基因打靶技术的研究进展

基因打靶在人类遗传病动物模型的构建,基因治疗和基因功能研究等方面都有重要的作用。本文综述了一些常用的基因打靶策略,并对这些技术的研究进展作一介绍。     

Microbial horizontal gene transfer and the DNA release from transgenic crop plants

Intraspecific and interspecific horizontal gene transfers among prokaryotes by mechanisms like conjugation, transduction and transformation are part of their life style. Experimental data and nucleotide sequence analyses show that these processes appear to occur in any prokaryotic habitat and have shaped microbial genomes throughout evolution over hundreds of million years. Here we summarize studies with a focus on the possibility of the transfer of free recombinant DNA released from transgenic plants to microorganisms by transformation. A list of 87 species capable of natural transformation is presented. We discuss monitoring techniques which allowed detection of the spread of intact DNA from plants during their growth, in the process of decay and by pollen dispersal including novel biomonitoring assays for measuring the transforming potential of DNA in the environment. Also, studies on the persistence of free DNA in soil habitats and the potential of bacteria to take up DNA in soil are summarized. On the other hand, the various barriers evolved in prokaryotes which suppress interspecific gene transfer and recombination will be addressed along with studies aiming to estimate the chance of a gene transfer from plant to microbe. The results suggest that, although such transfers could be possible in principle, each of the many steps involved from the release of intact DNA from a plant cell to integration into a prokaryotic genome has such a low probability that a successful transfer event be extremely rare. Further, interspecies transfer of chromosomal DNA is mostly negative for the recipient, and, if not, in the absence of a selective advantage the transformant will be lost. It is stressed that the nucleotide sequences introduced into transgenic plants are much less likely to be captured from the transgenic plants than directly from those organisms (often bacteria or viruses) from which they were originally derived.     

Contemporary gene targeting strategies for the novice

Gene targeting in mouse embryonic stem (ES) cells is a fundamental methodology for generating mice with precise genetic modifications. Although there are many complex gene targeting strategies for creating a variety of diverse mutations in mice, most investigators initially choose to generate a null allele. Here we provide a guide for the novice to generate a null allele for a protein coding gene using a fundamental gene targeting strategy. Ultimately, a well considered gene targeting strategy saves significant amounts of time, money, and research animal lives. The straightforward strategy presented here bypasses many of the pitfalls associated with gene knockouts generated by novices. This guide also serves as a foundation for subsequently designing more complex gene targeting strategies.     

游动放线菌中orf20基因敲除对雷莫拉宁合成的影响

雷莫拉宁生物合成基因簇中orf20与已知的卤化酶基因高度同源.本研究在大肠杆菌中构建同框敲除质粒pSM-3,将其转入游动放线菌Actinoplanes sp.ATCC 33076,通过同源重组双交换的方法将orf20基因内部编码64个氨基酸的序列敲除,筛选得到双交换阻断突变株SIPI-A.2001 dorf20(Δor...     

Gene targeting in plants: fingers on the move

Zinc-finger endonucleases (ZFNs) make targeted double-stranded breaks in genomic DNA and, thus, stimulate recombination and repair processes at specific sites. ZFNs can now be harnessed to stimulate homologous recombination and gene targeting in plants, which represents a major step towards modifying the plant genome more precisely. ZFN-mediated gene targeting is likely to become a powerful tool for genome research and genetic engineering.     

Positive selection on multiple antique allelic lineages of transferrin in the polyploid Carassius auratus

Transferrin polymorphism has been studied in the polyploid Carassius auratus by cloning and sequence analysis of cDNAs from its three subspecies C. auratus gibelio, C. auratus auratus, and C. auratus cuvieri. DNA polymorphism of extremely high extent was shown for the transferrin gene by the 248 segregation sites among coding region sequences of its alleles. The deduced amino acid sequences of the transferrin alleles showed variable theoretical physicochemical parameters, which might constitute molecular basis for their electrophoretic heterogeneity. Positive selection was inferred by the replacement/synonymous ratios larger than 1 in partial allelic lineages which was subsequently confirmed by likelihood simulation under neutral or selection models. Furthermore, the correspondent sites to these selected codons were collectively located at two planes in the crystallographic structure of rabbit transferrin, which suggested that the rapid evolution of C. auratus transferrin might correlate to its adaptation to variable environmental elements such as oxygen pressure. The minimal 26 recombination events were detected among coding sequences of C. auratus transferrin, with partial mosaic sequences and breakpoints identified by identity scanning and information site analyses. Phylogenetic analyses revealed multiple antique allelic lineages of transferrin, which was estimated to diverge fifteen to twenty MYA. All these features strongly suggested the role of balancing selection in long persistence of high transferrin polymorphism in C. auratus. Furthermore, owing to its particular evolutionary backgrounds, the silver crucian carp might possess a distinctive balancing selection mechanism.     

