Complete nucleotide sequence of the Escherichia coli gdhA gene

The DNA sequence of the gdhA gene of Escherichia coli K12, which encodes the 447 amino acid polypeptide subunit of NADP-specific glutamate dehydrogenase, is presented. The deduced protein sequence is strongly homologous to the corresponding enzyme of the eukaryotic fungus Neurospora crassa. The upstream DNA sequence includes several overlapping promoter consensus sequences. The downstream DNA sequence contains inverted repeats, predicted as forming long stable stem-loop structures in RNA, homologous to those found in several enterobacterial intergenic regions.     

The gdhA gene is located at 38.6 minutes on the Escherichia coli map.

We report here that the gdhA gene of Escherichia coli, which encodes the NADP-specific glutamate dehydrogenase, is located at 38.6 min on the map. We have confirmed this location by showing linkage with three Tn10 insertions that are linked to the aroD, pheS, and ansA loci, by complementation by a restriction-mapped lambda clone, and by showing correspondence between the restriction maps of the chromosome and the cloned and sequenced gdhA gene.     

Isolation of a Rhizobium phaseoli cytochrome mutant with enhanced respiration and symbiotic nitrogen fixation.

Cultured cells of a Rhizobium phaseoli wild-type strain (CE2) possess b-type and c-type cytochromes and two terminal oxidases: cytochromes o and aa3. Cytochrome aa3 was partially expressed when CE2 cells were grown on minimal medium, during symbiosis, and in well-aerated liquid cultures in a complex medium (PY2). Two cytochrome mutants of R. phaseoli were obtained and characterized. A Tn5-mob-induced mutant, CFN4201, expressed diminished amounts of b-type and c-type cytochromes, showed an enhanced expression of cytochrome oxidases, and had reduced levels of N,N,N',N'-tetramethyl-p-phenylenediamine, succinate, and NADH oxidase activities. Nodules formed by this strain had no N2 fixation activity. The other mutant, CFN4205, which was isolated by nitrosoguanidine mutagenesis, had reduced levels of cytochrome o and higher succinate oxidase activity but similar NADH and N,N,N',N'-tetramethyl-p-phenylenediamine oxidase activities when compared with the wild-type strain. Strain CFN4205 expressed a fourfold-higher cytochrome aa3 content when cultured on minimal and complex media and had twofold-higher cytochrome aa3 levels during symbiosis when compared with the wild-type strain. Nodules formed by strain CFN4205 fixed 33% more N2 than did nodules formed by the wild-type strain, as judged by the total nitrogen content found in plants nodulated by these strains. Finally, low-temperature photodissociation spectra of whole cells from strains CE2 and CFN4205 reveal cytochromes o and aa3. Both cytochromes react with O2 at -180 degrees C to give a light-insensitive compound. These experiments identify cytochromes o and aa3 as functional terminal oxidases in R. phaseoli.     

Overexpression of the dctA gene in Rhizobium meliloti: effect on transport of C4 dicarboxylates and symbiotic nitrogen fixation.

Symbiotic nitrogen fixation may be limited by the transport of C4 dicarboxylates into bacteroids in the nodule for use as a carbon and energy source. In an attempt to increase dicarboxylate transport, a plasmid was constructed in which the Rhizobium meliloti structural transport gene dctA was fused to a tryptophan operon promoter from Salmonella typhimurium, trpPO. This resulted in a functional dctA gene that was no longer under the control of the dctBD regulatory genes, but the recombinant plasmid was found to be unstable in R. meliloti. To stably integrate the trpPO-dctA fusion, it was recloned into pBR325 and recombined into the R. meliloti exo megaplasmid in the dctABD region. The resultant strain showed constitutive dctA-specific mRNA synthesis which was about 5-fold higher than that found in fully induced wild-type cells. Uptake assays showed that [14C]succinate transport by the trpPO-dctA fusion strain was constitutive, and the transport rate was the same as that of induced control cells. Acetylene reduction assays indicated a significantly higher rate of nitrogen fixation in plants inoculated with the trpPO-dctA fusion strain compared with the control. Despite this apparent increase, the plants had the same top dry weights as those inoculated with control cells.     

The effect of strA mutation on symbiotic nitrogen fixation by Rhizobium meliloti.

Studies on 3H-dihydrostreptomycin accumulation and binding to ribosomes showed that ineffective strain CMts17 carries strB type mutation changing its membrane permeability to the drug. Introduction of high level streptomycin resistance of strA type into strain CMts17 was correlated with acquisition of effectiveness and membrane permeability to the drug. This suggests that changes in membrane permeability, responsible for ineffectiveness of strain CMts17, can be reversed by strA mutation.     

