Visual exoproteomics of Clostridium thermocellum during anaerobic biomass-degradation identifies functional spirosomes

Abstract

Visual proteomics enables the study of low-abundance proteins and identification of unknown complexes from heterogeneous samples by complementing high-resolution cryogenic electron microscopy (cryoEM) with external inputs on protein identity such as mass spectrometry. Using this approach, we interrogated the exoproteome of the anaerobic cellulose-degrading bacterium Clostridium thermocellum as it carried out biomass degradation. Mass spectrometry indicated a broad exoproteome composition, including cellulose degrading machinery CelA and CipA. A focus on large exoproteome assemblies revealed abundant protein filaments and pleomorphic vesicular structures. Analysis of the most abundant protein filaments yielded an [~]4 {square} resolution native structure that, aided by mass spectrometry, de novo modeling, and structural searching, was found to be the aldehyde-alcohol dehydrogenase (AdhE) spirosome. AdhE contained both NAD+ and Fe in their expected binding sites and biochemical and structural analyses of enriched spirosome preparations indicated they were functional. Altered NADH solution concentrations triggered conformational changes in the exoproteomic spirosomes, and the constituent AdhE remained capable of ethanol production. Although the basis for functional extracellular spirosome accumulation in live anaerobic C. thermocellum cultures remains unclear, their abundance in crude exoproteomes suggests their presence could influence biomass fueled C. thermocellum growth.