A genomic analysis reveals the diversity of cellulosome displaying bacteria

Christine M Minor; Allen Takayesu; Sung Min Ha; Lukasz Salwinski; Michael R Sawaya; Matteo Pellegrini; Robert T Clubb

doi:10.3389/fmicb.2024.1473396

A genomic analysis reveals the diversity of cellulosome displaying bacteria

Front Microbiol. 2024 Oct 30:15:1473396. doi: 10.3389/fmicb.2024.1473396. eCollection 2024.

Authors

Christine M Minor^#^{1

2}, Allen Takayesu^#^{1

2}, Sung Min Ha³, Lukasz Salwinski⁴, Michael R Sawaya¹, Matteo Pellegrini⁴, Robert T Clubb^{1

2

5}

Affiliations

¹ Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States.
² UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, United States.
³ Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States.
⁴ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.
⁵ Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States.

^# Contributed equally.

Abstract

Introduction: Several species of cellulolytic bacteria display cellulosomes, massive multi-cellulase containing complexes that degrade lignocellulosic plant biomass (LCB). A greater understanding of cellulosome structure and enzyme content could facilitate the development of new microbial-based methods to produce renewable chemicals and materials.

Methods: To identify novel cellulosome-displaying microbes we searched 305,693 sequenced bacterial genomes for genes encoding cellulosome proteins; dockerin-fused glycohydrolases (DocGHs) and cohesin domain containing scaffoldins.

Results and discussion: This analysis identified 33 bacterial species with the genomic capacity to produce cellulosomes, including 10 species not previously reported to produce these complexes, such as Acetivibrio mesophilus. Cellulosome-producing bacteria primarily originate from the Acetivibrio, Ruminococcus, Ruminiclostridium, and Clostridium genera. A rigorous analysis of their enzyme, scaffoldin, dockerin, and cohesin content reveals phylogenetically conserved features. Based on the presence of a high number of genes encoding both scaffoldins and dockerin-fused GHs, the cellulosomes in Acetivibrio and Ruminococcus bacteria possess complex architectures that are populated with a large number of distinct LCB degrading GH enzymes. Their complex cellulosomes are distinguishable by their mechanism of attachment to the cell wall, the structures of their primary scaffoldins, and by how they are transcriptionally regulated. In contrast, bacteria in the Ruminiclostridium and Clostridium genera produce 'simple' cellulosomes that are constructed from only a few types of scaffoldins that based on their distinct complement of GH enzymes are predicted to exhibit high and low cellulolytic activity, respectively. Collectively, the results of this study reveal conserved and divergent architectural features in bacterial cellulosomes that could be useful in guiding ongoing efforts to harness their cellulolytic activities for bio-based chemical and materials production.

Keywords: AlphaFold2; Cellulosome; biomass; cohesin; comparative genomics; dockerin; lignocellulose.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This material is based upon work supported by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research program under Award Number DE-FC02-02ER63421. We also acknowledge support from NIH grant R01-AI052217 (R.T.C), a Cellular and Molecular Biology training grant T32GM145388 (CM), and the UCLA Quantitative & Computational Biosciences Collaboratory for assistance.