On the rate of molecular evolution

Summary There are at least two outstanding features that characterize the rate of evolution at the molecular level as compared with that at the phenotypic level. They are; (1) remarkable uniformity for each molecule, and (2) very high overall rate when extrapolated to the whole DNA content.The population dynamics for the rate of mutant substitution was developed, and it was shown that if mutant substitutions in the population are carried out mainly by natural selection, the rate of substitution is given byk = 4 N _e s ₁ v, whereN _e is the effective population number,s ₁ is the selective advantage of the mutants, andv is the mutation rate per gamete for such advantageous mutants (assuming that 4N _e s ₁ 1). On the other hand, if the substitutions are mainly carried out by random fixation of selectively neutral or nearly neutral mutants, we havek = v, wherev is the mutation rate per gamete for such mutants.Reasons were presented for the view that evolutionary change of amino acids in proteins has been mainly caused by random fixation of neutral mutants rather than by natural selection.It was concluded that if this view is correct, we should expect that genes of living fossils have undergone almost as many DNA base replacements as the corresponding genes of more rapidly evolving species.Contribution No. 789 from the National Institute of Genetics, Mishima, Shizuokaken 411 Japan. Aided in part by a grant-in-aid from the Ministry of Education, Japan.     

Protein phosphorylation: a motive force for adaptive evolution

Spontaneity and diversity are the intrinsic properties of protein phosphorylation. They provide living systems with opportunities for polyvariant transformation of expressed genetic information and alteration of their energy metabolism under change of living conditions. Thus, protein phosphorylation can be regarded as a molecular mechanism for adaptation and selection of mutant proteins useful for the cell, i.e. a motive force for adaptive evolution.     

基于生物适应进化原理论证生物进化的动力

文章从现有主流生物进化理论存在的问题入手, 以生物适应进化原理为认识基础, 讨论生物进化的动力, 以求对生物进化机制有一个新的认识。在薛定谔“生命赖负熵生存”观点的指导下, 提出了“负熵流”包括能量流、物质流和信息流, 以及负熵流是生命生存和发育的动力的观点。作者在原有生物适应进化原理基础上, 修改完善并提出了“DNA、RNA和蛋白质在环境作用下的生物适应进化调控系统”理论, 并根据系统发育是个体发育的“积分”的观点, 推论得出生物与环境的负熵差引起的负熵流也是生命进化的动力, 对生物进化机制作出了新的理解。基于这样的生物进化机制的认识, 提出了“进化是一个子系统在其上一等级系统中, 将自身全部或部分信息遗传给下一代子系统, 并在其适应上一等级系统过程中, 产生一些新质, 终止一些旧质, 从而在其上一等级系统中得以延续的变化过程”的概念, 并探讨了一些与进化有关的其他争议问题。     

On the nature of mutations in molecular evolution

In this work it is proposed that in evolution amino acid substitutions implying strong physico chemical and structural differences are more relevant and more frequent than substitutions between similar amino acids. This analysis is made over a group of protein families representing about 10 000 substitutions and as examples the evolutionary trees of fibrinopeptides A and calcitonins were constructed and compared.     

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

Background  

Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm.     

Pattern generation in molecular evolution: Exploitation of the variation in RNA landscapes

Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their ruggedness. Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively flat peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of neighboring RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences increases. The patterns that are generated in the RNA sequences and the RNA secondary structures are not directly selected for and can be regarded as a side effect of the evolutionary dynamics of the system. Correspondence to: M.A. Huynen     

Environmental adaptations as windows on molecular evolution

Changes in gene regulation may play an important role in adaptive evolution, particularly during adaptation to a changing environment. However, little is known about the molecular mechanisms underlying adaptively significant variation in gene regulation. To address this question, we are using environmental adaptations in populations of a fish, Fundulus heteroclitus as a window into the molecular evolution of gene regulation. F. heteroclitus are found along the East Coast of North America, with populations distributed along a steep thermal gradient. At the extremes of the species range, populations have undergone local adaptation to their habitat temperatures. A variety of genes differ in their regulation between these populations. We have determined the mechanism responsible for changes in lactate dehydrogenase-B (Ldh-B) gene regulation. A limited number of mutations in the regulatory sequence of this gene result in changes in its expression. Both the phenotypic (increased LDH activity) and genotypic (changes in Ldh-B regulatory sequences) differences between populations have been shown to be affected by natural selection, rather than genetic drift. Therefore, even a small number of mutations within important regulatory sequences can provide evolutionarily significant variation and have an impact on environmental adaptation.     

On the frequency of arginine in proteins and its implications for molecular evolution

Evidence is presented against the concept that arginine appeared later in the evolution of life that the other common amino acids, as an ‘evolutionary intruder’. Alternative explanations for the relatively low frequency of arginine in proteins are considered, based on the proposition that there has been selection for such low frequency because of special properties of the amino acid.     

