User:Nikhil Malvankar/Geobacter pilus structure and function: Difference between revisions

Revision as of 17:34, 30 June 2021

Structure of novel pili evolved for extracellular translocation of microbial nanowires.

Yangqi Gu, Vishok Srikanth, Ruchi Jain, Aldo I. Salazar-Morales, J. Patrick O'Brien, Sophia M. Yi, Rajesh K. Soni, Fadel A. Samatey, Sibel Ebru Yalcin, and Nikhil S. Malvankar. (journal article link here) (2021). (DOI link here)

Structure Tour

Background

Previously, pili of Geobacter sulfurreducens were thought to be composed of PilA-N, a 61-amino acid protein^[1]^[2]. Immediately downstream from the pilA-N gene is pilA-C, coding for a 104 amino acid protein suspected to be the missing C-terminal globular domain of PilA-N^[3]^[4]. Gene fission of pilins is widely distributed in Desulfuromonadales including Geobacteracae^[5]. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported^[6]^[7].

Pilus Structure

Our electron cryomicroscopic structure of Geobacter sulfurreducens pili (restore initial scene), 6vk9, reveals them to be composed of a core of PilA-N (61 amino acids) coated with an outer surface layer of PilA-C (104 amino acids). Here is a cutaway view (front half hidden). The C-termini of PilA-N protrude into sockets in PilA-C.

The PilA-N subunits have extensive hydrophobic contacts with each other, stabilizing the hydrophobic core of the filament. View PilA-N with PilA-C hidden. Each PilA-N chain contacts 75 carbon atoms from 11 adjacent PilA-N chains, and also has 4 hydrogen bonds and 4 salt bridges with adjacent PilA-N chains (not shown). In contrast, PilA-C subunits (view PilA-C with front half and PilA-N hidden) have little contact with each other: 14 atoms, which are mostly hydrogen bonded, with one salt bridge (not shown).

Heterodimers

The pilus filament is assembled from heterodimers. Dimer secondary structure: PilA-N consists of two alpha helices, while PilA-C includes a 3-stranded beta sheet. The C-terminal protrusion of PilA-N is held between two flaps (darker) of PilA-C. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of PilA-N. These flaps might be open before PilA-N arrives to form a dimer, reminiscent of the flaps of HIV protease^[8]. (See, for example, 1hxw and Flaps Morph for HIV Protease.) Four glycines (red: 10, 11, 31, 37) provide flexibility that could enable opening of the flaps.

Other Findings and Conclusions

As detailed in the journal publication, the PilA-N-C pili studied here are 50-fold less electrically conductive than the nanowires composed of cytochromes^[6]^[7]. These PilA-N-C pili lack the structural hallmarks of type 4 pili, but share structural characteristics with pseudopili. PilA-N and PilA-C remain in the inner membrane, unless the gene for OmcS (or OmcZ) is deleted, in which case they form the pili extending outside the cell studied here. When the pilA-N gene is deleted, OmcS nanowires fail to be produced. It is proposed in the journal publication that PilA-N-C is part of a secretion system required for production of OmcS/OmcZ nanowires.

↑ Malvankar NS, Vargas M, Nevin K, Tremblay PL, Evans-Lutterodt K, Nykypanchuk D, Martz E, Tuominen MT, Lovley DR. Structural basis for metallic-like conductivity in microbial nanowires. MBio. 2015 Mar 3;6(2):e00084. doi: 10.1128/mBio.00084-15. PMID:25736881 doi:https://dx.doi.org/10.1128/mBio.00084-15
↑ Lovley DR, Walker DJF. Geobacter Protein Nanowires. Front Microbiol. 2019 Sep 24;10:2078. doi: 10.3389/fmicb.2019.02078. eCollection , 2019. PMID:31608018 doi:https://dx.doi.org/10.3389/fmicb.2019.02078
↑ Richter LV, Sandler SJ, Weis RM. Two isoforms of Geobacter sulfurreducens PilA have distinct roles in pilus biogenesis, cytochrome localization, extracellular electron transfer, and biofilm formation. J Bacteriol. 2012 May;194(10):2551-63. doi: 10.1128/JB.06366-11. Epub 2012 Mar 9. PMID:22408162 doi:https://dx.doi.org/10.1128/JB.06366-11
↑ Holmes DE, Dang Y, Walker DJF, Lovley DR. The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer. Microb Genom. 2016 Aug 25;2(8):e000072. doi: 10.1099/mgen.0.000072. eCollection, 2016 Aug. PMID:28348867 doi:https://dx.doi.org/10.1099/mgen.0.000072
↑ Shu C, Xiao K, Yan Q, Sun X. Comparative Analysis of Type IV Pilin in Desulfuromonadales. Front Microbiol. 2016 Dec 21;7:2080. doi: 10.3389/fmicb.2016.02080. eCollection, 2016. PMID:28066394 doi:https://dx.doi.org/10.3389/fmicb.2016.02080
↑ ^6.0 ^6.1 Wang F, Gu Y, O'Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID:30951668 doi:https://dx.doi.org/10.1016/j.cell.2019.03.029
↑ ^7.0 ^7.1 Filman DJ, Marino SF, Ward JE, Yang L, Mester Z, Bullitt E, Lovley DR, Strauss M. Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire. Commun Biol. 2019 Jun 19;2(1):219. doi: 10.1038/s42003-019-0448-9. PMID:31925024 doi:https://dx.doi.org/10.1038/s42003-019-0448-9
↑ Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):915-20. doi:, 10.1073/pnas.0508452103. Epub 2006 Jan 17. PMID:16418268 doi:https://dx.doi.org/10.1073/pnas.0508452103

