Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins

Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic diversity and fitness through iterative directed evolution will accelerate improvements in engineered protein therapeutics.     

Engineering plant virus resistance: from RNA silencing to genome editing strategies

Viral diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant virus resistance is essential for sustainable agriculture. In the last decades, several modern technologies were applied in plant antiviral engineering. Here we summarized breakthroughs of the two major antiviral strategies, RNA silencing and genome editing. RNA silencing strategy has been used in antiviral breeding for more than thirty years, and many crops engineered to stably express small RNAs targeting various viruses have been approved for commercial release. Genome editing technology has emerged in the past decade, especially CRISPR/Cas, which provides new methods for genetic improvement of plant virus resistance and accelerates resistance breeding. Finally, we discuss the potential of these technologies for breeding crops, and the challenges and solutions they may face in the future.     

Metabolic engineering of <Emphasis Type="Italic">Agrobacterium</Emphasis> sp. ATCC31749 for curdlan production from cellobiose

Curdlan is a commercial polysaccharide made by fermentation of Agrobacterium sp. Its anticipated expansion to larger volume markets demands improvement in its production efficiency. Metabolic engineering for strain improvement has so far been limited due to the lack of genetic tools. This research aimed to identify strong promoters and to engineer a strain that converts cellobiose efficiently to curdlan. Three strong promoters were identified and were used to install an energy-efficient cellobiose phosphorolysis mechanism in a curdlan-producing strain. The engineered strains were shown with enhanced ability to utilize cellobiose, resulting in a 2.5-fold increase in titer. The availability of metabolically engineered strain capable of producing β-glucan from cellobiose paves the way for its production from cellulose. The identified native promoters from Agrobacterium open up opportunities for further metabolic engineering for improved production of curdlan and other products. The success shown here marks the first such metabolic engineering effort in this microbe.     

Improvement of microbial strains and fermentation processes

Improvement of microbial strains for the over-production of industrial products has been the hallmark of all commercial fermentation processes. Conventionally, strain improvement has been achieved through mutation, selection, or genetic recombination. Over-production of primary or secondary metabolites is a complex process, and successful development of improved strains requires a knowledge of physiology, pathway regulation and control, and the design of creative screening procedures. In addition, it requires mastery of the fermentation process for each new strain, as well as sound engineering know-how for media-optimization and the fine-tuning of process conditions. This review focuses on the various options that may be employed to improve microbial strains and addresses the complex problems of screening, the tools and technology behind the selection of targeted organisms, and the importance of process optimization. Furthermore, this review discusses new and emerging technologies and designing optimized media for tracking mutants with enhanced productivity or other desired attributes. Received: 7 February 2000 / Received revision: 2 May 2000 / Accepted: 2 May 2000     

Genetic characterization of naturally occurring Rhizobium meliloti populations and their potential to form effective symbioses with lucerne

Genetic characterization by Randomly Amplified Polymorphic DNA (RAPD) fingerprinting was employed to study the status of Rhizobium meliloti populations inhabiting nodules of lucerne. Rhizobium strains were isolated from nodules harvested from plants growing in inoculated or uninoculated experimental plots, uninoculated commercial fields and from lucerne grown in pots containing soils of different origin. Dry matter analyses were recorded and rhizobia were assessed for relative genetic diversity between treatments. Inoculated and uninoculated soils did not differ in terms of dry matter production, and lucerne grew, and was adequately nodulated, in soils with no history of lucerne cultivation. These findings, and the demonstration that there is a rich genetic diversity of Rh. meliloti in these soils, show that it is not always necessary to apply a standard commercial inoculant.     

