David H. Boxer

Involvement of the narJ and mob gene products in distinct steps in the biosynthesis of the molybdoenzyme nitrate reductase in Escherichia coli

The Escherichia coli mob locus is required for synthesis of active molybdenum cofactor, molybdopterin guanine dinucleotide. The mobB gene is not essential for molybdenum cofactor biosynthesis because a deletion of both mob genes can be fully complemented by just mobA. Inactive nitrate reductase, purified from a mob strain, can be activated in vitro by incubation with protein FA (the mobA gene product), GTP, MgCl2, and a further protein fraction, factor X. Factor X activity is present in strains that lack MobB, indicating that it is not an essential component of factor X, but over‐expression of MobB increases the level of factor X. MobB, therefore, can participate in nitrate reductase activation. The narJ protein is not a component of mature nitrate reductase but narJ mutants cannot express active nitrate reductase A. Extracts from narJ strains are unable to support the in vitro activation of purified mob nitrate reductase: they lack factor X activity. Although the mob gene products are necessary for the biosynthesis of all E. coli molybdoenzymes as a result of their requirement for molybdopterin guanine dinucleotide, NarJ action is specific for nitrate reductase A. The inactive nitrate reductase A derivative in a narJ strain can be activated in vitro following incubation with cell extracts containing the narJ protein. NarJ acts to activate nitrate reductase after molybdenum cofactor biosynthesis is complete.

Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli.

Synthesis of the [NiFe] hydrogenases 1 and 2 of Escherichia coli is induced in response to anaerobiosis and is repressed when nitrate is present in the growth medium. The hydrogenase 1 and hydrogenase 2 enzymes are encoded by the polycistronic hyaABCDEF and hybOABCDEFG operons, respectively. Primer extension analysis was used to determine the initiation site of transcription of both operons. This permitted the construction of single-copy lacZ operon fusions, which were used to examine the transcriptional regulation of the two operons. Expression of both was induced by anaerobiosis and repressed by nitrate, which is in complete accord with earlier biochemical studies. Anaerobic induction of the hyb operon was only partially dependent on the FNR protein and, surprisingly, was enhanced by an arcA mutation. This latter result indicated that ArcA suppresses anaerobic hyb expression and that a further factor, which remains to be identified, is involved in controlling anaerobic induction of operon expression. Nitrate repression of hyb expression was mediated by the NarL/NarX and NarP/NarQ two-component regulatory systems. Remarkably, a narP mutant lacked anaerobic induction of hyb expression, even in the absence of added nitrate. Anaerobic induction of hya expression was dependent on the ArcA and AppY regulators, which confirms earlier observations by other authors. Nitrate repression of the hya operon was mediated by both NarL and NarP. Taken together, these data indicate that although the hya and hyb operons share common regulators, there are important differences in the control of expression of the individual operons.

Molecular genetic analysis of the moa operon of Escherichia coli K-12 required for molybdenum cofactor biosynthesis

A 3.2 kb chromosomal DNA fragment which complements the defects in a series of twelve moa::Mucts insertion mutants has been sequenced. Five open reading frames (ORFs) were identified and these are arranged in a manner consistent with their forming an operon. The encoded proteins (MoaA‐MoaE) have predicted molecular weights of 37346, 18665, 17234, 8843 and 16981 respectively. Examination of subclones of the whole locus in an expression system demonstrated the predicted products. N‐terminal amino acid sequences for the moa A, B, C and E products confirmed the translational starts. Genetic analysis distinguished four classes of moa mutants corresponding to genes moaA, C, D and E. Potential promoter sequences upstream of moaA and a possible transcription termination signal have been identified. Genetic analysis of the chlA1 and chlM mutants, which have been biochemically characterized as defective in molybdopterin biosynthesis, indicates that these carry lesions in moaA and moaD respectively. The moa locus is orientated clockwise at 17.7 minutes in the chromosome.

