The problem of antibiotic resistant bacteria. The important role of environmentally responsive mutagenesis, its relevance to a new paradigm that may allow a solution

The frequent creation of antibiotic resistant bacteria through mutation poses a severe medical problem. As a way towards solving the problem, mutations conferring antibiotic sensitivity could be induced in such bacteria at very high frequency through the controlled process of environmentally responsive mutagenesis, an adaptively responsive mutator process. Such induction, as a necessary developmental stage towards global adaptation, would be enabled by patterns of mild stresses. The stresses and their patterns would be elucidated through in vitro experiments and clinical trials. The effective application of this ordered process, whose detection was allowed through a change in experimental design, requires a new and more comprehensive paradigm of mutagenesis than the one currently applied. This would be a new paradigm that has holistic and developmental features. Yet, the effective and ongoing emergence of such a paradigm will depend on experimental setups that will enable or provide, unlike previous experimental arrangements, new insights as to the developmental connections between innerly controlled mutagenesis and its environments. This should demonstrate controlled ways to generate and make manifest those genomic changes that, as developmental stages, give rise to antibiotic sensitivity in antibiotic resistant bacteria. The ultimate consequence of such a developed paradigm of mutagenesis may very well be a major and benign medical and biotechnical revolution.     

Environmentally responsive mutator systems: toward a unifying perspective.

Biology has long sought a unifying principle. The behaviour of genetically controlled mutator processes adaptively responsive to stress may reflect such a principle. Related mutators exist in diverse organisms from bacteria to mammals. Such systems have evolved from one another and have defined the very evolution of organisms. Many of these mutator systems can determine in a developmental manner a ultramutability or hypermutability throughout the genome. Though the genetic control of high levels of mutability can reflect molecular features, such mutagenic processes reflect a deeper parameter involving forces and their configurations. These configurations must generate stable or uniform configurations from unstable ones throughout the genome and organism. Directed mutation becomes a generative process attuned to non-uniform forces of local niches and to the more uniform forces of a universal niche. The manner of mutagenic, attuned response depends on the level of genomic and transgenomic organization. This is reflected in hierarchies of evolution. Directed mutation is a feature of a universal, generative ordering process, and this feature is marked by a universal dimensionless constant. It is the dynamic consequence of such directed generation which ultimately confers adaptation through dynamic completion. This suggests an underlying, unitary, and necessary dynamics connecting ultramutability systems in all organisms and would serve, in complementation with a molecular approach, to elicit new and productive research avenues. One outcome would be the illustration of a unifying principle governing biological and physical phenomena.     

Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation

In the lac adaptive mutation system of Cairns, selected mutant colonies but not unselected mutant types appear to arise from a nongrowing population of Escherichia coli. The general mutagenesis suffered by the selected mutants has been interpreted as support for the idea that E. coli possesses an evolved (and therefore beneficial) mechanism that increases the mutation rate in response to stress (the hypermutable state model, HSM). This mechanism is proposed to allow faster genetic adaptation to stressful conditions and to explain why mutations appear directed to useful sites. Analysis of the HSM reveals that it requires implausibly intense mutagenesis (10(5) times the unselected rate) and even then cannot account for the behavior of the Cairns system. The assumptions of the HSM predict that selected revertants will carry an average of eight deleterious null mutations and thus seem unlikely to be successful in long-term evolution. The experimentally observed 35-fold increase in the level of general mutagenesis cannot account for even one Lac(+) revertant from a mutagenized subpopulation of 10(5) cells (the number proposed to enter the hypermutable state). We conclude that temporary general mutagenesis during stress is unlikely to provide a long-term selective advantage in this or any similar genetic system.     