Notes & References

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

[1] Malvankar NS, Vargas M, Nevin K, Tremblay PL, Evans-Lutterodt K, Nykypanchuk D, Martz E, Tuominen MT, Lovley DR. Structural basis for metallic-like conductivity in microbial nanowires. MBio. 2015 Mar 3;6(2):e00084. doi: 10.1128/mBio.00084-15. PMID:25736881 doi:https://dx.doi.org/10.1128/mBio.00084-15

[2] Lovley DR, Walker DJF. Geobacter Protein Nanowires. Front Microbiol. 2019 Sep 24;10:2078. doi: 10.3389/fmicb.2019.02078. eCollection , 2019. PMID:31608018 doi:https://dx.doi.org/10.3389/fmicb.2019.02078

[3] Richter LV, Sandler SJ, Weis RM. Two isoforms of Geobacter sulfurreducens PilA have distinct roles in pilus biogenesis, cytochrome localization, extracellular electron transfer, and biofilm formation. J Bacteriol. 2012 May;194(10):2551-63. doi: 10.1128/JB.06366-11. Epub 2012 Mar 9. PMID:22408162 doi:https://dx.doi.org/10.1128/JB.06366-11

[4] Holmes DE, Dang Y, Walker DJF, Lovley DR. The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer. Microb Genom. 2016 Aug 25;2(8):e000072. doi: 10.1099/mgen.0.000072. eCollection, 2016 Aug. PMID:28348867 doi:https://dx.doi.org/10.1099/mgen.0.000072

[5] Shu C, Xiao K, Yan Q, Sun X. Comparative Analysis of Type IV Pilin in Desulfuromonadales. Front Microbiol. 2016 Dec 21;7:2080. doi: 10.3389/fmicb.2016.02080. eCollection, 2016. PMID:28066394 doi:https://dx.doi.org/10.3389/fmicb.2016.02080

[nw1-6] 6.0 ^6.1 Wang F, Gu Y, O'Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID:30951668 doi:https://dx.doi.org/10.1016/j.cell.2019.03.029

[nw2-7] 7.0 ^7.1 Filman DJ, Marino SF, Ward JE, Yang L, Mester Z, Bullitt E, Lovley DR, Strauss M. Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire. Commun Biol. 2019 Jun 19;2(1):219. doi: 10.1038/s42003-019-0448-9. PMID:31925024 doi:https://dx.doi.org/10.1038/s42003-019-0448-9

[8] Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):915-20. doi:, 10.1073/pnas.0508452103. Epub 2006 Jan 17. PMID:16418268 doi:https://dx.doi.org/10.1073/pnas.0508452103

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@@ Line 32: / Line 32: @@
 __NOTOC__
 ==Structure Tour==
-<StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/4'>
+<StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/7'>
 ===Background===
 Previously, pili of ''Geobacter sulfurreducens'' were thought to be composed of PilA-N, a 61-amino acid protein<ref>PMID: 25736881 </ref><ref>PMID: 31608018 </ref>. Immediately downstream from the ''pilA-N'' gene is ''pilA-C'', coding for a 104 amino acid protein suspected to be the missing C-terminal globular domain of PilA-N<ref>PMID:22408162 </ref><ref>PMID:28348867</ref>. Gene fission of pilins is widely distributed in ''Desulfuromonadales'' including ''Geobacteracae''<ref>PMID: 28066394</ref>. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported<ref name="nw1">PMID: 30951668</ref><ref name="nw2">PMID: 31925024</ref>.
@@ Line 38: / Line 38: @@
 ===Pilus Structure===
-Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili (<scene name='83/834714/Filament/4'>restore initial scene</scene>), [[6vk9]], reveals them to be <scene name='83/834714/Filament/1'>composed of a core</scene> of '''<font color='#e87000'>PilA-N</font>''' (61 amino acids) coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids). Here is a <scene name='83/834714/Filament/2'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.
+Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili (<scene name='83/834714/Filament/7'>restore initial scene</scene>), [[6vk9]], reveals them to be <scene name='83/834714/Filament/1'>composed of a core</scene> of '''<font color='#e87000'>PilA-N</font>''' (61 amino acids) coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids). Here is a <scene name='83/834714/Filament/2'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.
 The '''PilA-N''' subunits have extensive hydrophobic contacts with each other, stabilizing the hydrophobic core of the filament. <scene name='83/834714/Filament/5'>View PilA-N with PilA-C hidden</scene>. Each PilA-N chain contacts 75 carbon atoms from 11 adjacent PilA-N chains, and also has 4 hydrogen bonds and 4 salt bridges with adjacent PilA-N chains (not shown). In contrast, '''PilA-C''' subunits (<scene name='83/834714/Filament/6'>view PilA-C with front half and PilA-N hidden</scene>) have little contact with each other: 14 atoms, which are mostly hydrogen bonded, with one salt bridge (not shown).

User:Nikhil Malvankar/Geobacter pilus structure and function: Difference between revisions

Revision as of 17:34, 30 June 2021

Structure Tour

Contents

Background

Pilus Structure

Heterodimers

Other Findings and Conclusions

See Also

Notes & References

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