Large plasmids of fast-growing rhizobia: homology studies and location of structural nitrogen fixation (nif) genes

Non-oncogenic T-region mutants ofAgrobacterium tumefaciens do transfer, T-DNA into plant cells

A new procedure for site-directed mutagenesis has been applied to the shooting and rooting loci of T-DNA of an octopine Ti-plasmid ofAgrobacterium tumefaciens. Mutants have been obtained which induced tumours that either developed shoots or produced more roots than normally observed. Double mutations, in which both types of T-DNA loci were affected, resulted in non-oncogenic strains. Indications have been obtained, showing that T-DNA coded oncogenic functions can be eliminated without affecting T-DNA transfer into plant cells.

Site-directed mutagenesis in Escherichia coli of a stable R772::Ti cointegrate plasmid from Agrobacterium tumefaciens

The host range of an octopine Ti plasmid is limited to Rhizobiaceae. This has been extended also to Escherichia coli in the form of a stable cointegrate with the wide-host-range plasmid R772. Its structure was studied by constructing a physical map of R772 and of the R772::pTiB6 cointegrate. An insertion sequence present in R772, called IS70, turned out to be involved in cointegrate formation. We found one intact copy of IS70 and a small segment of IS70, respectively, at the junctions of R772 and Ti DNA. The absence of a complete second copy of IS70 is a likely explanation for the stability of the cointegrate plasmid. A procedure for site-directed mutagenesis of this cointegrate plasmid in E. coli is described. The effect of mutations in the Ti plasmid part can be studied subsequently by transferring the cointegrate into Agrobacterium tumefaciens. The advantage of this procedure for Ti plasmids over other methods used at present is discussed.

Comparison of Ti plasmids from three different biotypes of Agrobacterium tumefaciens isolated from grapevines

Twenty-six plasmids from grapevine isolates of Agrobacterium tumefaciens were analyzed by SmaI fingerprinting and by hybridization of nick-translated DNA to DNA of another plasmid. These experiments established that octopine Ti plasmids are not highly conserved, although octopine Ti plasmids from biotype 1 A. tumefaciens strains appeared to be very similar. Octopine Ti plasmids from biotype 3 strains are more variable in terms of host range and SmaI fingerprints, but share extensive DNA homology. Fingerprints of nopaline Ti plasmids from strains of a given biotype resemble each other but not fingerprints of Ti plasmids from strains of the other two biotypes. The wide host range octopine Ti plasmid from the biotype 3 strain Ag86 shares more DNA homology with narrow host range Ti plasmids, nopaline Ti plasmids, and octopine catabolism plasmids than with the wide host range octopine Ti plasmid from biotype 1 strain 20/1. pTiAg86 does share homology with the portion of pTi20/1 integrated and expressed in plant tumor cells. Since all wide host range Ti plasmids studied contain these sequences, we suggest that natural selection for a wide host range resulted in the presence of the common sequences in distantly related plasmids. The lack of homology between this "common DNA" and limited host range Ti plasmids shows that the DNA sequences per se are not required for tumorigenesis.

Cloning and expression of the cloacin DF13/aerobactin receptor of Escherichia coli (ColV-K30)

A DNA fragment derived from the ColV-K30 plasmid and coding for both sensitivity to cloacin DF13 and Fe3+-aerobactin uptake was cloned into pBR322. The cloned fragment coded for two polypeptides with molecular masses of 74,000 (the cloacin DF13/aerobactin receptor protein) and 50,000 daltons, respectively. When grown with sufficient iron, cells harboring pFS8 (with this fragment) possessed about 10 times as many receptor protein molecules as compared with cells of Escherichia coli (ColV-K30). The synthesis of the receptor protein specified by pFS8, however, was independent of the availability of iron, in contrast to strains harboring the intact ColV-K30 plasmid. Aerobactin was taken up but not synthesized by cells harboring pFS8. No growth occurred when iron-starved cultures of these cells were incubated with Fe3+-aerobactin, suggesting that expression of other ColV-K30-encoded genes is necessary to remove the iron from the Fe3+-aerobactin complex.

