Effects of gene duplication, epistasis, recombination and gene conversion on the fixation time of compensatory mutations.

Gene duplication is one of the major mechanisms of molecular evolution. Gene duplication enables copies of a gene to accumulate mutations through functional redundancy. If a gene encodes a specific protein that interacts with other proteins, RNA, or DNA, the relaxation of selective constraints caused by gene duplication might contribute to the fixation of compensatory mutations that occur at the interacting sites.

A model of compensatory molecular evolution involving multiple sites in RNA molecules.

Consider two sites under compensatory fitness interaction, such as a Watson-Crick base pair in an RNA helix or two interacting residues in a protein. A mutation at any one of these two sites may reduce the fitness of an individual. However, fitness may be restored by the occurrence of a second mutation at the other site.

Models of compensatory molecular evolution: effects of back mutation.

Compensatory mutations are individually deleterious but appropriate combinations of mutants are harmless. For several models of compensatory molecular evolution, we consider the effects of back mutation. It is shown that the effects of back mutation on the rate of compensatory molecular evolution are weak.

High expression level of levansucrase from Bacillus licheniformis RN-01 and synthesis of levan nanoparticles.

LsRN from Bacillus licheniformis was cloned and expressed in Escherichia coli. From a 1793 bp genomic sequence, the lsRN gene was found to be composed of a single 1446 bp ORF with a putative promoter consensus boxes and a ribosome-binding site. This ORF was predicted to encode for 482 amino acid residues.

Effective population size of a population with stochastically varying size.

For a Wright-Fisher model with mutation whose population size fluctuates stochastically from generation to generation, a heterozygosity effective population size is defined by means of the equilibrium average heterozygosity of the population. It is shown that this effective population size is equal to the harmonic mean of population size if and only if the stochastic changes of population size are uncorrelated. The effective population size is larger (resp.

Compensatory evolution in diploid populations.

Compensatory mutations are individually deleterious but harmless in appropriate combinations either at more than two sites within a gene or on separate genes. Considering that dominance effects of selection and heterodimer formation of gene products may affect the rate of compensatory evolution, we investigate compensatory neutral mutation models for diploid populations. Our theoretical analysis on the average time until fixation of compensatory mutations shows that these factors play an important role in reducing the fixation time of compensatory mutations if mutation rates are not low.

Coordinated expression of functionally diverse fructosyltransferase genes is associated with fructan accumulation in response to low temperature in perennial ryegrass.

* Fructan is the major nonstructural carbohydrate reserve in temperate grasses. To understand regulatory mechanisms in fructan synthesis and adaptation to cold environments, the isolation, functional characterization and genetic mapping of fructosyltransferase (FT) genes in perennial ryegrass (Lolium perenne) are described. * Six cDNAs (prft1-prft6) encoding FTs were isolated from cold-treated ryegrass plants, and three were positioned on a perennial ryegrass linkage map.

Evidence for the transglycosylation of complex type oligosaccharides of glycoproteins by endo-beta-N-acetylglucosaminidase HS.

Transglycosylation activity of endo-beta-N-acetylglucosaminidase HS (Endo HS) was investigated using native human transferrin as a donor of an asparagine-linked oligosaccharide and p-nitrophenyl-beta-d-glucose (PNP-beta-d-Glc) as an acceptor of the oligosaccharide. The amount of the product increased dependent on the concentration of the acceptors. Absorption spectrum, exoglycosidase digestion and matrix assisted laser desorption and ionization-time of flight (MALDI-TOF) mass analysis of the transglycosylation product indicated that the asialobiantennary complex type oligosaccharide of human transferrin was transferred to PNP-beta-d-Glc.

Molecular cloning and determination of the nucleotide sequence of raw starch digesting alpha-amylase from Aspergillus awamori KT-11.

Complementary DNAs encoding alpha-amylases (Amyl I, Amyl III) and glucoamylase (GA I) were cloned from Aspergillus awamori KT-11 and their nucleotide sequences were determined. The sequence of Amyl III that was a raw starch digesting alpha-amylase was found to consist of a 1,902 bp open reading frame encoding 634 amino acids. The signal peptide of the enzyme was composed of 21 amino acids.

Degradation of raw starch granules by alpha-amylase purified from culture of Aspergillus awamori KT-11.

Raw-starch-digesting alpha-amylase (Amyl III) was purified to an electrophoretically pure state from the extract of a koji culture of Aspergillus awamori KT-11 using wheat bran in the medium. The purified Amyl III digested not only soluble starch but also raw corn starch. The major products from the raw starch using Amyl III were maltotriose and maltose, although a small amount of glucose was produced.

Coalescent process with fluctuating population size and its effective size.

We consider a Wright-Fisher model whose population size is a finite Markov chain. We introduce a sequence of two-dimensional discrete time Markov chains whose components describe the coalescent process and the fluctuation of population size. For the limiting process of the sequence of Markov chains, the relationship of the expectation of coalescence time to the harmonic and the arithmetic means of population sizes is shown, and the Laplace transform of the distribution of coalescence time is calculated.

New action pattern of a maltose-forming alpha-amylase from Streptomyces sp. and its possible application in bakery.

An a-Amylase (EC 3.2.1.

A population genetic study on the transition from Jomon people to Yayoi people.

In the study on the origin of Japanese, one of main unsolved problems is the transition from the Jomon people to the Yayoi people. The main difficulty in solving this problem has been the lack of suitable skeletal materials belonging to the time between the two periods, i.e.

Characterization of a thermostable levansucrase from Bacillus sp. TH4-2 capable of producing high molecular weight levan at high temperature.

A thermoactive and thermostable levansucrase was purified from a newly isolated thermophilic Bacillus sp. from Thailand soil. The purification was achieved by alcohol precipitation, DEAE-Cellulose and gel filtration chromatographies.

A neutral model with fluctuating population size and its effective size.

We consider a diffusion model with neutral alleles whose population size is fluctuating randomly. For this model, the effects of fluctuation of population size on the effective size are investigated. The effective size defined by the equilibrium average heterozygosity is larger than the harmonic mean of population size but smaller than the arithmetic mean of population size.