# Uncovering Biochemical Features of Resistant Starch Degradation by R. bromii

> **NIH NIH F31** · UNIVERSITY OF MICHIGAN AT ANN ARBOR · 2021 · $39,636

## Abstract

Abstract
 The human gut microbial community influences many aspects of human physiology via the output of
short chain fatty acids from the fermentation of dietary carbohydrates. Ruminococcus bromii, a keystone
species in the human gut, degrades dietary resistant starch (RS) and cross-feeds other gut bacteria that
produce butyrate, a short chain fatty acid with potent anti-inflammatory and anti-tumorigenic properties. R.
bromii has an amylosome, a complex of secreted starch-active proteins, that is predicted to be responsible for
its unique ability to degrade resistant starch (RS). However, the molecular determinants of the amylosome that
confer RS degradation are poorly understood. The amylosome is predicted to be assembled via calcium-
dependent protein-protein interactions. Via proteomic analysis, I identified Doc20 as one of the most abundant
proteins enriched from EDTA-washed R. bromii. Doc20 is comprised of two starch-binding domains separated
by an extended Thr/Pro-rich linker followed by a dockerin domain, a calcium-dependent protein-protein
interaction domain that facilitates incorporation into the amylosome. While we have a theoretical framework by
which R. bromii assembles via dockerins, the nature of the discrete interactions between amylosome
components and molecular features of these proteins are unknown, preventing a mechanistic understanding of
how R. bromii degrades RS. I have solved the crystal structures of domain 1 and a close homolog of domain 2
of Doc20 to reveal that these are starch-binding domains. Despite these data being informative of the domains
of Doc20 in isolation, how the starch-binding capabilities of Doc20 may be influenced by the linker and how
these domains interact are unknown. I discovered that Doc20 binds to Sca5, a cell wall-anchored protein that
has two starch-binding domains. I aim to structurally analyze Doc20’s binding interface with Sca5 and define
Doc20’s interaction network with other amylosome proteins to understand how Doc20 contributes to the
amylosome. In some multiprotein systems that employ a dockerin-mediated protein interaction network, flexible
linkers of dockerin-containing proteins contract after binding to their target protein. I aim to characterize the
molecular dynamics of the linker region that separates domains 1 and 2 of Doc20 by using small angle x-ray
scattering (SAXS) and solve the crystal structure of the Doc20-Sca5 complex. I also aim to elucidate the
protein interaction network of Doc20 over time. My expected outcome is to create a temporal, molecular-scale
map of the starch-binding network of proteins that interact with the abundant amylosome protein Doc20. These
results are expected to have a positive impact as they will uncover the biochemical details of Doc20 within the
context of the amylosome which will provide essential insight into RS degradation by gut bacteria.

## Key facts

- **NIH application ID:** 10143381
- **Project number:** 1F31GM137488-01A1
- **Recipient organization:** UNIVERSITY OF MICHIGAN AT ANN ARBOR
- **Principal Investigator:** Filipe Muniz Cerqueira
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $39,636
- **Award type:** 1
- **Project period:** 2021-07-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10143381

## Citation

> US National Institutes of Health, RePORTER application 10143381, Uncovering Biochemical Features of Resistant Starch Degradation by R. bromii (1F31GM137488-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10143381. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*