applied to biopolymers that are not optimally adapted for particular technical or medical purposes. Information can also be stored in molecules with structures and chemical properties that are completely different from nucleic acids. Therefore, optimization processes that mimic the natural evolutionary strategies can also be applied to small organic molecules. Much effort has been made theoretically and practically to find a certain optimized species within the (hyper)astronomical number of possible sequence alternatives. From a series of computer experiments it can be concluded that it is not necessary to search the entire sequence space in order to find a particular structure; this is advantageous because the diversity of mutant libraries that can realistically be achieved in the laboratory never extends to the number of theoretically possible sequences. Molecular mutant libraries that serve as starting populations for in vitro selection have been constructed for nucleic acids, proteins, peptides and small organic molecules.
Journal Article↗
Molecular evolution caught in action: gene duplication and evolution of molecular isoforms of prothrombin activators in Pseudonaja textilis (brown snake).
BACKGROUND: The evolution of structurally and functionally similar proteins with highly diverse physiological roles within a single organism is of great interest. Australian elapid snakes offer an excellent opportunity to study the molecular evolution of prothrombin activators. Venom from Pseudonaja textilis contains pseutarin C, a group C prothrombin activator. Its enzymatic subunit is structurally and functionally similar to mammalian factor (F) Xa, whereas its non-enzymatic subunit is similar to FVa. As vertebrates, the snakes also contain a system to activate prothrombin in their own blood during injury. These hemostatic factors are produced in the liver. RESULTS: Here we describe the presence of two molecular forms of FX expressed in the liver of P. textilis. Both isoforms have molecular signatures and domain architecture of FX. However, one isoform shows approximately 94% sequence identity with the snake FX from Tropidechis carinatus, whereas the other is much closer (90% identity) to the catalytic subunit of pseutarin C (PCCS). Real-time polymerase chain reaction reveals that the latter isoform is expressed approximately 56 000 times lower in the liver of P. textilis. However, the isoforms are not expressed in the venom gland. CONCLUSION: A detailed analysis of deletions and insertions along with the sequence indicates that the second isoform is an intermediate caught in the evolution of venom prothrombin activator from the blood coagulation FX. Thus, this isoform represents a 'molecular fossil' and reveals the likely evolutionary path of recruitment of FX in the venom gland.
Amino Acid Sequence↗
Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus.
Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients (magnitude of > 0.42; P < 0.01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolutionarily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (pi), was estimated for HSV-1 genomes within (pi x or pi y) and between (pi xy) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0.0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (pi xy) was highest between isolates from the three Asian countries and Kenya (0.0075 to 0.0081) and lowest among those from the three Asian countries (0.0032 to 0.0040). The mutation rate (lambda) for HSV-1 was estimated to be 3.5 x 10(-8)/site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.
Biological Evolution↗
Sociality and the rate of molecular evolution.
The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of "nearly neutral" mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs, and nontranslated sequences). By including a wide range of social taxa, we were able to test whether there is a general influence of sociality on rates of molecular evolution and to test specific predictions of the hypothesis: (1) that social species have faster rates because they have reduced effective population sizes; (2) that mitochondrial genes would show a greater effect of sociality than nuclear genes; and (3) that rates of molecular evolution should be correlated with the degree of sociality. We find no consistent pattern in rates of molecular evolution between social and nonsocial lineages and no evidence that mitochondrial genes show faster rates in social taxa. However, we show that the most highly eusocial Hymenoptera do have faster rates than their nonsocial relatives. We also find that social parasites (that utilize the workers from related species to produce their own offspring) have faster rates than their social relatives, which is consistent with an effect of lower effective population size on rate of molecular evolution. Our results illustrate the importance of allowing for phylogenetic nonindependence when conducting investigations of determinants of variation in rate of molecular evolution.
Animals↗
Some aspects of E. coli promoter evolution observed in a molecular evolution experiment.
