Regulation of the ndh gene of Escherichia coli by integration host factor and a novel regulator, Arr

TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent Escherichia coli

IMPORTANCE

Energy generation pathways are a potential avenue for the development of novel antibiotics. However, bacteria possess remarkable resilience due to the compensatory pathways, which presents a challenge in this direction. NADH, the primary reducing equivalent, can transfer electrons to two distinct types of NADH dehydrogenases. Type I NADH dehydrogenase is an enzyme complex comprising multiple subunits and can generate proton motive force (PMF). Type II NADH dehydrogenase does not pump protons but plays a crucial role in maintaining the turnover of NAD+. To study the adaptive rewiring of energy metabolism, we evolved an Escherichia coli mutant lacking type II NADH dehydrogenase. We discovered that by modifying the flux through the tricarboxylic acid (TCA) cycle, E. coli could mitigate the growth impairment observed in the absence of type II NADH dehydrogenase. This research provides valuable insights into the intricate mechanisms employed by bacteria to compensate for disruptions in energy metabolism.

Catabolism of Amino Acids and Related Compounds

This review considers the pathways for the degradation of amino acids and a few related compounds (agmatine, putrescine, ornithine, and aminobutyrate), along with their functions and regulation. Nitrogen limitation and an acidic environment are two physiological cues that regulate expression of several amino acid catabolic genes. The review considers Escherichia coli, Salmonella enterica serovar Typhimurium, and Klebsiella species. The latter is included because the pathways in Klebsiella species have often been thoroughly characterized and also because of interesting differences in pathway regulation. These organisms can essentially degrade all the protein amino acids, except for the three branched-chain amino acids. E. coli, Salmonella enterica serovar Typhimurium, and Klebsiella aerogenes can assimilate nitrogen from D- and L-alanine, arginine, asparagine, aspartate, glutamate, glutamine, glycine, proline, and D- and L-serine. There are species differences in the utilization of agmatine, citrulline, cysteine, histidine, the aromatic amino acids, and polyamines (putrescine and spermidine). Regardless of the pathway of glutamate synthesis, nitrogen source catabolism must generate ammonia for glutamine synthesis. Loss of glutamate synthase (glutamineoxoglutarate amidotransferase, or GOGAT) prevents utilization of many organic nitrogen sources. Mutations that create or increase a requirement for ammonia also prevent utilization of most organic nitrogen sources.

Distinct physiological roles for the two L-asparaginase isozymes of Escherichia coli

Escherichia coli expresses two L-asparaginase (EC 3.5.1.1) isozymes: L-asparaginse I, which is a low affinity, cytoplasmic enzyme that is expressed constitutively, and L-asparaginase II, a high affinity periplasmic enzyme that is under complex co-transcriptional regulation by both Fnr and Crp. The distinct localisation and regulation of these enzymes suggest different roles. To define these roles, a set of isogenic mutants was constructed that lacked either or both enzymes. Evidence is provided that L-asparaginase II, in contrast to L-asparaginase I, can be used in the provision of an anaerobic electron acceptor when using a non-fermentable carbon source in the presence of excess nitrogen.

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

The authors analyze the role transcription plays in regulating bacterial metabolic flux. Of 91 transcriptional regulators studied, 2/3 affect absolute fluxes, but only a small number of regulators control the partitioning of flux between different metabolic pathways.

In contrast to the canonical respiro-fermentative glucose metabolism, fully respiratory galactose metabolism depends exclusively on the PEP-glyoxylate cycle.

Of 91 transcription factors, 2/3 affect absolute fluxes, but only one controls the distribution of fluxes on galactose and nine on glucose.

Transcriptional control of hexose flux distributions is confined to the acetyl-CoA branch point.

The PEP-glyoxylate cycle is controlled by cAMP-Crp in a hexose uptake rate-dependent manner.

Focusing on central carbon metabolism of Escherichia coli, we aim here to systematically identify transcriptional regulators that control the distribution of metabolic fluxes during aerobic growth on hexoses. To assess the condition dependence of transcriptional control of flux, we selected glucose and galactose as two substrates that are highly similar, yet lead to distinct growth rates (Soupene et al, 2003), overall metabolic rates (De Anda et al, 2006; Samir El et al, 2009) and levels of catabolite repression (Hogema et al, 1998; Bettenbrock et al, 2007).

