DNA-mediated genetic correction of thiamineless Arabidopsis thaliana

Tracing My Roots: How I Became a Plant Biologist

My trajectory to becoming a plant biologist was shaped by a complex mix of scientific, political, sociological, and personal factors. I was trained as a microbiologist and molecular biologist in the late 1960s and early 1970s, a time of political upheaval surrounding the Vietnam War. My political activism taught me to be wary of the potential misuses of scientific knowledge and to promote the positive applications of science for the benefit of society. I chose agricultural science for my postdoctoral work. Because I was not trained as a plant biologist, I devised a postdoctoral project that took advantage of my microbiological training, and I explored using genetic technologies to transfer the ability to fix nitrogen from prokaryotic nitrogen-fixing species to the model plant Arabidopsis thaliana with the ultimate goal of engineering crop plants. The invention of recombinant DNA technology greatly facilitated the cloning and manipulation of bacterial nitrogen-fixation ( nif) genes, but it also forced me to consider how much genetic engineering of organisms, including human beings, is acceptable. My laboratory has additionally studied host–pathogen interactions using Arabidopsis and the nematode Caenorhabditis elegans as model hosts.

Beyond the fringe: when science moves from innovative to nonsense

Microbiology has experienced examples of highly productive researchers who have gone beyond just interpreting their experimental results with hypotheses and published nonsense that was readily recognized as such by readers. Although the most discussed cases of this pathology come from physics, studies of single-celled microorganisms, virology, and immunology have provided many examples. Five cases are described here along with some generalizations. These are the Lamarckian inheritance of acquired characteristics reported by distinguished and experienced researchers, vectorless DNA transfer and incorporation of bacterial DNA into chromosomes of plants years before vector construction of genetically modified plants was invented, water with memory of immunoglobulin IgE, a new electromagnetic radiation method for identifying bacterial and viral pathogens by the discoverer of human immunodeficiency virus, and the claim of isolation of a new bacterial isolate with arsenic replacing phosphorus in DNA. These examples represent very dissimilar areas, and the only common factor is hubris on the part of experienced researchers. Secondarily, failure of peer review sometimes happens, and journal editors do not step in, sometimes even when alerted before publication. These failures of the publishing process teach us that unnecessary mistakes occur and should warn us all to watch our own enthusiasms.

The virtosome-a novel cytosolic informative entity and intercellular messenger

Studies on a range of prokaryote and eukaryote cells and tissues have shown that a newly synthesized DNA/RNA-lipoprotein complex is released in a regulated manner. This complex, termed a virtosome, is a novel cytosolic component of eukaryote cells. The released virtosomes can readily enter other cells where they can modify the biology of the recipient cells. Such modifications include immunological changes and transformation from normal to cancer cells. The virtosomes form a normal component of the circulating nucleic acids in plasma and serum currently used for clinical diagnostic purposes. Given the transformative powers of virtosomes released from tumour cells, the presence of such a complex in human plasma could readily offer the basis of an alternative mechanism for the initiation of metastases.

The development of Arabidopsis as a model plant

Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom.

Inherited metabolic disease: prospects for the future in both basic and clinical research

The birth of a child with an inherited disorder is often the beginning of a life-long problem for the whole family. About 8.5% of paediatric deaths and 4.7% of paediatric hospital admissions are due to autosomal and sex-linked recessive diseases. These figures are likely to be erroneously low because of incomplete ascertainment. The inherited metabolic diseases therefore merit study on economic as well as humanitarian grounds. Investigations of the disorders of purine metabolism have been conducted for more than a century and a half in the borderland between biochemistry and medicine, illuminating both disciplines and reflecting their separate developments. These studies are a general model for work in other branches of human intermediary metabolism. It is hoped that the basic study of the inborn errors or metabolism will expand our knowledge of the defective gene and of its product, the enzyme protein. Clinical studies should aim to improve the prenatal, postnatal and carrier-state diagnosis of these disorders, and to improve their treatment by methods which can be made practicable and generally available at the clinical level. There may be some hope for enzyme replacement in certain circumstances. The prospect for genetic modification at the clinical level is almost infinitely far away, where many would say that is should remain.