The Genetic Improvement of Entomopathogenic Nematodes and Their Symbiont Bacteria: Phenotypic Targets, Genetic Limitations and an Assessment of Possible Hazards

The methodologies of classical genetics and genetic engineering can be used for the genetic improvement of entomopathogenic nematodes (EPNs) and their symbiont bacteria. Many of the complex behavioural and physiological traits which are targets for genetic improvement are likely to be controlled polygenically, thus selective breeding for improvements to these traits would be appropriate. Much basic research needs to be carried out before researchers will be able to effect improvements to EPNs and their symbionts by genetic engineering. There is a lack of basic information on the genetics and biochemistry of the characteristics that might be altered by transgenic methods in EPNs, and their bacteria, and existing transformation protocols need to be made more effective.     

A proline tRNA(CGG) gene encompassing the attachment site of temperate phage 16-3 is functional and convertible to suppressor tRNA

Several temperate bacteriophage utilize chromosomal sequences encoding putative tRNA genes for phage attachment. However, whether these sequences belong to genes which are functional as tRNA is generally not known. In this article, we demonstrate that the attachment site of temperate phage 16-3 (attB) nests within an active proline tRNA gene in Rhizobium meliloti 41. A loss-of-function mutation in this tRNA gene leads to significant delay in switching from lag to exponential growth phase. We converted the putative Rhizobium gene to an active amber suppressor gene which suppressed amber mutant alleles of genes of 16-3 phage and of Escherichia coli origin in R. meliloti 41 and in Agrobacterium tumefaciens GV2260. Upon lysogenization of R. meliloti by phage 16-3, the proline tRNA gene retained its structural and functional integrity. Aspects of the co-evolution of a temperate phage and its bacterium host is discussed. The side product of this work, i.e. construction of amber suppressor tRNA genes in Rhizobium and Agrobacterium, for the first time widens the options of genetic study.     

Nuclear and plastid genetic engineering of plants: Comparison of opportunities and challenges

Plant genetic engineering is one of the key technologies for crop improvement as well as an emerging approach for producing recombinant proteins in plants. Both plant nuclear and plastid genomes can be genetically modified, yet fundamental functional differences between the eukaryotic genome of the plant cell nucleus and the prokaryotic-like genome of the plastid will have an impact on key characteristics of the resulting transgenic organism. So, which genome, nuclear or plastid, to transform for the desired transgenic phenotype? In this review we compare the advantages and drawbacks of engineering plant nuclear and plastid genomes to generate transgenic plants with the traits of interest, and evaluate the pros and cons of their use for different biotechnology and basic research applications, ranging from generation of commercial crops with valuable new phenotypes to ‘bioreactor’ plants for large-scale production of recombinant proteins to research model plants expressing various reporter proteins.     

Advances in cultivation of Gelidiales

Currently, Gelidium and Pterocladia (Gelidiales) are collected or harvested only from the sea. Despite several attempts to develop a cultivation technology for Gelidium, no successful methodology has yet been developed. Initial steps towards developmental efforts in Portugal, Spain, South Africa and Israel have been published. More developments have probably been performed but have not been published. Two different technological concepts have been tested for Gelidium cultivation: (1) the attachment of Gelidium fragments to concrete cylinders floating in the sea, and (2) free-floating pond cultivation technology. These vegetative cultivation technologies might be partially optimized by controlling physical, chemical and biological growth factors. The pond cultivation technology is the much more controllable option. The effects of all factors are discussed in detail in this review. It seems that the main difficulty with cultivation of Gelidium is its low growth rate. The claimed yields of the two technologies are far from being economically attractive at this stage of their development. It seems that in order to introduce Gelidium into commercial cultivation, major efforts in genetic improvement through selection or genetic engineering will be required. Only high yield strains will have the potential to compete economically with the present harvesting tradition. However, accumulated experience with genetic improvement of other useful seaweed species suggests that this is possible.     