Molybdenum Cofactor Biosynthesis THE PLANT PROTEIN Cnx1 BINDS MOLYBDOPTERIN WITH HIGH AFFINITY

The molybdenum cofactor is an essential part of all eukaryotic molybdoenzymes. It is a molybdopterin (MPT) revealing the same core structure in all organisms. The plant protein Cnx1 fromArabidopsis thaliana is involved in the multi-step biosynthesis of molybdenum cofactor. Previous studies (Stallmeyer, B., Nerlich, A., Schiemann, J., Brinkmann, H., and Mendel, R. R. (1995) Plant J. 8, 751–762) suggested a function of Cnx1 in a late step of cofactor biosynthesis distal to the formation of MPT,i.e. conversion of MPT into molybdenum cofactor. Here we present the first biochemical evidences confirming this assumption. The protein Cnx1 consists of two domains (E and G) homologous to two distinct Escherichia coli proteins involved in cofactor synthesis. Binding studies with recombinantly expressed and purified Cnx1 and with its single domains revealed a high affinity of the G domain to MPT (k D = 0.1 μm) with equimolar binding. In contrast, the E domain of Cnx1 binds MPT with lower affinity (k D = 1.6 μm) and in a cooperative manner (n H = 1.5). The entire Cnx1 showed a tight and cooperative MPT binding. Based on these data providing a common link between both domains that matches the previous characterization of plant and bacterial Cnx1 homologous mutants, we present a model for the function of Cnx1.

Nickel deficiency gives rise to the defective hydrogenase phenotype of hydc and fnr mutants in Escherichia coli

Hydrogenase activity and other hydrogenase‐related functions can be restored to hydC mutants by the specific addition of nickel salts to the growth medium. These mutants are defective in all three hydrogenase isoenzymes and the restoration is dependent upon protein synthesis. The cellular nickel content of the mutant when grown in LB medium is less than 1% of that of the parental strain. Partial suppression of the hydrogenase phenotype of hydC mutants occurs when growth takes place in a different medium. This correlates with an increased cellular nickel content. The phenotype of the mutant is also fully suppressed by growth in media of very low magnesium content. Such media facilitate nickel uptake via the magnesium transport system, which leads to the acquisition of a normal cellular nickel content. Mutations in the fnr gene, which encodes a transcriptional regulator for several anaerobically expressed enzymes, abolishes hydC expression and gives rise to a defective hydrogenase phenotype. The hydrogenase phenotype of fnr is closely similar to that of hydC in all respects examined. The hydrogenase activity of fnr strains can be restored by the presence of a functional hydC gene on a multicopy plasmid. The hydrogenase phenotype of fnr strains therefore arises indirectly via suppression of hydC, which leads to a low cellular nickel content. Nickel has no influence on fumarate reductase or nitrate reductase activities in fnr strains. The hydrogen‐metabolism phenotype of fnr strains is, therefore, dependent upon their ability to acquire nickel from growth media. It is likely that hydC encodes a specific transport system for nickel.

Pleiotropic hydrogenase mutants of Escherichia coli K12: growth in the presence of nickel can restore hydrogenase activity

Anaerobic growth in the presence of 0.6 mM NiCl2 was able to restore hydrogenase and benzyl-viologen-linked formate dehydrogenase activities to a mutant (FD12), which is normally defective in these activities. This mutant carries a mutation located near minute 58 in the genome. Hydrogenase isoenzyme I and II activities were restored along with the hydrogenase activity that forms part of the formate hydrogen lyase system. A plasmid (pRW1) was constructed, containing a 4.8 kb chromosomal DNA insert, which was able to complement the lesion in mutant FD12. Further mutants with mutations near 58 minutes on the chromosome, and which lacked hydrogenase and formate dehydrogenase activities were isolated. These mutants were divided into three groups. Class I mutants were restored to the wild-type phenotype either by growth with 0.6 mM NiCl2 or following transformation with pRW1. Class II mutants were also complemented by pRW1 but were unaffected by growth with NiCl2. Class III mutants were unaffected by both pRW1 and growth with NiCl2. The cloned 4.8 kb fragment of chromosomal DNA therefore encodes two genes essential for hydrogenase activity. Restriction analysis indicates that the cloned DNA is the same as a fragment that has previously been cloned and which complements the hydB locus (Sankar et al. (1985) J. Bacteriol., 162, 353-360). None of the three classes of mutants possess mutations in hydrogenase structural genes.