Gene transfer strategies in plants

In recent years, a large number of gene transfer methods have been developed. However, the results of these studies have often been published in such a way that it has been extremely difficult for researchers to assess the reliability and efficiency of the method, and to judge whether or not integrative transformation has occurred. Thus although an abundance of knowledge exists within the area of gene transfer, its documentation remains disjointed. This report summarises the recent progress which has been made in the field of gene transfer systems in plants and discusses the associated advantages, disadvantages and limitations in an attempt to clarify this issue.

Evidence that direct DNA uptake through cut shoots leads to genetic transformation of Solanum aviculare Forst

The reporter genes GUS, NPTII and BAR, either separately or in combination, have been exploited to determine if DNA which can directly enter plants, circulate within the plant and enter nuclei, can also integrate into the genome in a manner which will permit gene expression. Feeding of either seed-derived or adventitious cut shoots of Solanum aviculare with the GUS gene followed by rooting of the shoots and growing on, resulted in all tissues of the plant showing GUS activity as detected cytochemically. Southern blot analysis of plants derived from the adventitious shoots confirmed the presence of the reporter gene in roots. Reporter gene expression was observed also in the F1 generation. If GUS and NPTII or GUS, NPTII and BAR were fed together, then in each case it was possible to have both expression and Southern blot confirmation of each of the genes. There was a relatively high rate of transformation of approximately 5% of the fed stems across all experiments conducted during the present study.

A fortunate choice: the history of Arabidopsis as a model plant

During the past 20 years, the flowering plant Arabidopsis thaliana has been adopted as a model organism by thousands of biologists. This community has developed important tools, resources and experimental approaches that have greatly stimulated plant biological research. Here, we review some of the key events that led to the uptake of Arabidopsis as a model plant and to the growth of the Arabidopsis community.

On procaryotic gene expression in eucaryotic systems

Numerous types of interaction between pro- and eucaryotes exist in nature, from the endosymbiosis of some bacteria with unicellular organisms and insects to the complex systems of bacterial flora associated with the skin and intestines of animals and man, and nitrogen-fixation and crown-gall tumor induction in plants. Until recently, such interactions were not thought to include genetic transfer, but an increasing body of evidence points to the probability of similar naturally-occurring exchanges with wide-ranging implications for evolution and genetic manipulation. Experiments to elucidate the possible effects of procaryotic genes in eucaryotic systems have included in vitro and in vivo studies with both plant and animal systems, for instance the translation of bacterial messenger RNAs in the wheat germ and rabbit reticulocyte systems and the introduction of bacterial genes into plant protoplasts, animal cells and whole organisms. In the present paper we have tried to summarize the results of experiments involving the uptake, replication, transcription, translation and integration of procaryotic genes in various eucaryotic systems and to discuss the implications of such findings for basic research as well as for possible biomedical applications. Awareness of the possibility of procaryotic-eucaryotic genetic interactions may help to elucidate unresolved questions in pathology, such as possible involvement of the intestinal flora in carcinogenesis, as well as to provide valuable probes of eucaryotic control mechanisms and new approaches in agricultural genetic engineering.

Molecular mechanisms of the origin of chromosome aberrations and the structural organisation of eukaryotic DNA

A new hypothesis on the appearance of exchange chromosomal aberrations has been suggested. According to this hypothesis, temporal duplex polynucleotide structure should arise during G1 and G2 phases during the correction of DNA. The size of the duplex, as a rule, should be restricted to the size of complementary nucleotide sequences in the regions of repetitions. Any polynucleotide break in a duplex zone would result in chromosome breakage and if complementary broken ends interact with each other, then exchange chromosome aberrations may be formed. This hypothesis would explain such previously obscure phenomena as extremely high frequencies of exchanges after mutagen treatment, the nature of mitotic crossing-over, negative interference, change of aberration types before replication, the low frequency of damaged structural genes during aberration formation, etc.