Experimentally determined fluxes (Fischer and Sauer, 2003a) during growth on glucose and galactose reveal two distinct metabolic states. On glucose, high metabolic rates lead to high overflow metabolism and respiratory fluxes through the TCA cycle. On galactose, in contrast, metabolism was much slower without overflow metabolism and respiratory fluxes exclusively through the PEP-glyoxylate cycle (Fischer and Sauer, 2003b).

To determine which transcriptional events controlled these two distinct metabolic states, we determined intracellular fluxes in 91 transcription factor mutants. These genetic perturbations primarily affected absolute fluxes but not the distribution of fluxes. The distribution of flux between glycolysis and pentose–phosphate pathway in upper metabolism, e.g., remained constant in all mutants under all conditions. Transcriptional control of the flux distribution was exclusively seen at the acetyl-CoA branch point. On glucose, nine transcription factors controlled the distribution of fluxes at this branch point, five of which (ArcA, IHFA, IHFB, PdhR, Fur) did so presumably directly through their known targets in TCA cycle and/or respiration. Without known targets in the relevant pathways, the remaining four transcription factors (GlpR, QseB, HdfR, GlcC) may act either indirectly or directly through unknown targets. On galactose, transcriptional control focused exclusively on the PEP-glyoxylate cycle. While deletion of six transcription factors (Cra, Crp, IHFA, IHFB, Mlc, NagC) abolished or reduced the PEP-glyoxylate cycle flux, we demonstrate by substrate-limited chemostat experiments, derepression of galactose uptake and show by metabolomics that five of these transcription factors act indirectly through increased cAMP concentrations that allosterically activate Crp, the only direct transcription factors that controls the PEP-glyoxylate cycle (Nanchen et al, 2008).

Overall, our absolute flux data demonstrate that control of flux splitting during growth on hexoses was confined to the acetyl-CoA branch point in E. coli. Of the 36 transcription factors known to target genes in pathways that diverge from the acetyl-CoA branch point, only one transcription factor on galactose and five plus potentially four others on glucose showed altered flux splitting. The primary focus of steady state transcriptional control on the acetyl-CoA branch point, and thus the metabolic decision between the energetically efficient respiration and the less efficient but more rapid fermentation, was recently also demonstrated with only relative flux data for Saccharomyces cerevisiae (Fendt et al, 2010).

In contrast to glucose-grown Bacillus subtilis (Fischer et al, 2005), for batch glucose-grown E. coli, none of the investigated transcription factor mutants exhibited improved biomass productivity. However, the mutants Cra, IHF A, IHF B and NagC with increased uptake rates grew much faster at almost unaltered biomass yields. As the removal of the glucose PTS-based repression with a Crr mutant also resulted in increased galactose uptake, we provide evidence that E. coli actively represses its galactose uptake at the expense of otherwise possible rapid growth.

Despite our increasing topological knowledge on regulation networks in model bacteria, it is largely unknown which of the many co-occurring regulatory events actually control metabolic function and the distribution of intracellular fluxes. Here, we unravel condition-dependent transcriptional control of Escherichia coli metabolism by large-scale ¹³C-flux analysis in 91 transcriptional regulator mutants on glucose and galactose. In contrast to the canonical respiro-fermentative glucose metabolism, fully respiratory galactose metabolism depends exclusively on the phosphoenol-pyruvate (PEP)-glyoxylate cycle. While 2/3 of the regulators directly or indirectly affected absolute flux rates, the partitioning between different pathways remained largely stable with transcriptional control focusing primarily on the acetyl-CoA branch point. Flux distribution control was achieved by nine transcription factors on glucose, including ArcA, Fur, PdhR, IHF A and IHF B, but was exclusively mediated by the cAMP-dependent Crp regulation of the PEP-glyoxylate cycle flux on galactose. Five further transcription factors affected this flux only indirectly through cAMP and Crp by increasing the galactose uptake rate. Thus, E. coli actively limits its galactose catabolism at the expense of otherwise possible faster growth.

The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction

BACKGROUND

The Escherichia coli heterodimeric HU protein is a small DNA-bending protein associated with the bacterial nucleoid. It can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Cells lacking HU grow very poorly and display many phenotypes.

