Identification of silencer binding proteins from yeast: possible roles in SIR control and DNA replication

The 'silent' yeast mating-type loci (HML and HMR) are repressed by sequences (HMLE and HMRE) located over 1 kb from their promoters which have properties opposite those of enhancers, and are called 'silencers'. Both silencers contain autonomously replicating sequences (ARS). Silencer activity requires four trans-acting genes called SIR (silent information regulator). We have identified two DNA binding factors , SBF-B and SBF-E, which bind to known regulatory elements at HMRE. SBF-B binds to a region involved in both the silencer and ARS functions of HMRE, but doesn not bind to HMLE. This factor also binds to the unlinked ARS1 element. SBF-E recognizes a sequence found at both silencers. These results suggest that the two silencers may be composed of different combinations of regulatory elements at least one of which is common to both. Neither factor appears to be a SIR gene product. Hence the SIR proteins may not directly interact with the silencer control sites.     

Evidence for purifying selection acting on silent sites in BRCA1

In mammals, it is usually assumed that selection cannot be strong enough to act on nucleotide mutations that do not cause a change at the protein level (i.e. 'silent' or 'synonymous' mutations). Here we report the results of a molecular evolutionary analysis of BRCA1. We find a repeatable pronounced peak in the ratio of nonsynonymous to synonymous substitutions between codons 200-300. Unusually, this peak is caused by a plummet in the silent-site rate of evolution. The most parsimonious interpretation of these data is that purifying selection is acting on silent sites.     

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons

The patterns of synonymous codon usage in 91 Drosophila melanogaster genes have been examined. Codon usage varies strikingly among genes. This variation is associated with differences in G+C content at silent sites, but (unlike the situation in mammalian genes) these differences are not correlated with variation in intron base composition and so are not easily explicable in terms of mutational biases. Instead, those genes with high G+C content at silent sites, resulting from a strong "preference" for a particular subset of the codons that are mostly C- ending, appear to be the more highly expressed genes. This suggests that G+C content is reduced in sequences where selective constraints are weaker, as indeed seen in a pseudogene. These and other data discussed are consistent with the effects of translational selection among synonymous codons, as seen in unicellular organisms. The existence of selective constraints on silent substitutions, which may vary in strength among genes, has implications for the use of silent molecular clocks.      

A Cre-loxP based system for studying horizontal gene transfer

We have previously shown that DNA can be transferred to phagocytosing cells via the uptake of apoptotic cells. We report a model system that facilitates study of antigen presentation of genes transferred specifically via horizontal gene transfer. Constructs were generated encoding the LacZ gene or the influenza A nucleoprotein silenced by a STOP sequence flanked by two loxP sites. These reporter genes were demonstrated to be silent in donor cells and become activated after phagocytosis of Cre-expressing fibroblasts or macrophages. These results provide a model system for studying the influence of horizontally transferred antigens on activation of the immune system.     

An analysis of codon usage in mammals: Selection or mutation bias?

Summary A new statistical test has been developed to detect selection on silent sites. This test compares the codon usage within a gene and thus does not require knowledge of which genes are under the greatest selection, that there exist common trends in codon usage across genes, or that genes have the same mutation pattern. It also controls for mutational biases that might be introduced by the adjacent bases. The test was applied to 62 mammalian sequences, the significant codon usage biases were detected in all three species examined (humans, rats, and mice). However, these biases appear not to be the consequence of selection, but of the first base pair in the codon influencing the mutation pattern at the third position.     

