---
title: "FapA links the flagellar cage to cytoplasmic control of surface behaviors in Helicobacter pylori"
id: "biorxiv-1-fapa-extends-the-flagellar-cage-dependent-network-into-the-cytoplasm-to-control"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-1-fapa-extends-the-flagellar-cage-dependent-network-into-the-cytoplasm-to-control"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1?rss=1"
published_at: "2026-10-24T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# FapA links the flagellar cage to cytoplasmic control of surface behaviors in Helicobacter pylori
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-1-fapa-extends-the-flagellar-cage-dependent-network-into-the-cytoplasm-to-control
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1?rss=1)
- **Published At:** 2026-10-24T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors identified **FapA** as a member of the flagellar assembly protein A family that functions within the pathway connecting the flagellar cage to surface-associated behaviors in **Helicobacter pylori**. - Deletion of fapA phenocopied loss of the cage components PilM, PilN, and PilO: the ΔfapA strain showed increased soft-agar migration and reduced microcolony and biofilm formation. - Epistasis experiments placed **FapA** downstream of the PilMNO cage components in the regulatory pathway controlling motility versus a sessile lifestyle. - The study used fluorescent protein fusions and protein–protein interaction assays to map **FapA** localization to cell poles and to demonstrate interaction with the cytoplasmic PilM component. - Cryo-electron tomography detected a cytoplasmic density adjacent to PilM in wild-type cells that was absent in the ΔfapA mutant, supporting a structural role for **FapA** at the motor poles. - Phylogenetic analysis indicated that FapA homologs occur across multiple bacterial phyla (Campylobacterota, Bacillota, Spirochaetota, Desulfobacterota, Thermotogota, Synergistota, and Pseudomonadota), suggesting broader conservation. - The authors concluded that additional cytoplasmic components of the **flagellar cage** restrict motility and promote sessile/biofilm behaviors; the paper did not report detailed biochemical mechanisms or in vivo infection data. - Methods reported in the source included gene deletion, epistasis analysis, fluorescent fusion localization, protein–protein interaction experiments, cryo-electron tomography, and phylogenetic analyses; the source did not provide specific experimental parameters in this summary (for example, exact assays, sample sizes, or statistical values were not reported).
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Fong, Corey D. Witt, [ View ORCID Profile](http://orcid.org/0009-0000-0644-3070)Eric H.L. Huang, Jian Yue, [ View ORCID Profile](http://orcid.org/0000-0001-5891-4559)Xiaolin Liu, [ View ORCID Profile](http://orcid.org/0000-0001-8478-4751)Anne Roujeinikova, Jun Liu, [ View ORCID Profile](http://orcid.org/0000-0001-6265-7401)Karen Ottemann doi: https://doi.org/10.64898/2026.10.23.761471 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. Jiunn N.C. Fong 1 University of California, Santa Cruz; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jiunn%2BN.C.%2BFong%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Fong%20JN&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJiunn%2BN.C.%2BFong%2B) * [ORCID record for Jiunn N.C. Fong](http://orcid.org/0000-0003-3933-7885 "Open in new tab") Corey D. Witt 1 University of California, Santa Cruz; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Corey%2BD.%2BWitt%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Witt%20CD&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ACorey%2BD.%2BWitt%2B) Eric H.L. Huang 1 University of California, Santa Cruz; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Eric%2BH.L.%2BHuang%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Huang%20EH&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AEric%2BH.L.%2BHuang%2B) * [ORCID record for Eric H.L. Huang](http://orcid.org/0009-0000-0644-3070 "Open in new tab") Jian Yue 2 Yale University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jian%2BYue%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Yue%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJian%2BYue%2B) Xiaolin Liu 1 University of California, Santa Cruz; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Xiaolin%2BLiu%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Liu%20X&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AXiaolin%2BLiu%2B) * [ORCID record for Xiaolin Liu](http://orcid.org/0000-0001-5891-4559 "Open in new tab") Anne Roujeinikova 3 Monash University * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Anne%2BRoujeinikova%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Roujeinikova%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAnne%2BRoujeinikova%2B) * [ORCID record for Anne Roujeinikova](http://orcid.org/0000-0001-8478-4751 "Open in new tab") Jun Liu 2 Yale University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jun%2BLiu%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Liu%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJun%2BLiu%2B) Karen Ottemann 1 University of California, Santa Cruz; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Karen%2BOttemann%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Ottemann%20K&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AKaren%2BOttemann%2B) * [ORCID record for Karen Ottemann](http://orcid.org/0000-0001-6265-7401 "Open in new tab") * For correspondence: ottemann@ucsc.edu * [Abstract](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5901246/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5901246/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5901246/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5901246/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5901246/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Flagellar systems enable many host-associated bacteria to colonize successfully. One such pathogen is Helicobacter pylori, which assembles an elaborate, high-torque flagellar motor that has a wide C-ring, 18 stator complexes, and is surrounded by a cage that includes homologs of the type IV pilus proteins PilM, PilN, and PilO. PilMNO act to repress soft-agar migration while promoting cell aggregation, microcolony, and biofilm formation, but the pathway linking the flagellar cage to these behaviors is unknown. Here we identify FapA, a member of the flagellar assembly protein A (FapA) family, as a component of this pathway. Deletion of fapA increased soft-agar migration and reduced microcolony and biofilm formation, similar to deletion of pilMNO. Epistasis analysis placed FapA downstream of the PilMNO flagellar cage. Using fluorescent fusions and protein-protein interaction experiments, FapA was found to localize to the cell poles, the sites of flagellar motor placement, and interact with the cytoplasmic PilM component of the cage. Indeed, cryo-electron tomography experiments detected cytoplasmic density near PilM that was lost in the ΔfapA deletion mutant. Phylogenetic analysis suggests that FapA proteins are more widespread than previously appreciated, being found in multiple bacterial phyla including Campylobacterota, Bacillota, Spirochaetota, Desulfobacterota, Thermotogota, Synergistota, and Pseudomonadota. Together, these findings support that the H. pylori flagellar cage has additional components that reside in the cytoplasm but similarly function to limit motility and activate a sessile/biofilm lifestyle. Given the widespread nature of FapA, our results suggest that many other bacteria might employ FapA homologs for similar purposes. ### Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.23.761471.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.10.23.761471v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) FapA extends the flagellar cage-dependent network into the cytoplasm to control surface-associated behaviors in Helicobacter pylori Jiunn N.C. Fong, Corey D. Witt, Eric H.L. Huang, Jian Yue, Xiaolin Liu, Anne Roujeinikova, Jun Liu, Karen Ottemann bioRxiv 2026.10.23.761471; doi: https://doi.org/10.64898/2026.10.23.761471 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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