METHODOLOGY/PRINCIPAL FINDINGS

We analyzed the transcription profile of every Escherichia coli gene in the absence of one or both HU subunits. This genome-wide in silico transcriptomic approach, performed in parallel with in vivo genetic experimentation, defined the HU regulon. This large regulon, which comprises 8% of the genome, is composed of four biologically relevant gene classes whose regulation responds to anaerobiosis, acid stress, high osmolarity, and SOS induction.

CONCLUSIONS/SIGNIFICANCE

The regulation a large number of genes encoding enzymes involved in energy metabolism and catabolism pathways by HU explains the highly pleiotropic phenotype of HU-deficient cells. The uniform chromosomal distribution of the many operons regulated by HU strongly suggests that the transcriptional and nucleoid architectural functions of HU constitute two aspects of a unique protein-DNA interaction mechanism.

A critical phosphate concentration in the stationary phase maintains ndh gene expression and aerobic respiratory chain activity in Escherichia coli

Escherichia coli NADH dehydrogenase-2 (NDH-2) is a primary dehydrogenase in aerobic respiration that shows cupric-reductase activity. The enzyme is encoded by ndh, which is highly regulated by global transcription factors. It was described that the gene is expressed in the exponential growth phase and repressed in late stationary phase. We report the maintenance of NDH-2 activity and ndh expression in the stationary phase when cells were grown in media containing at least 37 mM phosphate. Gene regulation was independent of RpoS and other transcription factors described to interact with the ndh promoter. At this critical phosphate concentration, cell viability, oxygen consumption rate, and NADH/NAD+ ratio were maintained in the stationary phase. These physiological parameters gradually changed, but NDH-2 activity remained high for up to 94 h. Phosphate seems to trigger an internal signal in the stationary phase mediated by systems not yet described.

NADH as Donor

The number of NADH dehydrogenases and their role in energy transduction in Escherchia coli have been under debate for a long time. Now it is evident that E. coli possesses two respiratory NADH dehydrogenases, or NADH:ubiquinone oxidoreductases, that have traditionally been called NDH-I and NDH-II. This review describes the properties of these two NADH dehydrogenases, focusing on the mechanism of the energy converting NADH dehydrogenase as derived from the high resolution structure of the soluble part of the enzyme. In E. coli , complex I operates in aerobic and anaerobic respiration, while NDH-II is repressed under anaerobic growth conditions. The insufficient recycling of NADH most likely resulted in excess NADH inhibiting tricarboxylic acid cycle enzymes and the glyoxylate shunt. Salmonella enterica serovar Typhimurium complex I mutants are unable to activate ATP-dependent proteolysis under starvation conditions. NDH-II is a single subunit enzyme with a molecular mass of 47 kDa facing the cytosol. Despite the absence of any predicted transmembrane segment it has to be purified in the presence of detergents, and the activity of the preparation is stimulated by an addition of lipids.

PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli

The pyruvate dehydrogenase (PDH) multienzyme complex plays a key role in the metabolic interconnection between glycolysis and the citric acid cycle. Transcription of the Escherichia coli genes for all three components of the PDH complex in the pdhR-aceEF-lpdA operon is repressed by the pyruvate-sensing PdhR, a GntR family transcription regulator, and derepressed by pyruvate. After a systematic search for the regulation targets of PdhR using genomic systematic evolution of ligands by exponential enrichment (SELEX), we have identified two novel targets, ndh, encoding NADH dehydrogenase II, and cyoABCDE, encoding the cytochrome bo-type oxidase, both together forming the pathway of respiratory electron transport downstream from the PDH cycle. PDH generates NADH, while Ndh and CyoABCDE together transport electrons from NADH to oxygen. Using gel shift and DNase I footprinting assays, the PdhR-binding site (PdhR box) was defined, which includes a palindromic consensus sequence, ATTGGTNNNACCAAT. The binding in vitro of PdhR to the PdhR box decreased in the presence of pyruvate. Promoter assays in vivo using a two-fluorescent-protein vector also indicated that the newly identified operons are repressed by PdhR and derepressed by the addition of pyruvate. Taken together, we propose that PdhR is a master regulator for controlling the formation of not only the PDH complex but also the respiratory electron transport system.

