Sandbox

From Proteopedia

(Difference between revisions)

Revision as of 19:37, 10 November 2025

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 </td></tr></table>

Structure Tour

1 Background
2 Pilus Structure
3 Heterodimers
4 Other Findings and Conclusions

Background

Previously, 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

Click the green links below to change the molecular scene. Rotate to view the molecule from all sides (drag to rotate). Zoom with your mouse wheel, or Shift-Drag up/down.

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

The PilA-N subunits have extensive hydrophobic contacts with each other, stabilizing the hydrophobic core of the filament. . 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 () 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 . Dimer : PilA-N consists of two alpha helices, while PilA-C includes a 3-stranded beta sheet. The C-terminal protrusion of PilA-N is (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.) (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 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.

Notes & References

↑ Yalcin SE, Malvankar NS. The blind men and the filament: Understanding structures and functions of microbial nanowires. Curr Opin Chem Biol. 2020 Dec;59:193-201. doi: 10.1016/j.cbpa.2020.08.004. Epub, 2020 Oct 15. PMID:33070100 doi:http://dx.doi.org/10.1016/j.cbpa.2020.08.004
↑ 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:http://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:http://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:http://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:http://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:http://dx.doi.org/10.3389/fmicb.2016.02080
↑ ^7.0 ^7.1 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:http://dx.doi.org/10.1016/j.cell.2019.03.029
↑ ^8.0 ^8.1 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:http://dx.doi.org/10.1038/s42003-019-0448-9
↑ ^9.0 ^9.1 Yalcin SE, O'Brien JP, Gu Y, Reiss K, Yi SM, Jain R, Srikanth V, Dahl PJ, Huynh W, Vu D, Acharya A, Chaudhuri S, Varga T, Batista VS, Malvankar NS. Electric field stimulates production of highly conductive microbial OmcZ nanowires. Nat Chem Biol. 2020 Oct;16(10):1136-1142. doi: 10.1038/s41589-020-0623-9. Epub, 2020 Aug 17. PMID:32807967 doi:http://dx.doi.org/10.1038/s41589-020-0623-9
↑ 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:http://dx.doi.org/10.1073/pnas.0508452103

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox"

@@ Line 1: / Line 1: @@
-== NolR ==
-The symbiosis between rhizobial microbes and legume plants is fundamental to sustainable agriculture and ecological nitrogen cycling. This partnership requires coordinated expression of multiple genes to establish nitrogen-fixing nodules, with **NolR serving as a global transcriptional regulator** controlling this critical developmental process across diverse *Rhizobium* species.
+<span style="font-size:160%"><b>Structural basis for regulation of rhizobial nodulation
+and symbiosis gene expression by the regulatory
+protein NolR.</b></span>
-We present the first high-resolution X-ray crystal structures of NolR in both unliganded and DNA-bound forms, revealing its complex interactions with asymmetric operator sequences. Analysis of NolR complexed with two different 22-base pair operator DNA sequences (oligos AT and AA) demonstrates that this **homodimeric transcription factor adopts a winged helix-turn-helix fold** and recognizes DNA through a combination of positively charged surface residues that engage the DNA phosphate backbone and specific base contacts.
-The most striking finding is a **conformational switching mechanism involving Gln56**, which alters its position to accommodate variation in target DNA sequences without changing overall binding affinity. This elegant mechanism allows NolR to regulate multiple nodulation and symbiosis genes with different operator sequences through modulation of thermodynamic binding contributions. The conformational flexibility of this key residue represents a novel regulatory strategy in the ArsR/SmtB transcription factor family.
+<span style="font-size:100%">
+[[User:Yangqi Gu|Yangqi '''Gu''']],
+[[User:Vishok Srikanth|Vishok '''Srikanth''']],
+Aldo I. '''[https://www.linkedin.com/in/aldo-salazar-morales-7a866617 Salazar-Morales]''',
+Ruchi '''Jain''',
+J. Patrick '''[https://malvankarlab.yale.edu/group-members O'Brien]''',
+Sophia M. '''[https://malvankarlab.yale.edu/group-members Yi]''',
+Rajesh K. '''Soni''',
+Fadel A. [[User:Fadel A. Samatey|'''Samatey''']],
+Sibel Ebru '''[https://medicine.yale.edu/profile/sibel_yalcin/ Yalcin]''',
+and Nikhil S. '''[[User:Nikhil_Malvankar|Malvankar]]'''.
+[https://www.nature.com/articles/s41586-021-03857-w nature.com/articles/s41586-021-03857-w] (2021).
+[https://doi.org/10.1038/s41586-021-03857-w DOI 10.1038/s41586-021-03857-w]
+</span>
+</td></tr></table>
+__NOTOC__
+==Structure Tour==
+<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 name="blindmen">PMID: 33070100</ref><ref name="homolmod">PMID: 25736881 </ref><ref name="lovleyreview">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><ref name="omcz">PMID: 32807967</ref>.
-These structural studies provide unprecedented molecular insight into **how NolR functions as a global regulatory hub**, proposing two distinct regulatory models for differential gene expression during nodule formation and symbiotic nitrogen fixation. This work illuminates the structural basis for one of nature's most important agricultural and ecological partnerships.
+===Pilus Structure===
+{{Template:ClickGreenLinks}}
+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/9'>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/10'>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/11'>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/12'>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).
+===Heterodimers===
+The pilus filament is assembled from <scene name='83/834714/Dimer/5'>heterodimers</scene>. Dimer <scene name='83/834714/Dimer/6'>secondary structure</scene>: '''<font color='#e87000'>PilA-N</font>''' consists of two alpha helices, while '''<font color='00a0a0'>PilA-C</font>''' includes a 3-stranded beta sheet. The C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>''' is <scene name='83/834714/Flaps/7'>held between two flaps</scene> (darker) of '''<font color='00a0a0'>PilA-C</font>'''. 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 '''<font color='#e87000'>PilA-N</font>'''. These flaps might be open before '''<font color='#e87000'>PilA-N</font>''' arrives to form a dimer, reminiscent of the flaps of HIV protease<ref>PMID: 16418268</ref>. (See, for example, [[1hxw]] and [[Flaps Morph for HIV Protease]].) <scene name='83/834714/Flaps/8'>Four glycines</scene> (<font color="red">'''red: 10, 11, 31, 37'''</font>) 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 20-fold less electrically conductive than the nanowires composed of OmcS cytochromes<ref name="nw1" /><ref name="nw2" />, and 20,000-fold less conductive than OmcZ nanowires<ref name="omcz" />. 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.
+</StructureSection>
+<br>
+<hr><br>
+==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: [[Malvankar/2|2019, Cell: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.]]
+==Notes & References==
+<references />

Sandbox

From Proteopedia

Revision as of 19:37, 10 November 2025

Structure Tour

Contents

Background

Pilus Structure

Heterodimers

Other Findings and Conclusions

See Also

Notes & References

Views

Personal tools

Navigation

Search

Toolbox