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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.


Physical map of the B. azotoformans LMG 9581T (A) and Geobacillus thermodenitrificans NG80-2 (B) nos gene clusters. Arrows show the direction of transcription. Open reading frames are drawn to scale. Homologous genes are shown in identical colors.
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Figure 3: Physical map of the B. azotoformans LMG 9581T (A) and Geobacillus thermodenitrificans NG80-2 (B) nos gene clusters. Arrows show the direction of transcription. Open reading frames are drawn to scale. Homologous genes are shown in identical colors.

Mentions: The genome of B. azotoformans encodes no less than five nos gene clusters, with three clusters including a nosZ gene, and one orphan nosF (Table 2, Figure 3A). Gene arrangements differ in every cluster (Figure 3A), but they are most similar to the atypical nos gene cluster (nosCZ-ORF-nosDYF-ORF) found in the three other Gram-positives available in the databases with nos genes: Geobacillus thermodenitrificans NG80-2 (Figure 3B), Desulfitobacterium hafniense T51 (Liu et al., 2008), and Desulfotomaculum ruminis DSM 2154. Each nosZ gene is consistently preceded by nosC, coding for a cytochrome c, which is predicted (LipoP) to be a lipoprotein with the heme c part facing the periplasm. NosZ is followed by a conserved hypothetical open reading frame encoding a membrane protein with four predicted TMHs. Interestingly, the latter is also the case in W. succinogenes (Ws0918) (Simon et al., 2004). In W. succinogenes, the two copies of nosC are located downstream of nosZ and are flanked by nosG and nosH genes, which are absent in B. azotoformans. NosGH represent a membrane-bound quinone-oxidizing electron transfer module, resembling NapGH in the periplasmic NAR (Nap) system described above. B. azotoformans also lacks a nosA gene that codes for a periplasmic accessory protein involved in Cu binding. However, we note the presence of one of the four senC/SCO1 paralogs upstream of nosC3. As mentioned before, SenC has been implemented with the insertion of copper (CuA); genes coding for the other three paralogs are associated with the alternative NORs. NosL, which is present in three copies in the nos gene clusters (Figure 3A), is a lipoprotein that stoichiometrically binds Cu. This property suggests NosL to be a copper chaperone for metal-center assembly (Zumft, 2005a). NosDYF represent a Cu-ABC transport system with a periplasmic Cu-binding protein (NosD), a membrane-bound permease (NosY), and a cytoplasmic ATPase (NosF) that provides the driving force for Cu translocation (Zumft, 2005a). As can be seen from Figure 3A, nosDYF come in different arrangements in the genome of B. azotoformans, either with or not associated with NosZ. Moreover, sequence analysis reveals marked differences among the individual gene products. All five nosD gene products have a putative transmembrane helix at the C-terminus, but only three of these have a predicted Sec-signal (NosD1, BAZO_00130; NosD4, BAZO_18066; NosD5, BAZO_14249), as expected for periplasmic proteins. NosY3 contains a seventh TMH, one more than usual, while significant insertions without any known domain are found in NosY4 (39 AA at the N-terminus) and NosF1 (49 AA at the C-terminus). Regardless of these differences, B. azotoformans has the disposal of a multicopy factory that could supply NosZ, and possibly also other copper proteins like NirK, with the high demand on copper (Richardson et al., 2009).


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

Heylen K, Keltjens J - Front Microbiol (2012)

Physical map of the B. azotoformans LMG 9581T (A) and Geobacillus thermodenitrificans NG80-2 (B) nos gene clusters. Arrows show the direction of transcription. Open reading frames are drawn to scale. Homologous genes are shown in identical colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Physical map of the B. azotoformans LMG 9581T (A) and Geobacillus thermodenitrificans NG80-2 (B) nos gene clusters. Arrows show the direction of transcription. Open reading frames are drawn to scale. Homologous genes are shown in identical colors.
Mentions: The genome of B. azotoformans encodes no less than five nos gene clusters, with three clusters including a nosZ gene, and one orphan nosF (Table 2, Figure 3A). Gene arrangements differ in every cluster (Figure 3A), but they are most similar to the atypical nos gene cluster (nosCZ-ORF-nosDYF-ORF) found in the three other Gram-positives available in the databases with nos genes: Geobacillus thermodenitrificans NG80-2 (Figure 3B), Desulfitobacterium hafniense T51 (Liu et al., 2008), and Desulfotomaculum ruminis DSM 2154. Each nosZ gene is consistently preceded by nosC, coding for a cytochrome c, which is predicted (LipoP) to be a lipoprotein with the heme c part facing the periplasm. NosZ is followed by a conserved hypothetical open reading frame encoding a membrane protein with four predicted TMHs. Interestingly, the latter is also the case in W. succinogenes (Ws0918) (Simon et al., 2004). In W. succinogenes, the two copies of nosC are located downstream of nosZ and are flanked by nosG and nosH genes, which are absent in B. azotoformans. NosGH represent a membrane-bound quinone-oxidizing electron transfer module, resembling NapGH in the periplasmic NAR (Nap) system described above. B. azotoformans also lacks a nosA gene that codes for a periplasmic accessory protein involved in Cu binding. However, we note the presence of one of the four senC/SCO1 paralogs upstream of nosC3. As mentioned before, SenC has been implemented with the insertion of copper (CuA); genes coding for the other three paralogs are associated with the alternative NORs. NosL, which is present in three copies in the nos gene clusters (Figure 3A), is a lipoprotein that stoichiometrically binds Cu. This property suggests NosL to be a copper chaperone for metal-center assembly (Zumft, 2005a). NosDYF represent a Cu-ABC transport system with a periplasmic Cu-binding protein (NosD), a membrane-bound permease (NosY), and a cytoplasmic ATPase (NosF) that provides the driving force for Cu translocation (Zumft, 2005a). As can be seen from Figure 3A, nosDYF come in different arrangements in the genome of B. azotoformans, either with or not associated with NosZ. Moreover, sequence analysis reveals marked differences among the individual gene products. All five nosD gene products have a putative transmembrane helix at the C-terminus, but only three of these have a predicted Sec-signal (NosD1, BAZO_00130; NosD4, BAZO_18066; NosD5, BAZO_14249), as expected for periplasmic proteins. NosY3 contains a seventh TMH, one more than usual, while significant insertions without any known domain are found in NosY4 (39 AA at the N-terminus) and NosF1 (49 AA at the C-terminus). Regardless of these differences, B. azotoformans has the disposal of a multicopy factory that could supply NosZ, and possibly also other copper proteins like NirK, with the high demand on copper (Richardson et al., 2009).

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.