Directional mutation pressure,mutator mutations,and dynamics of molecular evolution

Using a general form of the directional mutation theory, this paper analyzes the effect of mutations in mutator genes on the G + C content of DNA, the frequency of substitution mutations, and evolutionary changes (cumulative mutations) under various degrees of selective constraints. Directional mutation theory predicts that when the mutational bias between A/T and G/C nucleotide pairs is equilibrated with the base composition of a neutral set of DNA nucleotides, the mutation frequency per gene will be much lower than the frequency immediately after the mutator mutation takes place. This prediction explains the wide variation of the DNA G + C content among unicellular organisms and possibly also the wide intragenomic heterogeneity of third codon positions for the genes of multicellular eukaryotes. The present analyses lead to several predictions that are not consistent with a number of the frequently held assumptions in the field of molecular evolution, including belief in a constant rate of evolution, symmetric branching of phylogenetic trees, the generality of higher mutation frequency for neutral sets of nucleotides, the notion that mutator mutations are generally deleterious because of their high mutation rates, and teleological explanations of DNA base composition. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

DNA fingerprinting analysis of Booroola pedigrees: a search for linkage to the Booroola gene

Seven minisatellite probes from a variety of sources were used to analyse 11 paternal half-sib families in which the Booroola gene was segregating. A total of 402 bands that showed segregation in the pedigrees were examined for linkage to the Booroola gene. None of the bands showed segregation with the Booroola gene. The most likely evidence for a linked band was produced by the HaRas HVR probe in Family 902 (=0.0; LOD 2.3). The conclusion, however, is that the minisatellite probes used in this study could not be used as markers for the Booroola gene. The study highlighted problems associated with the use of minisatellite probes in linkage studies in half-sib families. The complex banding patterns found on fingerprinting gels was a major source of scoring error. In a few cases both of the sire's alleles could be identified at a particular locus, but in most cases only one of the alleles could be identified. For the most part, the bands had to be treated as dominant alleles. The contribution of dam alleles to the banding pattern could only be estimated. There was an indication that minisatellite loci in sheep are clustered in particular regions of the sheep genome as the rate at which bands segregated with each other was higher than one would expect from loci randomly distributed throughout the genome.     

Strategies for selecting mutation sites for methionine enhancement in the bean seed storage protein phaseolin

The complete three-dimensional structure of the bean seed storage protein phaseolin was generated from -carbon coordinates by using molecular mechanic calculations. This structure was used as a template to simulate modifications aimed at increasing the methionine content of phaseolin. A hydrophilic, methionine-rich looping insert sequence was designed. Simulated mutagenesis shows that the insert might be accommodated in turn and loop regions of the protein, but not within an -helix. Methionine content was also increased by the replacement of hydrophobic amino acids with methionine in the central core -barrels of the phaseolin protein. Calculations indicated that methionine can effectively replace conserved or variant leucine, isolecuine, and valine residues. However, alanine residues were much more sensitive to substitution, and demonstrated high variability in the effects of methionine replacement. Introduction of multiple substitutions in the barrel interior demonstrated that the replaced residues could interact favorably to relieve local perturbations caused by individual substitutions. Molecular dynamics simulations were also utilized to study the structural organization of phaseolin. The calculations indicate that there are extensive packing interactions between the major domains of phaseolin, which have important implications for protein folding and stability. Since the proposed mutant proteins can be produced and studied, the results presented here provide an ideal test to determine if there is a correlation between the effects obtained by computer simulation and the effects of the mutations on the protein structure expressedin vivo.     

Specificity and regulation of the mutator transposable element system in maize

The Mutator transposable element system is exceptional in many of its basic attributes. The high frequency and low specificity of mutant induction are both unusual and useful characteristics of the Mutator system. Other basic features are at least equally fascinating: the existence of multiple Mu element subfamilies with apparently unrelated internal sequences; the lack of correlation between Mu element transposition and excision; the complex inheritance of Mutator activity; the tight developmental regulation of Afufaror‐conditioned events; and the coordinated processes of element modification/inactivation, to name a few.

Molecular and genetic studies over the last 10 years have begun to explain many of these interesting properties and have uncovered new mysteries of Mutator biology. Both positive and negative regulators of the system have been identified and characterized to varying degrees. Insertion specificity has been observed at several levels. Recent accomplishments include the isolation of an autonomous Mu element and the discovery of maize lines with altered developmental regulation of Mutator‐derived mutability. This review defines the Mutator system, describes the status of current experimentation in the Mutator field, proposes models that may explain some aspects of Mutator behavior, and details future studies that will help elucidate the nature of the Mutator phenomenon.     