Comparison of the nucleotide sequences of a yeast gene family. I. Distribution and spectrum of spontaneous base substitutions

The nucleotide sequences of closely related members of a gene family can be used to investigate spontaneous mutations. Here we analyse the sequences of different yeast invertase genes which are more than 93% identical in the coding region and share some very similar, but not identical sequences in the noncoding flanking regions. Since all except one of the invertase genes are active, most of the base substitutions are silent. Within the coding region the base substitutions are unevenly distributed, indicating that parts of the genes were homogenized, probably via gene conversion. Transitions occurred more frequently than transversions in both, coding and noncoding regions. In the coding region pyrimidine transitions were the most abundant event due to silent changes mainly in the third codon position. In the noncoding region pyrimidine and purine transitions were found at equal frequencies. Transversions inverting base pairs (A-T and G-C) outnumber transversions changing base pairs (A-C and G-T). While the spectrum of mutations in the coding region is influenced by selective pressure to maintain the amino acid sequence, the spectrum in the noncoding region may be much less affected by selective pressure.     

基因组重排技术在开发新代谢产物中的应用

基因组重排是一种基于原生质体融合,并对原生质进行递推式融合的新型技术。随着基因组重排技术的不断发展和成熟,通过基因组重排获得新代谢产物的例子不断出现,表明该项技术作为新代谢产物开发的途径具有一定的应用前景。在此列举了基因组重排在开发新代谢产物方面的成果,包括基因组重排激活沉默基因产生新代谢产物;基因组重排引入单酶基因产生新抗生素;基因组重排互换基因模块产生杂合抗生素和基因组重排替换前体基因产生新抗生素的例子,并展望了其发展的趋势。     

Nucleotide sequence analysis of the lemur beta-globin gene family: evidence for major rate fluctuations in globin polypeptide evolution

Lemur beta-related globin genes have been isolated and sequenced. Orthology of prosimian and human epsilon-, gamma-, and beta-related globin genes was established by dot-matrix analysis. All of these lemur globin genes potentially encode functional beta-related globin polypeptides, though precisely when the gamma-globin gene is expressed remains unknown. The organization of the 18-kb brown lemur beta-globin gene cluster (5' epsilon-gamma-[psi eta-delta]-beta 3') is consistent with its evolution by contraction via unequal crossing-over from the putative ancestral mammalian beta-globin gene cluster (5' epsilon-gamma- eta-delta-beta 3'). The dwarf lemur nonadult globin genes are arranged as in the brown lemur. Similar levels of synonymous (silent) nucleotide substitutions and noncoding DNA sequence differences have accumulated between species in all of these genes, suggesting a uniform rate of noncoding DNA divergence throughout primate beta-globin gene clusters. These differences are comparable with those observed in the nonfunctional psi eta pseudogene and have therefore accumulated at the presumably maximal neutral rate. In contrast, nonsynonymous (replacement) nucleotide substitutions show a significant heterogeneity in distribution for both the same gene in different lineages and different genes in the same lineage. These major fluctuations in replacement but not silent substitution rates cannot be attributed to changes in mutation rate, suggesting that changes in the rate of globin polypeptide evolution in primates is not governed solely by variable mutation rates.      

Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans

In the postgenomic era it has become increasingly apparent that the vast number of predicted biosynthesis genes of microorganisms is not reflected by the metabolic profile observed under standard fermentation conditions. In the absence of a particular (in most cases unknown) trigger these gene loci remain silent. Because these cryptic gene clusters may code for the biosynthesis of important virulence factors, toxins, or even drug candidates, new strategies for their activation are urgently needed to make use of this largely untapped reservoir of potentially bioactive compounds. The discovery of new microbial metabolites through genome mining has proven to be a very promising approach. Even so, the investigation of silent gene clusters is still a substantial challenge, particularly in fungi. Here we report a new strategy for the successful induction of a silent metabolic pathway in the important model organism Aspergillus nidulans, which led to the discovery of novel PKS-NRPS hybrid metabolites.     

A new method for calculating evolutionary substitution rates

Summary In this paper we present a new method for analysing molecular evolution in homologous genes based on a general stationary Markov process. The elaborate statistical analysis necessary to apply the method effectively has been performed using Monte Carlo technqiues. We have applied our method to the silent third position of the codon of the five mitochondrial genes coding for identified proteins of four mammalian species (rat, mouse, cow and man). We found that the method applies satisfactorily to the three former species, while the last appears to be outside the scope of the present approach. The method allows one to calculate the evolutionarily effective silent substitution rate (v_s) for mitochondrial genes, which in the species mentioned above is 1.4×10^–8 nucleotide substitutions per site per year. We have also determined the divergence time ratios between the couples mousecow/rat-mouse and rat-cow/rat-mouse. In both cases this value is approximately 1.4.     

