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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

Multiple sequence alignment of qNOR from B. azotoformans LMG 9581T, B. bataviensis LMG 21833T, and other bacteria. Two non-sense mutations in BABA_p08977 have been corrected in this figure (see text for further explanation). Amino acids involved in the binding of catalytic centers (cyt b, b3, FeB) are highlighted in red, residues for quinol binding in black, bulky residues in the hydrophilic part in gray, residues for Ca2+ binding in yellow, residues lining the long water channel from the cytoplasm in dark blue, residues at water channel 1 in green and water channel 2 in light blue; transmembrane regions are indicated in blue and numbered on top of the alignment [as described by Matsumoto et al. (2012)]. Ba_q1, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_3340); Ba_q2, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_1567); Ge, Geobacillus stearothermophilus (PDB 3AYF, 3AYG); St, Staphylococcus aureus (SAEMRSA15_02230); An, Anaerophaga sp. HS1 (AnHS1_010100003178); Fl, Flavobacterium johnsoniae UW101 (Fjoh_2413); Ng, Neisseria gonorrhoeae (NgonD_010100007739); Cu, Cupriavidus metallidurans CH34 (Rmet_3167); Sy, Synechocystis sp. PCC 6803 (sll0450). PDB, protein database accession number.
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FA2: Multiple sequence alignment of qNOR from B. azotoformans LMG 9581T, B. bataviensis LMG 21833T, and other bacteria. Two non-sense mutations in BABA_p08977 have been corrected in this figure (see text for further explanation). Amino acids involved in the binding of catalytic centers (cyt b, b3, FeB) are highlighted in red, residues for quinol binding in black, bulky residues in the hydrophilic part in gray, residues for Ca2+ binding in yellow, residues lining the long water channel from the cytoplasm in dark blue, residues at water channel 1 in green and water channel 2 in light blue; transmembrane regions are indicated in blue and numbered on top of the alignment [as described by Matsumoto et al. (2012)]. Ba_q1, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_3340); Ba_q2, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_1567); Ge, Geobacillus stearothermophilus (PDB 3AYF, 3AYG); St, Staphylococcus aureus (SAEMRSA15_02230); An, Anaerophaga sp. HS1 (AnHS1_010100003178); Fl, Flavobacterium johnsoniae UW101 (Fjoh_2413); Ng, Neisseria gonorrhoeae (NgonD_010100007739); Cu, Cupriavidus metallidurans CH34 (Rmet_3167); Sy, Synechocystis sp. PCC 6803 (sll0450). PDB, protein database accession number.

Mentions: While cNORs are absent in the genome of B. azotoformans, we could identify two genes coding for qNORs, BAZO_00190, and BAZO_08916. The preference for quinol-dependent NOR seems to be a common property of Gram-positive microorganisms. Although BAZO_00190 and BAZO_08916 share only 38% sequence identity, the comparison of their amino acid sequences with those of which the functions have been established, including qNOR from Geobacillus stearothermophilus having a known crystal structure (Matsumoto et al., 2012) (Figure A2), suggests functionality of both B. azotoformans proteins. Briefly, BAZO_00190 and BAZO_08916 are composed of one subunit in which 13 TMHs surround the catalytic module. A 14th (N-terminal) TMH precedes a soluble domain facing the periplasm with a heme c fold, but heme c itself is absent. In both proteins amino acids are conserved binding both heme b molecules, non-heme iron, a specific calcium atom, the quinol substrate as well as the amino acids lining a proposed water/proton channel down from cytoplasm to the catalytic side, hydrophobic amino acids along two other putative water channels, and aromatic amino acids that stabilize that heme c fold of the soluble domain (Figure A2).


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

Heylen K, Keltjens J - Front Microbiol (2012)

Multiple sequence alignment of qNOR from B. azotoformans LMG 9581T, B. bataviensis LMG 21833T, and other bacteria. Two non-sense mutations in BABA_p08977 have been corrected in this figure (see text for further explanation). Amino acids involved in the binding of catalytic centers (cyt b, b3, FeB) are highlighted in red, residues for quinol binding in black, bulky residues in the hydrophilic part in gray, residues for Ca2+ binding in yellow, residues lining the long water channel from the cytoplasm in dark blue, residues at water channel 1 in green and water channel 2 in light blue; transmembrane regions are indicated in blue and numbered on top of the alignment [as described by Matsumoto et al. (2012)]. Ba_q1, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_3340); Ba_q2, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_1567); Ge, Geobacillus stearothermophilus (PDB 3AYF, 3AYG); St, Staphylococcus aureus (SAEMRSA15_02230); An, Anaerophaga sp. HS1 (AnHS1_010100003178); Fl, Flavobacterium johnsoniae UW101 (Fjoh_2413); Ng, Neisseria gonorrhoeae (NgonD_010100007739); Cu, Cupriavidus metallidurans CH34 (Rmet_3167); Sy, Synechocystis sp. PCC 6803 (sll0450). PDB, protein database accession number.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

FA2: Multiple sequence alignment of qNOR from B. azotoformans LMG 9581T, B. bataviensis LMG 21833T, and other bacteria. Two non-sense mutations in BABA_p08977 have been corrected in this figure (see text for further explanation). Amino acids involved in the binding of catalytic centers (cyt b, b3, FeB) are highlighted in red, residues for quinol binding in black, bulky residues in the hydrophilic part in gray, residues for Ca2+ binding in yellow, residues lining the long water channel from the cytoplasm in dark blue, residues at water channel 1 in green and water channel 2 in light blue; transmembrane regions are indicated in blue and numbered on top of the alignment [as described by Matsumoto et al. (2012)]. Ba_q1, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_3340); Ba_q2, Bacillus sp. 1NLA3E (B1NLA3EDRAFT_1567); Ge, Geobacillus stearothermophilus (PDB 3AYF, 3AYG); St, Staphylococcus aureus (SAEMRSA15_02230); An, Anaerophaga sp. HS1 (AnHS1_010100003178); Fl, Flavobacterium johnsoniae UW101 (Fjoh_2413); Ng, Neisseria gonorrhoeae (NgonD_010100007739); Cu, Cupriavidus metallidurans CH34 (Rmet_3167); Sy, Synechocystis sp. PCC 6803 (sll0450). PDB, protein database accession number.
Mentions: While cNORs are absent in the genome of B. azotoformans, we could identify two genes coding for qNORs, BAZO_00190, and BAZO_08916. The preference for quinol-dependent NOR seems to be a common property of Gram-positive microorganisms. Although BAZO_00190 and BAZO_08916 share only 38% sequence identity, the comparison of their amino acid sequences with those of which the functions have been established, including qNOR from Geobacillus stearothermophilus having a known crystal structure (Matsumoto et al., 2012) (Figure A2), suggests functionality of both B. azotoformans proteins. Briefly, BAZO_00190 and BAZO_08916 are composed of one subunit in which 13 TMHs surround the catalytic module. A 14th (N-terminal) TMH precedes a soluble domain facing the periplasm with a heme c fold, but heme c itself is absent. In both proteins amino acids are conserved binding both heme b molecules, non-heme iron, a specific calcium atom, the quinol substrate as well as the amino acids lining a proposed water/proton channel down from cytoplasm to the catalytic side, hydrophobic amino acids along two other putative water channels, and aromatic amino acids that stabilize that heme c fold of the soluble domain (Figure A2).

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