Factors affecting the efficiency of introducing precise genetic changes in ES cells by homologous recombination: tag-and-exchange versus the Cre-loxp system

The introduction of genetic modifications in specific genes by homologous recombination provides a powerful tool for elucidation of structure-function relationships of proteins of biological interest. Presently, there are several alternative methods of homologous recombination that permit the introduction of small genetic modifications in specific loci. Two of the most widely used methods are the tag-and-exchange, based on the use of positive--negative selection markers, and the Cre-loxP system, based on the use of a site-specific recombinase. The efficiency of detection of targeting events at different loci using the two systems was compared. Additionally, we analysed how the distance between two gene markers placed within the region of homology of a targeting vector affects the rate at which both markers are introduced into the locus during the homologous recombination event. Our results indicate that the method based on the use of positive--negative selection markers was les s efficient than the Cre-loxP based system, irrespective of locus or type of positive--negative selection. It was also determined that as the distance between the selectable marker and the genetic modification being introduced increases, there is a progressive reduction in the efficiency of detecting events with the desired genetic modification     

Increased efficiency of homologous recombination in ES cells by cleavage at both ends of homology in the targeting vector

Transgenic Research -     

Mouse genetics in the 21st century: using gene targeting to create a cornucopia of mouse mutants possessing precise genetic modifications

Over 1500 mouse mutants have been identified, but few of the genes responsible for the defects have been identified. Recent developments in the area of gene targeting are revolutionizing the field of mouse genetics and our understanding of numerous genes, including those thought to be involved in cell proliferation and differentiation. Gene targeting was developed as a method for producing a predetermined mutation in a specific endogenous gene. Advances in the design of targeting vectors and in the use of embryonic stem cells have permitted the production of numerous mutant mice with null mutations in specific genes. These mutant mice will be critical for investigating thein vivo functions of many genes that have been cloned in recent years. This review discusses a wide range of new developments in the field of gene targeting with a focus on issues to be considered by those planning to use this new technology. It also examines some of the lessons learned from recent gene targeting studies and discusses different applications of the technology that are likely to generate scores of new animal models for a wide range of human diseases.Abbreviations ES embryonic stem - neo^r neomycin resistance gene - HSV herpes simplex virus - tk thymidine kinase gene - PCR polymerase chain reaction - LIF leukemia inhibitory factor - LTP long-term potentiation - Rb retinoblastoma gene product - CF cystic fibrosis     

Efficient targeting of the IL-4 gene in a BALB/c embryonic stem cell line

Embryonic stem (ES) cell lines have been derived from the inner cell mass of day 3.5 blastocysts of the inbred mouse strain BALB/cJ. Twenty-three lines were karyotyped and three were selected for injection into C57BL/6J host blastocysts. Two of the three lines, BALB/c-I and BALB/c-IV, produced germ-line chimaeras. The suitability of the BALB/c-I line for gene targeting experiments was tested by transfecting a targeting construct for the interleukin-4 (IL-4) gene. Transfected BALB/c-I cells exhibited efficient homologous recombination of the targeting vector and transmitted the induced mutation through the germline. This newly-characterized BALB/c-ES cell line thus provides an alternative to the traditional 129-derived and the recently described C57BL/6 embryonic stem cell lines, and will be useful in disrupting genes involved in the immune system. Furthermore, the genetically pure BALB/c IL-4 deficient mice will aid in studying the role of IL-4 in several infectious disease models in which the BALB/c mouse is a susceptible strain.This work is dedicated to the memory of Georges Köhler who died during the completion of these studies.     

The construction of a cloning vector designed for gene replacement in Bordetella pertussis

We report here the construction of a plasmid cloning vector, pRTP1, designed to facilitate exchange of cloned and chromosomal alleles of the human bacterial pathogen Bordetella pertussis. pRTP1 provides the ability to successively select two homologous recombination events within the cloned sequences. The first is by selection for maintenance of the ampicillin-resistance gene on the plasmid which is unable to replicate autonomously after transfer via conjugation. The second selection, via streptomycin (Sm) selection, is against the maintenance of vector sequences which contain a gene encoding the Sm-sensitive allele of the gene for ribosomal protein S12 thus rendering an otherwise Sm-resistant strain Sm-sensitive. We demonstrate the use of this vector to introduce an unmarked mutation, constructed in vitro, into the chromosomal locus encoding pertussis toxin.     