The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds.

The molybdate‐dependent transcriptional regulator (ModE) from Escherichia coli functions as a sensor of molybdate concentration and a regulator for transcription of operons involved in the uptake and utilization of the essential element, molybdenum. We have determined the structure of ModE using multi‐wavelength anomalous dispersion. Selenomethionyl and native ModE models are refined to 1.75 and 2.1 Å, respectively and describe the architecture and structural detail of a complete transcriptional regulator. ModE is a homodimer and each subunit comprises N‐ and C‐terminal domains. The N‐terminal domain carries a winged helix–turn–helix motif for binding to DNA and is primarily responsible for ModE dimerization. The C‐terminal domain contains the molybdate‐binding site and residues implicated in binding the oxyanion are identified. This domain is divided into sub‐domains a and b which have similar folds, although the organization of secondary structure elements varies. The sub‐domain fold is related to the oligomer binding‐fold and similar to that of the subunits of several toxins which are involved in extensive protein–protein interactions. This suggests a role for the C‐terminal domain in the formation of the ModE–protein–DNA complexes necessary to regulate transcription. Modelling of ModE interacting with DNA suggests that a large distortion of DNA is not necessary for complex formation.

Phosphorescence depolarization and the measurement of rotational motion of proteins in membranes.

Rotational relaxation times of the order of many microseconds are typical of the presumably uniaxial rotation of membrane proteins [ 11. So far measurements of rotational relaxation times have been limited to those proteins which are present at high occupancy either in the orginal membrane, as with the band-3 proteins of erythrocyte ghosts [2], or in highly purified fragments of membrane such as the acetylcholine receptor protein of the electric organ of Torpedo mamorata [3], or in reconstituted membranes [4]. This restriction arises from the relative insensitivity of the two measurement methods usually used, either saturation transfer EPR spectroscopy [5] or the decay of linear dichroism following flash photolysis of an attached triplet-forming probe such as eosin [6]. We describe here a method for determining rotational relaxation times

Requirement for nickel of the transmembrane translocation of NiFe-hydrogenase 2 in Escherichia coli.

1 ms) by measurement of the depolarization of laser flashinduced phosphorescence of erythrosin (tetraiodoflurorescein) attached to the protein of interest. This new method provides experimental realisation of many earlier suggestions [7,8]: it exceeds the sensitivity of the photodichroism method [6] by a factor of -lo’, and the saturation transfer method [S] by -104. We illustrate the use of our method by describing the slow isotropic rotation of proteins in viscous media, and the anisotropic rotation of Ca”dependent ATPase in sarcoplasmic reticulum membrane.

The mob locus of Escherichia coli K12 required for molybdenum cofactor biosynthesis is expressed at very low levels

The cellular location of membrane‐bound NiFe‐hydrogenase 2 (HYD2) from Escherichia coli was studied by immunoblot analysis and by activity staining. Treatment of spheroplasts with trypsin was able to release active HYD2 into the soluble fraction, indicating that HYD2 is attached to the periplasmic side of the cytoplasmic membrane and that HYD2 undergoes a trans‐membrane translocation during its biosynthesis. By using a nik mutant deficient in the high affinity specific nickel transport system, we show that the intracellular availability of nickel is essential for the processing of the large subunit and for the transmembrane translocation of HYD2. We also demonstrate that the processing of the precursor, which is related with nickel incorporation, can occur in the membrane‐depleted soluble fraction and that it is associated with the increase in resistance to proteolysis of the processed form of the large subunit. The mechanism of the transmembrane translocation of HYD2 is discussed.