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Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus.

Heylen K, Keltjens J - Front Microbiol (2012)

Bottom Line: The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed.In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found.Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbiology, Department of Biochemistry and Microbiology, University of Ghent Gent, Belgium.

ABSTRACT
The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. Results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in Gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. A considerable degree of functional redundancy was observed with marked differences between B. azotoformans LMG 9581(T) and B. bataviensis LMG 21833(T). In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found. Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants. Quite unexpectedly, both bacilli have the disposal of two parallel pathways for nitrite reduction enabling a life style as a denitrifier and as an ammonifying bacterium.

No MeSH data available.


Related in: MedlinePlus

A Multiple sequence alignment of NosZ from B. azotoformans LMG 9581T and other bacteria. Conserved histidine ligands of the CuZ center are highlighted in dark blue; cysteine and other ligands of the CuA center in yellow, and turquoise respectively; partially conserved histidine residues in brown; calcium atom and chloride ion ligands in pink and green, respectively [according to Simon et al. (2004)]. TAT sequences are printed in red, N-terminal cleavage in blue. Gt, Geobacillus thermodenitrificans NG80-2 (GTNG_1734); Dh, Desulfitobacterium hafniense T51 (DSY0261); Dr, Desulfotomaculum. ruminis DSM 2154 (Desru_1528), Pd, Paracoccus denitrificans DSM 413 (PDB 1FWX), Ac, Achromobacter cycloclastes 1013 (PDB 21WF); Ps, Pseudomonas stutzeri (PDB 3SBP). PDB, protein database accession number.
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FA5: A Multiple sequence alignment of NosZ from B. azotoformans LMG 9581T and other bacteria. Conserved histidine ligands of the CuZ center are highlighted in dark blue; cysteine and other ligands of the CuA center in yellow, and turquoise respectively; partially conserved histidine residues in brown; calcium atom and chloride ion ligands in pink and green, respectively [according to Simon et al. (2004)]. TAT sequences are printed in red, N-terminal cleavage in blue. Gt, Geobacillus thermodenitrificans NG80-2 (GTNG_1734); Dh, Desulfitobacterium hafniense T51 (DSY0261); Dr, Desulfotomaculum. ruminis DSM 2154 (Desru_1528), Pd, Paracoccus denitrificans DSM 413 (PDB 1FWX), Ac, Achromobacter cycloclastes 1013 (PDB 21WF); Ps, Pseudomonas stutzeri (PDB 3SBP). PDB, protein database accession number.

Mentions: The deduced primary structure of the three B. azotoformans NosZ proteins (between 76.5 and 83.1% sequence identity) show all conserved ligands of CuA and CuZ centers that have been identified in the crystal structures (Figure A5) (Brown et al., 2000; Paraskevopoulos et al., 2006). Nevertheless, the NosZ sequences contain insertions and deletions that are shared with nitrous oxide reductases from other Gram-positive species, likely placing these in a distinct family. The differences could be related with domain-specific interactions in Gram-positives and Gram-negatives with other components of the NosZ system. Another feature is that the N-terminal sequence in Gram-positive NosZ's is shorter (Figure A5). Moreover, SignalP and TatP prediction programs are somewhat ambiguous regarding the presence of N-terminal leader and TAT signal sequences. For instance, whereas NosZ1 from B. azotoformans is predicted to have a TAT leader, yet lacking an N-terminal cleavage side, the opposite holds for NosZ2 and NosZ3. These differences might point to, even protein-specific, differences in assembly, and transport. It is conceivable that transport proceeds not only by the TAT—but also by the Sec translocon. Indeed, it has been described for W. succinogenes that transport of non-folded NosZ and subsequent Cu insertion results in a fully functional protein (Heikkilä et al., 2001).


Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus.

Heylen K, Keltjens J - Front Microbiol (2012)

A Multiple sequence alignment of NosZ from B. azotoformans LMG 9581T and other bacteria. Conserved histidine ligands of the CuZ center are highlighted in dark blue; cysteine and other ligands of the CuA center in yellow, and turquoise respectively; partially conserved histidine residues in brown; calcium atom and chloride ion ligands in pink and green, respectively [according to Simon et al. (2004)]. TAT sequences are printed in red, N-terminal cleavage in blue. Gt, Geobacillus thermodenitrificans NG80-2 (GTNG_1734); Dh, Desulfitobacterium hafniense T51 (DSY0261); Dr, Desulfotomaculum. ruminis DSM 2154 (Desru_1528), Pd, Paracoccus denitrificans DSM 413 (PDB 1FWX), Ac, Achromobacter cycloclastes 1013 (PDB 21WF); Ps, Pseudomonas stutzeri (PDB 3SBP). PDB, protein database accession number.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475470&req=5

FA5: A Multiple sequence alignment of NosZ from B. azotoformans LMG 9581T and other bacteria. Conserved histidine ligands of the CuZ center are highlighted in dark blue; cysteine and other ligands of the CuA center in yellow, and turquoise respectively; partially conserved histidine residues in brown; calcium atom and chloride ion ligands in pink and green, respectively [according to Simon et al. (2004)]. TAT sequences are printed in red, N-terminal cleavage in blue. Gt, Geobacillus thermodenitrificans NG80-2 (GTNG_1734); Dh, Desulfitobacterium hafniense T51 (DSY0261); Dr, Desulfotomaculum. ruminis DSM 2154 (Desru_1528), Pd, Paracoccus denitrificans DSM 413 (PDB 1FWX), Ac, Achromobacter cycloclastes 1013 (PDB 21WF); Ps, Pseudomonas stutzeri (PDB 3SBP). PDB, protein database accession number.
Mentions: The deduced primary structure of the three B. azotoformans NosZ proteins (between 76.5 and 83.1% sequence identity) show all conserved ligands of CuA and CuZ centers that have been identified in the crystal structures (Figure A5) (Brown et al., 2000; Paraskevopoulos et al., 2006). Nevertheless, the NosZ sequences contain insertions and deletions that are shared with nitrous oxide reductases from other Gram-positive species, likely placing these in a distinct family. The differences could be related with domain-specific interactions in Gram-positives and Gram-negatives with other components of the NosZ system. Another feature is that the N-terminal sequence in Gram-positive NosZ's is shorter (Figure A5). Moreover, SignalP and TatP prediction programs are somewhat ambiguous regarding the presence of N-terminal leader and TAT signal sequences. For instance, whereas NosZ1 from B. azotoformans is predicted to have a TAT leader, yet lacking an N-terminal cleavage side, the opposite holds for NosZ2 and NosZ3. These differences might point to, even protein-specific, differences in assembly, and transport. It is conceivable that transport proceeds not only by the TAT—but also by the Sec translocon. Indeed, it has been described for W. succinogenes that transport of non-folded NosZ and subsequent Cu insertion results in a fully functional protein (Heikkilä et al., 2001).

Bottom Line: The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed.In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found.Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbiology, Department of Biochemistry and Microbiology, University of Ghent Gent, Belgium.

ABSTRACT
The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. Results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in Gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. A considerable degree of functional redundancy was observed with marked differences between B. azotoformans LMG 9581(T) and B. bataviensis LMG 21833(T). In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found. Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants. Quite unexpectedly, both bacilli have the disposal of two parallel pathways for nitrite reduction enabling a life style as a denitrifier and as an ammonifying bacterium.

No MeSH data available.


Related in: MedlinePlus