We devised a molecular evolution procedure to evolve E. coli promoter sequences and applied it to observe an arbitrary, nonfunctional sequence evolving into functional promoters. In the experiments, DNA sequence variations were generated with error-prone PCR and were inserted in the promoter region of the cat (chloramphenicol acetyl transferase) gene on a plasmid. Upon transforming the cells, functional promoters on the plasmid were selected according to the chloramphenicol resistance. Within a few cycles of mutation-selection, promoters emerged, and the sequences converged into a small number of groups. In the process, the extended minus 10 type of promoters emerged quickly, and small deletions were often involved in adjusting the length between the -35 and the -10 elements. Our results also suggest a possible selection for promoter stability against mutation.
Base Sequence↗
[Molecular evolution].
The molecular evolution is considered in several protein families. It can be studied with the data of an entirely known structure, like in hemoglobin or cytochrome, or of only partial structural data, as for proteases or immunoglobulins. In the case of isozymes the study of physico-chemical and kinetic properties is more indirect. Finally, it is shown that the molecular mechanisms are always the same, happening probably at the same frequency, the differences being due to a variable selection by molecular constraints and adaptation to the environment.
Biological Evolution↗
A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.
Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.
Animals↗
Creating novel enzymes by applied molecular evolution.
Recent molecular techniques have made it feasible to simulate evolutionary processes and apply in vitro selection to evolve enzymes with novel properties that may have potential benefits for medical and industrial applications. The characterization of such mutants has also provided new insights into how molecular structure determines enzyme function.
Amino Acid Sequence↗
Estimating the rate of evolution of the rate of molecular evolution.
A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.
Algorithms↗
Episodic evolution of protein hormones: molecular evolution of pituitary prolactin.
Previous studies have shown that pituitary growth hormone displays an episodic pattern of evolution, with a slow underlying evolutionary rate and occasional sustained bursts of rapid change. The present study establishes that pituitary prolactin shows a similar pattern. During much of tetrapod evolution the sequence of prolactin has been strongly conserved, showing a slow basal rate of change (approx 0.27x10(9) substitutions/amino acid site/year). This rate has increased substantially ( approximately 12- to 38-fold) on at least four occasions during eutherian evolution, during the evolution of primates, artiodactyls, rodents, and elephants. That these increases are real and not a consequence of inadvertant comparison of paralogous genes is shown (for at least the first three groups) by the fact that they are confined to mature protein coding sequence and not apparent in sequences coding for signal peptides or when synonymous substitutions are examined. Sequences of teleost prolactins differ markedly from those of tetrapods and lungfish, but during the course of teleost evolution the rate of change of prolactin has been less variable than that of growth hormone. It is concluded that the evolutionary pattern seen for prolactin shows long periods of near-stasis interrupted by occasional bursts of rapid change, resembling the pattern seen for growth hormone in general but not in detail. The most likely basis for these bursts appears to be adaptive evolution though the biological changes involved are relatively small.
Animals↗
Genomes and evolution Population genetics and molecular evolution of whole genomes.
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Alternative Splicing↗
Mutant library construction in directed molecular evolution: casting a wider net.
Directed molecular evolution imitates the natural selection process in the laboratory to find mutant proteins with improved properties in the expected aspects by exploring the encoding sequence space. The success of directed molecular evolution experiment depends on the quality of artificially prepared mutant libraries and the availability of convenient high-throughput screening methods. Well-prepared libraries promise the possibility of obtaining desired mutants by screening a library containing a relatively small number of mutants. This article summarizes and reviews the currently available methodologies widely used in directed evolution practices in the hope of providing a general reference for library construction. These methods include error-prone polymerase chain reaction (epPCR), oligonucleotide-based mutagenesis, and genetic recombination exemplified by DNA shuffling and its derivatives. Another designed method is also discussed, in which B-lymphocytes are fooled to mutate nonantibody foreign proteins through somatic hypermutation (SHM).
Animals↗
Testing the covarion hypothesis of molecular evolution.
