Sandbox
Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.
Yangqi Gu,
Vishok Srikanth,
Aldo I. Salazar-Morales,
Ruchi Jain,
J. Patrick O'Brien,
Sophia M. Yi,
Rajesh K. Soni,
Fadel A. Samatey,
Sibel Ebru Yalcin,
and Nikhil S. Malvankar.
nature.com/articles/s41586-021-03857-w (2021).
DOI 10.1038/s41586-021-03857-w
Structure Tour
BackgroundPreviously, pili of Geobacter sulfurreducens were thought to be composed of PilA-N, a 61-amino acid protein[1][2][3]. 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[4][5]. Gene fission of pilins is widely distributed in Desulfuromonadales including Geobacteracae[6]. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported[7][8][9]. 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). HeterodimersThe 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[10]. (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 ConclusionsAs detailed in the journal publication, the PilA-N-C pili studied here are 20-fold less electrically conductive than the nanowires composed of OmcS cytochromes[7][8], and 20,000-fold less conductive than OmcZ nanowires[9]. 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.
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See Also
- 6vk9, the structure described here.
- Malvankar: A list of all interactive 3D complements for publications from the Malvankar group, including:
- Structure of the OmcS conductive nanowire: 2019, Cell: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.
