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High-resolution structure of a type IV pilin from the metal-reducing bacterium Shewanella oneidensis.

Gorgel M, Ulstrup JJ, Bøggild A, Jones NC, Hoffmann SV, Nissen P, Boesen T - BMC Struct. Biol. (2015)

Bottom Line: Interestingly, our PilBac1 crystal structure reveals two unusual features compared to other type IVa pilins: an unusual position of the disulfide bridge and a straight α-helical section, which usually exhibits a pronounced kink.In this study we have described the first structure of a pilin from Shewanella oneidensis.The structure possesses features of the common type IV pilin core, but also exhibits significant variations in the α-helical part and the D-region.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark. manuela@mbg.au.dk.

ABSTRACT

Background: Type IV pili are widely expressed among Gram-negative bacteria, where they are involved in biofilm formation, serve in the transfer of DNA, motility and in the bacterial attachment to various surfaces. Type IV pili in Shewanella oneidensis are also supposed to play an important role in extracellular electron transfer by the attachment to sediments containing electron acceptors and potentially forming conductive nanowires.

Results: The potential nanowire type IV pilin PilBac1 from S. oneidensis was characterized by a combination of complementary structural methods and the atomic structure was determined at a resolution of 1.67 Å by X-ray crystallography. PilBac1 consists of one long N-terminal α-helix packed against four antiparallel β-strands, thus revealing the core fold of type IV pilins. In the crystal, PilBac1 forms a parallel dimer with a sodium ion bound to one of the monomers. Interestingly, our PilBac1 crystal structure reveals two unusual features compared to other type IVa pilins: an unusual position of the disulfide bridge and a straight α-helical section, which usually exhibits a pronounced kink. This straight helix leads to a distinct packing in a filament model of PilBac1 based on an EM model of a Neisseria pilus.

Conclusions: In this study we have described the first structure of a pilin from Shewanella oneidensis. The structure possesses features of the common type IV pilin core, but also exhibits significant variations in the α-helical part and the D-region.

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Related in: MedlinePlus

Positioning of the aromatic residues in PilBac1. A: Overall alignment in the pilus. B, C: Magnified view on pilus subunits. The aromatic residues are shown as sphere representation in blue. Round, red arrows show the shortest distances between two neighboring aromatics. The distances between the individual aromatics are shown in Å on the side and the distance between two clusters is shown in Å in red. e-: electron.
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Fig9: Positioning of the aromatic residues in PilBac1. A: Overall alignment in the pilus. B, C: Magnified view on pilus subunits. The aromatic residues are shown as sphere representation in blue. Round, red arrows show the shortest distances between two neighboring aromatics. The distances between the individual aromatics are shown in Å on the side and the distance between two clusters is shown in Å in red. e-: electron.

Mentions: Malvankar and co-workers have proposed that nanowires from G. sulfurreducens are conductive due to the close positioning of aromatic amino acids in PilA [27]. The NMR structure of PilA from G. sulfurreducens showed that the aromatic side chains were indeed closely spaced with a maximum distance of 15 Å [43]; yet, to the best of our knowledge, the maximum distance between aromatic groups that allows for electron transfer has not been defined so far. Similar to G. sulfurreducens, S. oneidensis forms conductive nanowires and, based on the overall similarity between these two organisms including metabolic pathways and the prevalence of multiheme cytochromes, a similar electron transfer mechanism is very likely. PilBac1 is the type IV pilin which is most closely related to PilA from G. sulfurreducens based on sequence comparisons (Additional file 2: Table S2). The full-length chimeric model of PilBac1 contained 14 aromatic residues including two phenylalanines and one tyrosine in the modelled transmembrane domain. In the modelled pilus of PilBac1 subunits, the aromatic side chains were evenly spaced throughout the whole structure, with some being closer to their neighbors than others (Figure 9A). A long chain of aromatic side chains wound along the modelled filament with two clusters on each subunit in which the aromatics are closely positioned to each other with distances between 4 to 7 Å. Yet, these two clusters are separated by a gap of 11 Å which can be defined as the maximum distance between two aromatics in the pilus model. This distance compares well to PilA from Geobacter; however, the arrangement of aromatic side chains in PilE from N. gonorrhoeae – which has not been shown to produce conductive nanowires yet – is similar with a maximum distance between individual aromatic side chains of around 13 Å (Additional file 8: Figure S4). This may argue against the hypothesis stating that conductivity is based on a specific alignment of aromatic side chains.Figure 9


High-resolution structure of a type IV pilin from the metal-reducing bacterium Shewanella oneidensis.

