Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum

Claire Overly Cottom; Eva Heinz; Satchal Erramilli; Anthony Kossiakoff; Daniel J. Slade; Nicholas Noinaj

doi:10.1016/j.str.2025.08.008

Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum

Claire Overly Cottom, Eva Heinz, Satchal Erramilli, Anthony Kossiakoff, Daniel J. Slade, Nicholas Noinaj^*

^*Corresponding author for this work

Strathclyde Institute Of Pharmacy And Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.

Original language	English
Journal	Structure
Early online date	1 Sept 2025
DOIs	https://doi.org/10.1016/j.str.2025.08.008
Publication status	E-pub ahead of print - 1 Sept 2025

Funding

We would like to thank members of the Noinaj Lab for comments and discussions on the manuscript. We thank Laurie Mueller (negative-stain) and Thomas Klose (cryo-EM) for assistance during EM training, screening, and data collection. Thank you to the Purdue Proteomics Facility and Venkatesh Thirumalaikumar for assistance with mass spectrometry data collection and analysis. Thanks to Tomasz Gawda and Nevin Brittain for assistance with phage display screening and validation. We thank Dr. Rolf Müller for providing the darobactin compounds. And a special thanks to Steve Wilson for maintaining and managing our EM computing resources and to the beamline staff of the BioCAT beamline at the Advanced Photon Source (APS), Argonne National Laboratory for their help with data collection. The BioCAT resources are supported by grant P30 GM138395 from the NIGMS of the NIH; use of the Pilatus 3 1M detector was provided by grant 1S10OD018090 from NIGMS. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. We would like to thank the Wellcome Sanger Institute Parasites and Microbes core informatics team for their expert support. We also acknowledge funding support from NIH grants 1R01GM127884 (N.N.), 1R01GM127896 (N.N.), 1R01AI127793 (N.N.), and 1R01GM117372 (A.K.). C.O.C. was supported as a trainee through the T32 Drug Discovery in Infectious Disease Program (T32AI148103) and through a Bilsland Dissertation Fellowship (Department of Biological Science, Purdue University).

Keywords

Fusobacterium nucleatum
Proteomics
Protein Folding
Membrane Protein
Structural Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.str.2025.08.008

Cottom-etal-Structure-2025-Characterization-of-the-OMP-biogenesis-machinery-inAccepted author manuscript, 11 MBLicence: CC BY 4.0

Cite this

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title = "Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum",

abstract = "F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.",

keywords = "Fusobacterium nucleatum, Proteomics, Protein Folding, Membrane Protein, Structural Biology",

author = "Cottom, {Claire Overly} and Eva Heinz and Satchal Erramilli and Anthony Kossiakoff and Slade, {Daniel J.} and Nicholas Noinaj",

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TY - JOUR

T1 - Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum

AU - Cottom, Claire Overly

AU - Heinz, Eva

AU - Erramilli, Satchal

AU - Kossiakoff, Anthony

AU - Slade, Daniel J.

AU - Noinaj, Nicholas

PY - 2025/9/1

Y1 - 2025/9/1

N2 - F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.

AB - F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.

KW - Fusobacterium nucleatum

KW - Proteomics

KW - Protein Folding

KW - Membrane Protein

KW - Structural Biology

U2 - 10.1016/j.str.2025.08.008

DO - 10.1016/j.str.2025.08.008

M3 - Article

SN - 0969-2126

JO - Structure

JF - Structure

ER -

Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum

Abstract

Funding

Keywords

UN SDGs

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