Genetic transformation and "graft-hybridization" in flowering plants

Recent pollination experiments with highly irradiated (100,000 r) pollen in Nicotiana have shown that radiation-"pulverized" pollen chromatin can cause genetic transformation of the egg. A new model is proposed here for integration of chromatin fragments into host chromosomes. It is also proposed that heterochromatin may be involved in the process of gene transfer, and in the phenomena of meiotic drive associated with gene transfer.It is suggested that this discovery throws new light on the phenomenon of "graft-hybridization". In spite of many reports to the contrary, "graft-hybrids" have so far been explained only on the basis of their being chimaeras. A mechanism is suggested here by which they may result from genetic transformation.

Genetic analysis by chromosome-mediated gene transfer

A general method is presented for stable transfer of genetic information to eukaryotic cells, utilizing metaphase chromosomes as the vehicle. Recent progress, current problems and large areas of uncertainty in this field are reviewed; particular consideration is given to frequency of transfer, size of the transgenome, evidence of cotransfer of linked genes and serial chromosome transfer. A reasonable model for chromosome transfer is considered with respect to the available information, and various descrepancies are noted. The utility of this method for fine structural mapping, cloning small regions of the eukaryotic genome and other potential applications are discussed.

Biophysical and genetic evidence for transformation in plants

In thiamine mutants of Arabiodopsis, genetic corrections have been obtained by treatment with DNA bearing a thiamine information. When correction is attempted under selective conditions, about 0.7% of the treated plants grow and set fruit. Their progeny and the following ones, obtained by selfing, behave as homozygotes. Segregation of characters is found only when correction is attempted under nonselective conditions or when the correcting genes were of plasmidian origin. The correction is hereditary; results of backcrosses and test crosses indicate that it is dominant, nuclear, and strongly bound to the genome. The corrective factor appears to be added to the mutated genome and not substituted for the mutation, as it can be suppressed by outcrossing with the wild type or with a plant corrected by another DNA.

Studies on the fate of homologous DNA applied to seedlings of Matthiola incana

Seedlings of Matthiola incana (crucifer) are able to take up exogenous homologous DNA by the roots. DNA homogenously labelled with [3H]adenine and 5-bromodeoxyuridine is incorporated into the plants in a macromolecular form. Intact donor DNA and a fraction with a buoyant density intermediate between that of the donor and the recipient DNA can be recovered. Analysis of this intermediate fraction by ultrasonication and alkali treatment allows the suggestion that homologous DNA is integrated as a double-stranded DNA which becomes covalently linked to the recipient DNA. Control experiments in which seedlings were incubated in a mixture simulating donor DNA degradation products in the presence and absence of unlabelled competitors suggest that these results are not due to the breakdown of donor DNA and reincorporation of the products during DNA synthesis in the recipient plants. When ultrasonicated or thermally denatured DNA is applied to the plants it may be degraded and reused for recipient DNA synthesis but it is not recovered in a macromolecular form. The possibility that the intermediate DNA fraction arises by bacterial contamination of the plants can be excluded by several arguments. Autoradiographic studies show that at least part of the radioactivity of the donor DNA taken up by the plants is associated with the cell nucleus.

Uptake of bacterial DNA by Chlamydomonas reinhardi

Escherichia coli [3H]DNA supplied to vegetative cultures of wild-type (mt+) and CW15 (mt+;mutant lacking the cell wall) Chlamydomonas reinhardi could bind to the cell wall of the wild-type and to the cell membrane of CW15 mutant cells. The extent of this binding decreased with time and was to a large degree (over 90%) DNA-ase-sensitive. Nevertheless, about 0.01% of the bacterial DNA remained irreversibly associated with the cells when they reached stationary phase. The irreversible binding of the donor bacterial DNA to Chlamydomonas cells could be increased by treatment of the cultures with polycations such as DEAE-dextran, poly-L-lysine and poly-L-ornithine. Although the CW15 cells rapidly degraded bacterial DNA in the culture medium wild-type cells showed only a small effect on the molecular weight of the donor DNA. The acid-insoluble radioactivity irreversibly bound to WT (+) cells consisted mainly of oligonucleotides with a small proportion present as less depolymerized donor DNA. No radioactivity, however, was found to be associated with the recipient high molecular weight Chlamydomonas DNA. No labeled donor DNA could be recognized in the cells given bacterial [3H]DNA in early stationary phase. Instead, radioactivity found in Chlamydomonas DNA corresponded to reutilization of [3H]thymine derivatives released as a result of [3H]DNA degradation. No evidence for the integration of detectable amounts of donor DNA sequences into the host cell DNA was obtained.