A Simple and Reproducible Method for Directed Evolution: Combination of Random Mutation with dITP and DNA Fragmentation with Endonuclease V

An alternative method to combine mutagenesis PCR with dITP and fragmentation by endonuclease V for directed evolution was developed. In comparison to the routine protocol for directed evolution, dITP was used as mutation reagent in the mutagenesis PCR. Subsequently, the incorporated dITP in the PCR products could represent as being the target of endonuclease V. Finally, the mutated dsDNA was fragmented by endonuclease V and then shuffled via assembly and reamplification as is usually done. In this study, the gene encoding kanamycin resistance has been used as reporter to verify the novel method for directed evolution. However, the mutation frequency could be easily adjusted by the amount of dITP used in the mutagenesis PCR reaction. Besides, this protocol yielded the mutation types with an obvious bias to transition substitutions as the normal error-prone PCR did. Conclusively, this novel method for directed evolution has been demonstrated to be efficient, reproducible, and easy to handle in actual practice. Using this protocol, we have successfully constructed a random mutation library for the gene encoding a serine alkaline protease.     

CRISPR/Cas9-based directed evolution in mammalian cells

An increasingly powerful set of new CRISPR/Cas-based methods is becoming available for directed evolution of proteins in mammalian cells. Although in vitro techniques or microbial expression systems have been dominating directed evolution, there are now promising approaches to diversify proteins in mammalian cells in situ. This can be achieved by simple indel mutagenesis or more sophisticated homology repair mechanisms for cassette mutagenesis of coding sequences. Cas9 variant fusions to base editors and other effectors pose another promising way to introduce diversity into proteins. CRISPR/Cas9-based directed evolution in mammalian cells opens a new exciting era of discovery for the many classes of proteins for which a mammalian cellular context is preferable.     

The development of gene expression systems for filamentous fungi

Filamentous fungi have been used for decades in the commercial production of enzymes, antibiotics, and specialty chemicals. Traditionally, improving the yields of these products has involved either mutagenesis and screening or modification of fermentation conditions. Generally, selective breeding of strains has not been successful, because most of the commercially important fungal species lack a sexual cycle. For a few species, strain improvements have been made possible by employing the parasexual cycle for genetic crosses (30). The recent development of DNA-mediated transformation systems for several industrially important fungal species has spawned a flurry of research activity directed toward the development of gene expression systems for these microorganisms. This technology is now a viable means for novel and more directed approaches to improving existing fungal strains which produce enzymes or antibiotics. In addition, fungal expression systems are now being tested for the production of heterologous gene products such as mammalian pharmaceutical proteins. The goal of this review is to present a summary of the gene expression systems which have recently been developed for some filamentous fungi of commercial importance. To insure that the most recent developments are presented we have included data from not only scientific papers, but also from personal communications, abstracts, symposia, and our own laboratory.     

Searching for Sequence Directed Mutagenesis in Eukaryotes

Sequence directed mutagenesis is a mechanism by which imperfect repeats “repair” each other to become perfect, generating mutations. This process is known to be prevalent in prokaryotes and it has been implicated in several human genetic diseases. Here we test whether sequence directed mutagenesis occurs in the protein coding sequences of eukaryotes using extensive DNA sequence data from humans, mice, Drosophila, nematodes, yeast, and Arabidopsis. Using two tests we find little evidence of sequence directed mutagenesis. We conclude that sequence directed mutagenesis is not prevalent in eukaryotes and that the examples of human diseases, apparently caused by sequence directed mutagenesis, are probably coincidental. [Reviewing Editor: Dr. Richard Kliman]     

Going in GTP cycles in the nucleolus

Proteins are directed to cellular compartments by specific localization signals. A GTP-driven cycle has now been identified as a mechanism for protein targeting to the nucleolus. The involvement of a GTP switch suggests that nucleolar localization can be regulated and may be responsive to extracellular stimuli via signaling pathways. The uncovered mechanism also implies that localization is determined by increased retention rather than directed targeting.     

Therapy of Fabry disease with pharmacological chaperones: from in silico predictions to in vitro tests

Background

Fabry disease is a rare disorder caused by a large variety of mutations in the gene encoding lysosomal alpha-galactosidase. Many of these mutations are unique to individual families. Fabry disease can be treated with enzyme replacement therapy, but a promising novel strategy relies on small molecules, so called "pharmacological chaperones", which can be administered orally. Unfortunately only 42% of genotypes respond to pharmacological chaperones.