The covarion hypothesis of molecular evolution states that the fixation of mutations may alter the probability that any given position will fix the next change. Tests of this hypothesis using the divergence of real sequences are compromised because models of rate variation among sites (e.g., the gamma version of the one-parameter equation) predict sequence divergence values similar to those for the covarion process. This study therefore focuses on the extent to which the varied and unvaried codons of two well-diverged taxa are the same, because fewer are expected by the covarion hypothesis than by the gamma model. The data for these tests are the protein sequences of Cu, Zn superoxide dismutase (SOD) for mammals and plants. Simulation analyses show that the covarion hypothesis makes better predictions about the frequencies of varied and unhit positions in common between these two taxa than does the gamma version of the one-parameter model. Furthermore, the analysis of SOD tertiary structure demonstrates that mammal and plant variabilities are distributed differently on the protein. These results support the conclusions that the variable and invariable codons of mammal and plant SODs are different and that the covarion model explains the evolution of this protein better than the gamma version of the one-parameter process. Unlike other models, the covarion hypothesis accounts for rate fluctuations among positions over time, which is an important parameter of molecular evolution.
Animals↗
Molecular evolution in bacteria: surfaces, cathodes and anodes.
Molecular evolution is examined in bacteria with an emphasis on mineral surfaces, membranes, cathodes and anodes. In early molecular evolution, cathode-anode system may have been naturally occurring on a nm to micron scale. Secondly, the cathode-anode system could have been separated by a primitive, permeable lipid or microsphere on a mineral surface, that was a precursor of a more advanced membrane with a charge differential on either side of the membrane. These aspects will be considered from a theoretical evolutionary perspective.
Bacteria↗
Molecular clocks in reptiles: life history influences rate of molecular evolution.
Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between body size and substitution rate for many molecular data sets. Both the generality and the cause of the negative body size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size, age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles, lizards, snakes, crocodile, and tuatara. Although this study was limited by the number of comparisons for which both sequence and life-history data were available, the results suggest that a negative body size trend in rate of molecular evolution may be a general feature of reptile molecular evolution, consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.
Aging↗
The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution.
Using a water-based prebiotic model of sugar synthesis involving glycolaldehyde self-condensation, we demonstrate that homochiral L-dipeptide catalysts lead to the stereospecific syntheses of tetroses. The asymmetric effect is largest for erythrose, which may reach a D-enantiomeric excess of >80% with L-Val-L-Val catalyst. Based on results obtained with various peptides, we propose a possible catalytic-reaction intermediate, consisting of an imidazolidinone ring formed between the two nitrogen atoms of the peptide catalyst and the C1 of one glycolaldehyde molecule. The study was motivated by the premise that exogenous material, such as the nonracemic amino acids found in meteorites, could have participated in the terrestrial evolution of molecular asymmetry by stereospecific catalysis. Because peptides might have formed readily on the early Earth, it is possible that their catalytic contribution was relevant in the prebiotic processes that preceded the onset of life.
Catalysis↗
Molecular evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts.
The transporters of the ATP-Binding Cassette (ABC) Superfamily involved in the Multidrug Resistance (MDR) phenomena are also known as ABC-Pleiotropic Drug Resistance (PDR) proteins. The homologs of the Saccharomyces cerevisiae SNQ2 and PDR18 genes were identified in 171 yeast genomes, representing 68 different hemiascomycetous species. All early-divergent yeast species analyzed in this work lack Snq2/Pdr18 homologs, suggesting that the origin of these ABC-PDR genes in hemiascomycete yeasts resulted from a horizontal transfer event. The evolutionary pathway of the Snq2/Pdr18 protein subfamily in pathogenic Candida species was also reconstructed, revealing a main gene lineage leading to the Candida albicans SNQ2 gene. The results indicate that, after the gene duplication event at the origin of the SNQ2/PDR18 paralogs, the PDR18 ortholog has been under strong diversifying selection and suggest that a small portion of the sequence of the SNQ2 ancestral ortholog might have been under mild positive selection. The results also showed that strong positive selection was exerted over one of the two paralogs generated by the Whole Genome Duplication (WGD) event, corresponding to the duplicate at the origin of a "short-lived" WGD sublineage.
Evolution, Molecular↗