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Carbon catabolite repression (CCR) limits microbial utilization of lignocellulose-derived pentoses. To relieve CCR in  Clostridium beijerinckii  NCIMB 8052, we sought to downregulate catabolite control protein A (CcpA) using the M1GS ribozyme technology. A CcpA-specific ribozyme was constructed by tethering the catalytic subunit of  Escherichia coli  RNase P (M1 RNA) to a guide sequence (GS) targeting CcpA mRNA (M1GS CcpA ). As negative controls, the ribozyme M1GS CcpA–Sc  (constructed with a scrambled GS CcpA ) or the empty plasmid pMTL500E were used. With a ∼3-fold knockdown of CcpA mRNA in  C. beijerinckii  expressing M1GS CcpA  ( C. beijerinckii _M1GS CcpA ) relative to both controls, a modest enhancement in mixed-sugar utilization and solvent production was achieved. Unexpectedly,  C. beijerinckii _M1GS CcpA–Sc  produced 50% more solvent than  C. beijerinckii _pMTL500E grown on glucose + arabinose. Sequence complementarity (albeit suboptimal) suggested that M1GS CcpA–Sc  could target the mRNA encoding DNA integrity scanning protein A (DisA), an expectation that was confirmed by a 53-fold knockdown in DisA mRNA levels. Therefore, M1GS CcpA–Sc  was renamed M1GS DisA . Compared to  C. beijerinckii _M1GS CcpA  and _pMTL500E,  C. beijerinckii _M1GS DisA  exhibited a 7-fold decrease in the intracellular c-di-AMP level after 24 h of growth and a near-complete loss of viability upon exposure to DNA-damaging antibiotics. Alterations in c-di-AMP-mediated signaling and cell cycling likely culminate in a sporulation delay and the solvent production gains observed in  C. beijerinckii _M1GS DisA . Successful knockdown of the CcpA and DisA mRNAs demonstrate the feasibility of using M1GS technology as a metabolic engineering tool for increasing butanol production in  C. beijerinckii .

Ribozyme-Mediated Downregulation Uncovers DNA Integrity Scanning Protein A (DisA) as a Solventogenesis Determinant in Clostridium beijerinckii