Expression of Rhizobium meliloti genes for nitrogen fixation in Escherichia coli minicells: Mapping of the subunit of the nitrogenase reductase

An EcoRI fragment of Rhizobium meliloti M2011 which shows homology to Klebsiella pneumoniae DNA carrying nifH and nifD was cloned in both orientations into the Cm gene of plasmid pACYC184 and expressed in Escherichia coli minicells. Fragment specific polypeptides of M_r 12 500, 21 000, 30 000, and 31 000 could be identified. By transposon mutagenesis it was shown that two of them (M_r 12 500 and 21 000) are fusion products with parts of the chloramphenicol acetyltransferase. The other two polypeptides are specified by one coding region which could be mapped by transposon mutagenesis. There are several reasons (homology to Klebsiella nifH, sequence data and molecular weight of the gene products) to assume that this coding region represents the R. meliloti nifH gene (gene for the subunit of the R. meliloti nitrogenase reductase, RmII).     

Repetitive extragenic palindromic (REP) sequences in the Escherichia coli gdhA gene

Deletions of the 3' flanking DNA region of the glutamate dehydrogenase (GDH) structural gene from Escherichia coli K-12, have been produced on a plasmid that carries the complete gdhA gene. Those deletions include part of the repetitive extragenic palindromic (REP) sequences proposed by Stern et al. [Cell 37 (1984) 1015-1026], as a novel and major feature of the bacterial genome. The effect of these deletions on the final GDH level in the cell, has been determined. A broader compilation, analysis and alternative functions of the REP sequences, is also presented.     

Regulation of nitrogen fixation in Rhizobium sp.

Regulation of nitrogen fixation by ammonium and glutamate was examined in Rhizobium sp. 32H1 growing in defined liquid media. Whereas nitrogenase synthesis in Klebsiella pneunoniae is normally completely repressed during growth on NH4+, nitrogenase activity was detected in cultures of Rhizobium sp. grown with excess NH4+. However, an "ammonium effect" on activity was invariably observed in cultures grown on NH4+ as sole nitrogen source; the nitrogenase activity was, depending on conditions, 14 to 36% of that of comparable glutamate-grown cultures. Glutamate inhibited utilization of exogenous NH4+ and, in one of two procedures described, glutamate partially alleviated the ammonium effect on nitrogenase activity. NH4+, apparently produced from N2, was excreted into the culture medium when growth was initiated on glutamate, but not when NH4+ was thesole source of fixed nitrogen for growth. These findings are discussed in relation to nitrogen fixation by Rhizobium bacteroids.     

Impaired nitrogen fixation and glutamine synthesis in methionine sulfoximine sensitive (MSs) mutants of Rhizobium phaseoli

Molecular Genetics and Genomics - Random Tn5 mutagenesis of antibiotic-resistant derivatives of Rhizobium phaseoli CFN42 yielded several independent mutants that were sensitive to methionine...     

fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti.

Nitrogen fixation genes are shown to undergo a complex positive and negative regulation in Rhizobium meliloti. Activation of fixN by fixLJ is shown to require a third regulatory gene, fixK. As fixK is activated by fixLJ, we propose a cascade model for fixN regulation such that fixLJ activates fixN via fixK. In addition fixK negatively regulates expression of the nif-specific activator nifA as well as its own expression by autoregulation. Thus nifA and fixK are subject to a mixed regulation, positive (by fixLJ) and negative (by fixK). The sequence of fixK shows homology with the Escherichia coli regulators fnr and crp, which makes fixK the third characterized member of this family of prokaryotic regulators.     

Introduction of single-copy sequences into the chromosome of Escherichia coli: application to gene and operon fusions.

We have developed a general method for the introduction of any cloned sequence into the chromosome of Escherichia coli. This method employs an Hfr strain which carries a fragment of bla (the pBR322 gene imparting ampicillin resistance) between lacI and lacZ. Plasmid-borne inserts which are flanked by sequences from bla and lacZ can be introduced at this locus by homologous recombination. The isolation of recombinants is enhanced by selection for transfer of an integrated copy of the plasmid during conjugation. Once introduced into the chromosome, the inserted sequences can be transferred to other strains by conventional methods such as P1 transduction or conjugation. This method is suitable for the transfer of any cloned sequence to the chromosome and is particularly well suited to the construction of chromosomal gene and operon fusions with lacZ.     

