Restriction map of native and cloned cauliflower mosaic virus DNA

The Dawn of Plant Molecular Biology: How Three Key Methodologies Paved the Way

The adoption of Arabidopsis thaliana in the 1980s as a universal plant model finally enabled researchers to adopt and take full advantage of the molecular biology tools and methods developed in the bacterial and animal fields since the early 1970s. It further brought the plant sciences up to speed with other research fields, which had been employing widely accepted model organisms for decades. In parallel with this major development, the concurrent establishment of the plant transformation methodology and the description of the cauliflower mosaic virus (CaMV) 35S promoter enabled scientists to create robust transgenic plant lines for the first time, thereby providing a valuable tool for studying gene function. The ability to create transgenic plants launched the plant biotechnology sector, with Monsanto and Plant Genetic Systems developing the first herbicide- and pest-tolerant plants, initiating a revolution in the agricultural industry. Here I review the major developments over a less than 10-year span and demonstrate how they complemented each other to trigger a revolution in plant molecular biology and launch an era of unprecedented progress for the whole plant field. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

From Bacteriophage to Plant Genetics

When first asked to write a review of my life as a scientist, I doubted anyone would be interested in reading it. In addition, I did not really want to compose my own memorial. However, after discussing the idea with other scientists who have written autobiographies, I realized that it might be fun to dig into my past and to reflect on what has been important for me, my life, my family, my friends and colleagues, and my career. My life and research has taken me from bacteriophage to Agrobacterium tumefaciens-mediated DNA transfer to plants to the plant genome and its environmentally induced changes. I went from being a naïve, young student to a postdoc and married mother of two to the leader of an ever-changing group of fantastic coworkers-a journey made rich by many interesting scientific milestones, fascinating exploration of all corners of the world, and marvelous friendships.

In vivo recombination of cauliflower mosaic virus DNA

LIGATION AND RECOMBINATION OF THE DNA OF CAULIFLOWER MOSAIC VIRUS (CAMV) IS DEMONSTRATED BY THE FOLLOWING EXPERIMENTS: (i) Ligation: Different noninfectious fragments of the CaMV genome (obtained after insertion into plasmid pBR322 followed by enzymatic excision) regained infectivity when mixtures of them were used to inoculate their host. The symptom appearance was delayed by comparison with a typical CaMV infection, and only the newly formed leaves were affected. (ii) Recombination: Pairs of noninfectious recombinant full-length CaMV genomes (integrated into pBR322 at different restriction endonuclease sites) regained infectivity upon simultaneous inoculation of a sensitive host. The symptomatology of the resulting infection was indistinguishable from that of a typical CaMV infection. We show that progeny DNA had the same characteristics (size, structure, restriction endonuclease digestion pattern) as bona fide CaMV DNA, and that the vector pBR322 had been completely eliminated. A cloned tandem dimer of CaMV DNA with a partial deletion similarly was infectious in the plant assays. This system should be useful to study the expression of mutant genomes, thus allowing characterization of the CaMV genes.

Physical maps of the genomes of dahlia mosaic virus and mirabilis mosaic virus-two members of the caulimovirus group

The nucleic acids of dahlia mosaic virus (DaMV) and mirabilis mosaic virus (MMV) have been isolated and compared with the native DNA of cauliflower mosaic virus (CaMV). The native DNAs of these viruses separated into circular and linear molecules during gel electrophoresis to produce patterns nearly identical to those of CaMV. The DNAS of DaMV and MMV were cloned in bacteria and used for mapping the cleavage sites for 14 different restriction endonucleases. These sites were confirmed with native viral DNA. The S1 nuclease cleavage sites and the sizes of single-stranded denaturation products of the native DNA of each virus was used to determine the location of the four single-stranded interruptions present in each virus. The largest denaturation fragment of each virus migrated in gels at about the same rate as the a strand (which has one discontinuity) of CaMV. These features have been used to construct physical maps of the viral genomes.

Identification of C-terminal amino acid residues of cauliflower mosaic virus open reading frame III protein responsible for its DNA binding activity

We cloned in Escherichia coli truncated versions of the protein p15 encoded by open reading frame III of cauliflower mosaic virus. We then compared the ability of the wild-type p15 (129 amino acids) and the deleted p15 to bind viral double-stranded DNA genome. Deletions of > 11 amino acids in the C-terminal proline-rich region resulted in loss of DNA binding activity of wild-type p15. Moreover, a point mutation of the proline at position 118 sharply reduced the interaction between the viral protein and DNA. These results suggest that cauliflower mosaic virus p15 belongs to the family of DNA binding proteins having a proline-rich motif involved in interaction with double-stranded DNA.

The cauliflower mosaic virus gene III product is a non-sequence-specific DNA binding protein

The interaction of the gene III product, P15, of cauliflower mosaic virus with different double-stranded DNA fragments of the viral genome was investigated. The results suggest that gene III product which showed DNA binding activity is a structural protein of the viral particle.