Enhancing the efficiency of introducing precise mutations into the mouse genome by hit and run gene targeting

The creation of precise clinical mutations by gene targeting is important in elucidating disease pathogenesis using mouse models. 'Hit and run' gene targeting is an elegant method to achieve this goal. This uses first a positive selection to introduce the targeting vector carrying the required mutation and then a negative selection to identify clones which have removed vector and wild-type sequences by intrachromosomal recombination. However, this approach has only been successfully used in a handful of cases. We used this procedure to introduce precise clinical mutations into the exon 10 region of the cystic fibrosis transmembrane conductance regulator (Cftr) gene. Using a CMV promoter driven hygromycin/thymidine kinase (hyg/tk) fusion gene as both our dominant and negative selectable marker, we targeted the Cftr locus very efficiently but only identified false runs after the negative selection step. This defect in thymidine kinase induced toxicity to gancyclovir correlated with methylation of the transgene. Consequently we devised a stringent screening procedure to select only true 'run' clones. Unfortunately these 'run' clones had lost the mutation so we altered the vector design to bias the run step to retain the mutation and used a different tk selection cassette with a HSVtk promoter sequence. This new vector design allowed both efficient 'hit and run' for two cystic fibrosis (CF) mutations with no false positives and successful germline transmission of the novel G480C missense mutation.     

Chromosomal promoter replacement in Saccharomyces cerevisiae: Construction of conditional lethal strains for the cloning of glycosyltransferases from various organisms

Heterologous complementation in yeast has been a successful tool for cloning and characterisation of genes from various organisms. Therefore we constructed conditionally lethal Saccharomyces cerevisiae strains by replacing the endogenous promoter from the genes of interest (glycosyltransferases) by the stringently regulated GAL1-promoter, by a technique called chromosomal promoter replacement. Such yeast strains were constructed for the genes Alg 1, Alg7, Sec59, Wbp1 involved in N-Glycosylation, the genes Gpi2, Gpi3/Spt14, Gaal, Pis1, involved in GPI-anchor biosynthesis and Dpm involved in both pathways. All strains show the expected conditionally lethal phenotype on glucose-containing medium when expression of the respective gene is turned off.     

Efficient gene targeting in ligase IV-deficient Monascus ruber M7 by perturbing the non-homologous end joining pathway

Inactivating the non-homologous end joining (NHEJ) pathway is a well established method to increase gene replacement frequency (GRF) in filamentous fungi because NHEJ is predominant for the repair of DNA double strand breaks (DSBs), while gene targeting is based on homologous recombination (HR). DNA ligase IV, a component of the NHEJ system, is strictly required for the NHEJ in Saccharomyces cerevisiae and Neurospora crassa. To enhance the GRF in Monascus ruber M7, we deleted the Mrlig4 gene encoding a homolog of N. crassa DNA ligase IV. The obtained mutant (MrΔlig4) showed no apparent defects in vegetative growth, colony phenotype, microscopic morphology, spore yield, and production of Monascus pigments and citrinin compared with the wild-type strain (M. ruber M7). Gene targeting of ku70 and triA genes revealed that GRF in the MrΔlig4 strain increased four-fold compared with that in the wild-type strain, reached 68 % and 85 %, respectively. Thus, the MrΔlig4 strain is a promising host for efficient genetic manipulation. In addition, the MrΔlig4 strain is more sensitive than M. ruber M7 to a DNA-damaging agent, methyl methanesulfonate.     

The size and ratio of homologous sequence to non-homologous sequence in gene disruption cassette influences the gene targeting efficiency in <Emphasis Type="Italic">Beauveria bassiana</Emphasis>

Targeted gene replacement via homologous recombination (HR) is a conventional approach for the analysis of gene function. However, this event is rare in Beauveria bassiana, which hampers efficient functional analysis in this widely used entomopathogenic fungus. To improve homologous recombination frequency in B. bassiana, we investigated the effect of the ratio of homologous sequence to non-homologous sequence (HS/NHS) in gene disruption cassette upon the HR frequency by two gene loci BbNtl and BbThi, using the herpes simplex virus thymidine kinase as a negative selectable marker against ectopic transformants. Our data revealed that an increase of the ratio of HS/NHS achieved by either extending homologous sequence or decreasing non-homologous sequence could improve HR frequency in B. bassiana. We determined empirically that (1) at least 700 bp of homology to both sides of a target gene was needed to get a reasonable number of disruptants, e.g., 6.7‰ to 13.3‰ in B. bassiana. (2) When the ratio of HS/NHS was above 0.8, an acceptable HR frequency could be achieved for gene replacement in B. bassiana, while when the ratio was below 0.3, few gene disrupted mutants were obtained.     

Establishment of Smad2 conditional gene targeting mice based on the Cre-LoxP system

Smads is a new gene family in transforming growth factor-β (TGF- β) signaling pathway. Smad2 mutated in multiple human tumors and may be a candidate tumor suppressor gene. Targeted disruption of murine Smad2 gene resulted in embryonic lethality at E6.5. To study the function of Smad2 in vertebrate organgenesis and tumorigenesis, we constructed the Smad2 conditional targeting vector in which two LoxP sequences were placed to flank the sequences encoding the C terminal functional domain of Smad2. The validity of the LoxP sites in the targeting construct was tested in E. coli that express the Cre recombinase constitutively. The vector was electroporated into ES cells and 3 targeted ES cell clones were obtained by Southern blot screening. Targeted ES cells were introduced into C57BL/6J blastocysts by microinjection to generate germ-line chimeras. Genotyping analysis showed that 2 progeny among these chimeras carried the Smad2 conditional targeted allele. The establishment of Smad2 conditional gene targeting mouse has laid a solid foundation for producing the tissue specific Smad2 gene knockout mice.     

