Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum

) from industrial waste gases and gasified waste into value-added products using gas-fermenting microbes, namely acetogens. However, our limited understanding of gene function and metabolic regulation is hindering rational engineering of acetogen cell factories. In this work, we aimed to identify genome-wide protein-RNA interactions contributing to autotrophy in the model-acetogen Clostridium autoethanogenum by combining steady-state chemostat cultivation, functional genomics, and computational methods. We first detected limited and uncoupled transcriptional and translational regulation between autotrophy and heterotrophy. Rigorous mapping of genome-wide transcriptional architecture revealed both differential usage and signal strength of transcriptional start and termination sites between genes and growth substrates. We then used computational tools to reconstruct protein-RNA interactions for differentially regulated genes, predicting 14 trans-acting regulatory RNA-binding proteins (RBPs) involved in post-transcriptional regulation but not linked to genes key for autotrophy. Most RBPs, one of which is translationally regulated, perform RNA modifications and regulate mRNA stability while others target translation-related genes. Our work provides valuable knowledge for metabolic engineering of acetogens and potentially contributes towards understanding primordial life on Earth.