Sulfur source-driven global remodeling of gene expression in the fuel-biodesulfurizing Rhodococcus qingshengii IGTS8

Abstract

ABSTRACT Recent proteomics and metabolomics studies have confirmed the significance of understanding the fuel biodesulfurization phenotype at a global scale beyond the desulfurization 4S pathway. To reveal the transcriptomic adaptations in the model strain Rhodococcus qingshengii IGTS8 under biodesulfurization conditions, we conducted a time series comparative RNA-seq study using cultures of IGTS8 grown on either dibenzothiophene (DBT) or MgSO4 as the sulfur source. The RNA-seq data revealed many differentially expressed genes (DEGs) depending on the sulfur source and growth phase, and the strongest transcriptomic response was evident during the late-log phase. In total, 6,690 transcripts were detected in the DBT and MgSO4 cultures, representing 99.5% of the total protein-coding genes. A substantial fraction of the DEGs encodes ABC-type transporters and hypothetical proteins. In the DBT culture, 623 DEGs were upregulated, and 587 DEGs were downregulated. Generally, the DEGs covered key physiological processes, such as stress response, regulation of gene expression, uptake of nutrients, metabolism of lipids, amino acids, carbohydrates, proteins, nucleotides, cell division, and cell wall biosynthesis/degradation. While genes of carbohydrate metabolism were mostly downregulated in the DBT culture, those encoding amino acid and fatty acid degradation, as well as energy conservation, were upregulated. Moreover, genes encoding mobile genetic elements, C1 metabolism enzymes, carbonic anhydrase, and nitrile hydratase were upregulated under biodesulfurization conditions. In contrast, dihydrofolate reductase was strongly downregulated. The growth phase-dependent transcriptomic rearrangements under biodesulfurization conditions appear to prioritize cellular homeostasis and protection rather than proliferation. IMPORTANCE Commercial application of fuel biodesulfurization requires exceptionally robust and catalytically active desulfurizing microbes that can tolerate and sustain activity under the harsh operational conditions in oil refineries. It is generally accepted that naturally occurring bacteria may not meet these industrial requirements. Therefore, synthetic biology and metabolic engineering hold promise. However, a thorough understanding of the physiology, metabolism, and stress response of fuel-desulfurizing bacteria, which is currently lacking, is key toward further developments in this field. Considering these knowledge gaps, our findings provide mechanistic insights into the transcriptional responses of the reference biodesulfurizing strain Rhodococcus qingshengii IGTS8, which, when integrated together with our recently reported proteomics and metabolomics data, enable a multifaceted and deeper understanding of the biodesulfurization phenotype, facilitating rational design of more efficient recombinant biodesulfurizers. Hence, this study represents a step forward toward developing a commercially viable fuel biodesulfurization process. Commercial application of fuel biodesulfurization requires exceptionally robust and catalytically active desulfurizing microbes that can tolerate and sustain activity under the harsh operational conditions in oil refineries. It is generally accepted that naturally occurring bacteria may not meet these industrial requirements. Therefore, synthetic biology and metabolic engineering hold promise. However, a thorough understanding of the physiology, metabolism, and stress response of fuel-desulfurizing bacteria, which is currently lacking, is key toward further developments in this field. Considering these knowledge gaps, our findings provide mechanistic insights into the transcriptional responses of the reference biodesulfurizing strain Rhodococcus qingshengii IGTS8, which, when integrated together with our recently reported proteomics and metabolomics data, enable a multifaceted and deeper understanding of the biodesulfurization phenotype, facilitating rational design of more efficient recombinant biodesulfurizers. Hence, this study represents a step forward toward developing a commercially viable fuel biodesulfurization process.