Efficient repetitive alteration of the mouse Huntington's disease gene by management of background in the tag and exchange gene targeting strategy

The introduction of subtle mutations to predetermined locations in the mouse genome has aided in the assessment of gene function and the precise modeling of inherited disorders. Subtle mutations can be engineered into the mouse genome by the tag and exchange gene targeting strategy (Askew et al., 1993; Stacey et al., 1994; Wu et al., 1994). This two-step method involves both a positive and a negative selection. The negative selection step typically generates a large amount of undesired background that may prevent the practical recovery of gene targeted clones (Vazquez et al., 1998). In this work we describe a strategy to effectively manage this background by calculation of a tolerable level of background for a specific targeting event, pre-screening for clones with low background, subcloning and growth of cell lines under selection. This strategy was used to repeatedly and efficiently alter the mouse Huntington's disease homologue (Hdh) resulting in an average of 15 percent of the clones having the desired modification. Analysis of the remaining background clones showed they arose de novo by a mechanism that involved physical loss of the marker rather than mutation or inactivation. We calculated the rate of loss of this marker as 8.3×10^–6 events/cell/generation. We further show that the exchanged clones retained the capacity to contribute to the mouse germline demonstrating the utility of this strategy in the production of mouse lines with Hdh variants.     

Enhancing phosphorus and zinc acquisition efficiency in rice: a critical review of root traits and their potential utility in rice breeding

Background

Rice is the world''s most important cereal crop and phosphorus (P) and zinc (Zn) deficiency are major constraints to its production. Where fertilizer is applied to overcome these nutritional constraints it comes at substantial cost to farmers and the efficiency of fertilizer use is low. Breeding crops that are efficient at acquiring P and Zn from native soil reserves or fertilizer sources has been advocated as a cost-effective solution, but would benefit from knowledge of genes and mechanisms that confer enhanced uptake of these nutrients by roots.

Scope

This review discusses root traits that have been linked to P and Zn uptake in rice, including traits that increase mobilization of P/Zn from soils, increase the volume of soil explored by roots or root surface area to recapture solubilized nutrients, enhance the rate of P/Zn uptake across the root membrane, and whole-plant traits that affect root growth and nutrient capture. In particular, this review focuses on the potential for these traits to be exploited through breeding programmes to produce nutrient-efficient crop cultivars.

Conclusions

Few root traits have so far been used successfully in plant breeding for enhanced P and Zn uptake in rice or any other crop. Insufficient genotypic variation for traits or the failure to enhance nutrient uptake under realistic field conditions are likely reasons for the limited success. More emphasis is needed on field studies in mapping populations or association panels to identify those traits and underlying genes that are able to enhance nutrient acquisition beyond the level already present in most cultivars.     

csd alleles in the red dwarf honey bee (Apis florea,Hymenoptera: Apidae) show exceptionally high nucleotide diversity

Abstract The single locus complementary sex determination (sl‐csd) gene is the primary gene determining the gender of honey bees (Apis spp.). While the csd gene has been well studied in the Western honey bee (Apis mellifera), and comparable data exist in both the Eastern honey bee (Apis cerana) and the giant honey bee (Apis dorsata), no studies have been conducted in the red dwarf honey bee, Apis florea. In this study we cloned the genomic region 3 of the A. florea csd gene from 60 workers, and identified 12 csd alleles. Analysis showed that similar to A. mellifera, region 3 of the csd gene contains a RS domain at the N terminal, a proline‐rich domain at the C terminal, and a hypervariable region in the middle. However, the A. florea csd gene possessed a much higher level of nucleotide diversity, compared to A. mellifera, A. cerana and Apis dorsata. We also show that similar to the other three Apis species, in A. florea, nonsynonymous mutations in the csd gene are selectively favored in young alleles.     

Existence of homologous sequences corresponding to cDNA of the ver gene in diverse higher plant species

INTRODUCT1ONIn the vast majority of higher plalls, a transitionfrom vegetative growth to reproductive developmentis strongly influenced by a set of environmental fac-tors, such as photoperiod, temperatu-re etc. Bothwinter trait and biennia1 plants require a period of1ow temperature fOr switching from vegetative to re-productive growth, and this process is known as ver-na1ization. Several physiological and genetic inves-tigations showed that the vrngenes control the ver-nalization traits of…