Evolution of new metabolic pathways: prospectives of biotechnology

Many microorganisms possess a remarkable ability to construct new metabolic pathways by modifying and utilizing their existing DNA. Regulatory mutations permit the deregulation or constitutive synthesis of enzymes that possess gratuitous catalytic activity for new substrates. Often silent or cryptic genes, genes not known to be expressed or utilized by the parent strain, are mobilized to catalyse a critical reaction in establishing the new pathway.     

Modeling the onset of virulence in a pectinolytic bacterium

Building up from experimental knowledge of the regulatory network of the pel genes in the bacteria E. chrysanthemi, we propose for the first time a qualitative modeling of the infectious transition of this bacteria when it is hosted in a plant. We show that this infectious transition can be understood as the excitable dynamics of a metabolico-genetic network. Our mathematical model can account for the main phases which are observed in the onset of the pathogenecity by Erwinia chrysanthemi, namely the silent, latent and virulent stages. Like in many infectious agents, the silent state corresponds to the growth phase of the bacteria, where they multiply without significantly producing molecules which could trigger a counter attack of the invaded host. The latent stage is characterized by a moderate but unequivocal expression of the virulence gene, waiting for a number of conditions which have to fulfill in order to trigger a fully developed infection. In the virulent state the bacteria synthesize a massive production of virulence factors including pectate lyases (Pel) which favor the invasion of the host plant tissues. Our model is able to show cases of transitions from the silent to the virulent stages of the infection, using the method of the piecewise-affine (PA) differential equations and its implementation in the genetic network analyser software (GNA). The obtained qualitative dynamics of the models are consistent with the current experimental data about this system. Moreover it can be interpreted with respect to the relatively complex structure of the binding sites of pel. From the biological point of view, our simulations validate the picture that the promoter of pel has evolved to form a security device preventing a hastened expression of these virulent genes. This first modeling of the regulation of pel genes opens the way to new confrontations between theoretical ideas with experiments and possible strategies to fight the soft-rot disease of plants.     

Expression, secretion and antigenic variation of bacterial S-layer proteins

The function of the S-layer, a regularly arranged structure on the outside of numerous bacteria, appears to be different for bacteria living in different environments. Almost no similarity exists between the primary sequences of S-proteins, although their amino acid composition is comparable. S-protein production is directed by single or multiple promoters in front of the S-protein gene, yielding stable mRNAs. Most bacteria secrete S-proteins via the general secretory pathway (GSP). Translocation of S-protein across the outer membrane of Gram-negative bacteria sometimes occurs by S-protein-specific branches of the GSP. O-polysaccharide side-chains of the lipopolysaccharide component of the cell wall of Gram-negative bacteria appear to function as receptors for attachment of the S-layer. Silent S-protein genes have been found in Campylobacter fetus and Lactobacillus acidophilus. These silent genes are placed in the expression site in a fraction of the bacterial population via inversion of a chromosomal segment.     

