Food Science and Technology Department
First Advisor
Dr. Yanbin Yin
Date of this Version
7-2023
Abstract
Cellulosomes are large multi-enzyme complexes encoded in the genomes of some microorganisms. Cellulosomes can degrade plant cell wall celluloses, commonly found in compost soils, forest floors and dietary fibers of farm animals. The hallmarks of cellulosome complexes are cohesins that form a large scaffoldin protein and dockerins that interact with cohesin to dock enzymes onto the scaffoldin. The dockerin-containing proteins often contain Carbohydrate Active Enzymes (CAZyme) domains, predominantly the cellulases (e.g., GH48 and GH9 enzymes), which enable them to break down celluloses. A fascinating question is, has Nature also evolved other similar protein complexes that target other types of complex carbohydrates? Only one cellulosome-containing bacterium (Ruminoccocus champallensis) has been characterized in the human gut microbiome. Existing research also suggests that due to diet differences amongst different human populations on different continents, the composition of the human gut microbiome differs. Recently, a cellulosome-like complex (named “Amylosome”) that degrades resistant starch instead of cellulose was identified in the human gut bacterium, Ruminococcus bromii. This sparks the idea that there could possibly be other gut microbes that possess the complex but encode for different CAZymes that enable them to degrade other complex carbohydrates. Thus, the central hypothesis of our study is that cohesin-dockerin interactions are prevalent in human, animal and other gut microbiomes. We developed a bioinformatic pipeline that enabled us to mine large and diverse gut microbiome databases using cellulosomal hallmark modules and domains such as cohesins, dockerins and CAZymes. We also searched for these cellulosome-like systems in (pro)phage metagenome assembled genomes (MAGs) and isolate genomes of various environmental microbiomes. Our main findings include: (1) (pro)phage genomes of animal gut microbiomes also encode dockerins and cohesins, (2) microbiomes of African population has higher percentages of MAGs with dockerins and cohesins than microbiomes of other human populations, and (3) a putative cellulosome-like system from the human gut Anaeromassilibacillus bacteria contains two scaffoldins consisting of multiple cohesin repeats and CBMs, likely for host glycan degradation.
Advisor: Yanbin Yin
Comments
A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Food Science and Technology, Under the Supervision of Professor Yanbin Yin. Lincoln, Nebraska: July 2023
Copyright © 2023 Jerry Elorm Akresi