Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation

Saskia Tabea Baur; Anja Poehlein; Niklas Jan Renz; Stefanie Karolina Hollitzer; José David Montoya Solano; Bettina Schiel-Bengelsdorf; Rolf Daniel; Peter Dürre

doi:10.3389/fgene.2022.966643

Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation

Front Genet. 2022 Aug 11:13:966643. doi: 10.3389/fgene.2022.966643. eCollection 2022.

Authors

Saskia Tabea Baur¹, Anja Poehlein², Niklas Jan Renz¹, Stefanie Karolina Hollitzer¹, José David Montoya Solano¹, Bettina Schiel-Bengelsdorf¹, Rolf Daniel², Peter Dürre¹

Affiliations

¹ Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
² Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany.

Abstract

Solvents such as butanol are important platform chemicals and are often produced from petrochemical sources. Production of butanol and other compounds from renewable and sustainable resources can be achieved by solventogenic bacteria, such as the hyper-butanol producer Clostridium saccharoperbutylacetonicum. Its sol operon consists of the genes encoding butyraldehyde dehydrogenase, CoA transferase, and acetoacetate decarboxylase (bld, ctfA, ctfB, adc) and the gene products are involved in butanol and acetone formation. It is important to understand its regulation to further optimize the solvent production. In this study, a new long non-coding antisense transcript complementary to the complete sol operon, now called Assolrna, was identified by transcriptomic analysis and the regulatory mechanism of Assolrna was investigated. For this purpose, the promoter-exchange strain C. saccharoperbutylacetonicum ΔP _asr ::P _asr ^** was constructed. Additionally, Assolrna was expressed plasmid-based under control of the native P _asr promoter and the lactose-inducible P _bgaL promoter in both the wild type and the promoter-exchange strain. Solvent formation was strongly decreased for all strains based on C. saccharoperbutylacetonicum ΔP _asr ::P _asr ^** and growth could not be restored by plasmid-based complementation of the exchanged promoter. Interestingly, very little sol mRNA expression was detected in the strain C. saccharoperbutylacetonicum ΔP _asr ::P _asr ^** lacking Assolrna expression. Butanol titers were further increased for the overexpression strain C. saccharoperbutylacetonicum [pMTL83151_asr_P _bgaL ] compared to the wild type. These results suggest that Assolrna has a positive effect on sol operon expression. Therefore, a possible stabilization mechanism of the sol mRNA by Assolrna under physiological concentrations is proposed.

Keywords: ABE fermentation; Assolrna; Clostridium saccharoperbutylacetonicum; antisense RNA; sol operon; stabilizing antisense RNA.