TILLING,high-resolution melting (HRM), and next-generation sequencing (NGS) techniques in plant mutation breeding

Induced mutations have been used effectively for plant improvement. Physical and chemical mutagens induce a high frequency of genome variation. Recently, developed screening methods have allowed the detection of single nucleotide polymorphisms (SNPs) and the identification of traits that are difficult to identify at the molecular level by conventional breeding. With the assistance of reverse genetic techniques, sequence variation information can be linked to traits to investigate gene function. Targeting induced local lesions in genomes (TILLING) is a high-throughput technique to identify single nucleotide mutations in a specific region of a gene of interest with a powerful detection method resulted from chemical-induced mutagenesis. The main advantage of TILLING as a reverse genetics strategy is that it can be applied to any species, regardless of genome size and ploidy level. However, TILLING requires laborious and time-consuming steps, and a lack of complete genome sequence information for many crop species has slowed the development of suitable TILLING targets. Another method, high-resolution melting (HRM), which has assisted TILLING in mutation detection, is faster, simpler and less expensive with non-enzymatic screening system. Currently, the sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Impressive progress in next-generation sequencing (NGS) technologies has paved the way for the detection and exploitation of genetic variation in a given DNA or RNA molecule. This review discusses the applications of TILLING in combination with HRM and NGS technologies for screening of induced mutations and discovering SNPs in mutation breeding programs.     

Studies of natural populations and mutants of rhizobium in the improvement of legume inoculants

Summary A study has been made of the symbiotic effectiveness ofRhizobium trifolii in fields ofTrifolium subterraneum in south-eastern Australia, with the purpose of providing background information for a programme of inoculant strain improvement. The strains found varied widely in symbiotic effectiveness. The distribution patterns of effectiveness varied from year to year and from locality to locality. From 24 to 65% of strains ofR. trifolii from different localities exhibited antagonism to selectedR. trifolii indicator strains. These reactions were mainly due to mild antibiotic effects but bacteriocinogenic strains and strains producing specific, virulent or wide-range, temperate phages, were also common. Factors to be considered in the selection and evaluation of inoculant strains from among natural populations are discussed and the possible role of genetic manipulation is examined. It is concluded that the general application of DNA transformation and transduction is restricted because of the limited degree of DNA homology among strains, the limited host-range of transducing phages and the lack of suitablein vitro screening procedures for symbiotic characters. A mutational model is presented in which characters known to be associated with symbiotic effectiveness would be manipulated by mutation and back-mutation to effect quantitative increases in effectiveness.     

Weeding with transgenes

Transgenes promise to reduce insecticide and fungicide use but relatively little has been done to significantly reduce herbicide use through genetic engineering. Recently, three strategies for transgene utilization have been developed that have the potential to change this. These are the improvement of weed-specific biocontrol agents, enhancement of crop competition or allelopathic traits, and production of cover crops that will self-destruct near the time of planting. Failsafe risk mitigation technologies are needed for most of these strategies.     

Enabling inverse metabolic engineering through genomics

Inverse metabolic engineering (IME) is a powerful framework for engineering cellular phenotypes. Progress in this field has been limited by a lack of comprehensive methods for efficiently identifying the genetic basis of relevant phenotypes. Advances in genomics technologies, including DNA microarrays and gene sequencing, have dramatically improved our ability to relate changes in phenotype with associated changes in genotype. When applied in the context of IME, these tools should enable the integration of "evolutionary" and "direct" approaches to engineering cell physiology, which should improve our understanding of the complex interactions affecting the expression, evolution and engineering of traits in natural and industrial hosts.     

Mapping of complementation groups within a Rhizobium leguminosarum CFN42 chromosomal region required for lipopolysaccharide synthesis

Summary A major genetic region specifying portions of the carbohydrate structure of Rhizobium leguminosarum CFN42 lipopolysaccharide was analyzed by Tn5 mutagenesis, constructing deletions in cloned DNA, restriction mapping, and complementation analysis. Mutations affecting lipopolysaccharide synthesis were arranged in nine complementation groups spanning 18 kb of DNA. One mutation resulted in O-polysaccharide-containing lipopolysaccharide having a slightly increased mobility in gel electrophoresis. This mutation did not affect the symbiosis with bean plants. The other mutations eliminated the 0-polysaccharide-containing lipopolysaccharide and resulted in strains defective in eliciting bean nodule development.     