Results

A procedure to predict which genotypes responsive to pharmacological chaperones in Fabry disease has been recently proposed. The method uses a position-specific substitution matrix to score the mutations. Using this method, we have screened public databases for predictable responsive cases and selected nine representative mutations as yet untested with pharmacological chaperones. Mutant lysosomal alpha galactosidases were produced by site directed mutagenesis and expressed in mammalian cells. Seven out of nine mutations responded to pharmacological chaperones. Nineteen other mutations that were tested with pharmacological chaperones, but were not included in the training of the predictive method, were gathered from literature and analyzed in silico. In this set all five mutations predicted to be positive were responsive to pharmacological chaperones, bringing the percentage of responsive mutations among those predicted to be positive and not used to train the classifier to 86% (12/14). This figure differs significantly from the percentage of responsive cases observed among all the Fabry mutants tested so far.

Conclusions

In this paper we provide experimental support to an "in silico" method designed to predict missense mutations in the gene encoding lysosomal alpha galactosidase responsive to pharmacological chaperones. We demonstrated that responsive mutations can be predicted with a low percentage of false positive cases. Most of the mutations tested to validate the method were described in the literature as associated to classic or mild classic phenotype. The analysis can provide a guideline for the therapy with pharmacological chaperones supported by experimental results obtained in vitro. We are aware that our results were obtained in vitro and cannot be translated straightforwardly into benefit for patients, but need to be validated by clinical trials.

     

Development of NaCl-tolerant strain in Chrysanthemum morifolium Ramat. through in vitro mutagenesis

One NaCl-tolerant chrysanthemum (Chrysanthemum morifolium Ramat.) variant (E2) has been developed in a stable form through IN VITRO mutagenesis using ethylmethane sulfonate (EMS) as the chemical mutagen. Salt tolerance was evaluated by the capacity of the plant to maintain both flower quality and yield under stress conditions. Enhanced tolerance of the E2 variant has been attributed to the increased activity of superoxide dismutase (SOD), ascorbate peroxidase (APX), and dehydroascorbate reductase (DHAR), and, to a lesser extent of membrane damage than NaCl-treated control plants. Isoform analysis revealed that an increase in total SOD activity in the E2 variant was solely due to significant activation of the Cu/Zn isoform. Elevated levels of carotenoids and ascorbate in E2 leaves have been reflected in their higher free radical scavenging capacity (RSC) expressed in terms of DPPH (2,2-diphenyl-1-picrylhydrazyl) scavenging ability. Data reflect that a proper balance between enzymatic and non-enzymatic defence systems is required for combating salinity stress in chrysanthemum. Better performance of the E2 progeny under same salinity stress condition, even in the second year, confirms the genetic stability of the salt-tolerance character. On the whole, the E2 variant, developed through 0.025 % EMS treatment, might be considered as a NaCl-tolerant strain showing positive characters towards NaCl stress.     

Protein and Genome Evolution in Mammalian Cells for Biotechnology Applications

Mutation and selection are the essential steps of evolution. Researchers have long used in vitro mutagenesis, expression, and selection techniques in laboratory bacteria and yeast cultures to evolve proteins with new properties, termed directed evolution. Unfortunately, the nature of mammalian cells makes applying these mutagenesis and whole-organism evolution techniques to mammalian protein expression systems laborious and time consuming. Mammalian evolution systems would be useful to test unique mammalian cell proteins and protein characteristics, such as complex glycosylation. Protein evolution in mammalian cells would allow for generation of novel diagnostic tools and designer polypeptides that can only be tested in a mammalian expression system. Recent advances have shown that mammalian cells of the immune system can be utilized to evolve transgenes during their natural mutagenesis processes, thus creating proteins with unique properties, such as fluorescence. On a more global level, researchers have shown that mutation systems that affect the entire genome of a mammalian cell can give rise to cells with unique phenotypes suitable for commercial processes. This review examines the advances in mammalian cell and protein evolution and the application of this work toward advances in commercial mammalian cell biotechnology.     