Proton motive force generation from stored polymers for the uptake of acetate under anaerobic conditions

The bacteria facilitating enhanced biological phosphorus removal gain a selective advantage from intracellularly stored polymer-driven substrate uptake under anaerobic conditions during sequential anaerobic : aerobic cycling. Mechanisms for these unusual membrane transport processes were proposed and experimentally validated using selective inhibitors and highly-enriched cultures of a polyphosphate-accumulating organism, Accumulibacter, and a glycogen-accumulating organism, Competibacter. Acetate uptake by both Accumulibacter and Competibacter was driven by a proton motive force (PMF). Stored polymers were used to generate the PMF -Accumulibacter used phosphate efflux through the Pit transporter, while Competibacter generated a PMF by proton efflux through the ATPase and fumarate reductase in the reductive TCA cycle.     

On the molecular mechanism of the evolution of genetic code alterations

Alterations to the standard genetic code have been found in both prokaryotes and eukaryotes. This finding demolished the central dogma of molecular biology, postulated by Crick in 1968, of an immutable and universal genetic code, and raised the question of how organisms survive genetic code alterations. Recent studies suggest that genetic code alterations are driven by selection using a mechanism that requires translational ambiguity. In C. albicans, the leucine CUG codon is decoded as serine through structural alterations of the translational machinery, in particular, of Ser-tRNA_CAG, which has dual identity and novel decoding properties. Here, we review the molecular mechanism of CUG reassignment, focusing on the structural change of the translational machinery and on the impact that such alteration had on the evolution of the Candida albicans genome. Published in Russian in Molekulyarnaya Biologiya, 2006, Vol. 40, No. 4, pp. 634–639. The text was submitted by the authors in English.     

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

The selective pressure at the protein level is usually measured by the nonsynonymous/synonymous rate ratio (omega = dN/dS), with omega < 1, omega = 1, and omega > 1 indicating purifying (or negative) selection, neutral evolution, and diversifying (or positive) selection, respectively. The omega ratio is commonly calculated as an average over sites. As every functional protein has some amino acid sites under selective constraints, averaging rates across sites leads to low power to detect positive selection. Recently developed models of codon substitution allow the omega ratio to vary among sites and appear to be powerful in detecting positive selection in empirical data analysis. In this study, we used computer simulation to investigate the accuracy and power of the likelihood ratio test (LRT) in detecting positive selection at amino acid sites. The test compares two nested models: one that allows for sites under positive selection (with omega > 1), and another that does not, with the chi2 distribution used for significance testing. We found that use of the chi(2) distribution makes the test conservative, especially when the data contain very short and highly similar sequences. Nevertheless, the LRT is powerful. Although the power can be low with only 5 or 6 sequences in the data, it was nearly 100% in data sets of 17 sequences. Sequence length, sequence divergence, and the strength of positive selection also were found to affect the power of the LRT. The exact distribution assumed for the omega ratio over sites was found not to affect the effectiveness of the LRT.     

Enzyme-coding genes as molecular clocks: The molecular evolution of animal alpha-amylases

Summary We constructed a cDNA library for the beetle,Tribolium castaneum. This library was screened using a cloned amylase gene fromDrosophila melanogaster as a molecular probe. Beetle amylase cDNA clones were isolated from this bank, and the nucleotide sequence was obtained for a cDNA clone with a coding capacity for 228 amino acids. Both the nucleotide sequence and predicted amino acid sequence were compared to our recent results forD. melanogaster alpha-amylases, along with published sequences for other alpha-amylases. The results show that animal alpha-amylases are highly conserved over their entire length. A borader comparison, which includes plant and microbial alpha-amylase sequences, indicates that parts of the gene are conserved between prokaryotes, plants, and animals. We discuss the potential importance of this and other enzyme-coding genes for the construction of molecular phylogenies and for the study of the general question of molecular clocks in evolution.     

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx)

Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were subsequently replaced with a randomized trinucleotide sequence donated by the DNA cassette termed SubSeq(NNN). The bla gene encoding TEM-1 beta-lactamase was used as a model to demonstrate the effectiveness of TriNEx. Sequence analysis revealed that the mutations were distributed throughout bla, with variants containing single, double and triple nucleotide changes. Many of the resulting amino acid substitutions had significant effects on the in vivo activity of TEM-1, including up to a 64-fold increased activity toward ceftazidime and up to an 8-fold increased resistance to the inhibitor clavulanate. Many of the observed amino acid substitutions were only accessible by exchanging at least two nucleotides per codon, including charge-switch (R164D) and aromatic substitution (W165Y) mutations. TriNEx can therefore generate a diverse range of protein variants with altered properties by combining the power of site-directed saturation mutagenesis with the capacity of whole-gene mutagenesis to randomly introduce mutations throughout a gene.     