The three families of respiratory NADH dehydrogenases

Most reducing equivalents extracted from foodstuffs during oxidative metabolism are fed into the respiratory chains of aerobic bacteria and mitochondria by NADH:quinone oxidoreductases. Three families of enzymes can perform this task and differ remarkably in their complexity and role in energy conversion. Alternative or NDH-2-type NADH dehydrogenases are simple one subunit flavoenzymes that completely dissipate the redox energy of the NADH/quinone couple. Sodium-pumping NADH dehydrogenases (Nqr) that are only found in procaryotes contain several flavins and are integral membrane protein complexes composed of six different subunits. Proton-pumping NADH dehydrogenases (NDH-1 or complex I) are highly complicated membrane protein complexes, composed of up to 45 different subunits, that are found in bacteria and mitochondria. This review gives an overview of the origin, structural and functional properties and physiological significance of these three types of NADH dehydrogenase.

Contributions of [4Fe-4S]-FNR and integration host factor to fnr transcriptional regulation

Maintaining appropriate levels of the global regulator FNR is critical to its function as an O(2) sensor. In this study, we examined the mechanisms that control transcription of fnr to increase our understanding of how FNR protein levels are regulated. Under anaerobic conditions, one mechanism that controls fnr expression is negative autoregulation by the active [4Fe-4S] form of FNR. Through DNase I footprinting and in vitro transcription experiments, we observed that direct binding of [4Fe-4S]-FNR to the predicted downstream FNR binding site is sufficient for repression of the fnr promoter in vitro. In addition, the downstream FNR binding site was required for repression of transcription from fnr'-lacZ fusions in vivo. No repression of fnr was observed in vivo or in vitro with the apoprotein form of FNR, indicating that repression requires the dimeric, Fe-S cluster-containing protein. Furthermore, our in vitro and in vivo data suggest that [4Fe-4S]-FNR does not bind to the predicted upstream FNR binding site within the fnr promoter. Rather, we provide evidence that integration host factor binds to this upstream region and increases in vivo expression of Pfnr under both aerobic and anaerobic conditions.

Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy

Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex.

New insights into type II NAD(P)H:quinone oxidoreductases

Type II NAD(P)H:quinone oxidoreductases (NDH-2) catalyze the two-electron transfer from NAD(P)H to quinones, without any energy-transducing site. NDH-2 accomplish the turnover of NAD(P)H, regenerating the NAD(P)(+) pool, and may contribute to the generation of a membrane potential through complexes III and IV. These enzymes are usually constituted by a nontransmembrane polypeptide chain of approximately 50 kDa, containing a flavin moiety. There are a few compounds that can prevent their activity, but so far no general specific inhibitor has been assigned to these enzymes. However, they have the common feature of being resistant to the complex I classical inhibitors rotenone, capsaicin, and piericidin A. NDH-2 have particular relevance in yeasts like Saccharomyces cerevisiae and in several prokaryotes, whose respiratory chains are devoid of complex I, in which NDH-2 keep the balance and are the main entry point of electrons into the respiratory chains. Our knowledge of these proteins has expanded in the past decade, as a result of contributions at the biochemical level and the sequencing of the genomes from several organisms. The latter showed that most organisms contain genes that potentially encode NDH-2. An overview of this development is presented, with special emphasis on microbial enzymes and on the identification of three subfamilies of NDH-2.

Regulation of ndh expression in Escherichia coli by Fis

The Escherichia coli ndh gene encodes NADH dehydrogenase II, a primary dehydrogenase used during aerobic and nitrate respiration. The anaerobic transcription factor FNR represses ndh expression by binding at two sites centred at −94·5 and −50·5. In vivo transcription studies using promoter fusions with 5′ deletions confirmed that both FNR sites are required for maximum repression under anaerobic conditions. The histone-like protein Fis binds to three sites [centred at −123 (Fis I), −72, (Fis II) and +51 (Fis III)] in the ndh promoter. Using ndh : : lacZ promoter fusions carrying 5′ deletions, or replacement mutations it is shown that Fis III is a repressing site and that Fis I and II are activating sites, with the greatest contribution from Fis II. Deletion of the C-terminal domain of the RNA polymerase α-subunit abolished Fis-mediated activation of ndh expression, suggesting that ndh has a Class I Fis-activated promoter. In accordance with the established pattern of Fis synthesis, ndh transcription was greatest during exponential growth. Thus, it is suggested that Fis enhances ndh expression during periods of rapid growth, by acting as a Class I activator, and that the binding of tandem FNR dimers represses ndh expression by preventing interaction of the RNA polymerase α-subunit with DNA and Fis.