Localization of symbiotic mutations in Rhizobium meliloti

A total of 5 Nod- and 57 Fix- symbiotic mutants of Rhizobium meliloti strain 41 have been isolated after either nitrosoguanidine or Tn5 transposition mutagenesis. Chromosomal locations of mutations in 1 Nod- and 11 Fix- derivatives were ascertained by transferring the chromosome (mobilized by plasmid R68.45), in eight fragments, into symbiotically effective recipients and testing the recombinants for symbiotic phenotype. Alternatively, the kanamycin resistance marker of Tn5 was mapped. In five mutants the fix alleles were localized on different chromosomal regions, but six other fix mutations and one nod mutation tested did not map onto the chromosome. It was shown that the chromosome-mobilizing ability (Cma+) of R68.45 was not involved in the mobilization of genes located extrachromosomally. Moreover, Cma- derivatives of R68.45 could mobilize regions of the indigenous plasmid pRme41b but not chromosomal genes. Thus, mobilization of a marker by Cma- R68.45 indicates its extrachromosomal location. With a 32P-labeled DNA fragment carrying Tn5 as a hybridization probe, it was shown that in five extrachromosomally located Tn5-induced fix mutants and one nod mutant Tn5 was localized on plasmid pRme41b. This is in agreement with the genetic mapping data.

Nitrogen fixation (nif) genes and large plasmids of Rhizobium japonicum

The location of structural nitrogen-fixation genes was determined for the slow- and fast-growing types of Rhizobium japonicum. Slow-growing R. japonicum strains do not harbor structural nif genes, homologous to nifD and nifH, on large plasmids (100 to 200 megadaltons). In contrast, all fast-growing R. japonicum strains, except PRC194, contain structural nif genes on large plasmids.

Plasmids and stability of symbiotic properties of Rhizobium trifolii

A conjugal plasmid which encodes both peak nodulation genes and nitrogenase genes, and which is labeled with the transposon Tn5, was transferred to a wild-type Rhizobium trifolii strain to examine the stability and expression of the host range and fixation (Fix+) phenotypes. Transconjugates were isolated which were shown to initially form nitrogen-fixing nodules (Nod+ Fix+) on both clovers and peas. These hybrid strains were then repeatedly passaged through either pea or clover nodules or onto a solid agar medium to determine whether these broadened-host-range characteristics were stably maintained. An instability was noted in the capacity of some of these hybrids to form nitrogen-fixing nodules on all of the host plants used. The broadened nodulation ability was, however, more readily maintained. In some cases, the changes in the Nod+ Fix+ phenotype could be attributed to demonstrable changes in the plasmid profile of the hybrid strains, whereas in other cases no demonstrable plasmid alterations could be detected.

On the operon structure of the nitrogenase genes of Rhizobium leguminosarum and Azotobacter vinelandii

The transcription of the nitrogenase genes in Rhizobium leguminosarum was studied by analysing total cellular RNA from bacteroids for the presence of nitrogenase messenger RNA. The RNA was separated by agarose gel electrophoresis and blotted onto nitrocellulose filters. Messenger RNA for nitrogenase was detected by hybridization with probes derived from plasmid pSA30, a recombinant plasmid carrying the nitrogenase genes of Klebsiella pneumoniae. In the same way nitrogenase mRNA was detected in RNA isolated from Azotobacter vinelandii and from Klebsiella pneumoniae, but only if both were cultured under conditions of derepression of the nitrogenase genes. The size of the RNA hybridizing with the probes indicates that in all three organisms the genes for the subunits of the two components of nitrogenase constitute a single operon.

