The identification and partial characterization of a plasmid containing the gene for the membrane-associated hydrogenase from E. coli

The hydrogenases and formate dehydrogenases of Escherichia coli

Escherichia coli has the capacity to synthesise three distinct formate dehydrogenase isoenzymes and three hydrogenase isoenzymes. All six are multisubunit, membrane-associated proteins that are functional in the anaerobic metabolism of the organism. One of the formate dehydrogenase isoenzymes is also synthesised in aerobic cells. Two of the formate dehydrogenase enzymes and two hydrogenases have a respiratory function while the formate dehydrogenase and hydrogenase associated with the formate hydrogenlyase pathway are not involved in energy conservation. The three formate dehydrogenases are molybdo-selenoproteins while the three hydrogenases are nickel enzymes; all six enzymes have an abundance of iron-sulfur clusters. These metal requirements alone invoke the necessity for a profusion of ancillary enzymes which are involved in the preparation and incorporation of these cofactors. The characterisation of a large number of pleiotropic mutants unable to synthesise either functionally active formate dehydrogenases or hydrogenases has led to the identification of a number of these enzymes. However, it is apparent that there are many more accessory proteins involved in the biosynthesis of these isoenzymes than originally anticipated. The biochemical function of the vast majority of these enzymes is not understood. Nevertheless, through the construction and study of defined mutants, together with sequence comparisons with homologous proteins from other organisms, it has been possible at least to categorise them with regard to a general requirement for the biosynthesis of all three isoenzymes or whether they have a specific function in the assembly of a particular enzyme. The identification of the structural genes encoding the formate dehydrogenase and hydrogenase isoenzymes has enabled a detailed dissection of how their expression is coordinated to the metabolic requirement for their products. Slowly, a picture is emerging of the extremely complex and involved path of events leading to the regulated synthesis, processing and assembly of catalytically active formate dehydrogenase and hydrogenase isoenzymes. This article aims to review the current state of knowledge regarding the biochemistry, genetics, molecular biology and physiology of these enzymes.

Cloning of the gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough) and determination of the NH2-terminal sequence

The gene encoding the hydrogenase from Desulfovibrio vulgaris (Hildenborough) has been cloned in Escherichia coli. D. vulgaris DNA was digested with the restriction endonucleases EcoRI and SalI and ligated into the vector pUC9 [Vieira, J. & Messing, J. (1982) Gene 19, 259-268], which had been cut with these same enzymes. Approximately 9000 recombinant clones were obtained by transformation of E. coli JM 101 followed by growth on rich plates with ampicillin for selection and isopropyl-beta-D-thiogalactoside and 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside present for detection of recombinants. The recombinant clones were then screened for production of immunoreactive proteins with rabbit antisera against purified hydrogenase and 125I-labelled protein A. 28 positive clones were found in this initial screening. These were further tested in an immunocompetition experiment, which showed that the protein product from one clone behaved identically to purified hydrogenase. The plasmid pHV15 isolated from this clone has a 4.7 X 10(3)-base-pair SalI/EcoRI insert. Cells of E. coli JM 101 transformed with pHV 15 produce a hydrogenase polypeptide of molecular mass 46 kDa as detected by Western blotting. The mass, as well as the Cleveland mapping pattern of the polypeptide produced by E. coli, are identical with those of the hydrogenase isolated from D. vulgaris (Hildenborough). Southern blotting of restriction-enzyme-digested D. vulgaris DNA, using the nick-translated 4.7 X 10(3)-base-pair SalI/EcoRI fragment as a probe, indicates the presence of a single gene with an internal PstI site. The NH2-terminal sequence of the hydrogenase was determined to be: (sequence in text). This information should allow an unambiguous identification of the hydrogenase gene.

Cloning of hydrogenase genes and fine structure analysis of an operon essential for H2 metabolism in Escherichia coli

Escherichia coli has two unlinked genes that code for hydrogenase synthesis and activity. The DNA fragments containing the two genes (hydA and hydB) were cloned into a plasmid vector, pBR322. The plasmids containing the hyd genes (pSE-290 and pSE-111 carrying the hydA and hydB genes, respectively) were used to genetically map a total of 51 mutant strains with defects in hydrogenase activity. A total of 37 mutants carried a mutation in the hydB gene, whereas the remaining 14 hyd were hydA. This complementation analysis also established the presence of two new genes, so far unidentified, one coding for formate dehydrogenase-2 (fdv) and another producing an electron transport protein (fhl) coupling formate dehydrogenase-2 to hydrogenase. Three of the four genes, hydB, fhl, and fdv, may constitute a single operon, and all three genes are carried by a 5.6-kilobase-pair chromosomal DNA insert in plasmid pSE-128. Plasmids carrying a part of this 5.6-kilobase-pair DNA (pSE-130) or fragments derived from this DNA in different orientations (pSE-126 and pSE-129) inhibited the production of active formate hydrogenlyase. This inhibition occurred even in a prototrophic E. coli, strain K-10, but only during an early induction period. These results, based on complementation analysis with cloned DNA fragments, show that both hydA and hydB genes are essential for the production of active hydrogenase. For the expression of active formate hydrogenlyase, two other gene products, fhl and fdv are also needed. All four genes map between 58 and 59 min in the E. coli chromosome.

