Related Experiment Video
Updated: Aug 6, 2026
11:34
Investigating Receptor-ligand Systems of the Cellulosome with AFM-based Single-molecule Force Spectroscopy
Published on: December 20, 2013
AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts
Christine Minor1,2, Allen Takayesu1,2, Mark A Arbing2,3
1Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA.
Mbio
|July 23, 2026
Summary
Cellulosomes, enzyme complexes for breaking down plant matter, are more common and diverse in the human gut than previously thought. Structural analysis revealed new Ruminococcus species and cellulosome types, highlighting their importance in the gut microbiome.
Area of Science:
- Microbiology
- Structural Biology
- Bioinformatics
Background:
- Cellulosomes are crucial for degrading plant polysaccharides but were considered rare in the human gut.
- Sequence-based methods often fail to detect diverse cellulosome-producing bacteria due to sequence divergence.
Purpose of the Study:
- To investigate the prevalence and diversity of cellulosomes in human gut Ruminococcus species.
- To leverage structural proteomics to identify novel cellulosome architectures and producers.
Main Methods:
- Proteome-scale AlphaFold2 structural predictions were used to identify putative cellulosome-producing Ruminococcus species.
- Structure-based clustering was employed to analyze novel cohesin families and cellulosome architectures.
- Experimental validation was combined with computational predictions.
Main Results:
- A significantly expanded set of Ruminococcus species, including previously unrecognized symbionts, were identified as putative cellulosome producers.
- Novel cohesin families with conserved folds despite sequence divergence were discovered, defining distinct cellulosome architectures.
- Ruminococcus species possess elaborate cellulosomes, some invisible to sequence-based annotation, and others enriched in starch-degrading enzymes.
Conclusions:
- Ruminococcal cellulosomes are more prevalent and diverse in the human gut than previously understood.
- Structural proteomics is a powerful tool for uncovering deeply divergent functional systems like cellulosomes.
- These findings redefine the distribution and evolution of cellulosomes in gut microbes and their role in dietary substrate degradation.
Related Concept Videos
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
01:27Microbiota of the Large Intestine
The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...
01:24Bacterial Phylum Tenericutes
The phylum Tenericutes, which includes the single class Mollicutes, comprises bacteria that lack cell walls. The term "Mollicutes" derives from the Latin word mollis, meaning "soft." These organisms are among the smallest known and are commonly referred to as mycoplasmas due to the prominence of the genus Mycoplasma, which includes well-known human pathogens. Despite their inability to stain gram-positively (a result of their lack of cell walls), mycoplasmas are phylogenetically related to the...
01:26Bacterial Phylum Bacteroidota
The phylum Bacteroidota includes over 700 species classified into four primary orders: Bacteroidales, Cytophagales, Flavobacteriales, and Sphingobacteriales. These gram-negative, non-sporulating rods exhibit saccharolytic capabilities and can be aerobic or fermentative, encompassing obligate aerobes, facultative aerobes, and obligate anaerobes. Many species display gliding motility, though some are nonmotile or use flagella. The genus Bacteroides is well-studied due to its significant role in...
01:26Bacterial Phylum Proteobacteria
Proteobacteria, one of the largest and most diverse bacterial phyla, encompasses a wide range of Gram-negative bacteria distinguished by their outer membrane composed of lipopolysaccharides. These microorganisms exhibit various metabolic capabilities, including phototrophy, chemolithotrophy, and heterotrophy, and thrive in diverse environments from soil to aquatic systems and host-associated niches. The phylum is divided into six classes: Alphaproteobacteria, Betaproteobacteria,...
01:27Bacterial Phylum Firmicutes
Firmicutes is a diverse phylum of Gram-positive bacteria characterized by a low GC content in their genomes. This phylum includes organisms with monoderm or diderm cell envelopes, highlighting a complex evolutionary history. Firmicutes comprises several major orders, including Lactobacillales, Clostridiales, and Bacillales, which exhibit remarkable diversity in their morphology, metabolism, and ecological roles.The order Lactobacillales includes lactic acid bacteria, which are fermentative...