Expression of CaMV ORF IV in Escherichia coli

A CaMV DNA fragment corresponding to nucleotides 2200-3992 and including the coding sequence (2200-3670) of open reading frame IV was inserted in the pTG908 prokaryotic expression vector. In the recombinant pTG-IV plasmid, ORF IV, which codes for the coat protein precursor, was fused to the N-terminal coding sequence of the lambda CII gene, which is under transcriptional control of the lambda PL promoter. The expected fusion protein CII-ORF IV had a calculated molecular weight of 58.4 Kd. Nevertheless, temperature induction of the PL promoter resulted in synthesis of a major 76-Kd fusion protein: the coat protein precursor migrated abnormally on SDS polyacrylamide gel.

Translation products of cauliflower mosaic virus ORF V, the coding region corresponding to the retrovirus pol gene

Open reading frame (ORF) V of cauliflower mosaic virus (CaMV), the candidate for the reverse transcriptase gene, has been expressed in E. coli under control of the PR promoter of bacteriophage lambda either as an N-terminal polypeptide fused to beta-galactosidase or as the total ORF V without fusion. Antibodies against these proteins were used to analyze extracts from CaMV-infected plants by immunoblotting. ORF V-specific polypeptides of 80, 62, 58, 22, and 18 kD apparent molecular weights were detected, with the largest species corresponding to the full length translation product. The 62 and 22 kD species could be assigned to the N-terminus and the remaining two species to the C-terminus of the ORF.

Expression in plants of two bacterial antibiotic resistance genes after protoplast transformation with a new plant expression vector

Two bacterial antibiotic resistance genes, one coding for the neomycin phosphotransferase (NPT I) from Tn903, and the other coding for the chloramphenicol acetyltransferase from Tn9 were used as plant selectable markers. Both genes were introduced into the Nicotiana tabacum genome in a new plant expression vector, using the direct gene transfer method. The vector pDH51, used in these experiments contains a plant expression unit as a movable cassette, consisting of the strong cauliflower mosaic virus (CaMV) 35S RNA promoter and transcription terminator separated by a polylinker containing several unique restriction sites.

Electron microscopic mapping of single-stranded discontinuities in cauliflower mosaic virus DNA by means of the biotin-avidin technique

Biotin-labeled deoxyuridine triphosphate has been used to label the three natural single-stranded discontinuities of Cauliflower Mosaic Virus DNA. The presence of biotin permitted the direct visualization and mapping of the discontinuities by electron microscopy, using ferritin-labeled avidin.

Replication of the cauliflower mosaic virus: role and stability of the cloned delta 3 discontinuity sequence

A fragment of cauliflower mosaic virus (CaMV) DNA, containing delta 3, one of the three discontinuity sequences, was cloned in various ways into CaMV DNA deleted for the delta 3 sequence. The series of constructions was monitored for the appearance of the typical single-strand (ss) discontinuity after hybrid CaMV replication in plants. The delta 3 discontinuity was observed only if the orientation of inserted DNA sequence was the same as in the wild-type virus. Long polylinker sequences used for insertion of the fragment into cloned viral DNA, affected the stability of the insert in progeny viral DNA in plants by acting as recombination targets.

Mutagenesis of cauliflower mosaic virus

A series of insertion mutants of cauliflower mosaic virus (CaMV) DNA has been constructed in vitro. These insertions consist of a short DNA sequence (10 or 22 bp) containing a restriction endonuclease site (SmaI) not represented on the viral DNA. Viral infectivity was analyzed by inoculating plants with the mutated cloned viral DNA and observing symptoms. Insertions within ORFVII, and in one site within the large intergenic region, did not interfere with viral infectivity, whilst insertions within ORFII and at the end of ORFIV retarded the development of viral symptoms. All other insertion mutants analyzed were lethal. CaMV with a deletion of 105 bp within ORFVII was viable. Such viable mutants can be used to construct additional deletions or to insert foreign DNA into the viral genome.

Plasmid-encoded hygromycin B resistance: the sequence of hygromycin B phosphotransferase gene and its expression in Escherichia coli and Saccharomyces cerevisiae

The plasmid-borne gene hph coding for hygromycin B phosphotransferase (HPH) in Escherichia coli has been identified and its nucleotide sequence determined. The hph gene is 1026 nucleotides long, coding for a protein with a predicted Mr of 39 000. The hph gene was placed in a shuttle plasmid vector, downstream from the promoter region of the cyc 1 gene of Saccharomyces cerevisiae, and an hph construction containing a single AUG in the 5' noncoding region allowed direct selection following transformation in yeast and in E. coli. Thus the hph gene can be used in cloning vectors for both pro- and eukaryotes.

Isolation and characterization of faithful and altered clones of the genomes of cauliflower mosaic virus isolates Cabb B-JI, CM4-184, and Bari I

Full-length genomes of cauliflower mosaic virus (CaMV) isolates Cabb B-JI, CM4-184, and Bari I have been cloned in the SalGI site of plasmid pAT 153. The cloned DNAs were characterized by restriction mapping and infectivity assays. All the sites present in the virion DNAs were found in the cloned DNAs. Comparison of restriction maps with those of DNA from two other isolates which have been recently completely sequenced revealed a close relationship among the different isolates. Some of the clones appear to be faithful copies of the viral genomes and these viral inserts are infectious when inoculated into turnip plants. Various clones with deletions in the CaMV DNA have been isolated and characterized. Some of them may correspond to deletions naturally occurring in a subpopulation of the virus whereas others occurred during cloning. None of the deleted fragments are infectious when inoculated into plants. Strikingly, all the deletions overlap one or two of the specific single-stranded breaks characteristic of caulimoviruses, suggesting that sequences surrounding the breaks are not dispensable.

