Multiple transcription factors of the FNR family in denitrifying <i>Pseudomonas stutzeri</i>: characterization of four <i>fnr</i>‐like genes, regulatory responses and cognate metabolic processes

Vollack, Kai-Uwe; Härtig, Elisabeth; Körner, Heinz; Zumft, Walter G.

doi:10.1046/j.1365-2958.1999.01494.x

Cited by 28 publications

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“…Northern blot analysis of the nirSTM operon of Ps. stutzeri (ZoBell) showed that two transcripts originated from the nirS promoter, one containing nirS alone, the other nirS, T and M (Ha$ rtig & Zumft, 1999). In neither pseudomonad is the nirS gene followed by a terminator such as that identified in Pa. pantotrophus (Fig.…”

Section: Northern Blot Studiesmentioning

confidence: 99%

“…aeruginosa (Arai et al, 1997 ;Hasegawa et al, 1998) and the set of regulatory proteins named DnrE, DnrS and DnrD in Ps. stutzeri (Vollack et al, 1999). All these proteins bear a high similarity to the transcriptional activator Fnr of Escherichia coli, but lack the N-terminal cysteines which allow the formation of an oxygen-labile iron-sulphur cluster in Fnr (Khoroshilova et al, 1995 (Zumft, 1997 ;Baker et al, 1998), but the environmental signals which trigger denitrification are different as well.…”

Section: Introductionmentioning

confidence: 99%

“…It would appear that in Ps. stutzeri nitrate and the absence of oxygen are sensed, directly or indirectly, by DnrE, DnrS and DnrD (Vollack et al, 1999) and these proteins then activate the nir and nor operons. In Pa. denitrificans and Ps.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional analysis of the nirS gene, encoding cytochrome cd 1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63 The GenBank accession number for the sequence in this paper is U75413.

2000

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The gene for cytochrome cd 1 nitrite reductase of Paracoccus pantotrophus, a protein of known crystal structure, is nirS. This gene is shown to be flanked by genes previously recognized in other organisms to encode proteins involved in the control of its transcription (nirI) and the biosynthesis of the d 1 cofactor (nirE). Northern blot analysis has established under anaerobic conditions that a monocistronic transcript is produced from nirS, in contrast to observations with other denitrifying bacteria in which arrangement of flanking genes is different and the messages produced are polycistronic. The lack of a transcript under aerobic conditions argues against a role for cytochrome cd 1 in the previously proposed aerobic denitrification pathway in Pa. pantotrophus. A putative rho-independent transcription termination sequence immediately following nirS, and preceding nirE, can be identified. The independent transcription of nirS and nirE indicates that it should be possible to produce site-directed mutants of nirS borne on a plasmid in a nirS deletion mutant

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Section: Northern Blot Studiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Transcriptional analysis of the nirS gene, encoding cytochrome cd 1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63 The GenBank accession number for the sequence in this paper is U75413.

2000

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“…We set the pH of the culture medium to 7.5 or 6.5 and grew completely consuming cells (strain A1601) alone in the presence or absence of 10 mM of exogenous nitrite. We incubated the cells under fully aerobic conditions because oxygen represses nitrite reductase activity (Vollack et al, 1999), thus preventing nitrite reduction-and consequently detoxification-during the experiment. We measured cell density over time (measured as OD 600 ; Figures 4a and b) and quantified the maximum specific growth rate (u max (min − 1 )) for each culture (Figure 4c).…”

Section: Alternative Explanations For the Accumulation Of Nitritementioning

confidence: 99%

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

2016

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Different microbial cell types typically specialize at performing different metabolic processes. A canonical example is substrate cross-feeding, where one cell type consumes a primary substrate into an intermediate and another cell type consumes the intermediate. While substrate cross-feeding is widely observed, its consequences on ecosystem processes is often unclear. How does substrate cross-feeding affect the rate or extent of substrate consumption? We hypothesized that substrate cross-feeding eliminates competition between different enzymes and reduces the accumulation of growth-inhibiting intermediates, thus accelerating substrate consumption. We tested this hypothesis using isogenic mutants of the bacterium Pseudomonas stutzeri that either completely consume nitrate to dinitrogen gas or cross-feed the intermediate nitrite. We demonstrate that nitrite crossfeeding eliminates inter-enzyme competition and, in turn, reduces nitrite accumulation. We further demonstrate that nitrite cross-feeding accelerates substrate consumption, but only when nitrite has growth-inhibiting effects. Knowledge about inter-enzyme competition and the inhibitory effects of intermediates could therefore be important for deciding how to best segregate different metabolic processes into different microbial cell types to optimize a desired biotransformation.

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“…Crp/Fnr regulators are generally classified into different subfamilies (e.g., CooA, Crp, Dnr, FixK, Fnr, HbaR, NnrR, etc.) according to phylogenetic affiliations (50). The increasing number of sequenced whole genomes has added to a growing list of Crp/Fnr family regulators identified in bacteria (9,26); however, functions for most are not well defined.…”

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confidence: 99%

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

Zhou

Chen

Zane

et al. 2012

Appl Environ Microbiol

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Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ⌬DVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ⌬DVU2547 mutant (JW9011) under nitrite stress conditions and a ⌬DVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.T ranscription factors, promoter sequences, and regulatory circuit architecture are often referred as "the regulatory genome" (27, 33), and transcription factors are central to the function of regulatory networks (5). Organisms rely on regulatory networks to orchestrate the transcription of genes in response to internal or external environmental changes in order to optimize metabolism and enhance survival. Crp/Fnr regulators are global transcriptional regulators widely distributed in bacteria. The characteristic structure of Crp/Fnr is a C-terminal helix-turn-helix (HTH) motif that fits the DNA major groove and an N-terminal nucleotide binding domain (34). This class of transcriptional factors is named after the first two representatives discovered in Escherichia coli, i.e., the Crp (cyclic AMP [cAMP] receptor protein) and Fnr (fumarate and nitrate reductase regulator protein) (4, 21, 24, 27). Crp/Fnr regulators are generally classified into different subfamilies (e.g., CooA, Crp, Dnr, FixK, Fnr, HbaR, NnrR, etc.) according to phylogenetic affiliations (50). The increasing number of sequenced whole genomes has added to a growing list of Crp/Fnr family regulators identified in bacteria (9, 26); however, functions for most are not well defin...

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Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr‐like genes, regulatory responses and cognate metabolic processes

Cited by 28 publications

References 0 publications

Transcriptional analysis of the nirS gene, encoding cytochrome cd 1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63 The GenBank accession number for the sequence in this paper is U75413.

Transcriptional analysis of the nirS gene, encoding cytochrome cd 1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63 The GenBank accession number for the sequence in this paper is U75413.

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

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