Regulation of the synthesis of hydrogenase (formate hydrogen-lyase linked) of E. coli

The regulation of synthesis of the hydrogenase which is a component of the formate hydrogen-lyase complex was studied by means of a strain of Escherichia coli possessing a transcriptional fusion of the hydrogenase gene (hyd) with the lacZ gene (hyd::lac fusion). Formation of active hydrogenase in the wild strain requires the presence of nickel in the medium; transcription of the hyd gene, however, is independent from the presence of Ni2+. Ni2+ addition to Ni2+-prestarved cells did not lead to any activation of presumptive hydrogenase apoprotein. Regulatory mutants were isolated in which nitrate repression of hyd::lac expression was relieved. Two main classes of regulatory mutants were identified: (i) Mutants with a defect in nitrate reductase; (ii) mutants with a cis-dominant regulatory mutation closely linked to the hyd::lac fusion. In the presence of formate which acts as an inducer, the hyd::lac fusion was also expressed under aerobic conditions. The results infer that nitrate repression of transcription of the hydrogenase structural gene is not effected by nitrate itself but requires the function of the electron transport chain leading to nitrate and that mutations in the promoter/operator region of the hyd cistron may confer insensitivity to redox control both by oxygen and nitrate.

Anaerobiosis induces expression of ant, a new Escherichia coli locus with a role in anaerobic electron transport

Escherichia coli has a formate hydrogenlyase system which allows it to maintain an electron balance during anaerobic growth by passing electrons from formate to H+ ions, thus generating H2. The Mu d1(Ap lac) bacteriophage was used to generate mutants that were defective in passing electrons from formate to benzyl viologen, an artificial electron acceptor. A subset of these mutants was studied in which beta-galactosidase was expressed at much higher levels under anaerobic conditions than under aerobic conditions. If nitrate was present during anaerobic growth, the same levels of beta-galactosidase were seen in these fusion strains as were seen under aerobic conditions. The Mu d1(Ap lac) insertions in these mutants were genetically mapped between mutS and srl and thus define a new locus we have termed ant (anaerobic electron transport). Recombinant lambda derivatives were isolated which complemented the deficiency of the ant mutants in anaerobic electron transport and also carried a trans-acting region of DNA which reduced expression of the ant-lac fusions under anaerobic conditions; a probe to the ant region was generated from one of these recombinant lambda derivatives. Southern hybridization analysis revealed that the four independent ant::Mu d1(Ap lac) fusions we isolated spanned an approximately 5-kilobase region and that all were transcribed in the same direction, counterclockwise on the E. coli genetic map.

On the redox control of synthesis of anaerobically induced enzymes in enterobacteriaceae

Mutants of Escherichia coli were isolated in which transcription of the structural genes for hydrogenase (hyd) and for one of the components of formate dehydrogenase (fdh) (of the formate hydrogen-lyase complex) is coupled with that of the lacZ gene. They were--together with lac fusions of the nifH and nifL genes from Klebsiella--used to study regulation by redox control, of the expression of the respective structural genes. The following results were obtained: (i) beta-galactosidase synthesis was fully repressed in the presence of O2 or nitrate (anaerobically), and induced in the absence of an external electron acceptor. Fumarate as terminal electron acceptor only marginally affected nif expression and partially repressed hyd and fdh expression. Redox control of the synthesis of hydrogenase and formate dehydrogenase, therefore, (as well as that of nif) acts at the level of transcription; the size of the redox potential seems to be correlated with the amount of repression; (ii) beta-galactosidase synthesis in the hyd:: lac and fdh::lac fusion strains is induced by formate. At high concentrations formate reverses the repression by nitrate and fumarate but not that by oxygen.

A method for the purification of E. coli plasmid DNA by homogeneous lysis and polyethylene glycol precipitation

A procedure is described for the isolation and purification of E. coli plasmid DNA by polyethylene glycol precipitation. The method is rapid, simple, inexpensive and amenable to both small and large scale manipulation. This procedure involves lysis of bacterial cells by treatment with pronase in sodium dodecyl sulfate, removal of chromosomal DNA by centrifugation, precipitation of residual nucleic acids with polyethylene glycol and removal of RNA by precipitation with LiCl. Plasmid DNA purified as described is pure enough for restriction endonuclease analysis, for use as a vector for the cloning of cDNA or synthetic DNA, or for use as a template in an E. coli transcription-translation cell-free system.

Cloning and expression of the hydrogenase gene from Clostridium butyricum in Escherichia coli

Hydrogenase gene from Clostridium butyricum was cloned in Escherichia coli HK16 (Hyd-) using pBR322 and PstI. The plasmid, pCBH1, containing hydrogenase gene was 7.3 MDa and pCBH1 had 5 PstI-DNA fragments (3.9, 2.6, 0.7, 0.03-0.04, less than 0.02 MDa, respectively). The hydrogenase activity of HK16 (pCBH1) was about 3.1-3.5-times as high as those of the present strains, such as C.butyricum and E.coli C600 (Hyd+).