Speed versus efficiency in microbial growth and the role of parallel pathways

Many microorganisms have sets of parallel pathways for ATP production in respiration and for ATP utilization in glutamate synthesis. The alternatives differ in efficiency of ATP production and utilization. The choice among these parallel pathways has been hypothesized to control the speed and efficiency of growth. Thus, the organism should be able to alleviate (or exaggerate) deficiency in one pathway by deleting another. I show here that in Escherichia coli the effect of lack of the glutamate-synthesizing enzyme glutamate dehydrogenase on glucose-limited growth is altered predictably by ndh, cyo, and cyd mutations affecting parallel pathways leading to ATP synthesis in respiration.

YeiL, the third member of the CRP-FNR family in Escherichia coli

The yeiL open reading frame located at 48.5 min (2254 kb) in the nfo-fruA region of the Escherichia coli chromosome was predicted to encode a CRP and FNR paralogue capable of forming inter- or intra-molecular disulphide bonds and incorporating one iron-sulphur centre per 25 kDa subunit. Purified MBP-YeiL (a maltose-binding-protein-YeiL fusion protein) was a high-molecular-mass oligomer or aggregate which released unstable monomers (68 kDa) under reducing conditions. The MBP-YeiL protein contained substoichiometric amounts of iron and acid-labile sulphide, and an average of one disulphide bond per monomer. The iron and sulphide contents increased consistent with the acquisition of one [4Fe-4S] cluster per monomer after anaerobic NifS-catalysed reconstitution. By analogy with FNR and FLP (the FNR-like protein of Lactobacillus casei) it was suggested that the transcription-regulatory activity of YeiL might be modulated by a sensory iron-sulphur cluster and/or by reversible disulphide bond formation. A yeiL-lacZ transcriptional fusion showed that aerobic yeiL expression increases at least sixfold during stationary phase, requires RpoS, and is positively autoregulated by YeiL, positively activated by Lrp (and IHF in the absence of FNR) and negatively regulated by FNR. A regulatory link between the synthesis of YeiK (a potential nucleoside hydrolase) and YeiL was inferred by showing that the yeiK and yeiL genes are divergently transcribed from overlapping promoters. A 10-15% deficiency in aerobic growth yield and an enhanced loss of viability under nitrogen starvation conditions were detected with a yeiL::kan(R) mutant, suggesting that YeiL might function as a post-exponential-phase nitrogen-starvation regulator.

Global gene expression profiling in Escherichia coli K12. The effects of integration host factor

We have used nylon membranes spotted in duplicate with full-length polymerase chain reaction-generated products of each of the 4,290 predicted Escherichia coli K12 open reading frames (ORFs) to measure the gene expression profiles in otherwise isogenic integration host factor IHF(+) and IHF(-) strains. Our results demonstrate that random hexamer rather than 3' ORF-specific priming of cDNA probe synthesis is required for accurate measurement of gene expression levels in bacteria. This is explained by the fact that the currently available set of 4,290 unique 3' ORF-specific primers do not hybridize to each ORF with equal efficiency and by the fact that widely differing degradation rates (steady-state levels) are observed for the 25-base pair region of each message complementary to each ORF-specific primer. To evaluate the DNA microarray data reported here, we used a linear analysis of variance (ANOVA) model appropriate for our experimental design. These statistical methods allowed us to identify and appropriately correct for experimental variables that affect the reproducibility and accuracy of DNA microarray measurements and allowed us to determine the statistical significance of gene expression differences between our IHF(+) and IHF(-) strains. Our results demonstrate that small differences in gene expression levels can be accurately measured and that the significance of differential gene expression measurements cannot be assessed simply by the magnitude of the fold difference. Our statistical criteria, supported by excellent agreement between previously determined effects of IHF on gene expression and the results reported here, have allowed us to identify new genes regulated by IHF with a high degree of confidence.