Gorgel M, Ulstrup JJ, Bøggild A, Jones NC, Hoffmann SV, Nissen P, Boesen T - BMC Struct. Biol. (2015)

Positioning of the aromatic residues in PilBac1. A: Overall alignment in the pilus. B, C: Magnified view on pilus subunits. The aromatic residues are shown as sphere representation in blue. Round, red arrows show the shortest distances between two neighboring aromatics. The distances between the individual aromatics are shown in Å on the side and the distance between two clusters is shown in Å in red. e-: electron.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4376143&req=5

Fig9: Positioning of the aromatic residues in PilBac1. A: Overall alignment in the pilus. B, C: Magnified view on pilus subunits. The aromatic residues are shown as sphere representation in blue. Round, red arrows show the shortest distances between two neighboring aromatics. The distances between the individual aromatics are shown in Å on the side and the distance between two clusters is shown in Å in red. e-: electron.
Mentions: Malvankar and co-workers have proposed that nanowires from G. sulfurreducens are conductive due to the close positioning of aromatic amino acids in PilA [27]. The NMR structure of PilA from G. sulfurreducens showed that the aromatic side chains were indeed closely spaced with a maximum distance of 15 Å [43]; yet, to the best of our knowledge, the maximum distance between aromatic groups that allows for electron transfer has not been defined so far. Similar to G. sulfurreducens, S. oneidensis forms conductive nanowires and, based on the overall similarity between these two organisms including metabolic pathways and the prevalence of multiheme cytochromes, a similar electron transfer mechanism is very likely. PilBac1 is the type IV pilin which is most closely related to PilA from G. sulfurreducens based on sequence comparisons (Additional file 2: Table S2). The full-length chimeric model of PilBac1 contained 14 aromatic residues including two phenylalanines and one tyrosine in the modelled transmembrane domain. In the modelled pilus of PilBac1 subunits, the aromatic side chains were evenly spaced throughout the whole structure, with some being closer to their neighbors than others (Figure 9A). A long chain of aromatic side chains wound along the modelled filament with two clusters on each subunit in which the aromatics are closely positioned to each other with distances between 4 to 7 Å. Yet, these two clusters are separated by a gap of 11 Å which can be defined as the maximum distance between two aromatics in the pilus model. This distance compares well to PilA from Geobacter; however, the arrangement of aromatic side chains in PilE from N. gonorrhoeae – which has not been shown to produce conductive nanowires yet – is similar with a maximum distance between individual aromatic side chains of around 13 Å (Additional file 8: Figure S4). This may argue against the hypothesis stating that conductivity is based on a specific alignment of aromatic side chains.Figure 9

Bottom Line: Interestingly, our PilBac1 crystal structure reveals two unusual features compared to other type IVa pilins: an unusual position of the disulfide bridge and a straight α-helical section, which usually exhibits a pronounced kink.In this study we have described the first structure of a pilin from Shewanella oneidensis.The structure possesses features of the common type IV pilin core, but also exhibits significant variations in the α-helical part and the D-region.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark. manuela@mbg.au.dk.

ABSTRACT

Background: Type IV pili are widely expressed among Gram-negative bacteria, where they are involved in biofilm formation, serve in the transfer of DNA, motility and in the bacterial attachment to various surfaces. Type IV pili in Shewanella oneidensis are also supposed to play an important role in extracellular electron transfer by the attachment to sediments containing electron acceptors and potentially forming conductive nanowires.

Results: The potential nanowire type IV pilin PilBac1 from S. oneidensis was characterized by a combination of complementary structural methods and the atomic structure was determined at a resolution of 1.67 Å by X-ray crystallography. PilBac1 consists of one long N-terminal α-helix packed against four antiparallel β-strands, thus revealing the core fold of type IV pilins. In the crystal, PilBac1 forms a parallel dimer with a sodium ion bound to one of the monomers. Interestingly, our PilBac1 crystal structure reveals two unusual features compared to other type IVa pilins: an unusual position of the disulfide bridge and a straight α-helical section, which usually exhibits a pronounced kink. This straight helix leads to a distinct packing in a filament model of PilBac1 based on an EM model of a Neisseria pilus.

Conclusions: In this study we have described the first structure of a pilin from Shewanella oneidensis. The structure possesses features of the common type IV pilin core, but also exhibits significant variations in the α-helical part and the D-region.

Show MeSH
Related in: MedlinePlus