On the trends in protein molecular evolution: Amino acid composition

Data on the amino acid composition of proteins having various functions from organisms representing different evolutionary levels (83 superfamilies) are used in order to elucidate the trends in protein molecular evolution. The interconnections evolutionary rate (rate of mutation acceptance) — amino acid composition, and evolutionary level of the organism — amino acid composition (in case of proteins of the same or very similar function) are studied. The amino acid compositions of proteins performing jointly an evolutionarily old functions are also juxtaposed. The mean contemporary protein composition is used as a basis for comparison. The obtained results are evidence in favour of the existence of a trend for an increase of the special amino acids (Met, Ile, Gln, His, Lys, Asn, Phe, Tyr, Trp, Cys) at the expense of the usual ones (Thr, Pro, Ala, Ser, Arg, Gly, Leu, Val, Glu, Asp). The tests of statistical significance of the obtained results (comparison of the mean compositions of proteins from low evolutionary level organisms with that of all sequenced proteins; comparison of the mean contemporary protein composition with that obtained after simulation of the evolutionary process) confirm and universalize the observed trend. The above results direct the attention to the concept of a smaller number of amino acids in the ancient proteins and respectively simpler genetic code. A fluctuation around the initial primitive level is suggested to explain the conservatism of proteins of the same function in evolutionarily low level organisms. The observed trend could be applied for designing new proteins.     

The evolution of the avian genome as revealed by comparative molecular cytogenetics

Birds are characterised by feathers, flight, a small genome and a very distinctive karyotype. Despite the large numbers of chromosomes, the diploid count of 2n approximately 80 has remained remarkably constant with 63% of birds where 2n = 74-86, 24% with 2n = 66-74 and extremes of 2n = 40 and 2n = 142. Of these, the most studied is the chicken (2n = 78), and molecular cytogenetic probes generated from this species have been used to further understand the evolution of the avian genome. The ancestral karyotype is, it appears, very similar to that of the chicken, with chicken chromosomes 1, 2, 3, 4q, 5, 6, 7, 8, 9, 4p and Z representing the ancestral avian chromosomes 1-10 + Z; chromosome 4 being the most ancient. Avian evolution occurred primarily in three stages: the divergence of the group represented by extant ratites (emu, ostrich etc.) from the rest; divergence of the Galloanserae (chicken, turkey, duck, goose etc.)--the most studied group; and divergence of the 'land' and 'water' higher birds. Other than sex chromosome differentiation in the first divergence there are no specific changes associated with any of these evolutionary milestones although certain families and orders have undergone multiple fusions (and some fissions), which has reduced their chromosome number; the Falconiformes are the best described. Most changes, overall, seem to involve chromosomes 1, 2, 4, 10 and Z where the Z changes are intrachromosomal; there are also some recurring (convergent) events. Of these, the most puzzling involves chromosomes 4 and 10, which appear to have undergone multiple fissions and/or fusions throughout evolution - three possible hypotheses are presented to explain the findings. We conclude by speculating as to the reasons for the strange behaviour of these chromosomes as well as the role of telomeres and nuclear organisation in avian evolution.     

Loops and repeats in proteins as footprints of molecular evolution

This review is devoted to substantiation of new characteristics for classification of living organisms. The novel view of a role of flexible regions in protein functioning and evolution is suggested. It is based on the newly revealed correlation between the number of loops in elongation factors and the complexity of organisms. This correlation allowed us to formulate a hypothesis of evolution of this protein family. In addition, the study of the ribosomal protein S1 family made it possible to consider the number of structural domains as a reliable indicator of a microorganism’s affiliation with a particular division and to judge about “direction” of their evolution. The findings allow us to consider the loops and repeats in these proteins as unique imprints of molecular evolution.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.

Zusammenfassung

Ein fundamentaler Unterschied zwischen der einzelnen Sequenzposition oder auch numerischen Merkmalen und komplexen morphologischen Merkmalen ist ihr Informationsgehalt. Merkmalsreihen komplexer Strukturen enthalten meist genügend Information, um a priori die Bestimmung der Lesrichtung zu ermöglichen. Die Feststellung des Ursprunges eines Dendrogramms ist somit ohne kladistischen Außengruppenvergleich möglich, während Bäume (Topologien), die auf wenig informativen Merkmalen beruhen, allgemein nur mit dem kladistischen Außengruppenvergleich 'gewurzelt' werden können. Die Qualität der insgesamt verwendeten Information ist entscheidend für die Wahl zwischen alternativen Verwandtschaftshypothesen. Numerische Methoden der Rekonstruktion der Phylogenese sind nützlich bei Verwendung einer gro β en Zahl informationsarmer Merkmale; das Hennigsche Verfahren ist für komplexe Merkmale vorzuziehen.