A novel high-throughput genetic screen for stress-responsive mutants of Arabidopsis thaliana reveals new loci involving stress responses

Activation sequence-1 (as-1) cognate promoter elements are widespread in the promoters of plant defense-related genes as well as in plant pathogen promoters, and may play important roles in the activation of defense-related genes. The as-1-type elements are highly responsive to multiple stress stimuli such as jasmonic acid (JA), salicylic acid (SA), H(2)O(2), xenobiotics and heavy metals, and therefore provide a unique opportunity for identifying additional signaling components and cross-talk points in the various signaling networks. A single as-1-type cis-element-driven GUS reporter Arabidopsis line responsive to JA, SA, H(2)O(2), xenobiotics and heavy metals was constructed for mutagenesis. A large-scale T-DNA mutagenesis has been conducted in the reporter background, and an efficient high-throughput mutant screen was established for isolating mutants with altered responses to the stress chemicals. A number of mutants with altered stress responses were obtained, some of which appear to identify new components in the as-1-based signal transduction pathways. We characterized a mutant (Delta8L4) with a T-DNA insertion in the coding sequence of the gene At4g24275. The as-1-regulated gene expression and GUS reporter gene expression were altered in the Delta8L4 mutant, but there was no change in the expression of genes lacking as-1 elements in their promoters. The phenotype observed with the Delta8L4 mutant was further verified using RNAi plants for At4g24275 (8L4-RNAi), suggesting the feasibility of use of this high-throughput mutant screening in isolating stress-signaling mutants.     

Generation and analysis of drought stressed subtracted expressed sequence tags from safflower (Carthamus tinctorius L.)

Drought is the most crucial environmental factor that limits productivity of many crop plants. Exploring novel genes and gene combinations is of primary importance in plant drought tolerance research. Stress tolerant genotypes/species are known to express novel stress responsive genes with unique functional significance. Hence, identification and characterization of stress responsive genes from these tolerant species might be a reliable option to engineer the drought tolerance. Safflower has been found to be a relatively drought tolerant crop and thus, it has been the choice of study to characterize the genes expressed under drought stress. In the present study, we have evaluated differential drought tolerance of two cultivars of safflower namely, A1 and Nira using selective physiological marker traits and we have identified cultivar A1 as relatively drought tolerant. To identify the drought responsive genes, we have constructed a stress subtracted cDNA library from cultivar A1 following subtractive hybridization. Analysis of?~1,300 cDNA clones resulted in the identification of 667 unique drought responsive ESTs. Protein homology search revealed that 521 (78?%) out of 667 ESTs showed significant similarity to known sequences in the database and majority of them previously identified as drought stress-related genes and were found to be involved in a variety of cellular functions ranging from stress perception to cellular protection. Remaining 146 (22?%) ESTs were not homologous to known sequences in the database and therefore, they were considered to be unique and novel drought responsive genes of safflower. Since safflower is a stress-adapted oil-seed crop this observation has great relevance. In addition, to validate the differential expression of the identified genes, expression profiles of selected clones were analyzed using dot blot (reverse northern), and northern blot analysis. We showed that these clones were differentially expressed under different abiotic stress conditions. The implications of the analyzed genes in abiotic stress tolerance are discussed in our study.     

Possible mechanisms of the occurrence of chromosome restructurings. IV. Chromosome restructurings in spontaneous mutagenesis