Pan-Cancer analyses of Necroptosis-Related genes as a potential target to predict immunotherapeutic outcome

Necroptosis is a unique programmed death mechanism of necrotic cells. However, its role and specific mechanism in cancer remain unclear, and a systematic pan-cancer analysis of necroptosis is yet to be conducted. Thus, we performed a specific pan-cancer analysis using The Cancer Genome Atlas and Genotype-Tissue Expression databases to analyse necroptosis expression in terms of cancer prognosis, DNA methylation status, tumour mutative burden, microsatellite instability, immune cell infiltration in different types of cancer and molecular mechanisms. For the first time, we explored the correlation between necroptosis and immunotherapy prognosis. Thus, our study provides a relatively comprehensive understanding of the carcinogenicity of necroptosis in different types of cancer. It is suggested that necroptosis can be used to evaluate the sensitivity of different patients to immunotherapy and may become a potential target for tumour immunotherapy.     

3. Genetic conservation in seed banks

The safest and most economical and convenient way of preserving the genetic resources of the majority of crop plants is by long-term seed storage. The technology is well developed, but recent research resulting from a greater understanding of behaviour at very low water potentials is leading to further improvements     

DEVELOPMENTAL MUTANTS OF VOLVOX: DOES MUTATION RECREATE THE PATTERNS OF PHYLOGENETIC DIVERSITY?

The nature of the variation which is created by mutation can show how the direction of evolution is constrained by internal biases arising from development and pre-existing design. We have attempted to quantify these biases by measuring eight life history characters in developmental mutants of Volvox carteri. Most of the mutants in our sample were inferior to the wild type, but deviated by less than tenfold from the wild-type mean. Characters differed in mutability, suggesting different levels of canalisation. Most correlations between life history characters among strains were positive, but there was a significant negative correlation between the size and the number of reproductive cells, suggesting an upper limit to the total quantity of germ produced by individuals. The most extreme phenotypes in our sample were very vigorous, showing that not all mutations of large effect are unconditionally deleterious. We investigated the effect of developmental constraints on the course of evolution by comparing the variance and covariance patterns among mutant strains with those among species in the family Volvocaceae. A close correspondence between patterns at these two levels would suggest that pre-existing design has a strong influence on evolution, while little or no correspondence shows the action of selection. The variance generated by mutation was equal to that generated by speciation in the family Volvocaceae, the genus Volvox, or the section Merillosphaera, depending on the character considered. We found that mutation changes the volume of somatic tissue independently of the quantity of germ tissue, so that the interspecific correlation between soma and germ can be attributed to selection. The negative correlation between size and number of germ cells among mutants of V. carteri is also seen among the larger members of the family (Volvox spp.), but not among the smaller members, suggesting a powerful design constraint that may be responsible for the absence of larger forms in the entire group.     

Variegation patterns caused by excision of the maize transposable element Dissociation (Ds) are autonomously regulated by allele-specific Activator (Ac) elements and are not due to trans-acting modifier genes

The Ac elements present in the unstable wxm7 and wx-m9 alleles of maize trigger different patterns of Ds excision in trans. To determine whether this differential regulation is a feature of the Ac alleles themselves or is mediated by genetically distinct factors, maize plants heterozygous for the wx-m7 and wx-m9 alleles were crossed to tester strains homozygous for Ds reporter alleles. Kernels showing the variegation pattern characteristic for the Ac elements carried in the wx-m7 and wx-m9 alleles were found to be present in the ratios expected from the genetic constitution of the strains. The aleurone variegation caused by excision of the Ds reporter element and the endosperm variegation caused by excision of Ac from the wx-m7 and wx-m9 alleles themselves segregated with the original wx-m alleles. In addition, stable Wx and wx derivatives of wx-m9 that have lost Ac no longer exert any trans effect on the wx-m7 allele (and vice versa). Therefore it is concluded that the observed variegation patterns are autonomously determined by specific trans effects of the particular Ac element.     

Analysis of the proposed Fe-SX binding region of Photosystem 1 by site directed mutation of PsaA in Chlamydomonas reinhardtii

The psaA and psaB genes of the chloroplast genome in oxygenic photosynthetic organisms code for the major peptides of the Photosystem 1 reaction center. A heterodimer of the two polypeptides PsaA and PsaB is thought to bind the reaction center chlorophyll, P700, and the early electron acceptors A₀, A₁ and Fe-S_X. Fe-S_X is a 4Fe4S center requiring 4 cysteine residues as ligands from the protein. As PsaA and PsaB have only three and two conserved cysteine residues respectively, it has been proposed by several groups that Fe-S_X is an unusual inter-peptide center liganded by two cysteines from each peptide. This hypothesis has been tested by site directed mutagenesis of PsaA residue C575 and the adjacent D576. The C575D mutant does not assemble Photosystem 1. The C575H mutant contains a photoxidisable chlorophyll with EPR properties of P700, but no other Photosystem 1 function has been detected. The D576L mutant assembles a modified Photosystem 1 in which the EPR properties of the Fe-S_A/B centers are altered. The results confirm the importance of the conserved cysteine motif region in Photosystem 1 structure.Dedicated to the memory of Daniel I. Arnon.