Fresh approaches to antibiotic production

New antibiotics are needed, (a) to control diseases that are refractory to existing ones either because of intrinsic or acquired drug resistance of the pathogen or because inhibition of the disease is difficult, at present, without damaging the host (fungal and viral diseases, and tumours), (b) for the control of plant pathogens and of invertebrates such as helminths, insects, etc., and (c) for growth promotion in intensive farming. Numerous new antibiotics are still being obtained from wild microbes, especially actinomycetes. Chemical modification of existing compounds has also had notable success. Here we explore the uses, actual and potential, of genetics to generate new antibiotics and to satisfy the ever-present need to increase yield. Yield improvement has depended in the past on mutation and selection, combined with optimization of fermentation conditions. Progress would be greatly accelerated by screening random recombinants between divergent high-yielding strains. Strain improvement may also be possible by the introduction of extra copies of genes of which the products are rate-limiting, or of genes conferring beneficial growth characteristics. Although new antibiotics can be generated by mutation, either through disturbing known biosyntheses or by activating 'silent' genes, we see more promise in interspecific recombination between strains producing different secondary metabolities, generating producers of 'hybrid' antibiotics. As with proposals for yield improvement, there are two major strategies for obtaining interesting recombinants of this kind: random recombination between appropriate strains, or the deliberate movement of particular biosynthetic abilities between strains. The development of protoplast technology in actinomycetes, fungi and bacilli has been instrumental in bringing these idealized strategies to the horizon. Protoplasts of the same or different species can be induced to fuse by polyethylene glycol. At least in intraspecific fusion of streptomyces, random and high frequency recombination follows. Protoplasts can also be used as recipients for isolated DNA, again in the presence of polyethylene glycol, so that the deliberate introduction of particular genes into production strains can be realistically envisaged. Various kinds of DNA cloning vectors are being developed to this end. Gene cloning techniques also offer rich possibilities for the analysis of the genetic control of antibiotic biosynthesis, knowledge of which is, at present, minimal. The information that should soon accrue can be expected to have profound effects on the application of genetics to industrial microbiology.     

Identification of functional open reading frames in chloroplast genomes

We have used a rapid computer dot-matrix comparison method to identify all DNA regions which have been evolutionarily conserved between the completely sequenced chloroplast genomes of tobacco and a liverwort. Analysis of these regions reveals 74 homologous open reading frames (ORFs) which have been conserved as to length and amino acid sequence; these ORFs also have an excess of nucleotide substitutions at silent sites of codons. Since the nonfunctional parts of these genomes have become saturated with mutations and show no sequence similarity whatsoever, the homologous ORFs are almost certainly functional. A further four pairs of ORFs show homology limited to only a short part of their putative gene products. Amino acid sequence identities range between 50 and 99%; some chloroplast proteins are seen to be among the most slowly evolving of all known proteins. A search of the nucleotide and amino acid sequence databanks has revealed several previously unidentified genes in chloroplast sequences from other species, but no new homologies to prokaryotic genes.     

Selection against accumulating mutations in niche-preference genes can drive speciation

Our current understanding of sympatric speciation is that it occurs primarily through disruptive selection on ecological genes driven by competition, followed by reproductive isolation through reinforcement-like selection against inferior intermediates/heterozygotes. Our evolutionary model of selection on resource recognition and preference traits suggests a new mechanism for sympatric speciation. We find speciation can occur in three phases. First a polymorphism of functionally different phenotypes is established through evolution of specialization. On the gene level, regulatory functions have evolved in which some alleles are conditionally switched off (i.e. are silent). These alleles accumulate harmful mutations that potentially may be expressed in offspring through recombination. Second mating associated with resource preference invades because harmful mutations in parents are not expressed in the offspring when mating assortatively, thereby dividing the population into two pre-zygotically isolated resource-specialist lineages. Third, silent alleles that evolved in phase one now accumulate deleterious mutations over the following generations in a Bateson-Dobzhansky-Muller fashion, establishing a post-zygotic barrier to hybridization.     

On the rate of DNA sequence evolution inDrosophila

Summary Analysis of the rate of nucleotide substitution at silent sites inDrosophila genes reveals three main points. First, the silent rate varies (by a factor of two) among nuclear genes; it is inversely related to the degree of codon usage bias, and so selection among synonymous codons appears to constrain the rate of silent substitution in some genes. Second, mitochondrial genes may have evolved only as fast as nuclear genes with weak codon usage bias (and two times faster than nuclear genes with high codon usage bias); this is quite different from the situation in mammals where mitochondrial genes evolve approximately 5–10 times faster than nuclear genes. Third, the absolute rate of substitution at silent sites in nuclear genes inDrosophila is about three times hihger than the average silent rate in mammals.