Cultivar and Rhizobium strain effect on nitrogen fixation and transport inPhaseolus vulgaris L.

The effects of Rhizobium strain and its interaction with plant cultivar were examined in glasshouse-grownPhaseolus vulgaris in two experiments where the physiological attributes defining the symbiotic efficiency were determined. Strains of Rhizobium significantly affected nodulation, rates of N accumulation, partitioning of N within the mature shoot and remobilizaton of the N stored in the vegetative organs to the seeds. The most efficient symbiosis (strain CO5 with Negro Argel), in comparison with the least efficient symbiosis (strain 127 K-17 with Venezuela-350) showed higher rates of C₂H₂ reduction from flowering to mid pod fill stage, evolved less hydrogen from nodules and showed higher rates of N transport as well as higher percentages of ureide-N in the xylem sap. At maturity, the best cultivar/strain association exceeded the total N accumulated in the seed and the harvest index of the poorest symbiosis in 88% and 20%, respectively. The other symbiotic combinations were intermediate in all characteristics. Nitrogen accumulation in plant shoot showed highly significant correlation with acetylene reduction rates, nodule relative efficiency, total N transport in the xylem sap and percentage of N transported as ureides.     

Conservation of symbiotic nitrogen fixation gene sequences in Rhizobium japonicum and Bradyrhizobium japonicum.

Southern hybridization with nif (nitrogen fixation) and nod (nodulation) DNA probes from Rhizobium meliloti against intact plasmid DNA of Rhizobium japonicum and Bradyrhizobium japonicum strains indicated that both nif and nod sequences are on plasmid DNA in most R. japonicum strains. An exception is found with R. japonicum strain USDA194 and all B. japonicum strains where nif and nod sequences are on the chromosome. In R. japonicum strains, with the exception of strain USDA205, both nif and nod sequences are on the same plasmid. In strain USDA205, the nif genes are on a 112-megadalton plasmid, and nod genes are on a 195-megadalton plasmid. Hybridization to EcoRI digests of total DNA to nif and nod probes from R. meliloti show that the nif and nod sequences are conserved in both R. japonicum and B. japonicum strains regardless of the plasmid or chromosomal location of these genes. In addition, nif DNA hybridization patterns were identical among all R. japonicum strains and with most of the B. japonicum strains examined. Similarly, many of the bands that hybridize to the nodulation probe isolated from R. meliloti were found to be common among R. japonicum strains. Under reduced hybridization stringency conditions, strong conservation of nodulation sequences was observed in strains of B. japonicum. We have also found that the plasmid pRjaUSDA193, which possess nif and nod sequences, does not possess sequence homology with any plasmid of USDA194, but is homologous to parts of the chromosome of USDA194. Strain USDA194 is unique, since nif and nod sequences are present on the chromosome instead of on a plasmid as observed with all other strains examined.     

Positive selection of nodulation-deficient Rhizobium phaseoli.

A high proportion of Rhizobium phaseoli mutants that survived infection with phage F1 were found to be nodulation deficient. Two that were examined in detail had internal defects in addition to the expected surface defects. One internal defect was in the enzyme phosphoglucose isomerase. The use of phages to select appropriate mutants should apply generally in any system in which surface components are involved.     

Rhizobium japonicum mutants defective in symbiotic nitrogen fixation.

Rhizobium japonicum strains 3I1b110 and 61A76 were mutagenized to obtain 25 independently derived mutants that produced soybean nodules defective in nitrogen fixation, as assayed by acetylene reduction. The proteins of both the bacterial and the plant portions of the nodules were analyzed by two-dimensional polyacrylamide gel electrophoresis. All of the mutants had lower-than-normal levels of the nitrogenase components, and all but four contained a prominent bacteroid protein not observed in wild-type bacteroids. Experiments with bacteria grown ex planta suggested that this protein was derepressed by the absence of ammonia. Nitrogenase component II of one mutant was altered in isoelectric point. The soluble plant fraction of the nodules of seven mutants had very low levels of heme, yet the nodules of five of these seven mutants contained the polypeptide of leghemoglobin. Thus, the synthesis of the globin may not be coupled to the content of available heme in soybean nodules. The nodules of the other two of these seven mutants lacked not only leghemoglobin but most of the other normal plant and bacteroid proteins. Ultrastructural examination of nodules formed by these two mutants indicated normal ramification of infection threads but suggested a problem in subsequent survival of the bacteria and their release from the infection threads.