Coactivation of the RpoS-dependent proP P2 promoter by fis and cyclic AMP receptor protein

The Escherichia coli proP P2 promoter, which directs the expression of an integral membrane transporter of proline, glycine betaine, and other osmoprotecting compounds, is induced upon entry into stationary phase to protect cells from osmotic shock. Transcription from the P2 promoter is completely dependent on RpoS (sigma(38)) and Fis. Fis activates transcription by binding to a site centered at -41, which overlaps the promoter, where it makes a specific contact with the C-terminal domain of the alpha subunit of RNA polymerase (alpha-CTD). We show here that Fis and cyclic AMP (cAMP) receptor protein (CRP)-cAMP collaborate to activate transcription synergistically in vitro. Coactivation both in vivo and in vitro is dependent on CRP binding to a site centered at -121.5, but CRP without Fis provides little activation. The contribution by CRP requires the correct helical phasing of the CRP site and a functional activation region 1 on CRP. We provide evidence that coactivation is achieved by Fis and CRP independently contacting each of the two alpha-CTDs. Efficient transcription in vitro requires that both activators must be preincubated with the DNA prior to addition of RNA polymerase.

Differential expression of over 60 chromosomal genes in Escherichia coli by constitutive expression of MarA

In Escherichia coli, the MarA protein controls expression of multiple chromosomal genes affecting resistance to antibiotics and other environmental hazards. For a more-complete characterization of the mar regulon, duplicate macroarrays containing 4,290 open reading frames of the E. coli genome were hybridized to radiolabeled cDNA populations derived from mar-deleted and mar-expressing E. coli. Strains constitutively expressing MarA showed altered expression of more than 60 chromosomal genes: 76% showed increased expression and 24% showed decreased expression. Although some of the genes were already known to be MarA regulated, the majority were newly determined and belonged to a variety of functional groups. Some of the genes identified have been associated with iron transport and metabolism; other genes were previously known to be part of the soxRS regulon. Northern blot analysis of selected genes confirmed the results obtained with the macroarrays. The findings reveal that the mar locus mediates a global stress response involving one of the largest networks of genes described.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Periplasmic nitrate-reducing system of the phototrophic bacterium Rhodobacter sphaeroides DSM 158: transcriptional and mutational analysis of the napKEFDABC gene cluster

The phototrophic bacterium Rhodobacter sphaeroides DSM 158 is able to reduce nitrate to nitrite by means of a periplasmic nitrate reductase which is induced by nitrate and is not repressed by ammonium or oxygen. Recently, a 6.8 kb PstI DNA fragment carrying the napABC genes coding for this periplasmic nitrate-reducing system was cloned [Reyes, Roldán, Klipp, Castillo and Moreno-Vivián (1996) Mol. Microbiol. 19, 1307-1318]. Further sequence and genetic analyses of the DNA region upstream from the napABC genes reveal the presence of four additional nap genes. All these R. sphaeroides genes seem to be organized into a napKEFDABC transcriptional unit. In addition, a partial open reading frame similar to the Azorhizobium caulinodans yntC gene and the Escherichia coli yjcC and yhjK genes is present upstream from this nap gene cluster. The R. sphaeroides napK gene codes for a putative 6.3 kDa transmembrane protein which is not similar to known proteins and the napE gene codes for a 6.7 kDa transmembrane protein similar to the Thiosphaera pantotropha NapE. The R. sphaeroides napF gene product is a 16.4 kDa protein with four cysteine clusters that probably bind four [4Fe-4S] centres. This iron-sulphur protein shows similarity to the NapF and NapG proteins of E. coli and Haemophilus influenzae. Finally, the napD gene product is a 9.4 kDa soluble protein which is also found in E. coli and T. pantotropha. The 5' end of the nap transcript has been determined by primer extension, and a sigma70-like promoter has been identified upstream from the napK gene. The same transcriptional start site is found for cells growing aerobically or anaerobically with nitrate. Different mutant strains carrying defined polar and non-polar insertions in each nap gene were constructed. Characterization of these mutant strains demonstrates the participation of the nap gene products in the periplasmic nitrate reduction in R. sphaeroides.