Enzymic starch utilization and genetic engineering

Starch is widely used in the food and beverage, paper and textile industries. Genetic engineering will allow optimization of starch conversion technologies both by creating novel enzymes/micro organisms of the desired efficiency, stability and activity to fit any process, and by ensuring they are produced in commercial quantities. Plants could also be genetically engineered to produce starches of the desired amylopectin: amylose ratio. To ensure a continuous supply of starch, starch-producing plants could be genetically engineered to be disease- and insect-resistant, high yielding, and able to grow under any climatic and soil conditions. However, screening for novel microorganisms should not be neglected and should be used to complement genetic engineering.     

酿酒酵母的"组学"技术研究进展及其在工程菌株构建中的应用

酿酒酵母是真核模式生物,已被广泛用于 "组学"水平的研究。"组学"技术主要由基因组学、转录组学、蛋白质组学及代谢组学构成。综述了酵母菌"组学"的研究进展,并论述了酵母菌"组学"技术在酵母菌菌株改造中的应用,包括酒类及生物燃料乙醇工业生产菌株的基因工程改造等。     

Genetic improvement of Citrus for disease resistance

Progress in the genetic improvement of Citrus species was reviewed. Tools used for the genetic improvement of Citrus were categorised as conventional (introduction, selection and hybridisation) and non-conventional methods (mutation, somatic cell hybridisation and genetic engineering) of improvement. Genes linked with the disease resistance were characterised and tagged through molecular marker techniques such as Sequenced Characterised Amplified Region and Cleaved Amplified Polymorphic Sequences. Disease resistance genes showed both monogenic and polygenic inheritance. Conventional methods for disease resistance improvement of Citrus were bottleneck due to inadequate and lengthy breeding procedures. However, non-conventional methods, such as mutation breeding and protoplast fusion, have been routinely utilised for the production of disease resistant germplasm while novel genes from variable sources were used to transform Citrus species to induce resistance against diseases. These non-conventional techniques have been shown to overcome the disadvantages of conventional breeding procedures and could be regarded as rapid methods of genetic improvement as well as helpful to overcome the interspecies barrier.     

Recombination deficient mutants of Rhizobium meliloti 41

Two mutants deficient in homologous genetic recombination have been isolated from Rhizobium meliloti 41 after Tn5 mutagenesis. Both mutants are defective in the induction of temperate phage 16-3 by UV-light, Mytomycin-C or Bleomycin, their UV sensitivity is more pronounced than that of the wild-type strain, and they lack the 'SOS activity' responsible for induced mutations.     

Screening of sunflower cultivars for metal phytoextraction in a contaminated field prior to mutagenesis

Sunflower can be used for the remediation of metal-contaminated soils. Its high biomass production makes this plant species interestingfor phytoextraction and using sunflower oil for a technical purpose may improve the economic balance of phytoremediation. The aim of the present field study was to screen 15 commercial cultivars of Helianthus annuus L. grown on metal-contaminated soil, to find out the variety with the highest metal extraction, which can be further improved by mutation or in vitro breeding procedures. Two different fertilizers (ammonium sulphate and ammonium nitrate) were also used to enhance the bioavailability of metals in soil Highly significant differences were observed within tested varieties for metal accumulation and extraction efficiency. Furthermore, ammonium nitrate increased cadmium extraction, whereas ammonium sulphate enhanced zinc and lead uptake in most tested cultivars. In this field-based sunflower screening, we found enhanced cumulative Cd, Zn, and Pb extraction efficiency by a factor 4.4 for Salut cultivar. We therefore emphasize that prior to any classical breeding or genetic engineering enhancing metal uptake potential, a careful screening of various genotypes should be done to select the cultivar with the naturally highest metal uptake and to start the genetic improvement with the best available plant material.