Nucleotide sequence of DNA from an altered-virulence isolate D/H of the cauliflower mosaic virus

The double-stranded DNA from the isolate D/H with an altered virulence of the cauliflower mosaic virus (CaMV) contains 8016 bp. The DNA is circular and possesses, like the DNA of most CaMV strains, three sequence interruptions. The comparison of its sequence with the previously published sequences of two other CaMV strains (Cabb-S and CM 1841) leads to the following conclusions: (1) The genetic organization of all three CaMV strains is identical with six potential genes (open reading frames) and two intergenic regions; (2) considered pairwise, the three DNAs differ from one another by only about 5% with base substitutions accounting for most of the changes although several deletions and insertions are also observed. The sequence differences among the three strains are spread in a uniform manner upon the genome except for the two intergenic regions, which are more highly conserved. The stability of the noncoding regions is probably linked to the fact that they carry sequences important for the initiation and termination of transcription. On the other hand, the sequence variation in the open reading frames has relatively little effect on the sequence of the corresponding polypeptides as changes occur preferentially in the third position of the reading frame triplets. It is anticipated that knowledge of the DNA sequences of several CaMV strains will facilitate construction of inter-strain recombinants which, once available, can be used to correlate gene structure and function.

Characterisation of cauliflower mosaic virus DNA sequences which encode major polyadenylated transcripts

Cauliflower mosaic virus DNA sequences which encode two major polyadenylated RNA species, the 1.9 kb messenger RNA for the 62,000 MW virus inclusion body polypeptide and 35S RNA, were mapped using the nuclease 51 procedure. The 1.9 kb RNA has an eleven nucleotide leader sequence transcribed from alpha-strand DNA located at co-ordinate 0.72 m.u. (map units), immediately upstream of the AUG initiation codon of reading frame VI. The 3'-end of 1.9 kb RNA maps at 0.95 m.u. and is co-terminal with the 3'-end of 35S RNA, a complete transcript of the DNA alpha-strand. The 5'-end of 35S RNA maps at 0.93 m.u. and is located upstream of the discontinuity G1 (zero m.u.) in the alpha-strand and some 200 nucleotides upstream of the sequence encoding its own 3'-terminus.

The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing

We have determined the complete primary structure (8031 base pairs) of an infectious clone of cauliflower mosaic virus strain CM1841. The sequence was obtained using the strategy of cloning shotgun restriction fragments in the sequencing vector M13mp7. Comparison of the CM1841 sequence with that published for another caMV strain (Strasbourg) reveals 4.4% changes, mostly nucleotide substitutions with a few small insertions and deletions. The six open reading frames in the sequence of the Strasbourg isolate are also present in CM1841.

Infectivities of native and cloned DNA of cauliflower mosaic virus

Infectivity assays on turnips reveal that (i) cauliflower mosaic virus (CaMV) DNA, whether circular or linear, is as infectious as the complete virus; (ii) linear DNA obtained with restriction enzymes from the native CaMV DNA has the same specific infectivity as when first cloned in plasmid (pBR322) or bacteriophage (lambda gtWES) vectors and then restricted at the cloning site; (iii) in all cases studied mosaic symptoms are accompanied by virus production. DNA isolated from these viruses is again circular and possesses the three "gaps" characteristic of CaMV DNA. The cloned CaMV DNA, when linked to the vector DNA, is noninfectious or exhibits very low infectivity.

Nucleotide sequence of cauliflower mosaic virus DNA

The complete nucleotide sequence (8024 nucleotides) of the circular double-stranded DNA of cauliflower mosaic virus has been established. The DNA molecule is known to possess three discrete single-stranded discontinuities, often referred to as "gaps," two in one strand and one in the other. The sequence data indicate that gap 1, the single discontinuity in the alpha strand, corresponds to the absence of no more than one or two nucleotides with respect to the complementary beta strand. The two discontinuities in the beta strand, however, are not authentic gaps since no nucleotides are missing, but are instead regions of sequence overlap: a short sequence (19 residues for gap 2, t least 2 residues for gap 3) at one terminus of each discontinuity, probably the 5' terminus, is displaced from the double helix by an identical sequence at the other boundary of the discontinuity. Analysis of the distribution of nonsense codons in the DNA sequence is consistent with other evidence that only the alpha strand is transcribed. The coding region extends around the circular molecule from 4 map units of gap 1, the map origin, to map position 91, and consists of six long open reading frames. Our findings suggest, but do not prove, that the DNA sequence of the open reading frames is colinear with viral protein sequences. The cistron for the viral coat protein, which is probably synthesized in the form of a precursor, has been situated in coding region IV on the basis of its unusual amino acid composition.