On the question of the integration of exogenous bacterial DNA into plant DNA

Extensive studies with pea, tomato, and barley failed to confirm the evidence presented by previous investigators for integration or replication of exogenously applied bacterial DNA in these plants. Labeled DNA of buoyant density in CsCl intermediate between that of high density donor bacterial DNA and of plant DNA was never observed with axenic plants. Intermediate peaks, similar to those used as evidence for recombination by earlier investigators, were observed only when the plants were contaminated with bacteria. Plant DNA prepared by a published procedure [Ledoux, L. & Huart, R. (1969) J. Mol. Biol. 43, 243-262] was found to be contaminated with unidentified impurities. Such DNA was partially protected from the action of DNase and produced aberrant banding patterns in CsCl after shearing. Much of the published evidence for integration of foreign DNA in plants is based upon experiments with plant DNA prepared by this procedure. We conclude that contamination is the likely explanation for what has been interpreted as evidence for integration.

Transfer of the human gene for hypoxanthine-guanine phosphoribosyltransferase via isolated human metaphase chromosomes into mouse L-cells

We have transferred the human gene for hypoxanthine-guanine phosphoribosyltransferase (HPRT, EC 2.4.2.8; IMP:pyrophosphate phosphoribosyltransferease) via isolated metaphase chromosomes from human HeLa S3 cells into murine A9 cells which lack functional murine HPRT activity, using the technique of McBride and Ozer (Proc, Nat. Acad. Sci. USA 70, 1258-1262, 1973). Three transformed clones were isolated which contained human HPRT activity as determined by electrophoretic and immunochemical assays. Twenty human isozymes other than HPRT whose genes have been assigned to 14 human chromosomes were found to be absent in our transformed clones. Moreover, the human isozymes of hlucose-6-phosphate dehydrogenase (EC 1.1.1.49; D-glucose 6-phosphate:NADP 1-oxidoreductase) and phosphoglycerate kinase (EC 2.7.2.3;ATP:3-phospho-D-glycerate 1-phosphotransferase), whose genes have been linked with the HPRT gene to the long are of the human X chromosome, were also absent. On the basis of the known linkage relationships of the three markers, we thereby suggest that the transferred piece of human genetic material is smaller than 20% of the human X chromosome or less than 1% of the human genome. This estimate assumes a normal syntenic relationship for the long arm of the X chromosome in HeLa S3 cells. In agreement with this conclusion, no human chromosomes could be detected in our transformed clones. When grown under nonselective conditions about 3% of the gene transfer cells lost the human HPRT marker per cell generation. Transformants that had lost human HPRT activity were subjected to hypoxanthine-aminopterin-thymidine selection. The frequency of revertants to the HPRT(+) phenotype was less than 1 x 10(-6), and two revertants that were obtained possessed the mouse electrophoretic phenotype. These results argue against a stable integration of the human donor genetic material into the mouse recipient genome.

Dosage compensation and ontogenic expression of suppressed and transformed Vermilion flies in Drosophila

A spectrofluorometric assay system for tryptophan oxygenase was used to compare dosage compensation properties and ontogenic expression of suppressed, "transformed," and wild-type vermilion flies. The results indicate that, although different stocks showed different levels of oxygenase activity, all showed dosage compensation properties. The ontogenic expression of tryptophan oxygenase was observed to be different in the various genotypes. Whereas suppressed vermilion resembled wild type in its pattern, the ontogenic profiles of "transformed" flies were different.