Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas aeruginosa: sequencing and identification of a locus for heme d1 biosynthesis

Kawasaki, Shinji; Arai, Hiroyuki; Kodama, Tohru; Igarashi, Yasuo

doi:10.1128/jb.179.1.235-242.1997

Cited by 85 publications

(100 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…3). Although sequence analysis highlighted a significant sequence identity (35.3%) and similarity (47.1%) between pairs of NirD-L, NirG, and NirH, these proteins are, on the basis of mutagenesis, functionally nonredundant (9,19). Subsequently, we found that extracts of E. coli overproducing NirD (where the C-terminal NirL encoding sequence was removed from the plasmid) or NirH could catalyze a single decarboxylation reaction of siroheme (Table S1).…”

Section: Nirdl-g-h Carries An Oxygen-independent Siroheme Decarboxylasementioning

confidence: 99%

Molecular hijacking of siroheme for the synthesis of heme and d ₁ heme

Bali

Lawrence

Lobo

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

110

148

View full text Add to dashboard Cite

Modified tetrapyrroles such as chlorophyll, heme, siroheme, vitamin B 12 , coenzyme F 430 , and heme d 1 underpin a wide range of essential biological functions in all domains of life, and it is therefore surprising that the syntheses of many of these life pigments remain poorly understood. It is known that the construction of the central molecular framework of modified tetrapyrroles is mediated via a common, core pathway. Herein a further branch of the modified tetrapyrrole biosynthesis pathway is described in denitrifying and sulfate-reducing bacteria as well as the Archaea. This process entails the hijacking of siroheme, the prosthetic group of sulfite and nitrite reductase, and its processing into heme and d 1 heme. The initial step in these transformations involves the decarboxylation of siroheme to give didecarboxysiroheme. For d 1 heme synthesis this intermediate has to undergo the replacement of two propionate side chains with oxygen functionalities and the introduction of a double bond into a further peripheral side chain. For heme synthesis didecarboxysiroheme is converted into Fe-coproporphyrin by oxidative loss of two acetic acid side chains. Fe-coproporphyrin is then transformed into heme by the oxidative decarboxylation of two propionate side chains. The mechanisms of these reactions are discussed and the evolutionary significance of another role for siroheme is examined.

show abstract

Section: Nirdl-g-h Carries An Oxygen-independent Siroheme Decarboxylasementioning

confidence: 99%

Molecular hijacking of siroheme for the synthesis of heme and d ₁ heme

Bali

Lawrence

Lobo

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

110

148

View full text Add to dashboard Cite

show abstract

“…The nitrate respiration nap and nar genes form a gene cluster (Peg.1539-Peg.1548), and are predicted to catalyze the reduction of nitrate to nitrite. The nirS gene for cytochrome cd 1 nitrite reductase, together with nirDFJNJ genes (Peg.1589-Peg.1594) that are involved in heme d 1 biosynthesis (Kawasaki et al, 1997), may reduce nitrite to NO. NO may be further reduced to nitrous oxide, and finally to N 2 using NO reductases (NorBC) and nitrous oxide reductases (NosZRDFY), respectively.…”

Section: Nitrogen Metabolismmentioning

confidence: 99%

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

et al. 2014

View full text Add to dashboard Cite

Magnetotactic bacteria (MTB) of the genus 'Candidatus Magnetobacterium' in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named 'Ca. Magnetobacterium casensis' isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood-Ljungdahl pathway for CO 2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood 'Ca. Magnetobacterium' genus.

show abstract

“…The monomeric NirN was able to bind heme d 1 in vitro and transferred the cofactor to NirS when the two proteins were mixed (12). The deletion of the nirN gene in different denitrifiers led to a mild growth phenotype, and cellfree extracts prepared from the corresponding ⌬nirN strains exhibited reduced NirS activity compared with the WT strains (9,12,16). From these observations it was deduced that NirN is not required for heme d 1 biosynthesis but, rather, might be involved in the insertion of the cofactor into NirS.…”

mentioning

confidence: 82%

NirN Protein from Pseudomonas aeruginosa is a Novel Electron-bifurcating Dehydrogenase Catalyzing the Last Step of Heme d1 Biosynthesis

Adamczack

Hoffmann

Papke

et al. 2014

Journal of Biological Chemistry

View full text Add to dashboard Cite

Heme d1 plays an important role in denitrification as the essential cofactor of the cytochrome cd1 nitrite reductase NirS. At present, the biosynthesis of heme d1 is only partially understood. The last step of heme d1 biosynthesis requires a so far unknown enzyme that catalyzes the introduction of a double bond into one of the propionate side chains of the tetrapyrrole yielding the corresponding acrylate side chain. In this study, we show that a Pseudomonas aeruginosa PAO1 strain lacking the NirN protein does not produce heme d1. Instead, the NirS purified from this strain contains the heme d1 precursor dihydro-heme d1 lacking the acrylic double bond, as indicated by UV-visible absorption spectroscopy and resonance Raman spectroscopy. Furthermore, the dihydro-heme d1 was extracted from purified NirS and characterized by UV-visible absorption spectroscopy and finally identified by high-resolution electrospray ionization mass spectrometry. Moreover, we show that purified NirN from P. aeruginosa binds the dihydro-heme d1 and catalyzes the introduction of the acrylic double bond in vitro. Strikingly, NirN uses an electron bifurcation mechanism for the two-electron oxidation reaction, during which one electron ends up on its heme c cofactor and the second electron reduces the substrate/product from the ferric to the ferrous state. On the basis of our results, we propose novel roles for the proteins NirN and NirF during the biosynthesis of heme d1.

show abstract

Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas aeruginosa: sequencing and identification of a locus for heme d1 biosynthesis

Cited by 85 publications

References 53 publications

Molecular hijacking of siroheme for the synthesis of heme and d ₁ heme

Molecular hijacking of siroheme for the synthesis of heme and d ₁ heme

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

NirN Protein from Pseudomonas aeruginosa is a Novel Electron-bifurcating Dehydrogenase Catalyzing the Last Step of Heme d1 Biosynthesis

Contact Info

Product

Resources

About

Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas aeruginosa: sequencing and identification of a locus for heme d1 biosynthesis

Cited by 85 publications

References 53 publications

Molecular hijacking of siroheme for the synthesis of heme and d 1 heme

Molecular hijacking of siroheme for the synthesis of heme and d 1 heme

Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae

NirN Protein from Pseudomonas aeruginosa is a Novel Electron-bifurcating Dehydrogenase Catalyzing the Last Step of Heme d1 Biosynthesis

Contact Info

Product

Resources

About

Molecular hijacking of siroheme for the synthesis of heme and d ₁ heme

Molecular hijacking of siroheme for the synthesis of heme and d ₁ heme