An attempt was undertaken to modify the spontaneous mutation process by varying its conditions in somatic cells of different species and tissues. The rate of chromosome aberrations and their types were studied in anaphase and metaphase. Under normal conditions, chromosome breaks were only found to occur. Breakage of chromosomes occurs during interphase, and as a result, acentric fragments are located outside the equatorial plate during metaphase. This process of chromosome breakage leads to elimination of some genetic material, without concomitant exchanges, and therefore, it has been named "elimination" process. Spontaneous chromosome mutagenesis manifesting itself at cytogenetic level was concluded to be an elimination process directed to elimination of a portion of chromatin from chromosomes. When the conditions of spontaneous mutagenesis are altered, in particular, by cardiovascular diseases in man, by partial inhibition of DNA repair in mice and pea cells, by transformation of Chinese hamster cells, upon ageing of pea seeds-qualitative changes in the chromosomal aberrations are registered, connected with the appearance of chromosome exchanges and acentric fragments situated within the equatorial plate during metaphase. These two types of chromosome aberrations are proposed to be considered as new criteria of pathology. A system of processes was suggested to exist, preventing the appearance of aberrations during mitosis, and it is supposed to be one of the most significant homeostatic systems.     

Germline mutagenesis mediated by <Emphasis Type="Italic">Sleeping Beauty</Emphasis>transposon system in mice

Following the descovery of its transposition activity in mammalian culture systems, the Sleeping Beauty (SB) transposon has since been applied to achieve germline mutagenesis in mice. Initially, the transposition efficiency was found to be low in cultured systems, but its activity in germ cells was unexpectedly high. This difference in transposition efficiency was found to be largely dependent on chromosomal status of the host genomic DNA and transposon vector design. The SB transposon system has been found to be suitable for comprehensive mutagenesis in mice. Therefore, it is an effective tool as a forward genetics screen for tagged insertional mutagenesis in mice.     

A Review of Multi-Responsive Membranous Systems for Rate-Modulated Drug Delivery

Membrane technology is broadly applied in the medical field. The ability of membranous systems to effectively control the movement of chemical entities is pivotal to their significant potential for use in both drug delivery and surgical/medical applications. An alteration in the physical properties of a polymer in response to a change in environmental conditions is a behavior that can be utilized to prepare ‘smart’ drug delivery systems. Stimuli-responsive or ‘smart’ polymers are polymers that upon exposure to small changes in the environment undergo rapid changes in their microstructure. A stimulus, such as a change in pH or temperature, thus serves as a trigger for the release of drug from membranous drug delivery systems that are formulated from stimuli-responsive polymers. This article has sought to review the use of stimuli-responsive polymers that have found application in membranous drug delivery systems. Polymers responsive to pH and temperature have been extensively addressed in this review since they are considered the most important stimuli that may be exploited for use in drug delivery, and biomedical applications such as in tissue engineering. In addition, dual-responsive and glucose-responsive membranes have been also addressed as membranes responsive to diverse stimuli.     

基于PCR的质粒快速定点诱变方法建立与评价

基因突变对生命的进化具有重要意义,针对质粒的DNA定点诱变技术也是基因工程、蛋白质工程研究中的重要手段之一。为了提高质粒定点诱变的效率,本研究利用引物部分重叠的设计方案,使用Tm值相对固定的引物设计模式,将同一引物分为重叠区（Tm=50±2℃）和非重叠区（Tm=60±2℃）,并在严格控制模板用量（2 pg/kb）的基础上,通过20个PCR循环对目标质粒进行定点诱变扩增,随后取0.5 μL产物直接用于转化。在FastPfu Fly酶系中,利用此法构建了6个含碱基替换、缺失和插入的质粒,均获得成功,突变效率可达96%以上,阳性克隆获得数达70个以上。此外,利用4种不同PCR酶系对该法的适用性进行了评价,结果表明突变效率均可达93%以上,阳性克隆获得数均在10个以上。通过适当增加PCR模板用量（10 pg/kb）并使用纯化后的PCR产物进行转化,该法可适用于转化效率大于106（cfu/μg）的任意感受态细胞,对应的突变效率可大于91%,阳性克隆获得数大于20。根据本法的作用原理,该方案适合质粒中10～20 bp（因重叠区GC含量及碱基序列的不同而改变）以内的任意碱基替换和插入,以及任意长度的DNA片段缺失。且具有通用性强、耗时少、诱变成功率高、成本低、对感受态及转化效率无特殊要求等优点,适合各实验室的日常研究使用。