Cloning of a nitrogen fixation (nif) gene cluster of Azospirillum brasilense

Homology was detected between the structural genes for the nitrogenase complex of K. pneumoniae (nifHDK genes) and the total DNA of several Azospirillum strains. Bacteriophage lambda gt 7-ara6 was used to construct a gene bank of A. brasilense strain 7000 DNA and a recombinant phage carrying a 6.7 kb Eco RI fragment, termed AbRI, was selected by hybridization with the K. pneumoniae nif probe. Using heteroduplex analysis the extent of the homology of the AbRI fragment and the K. pneumoniae nif genes was found to be approximately 5 kb. Proteins encoded by the AbRI fragment were examined after infection of E. coli minicells.

Directed transposon Tn5 mutagenesis and complementation analysis of Rhizobium meliloti symbiotic nitrogen fixation genes

An 18 kb region adjacent to and surrounding the genes for nitrogenase (nif) was cloned from the genome of the symbiotic nitrogen-fixing species Rhizobium meliloti. A total of 31 Tn5 insertions in the nif region were constructed and assayed for their effect on symbiotic nitrogen fixation (Fix phenotype). Fix- insertions were found in two clusters, one 6.3 kb region not containing essential symbiotic genes. The locations of at least three transcription units containing Fix genes were deduced from complementation analysis between genomic nif::Tn5 insertions and nif::Tn5 insertions on mobilizable cloning vectors. The locations of R. meliloti genes nifH, nifD and nifK, which code for the single subunit of the nitrogenase Fe protein and for the two subunits of the nitrogenase MoFe protein respectively, were determined by DNA hybridization to cloned Klebsiella pneumoniae nif genes and by comparison of partial R. meliloti DNA sequences with K. pneumoniae nif gene sequences. R. meliloti nifH, D and K are located in the 6.3 kb fix-::Tn5 cluster and are transcribed in the order nifH, nifD, nifK, which is the same order as in K. pneumoniae.

Relationship between Nif plasmids of fast-growing Rhizobium species and Ti plasmids of Agrobacterium tumefaciens

By use of the Southern blot hybridization technique the extent of DNA homology was determined between the Nif plasmid of a number of fast-growing Rhizobium species and Ti plasmids of the octopine (pTiAch5) and nopaline (pTiC58) type. DNA sequences common to these plasmids were located on functional maps of the Ti plasmids. No homology between Nif plasmids and the T region of Ti plasmids was detected.

Clustering of nitrogen fixation (nif) genes in Rhizobium meliloti

A cloned 17.3-kilobase region of the Rhizobium meliloti genome with homology to the Klebsiella pneumoniae nitrogenase structural genes was studied. Limits on the extent of homology were determined. Transposon mutagenesis of this region of the genome verified that it contained functional nif genes, Some transposon insertions resulted in a defective symbiotic phenotype, whereas others had no noticeable effect on symbiotic competence. The relative position of insertions yielding these two phenotypic classes suggested that at least three distinct units of gene expression are present in this region. Hybridization of RNA from alfalfa root nodules and from vegetatively grown Rhizobium to this cloned DNA showed that at least 11.1 kilobases of the region was transcribed actively and that transcription was specific for the symbiotic state.

Genes controlling early and late functions in symbiosis are located on a megaplasmid in Rhizobium meliloti

Large plasmids of molecular weight varying from 90 to around 200 x 10(6) have earlier been detected in most Rhizobium meliloti strains using an alkaline denaturation - phenol extraction procedure. With a less destructive method (Eckardt 1978) it was possible additionally to detect one plasmid of molecular weight clearly greater than 300 x 10(6) (= megaplasmid) in all of twenty-seven R. meliloti strains of various geographical origins and nodulation groupings investigated. Four strains (RCR 2011, A145, S26 and CC2013) were found to carry one megaplasmid and no smaller plasmids. Hybridization experiments with Klebsiella pneumoniae and R. meliloti cloned nitrogenase structural genes D and H showed that these genes are located on the megaplasmid and not on the smaller plasmids. All of the ten independent spontaneous non-nodulating derivatives of three strains of R. meliloti were shown to have suffered a deletion in the nifDH region of the megaplasmid. These results indicate that a gene controlling an early step in nodule formation is located in the nifDH region of the megaplasmid. This indicates that the same replicon carries genes controlling early and late functions in symbiosis.