Functional characterization of the transcription regulator WhiB1 from Gordonia sp. IITR100

Regulation of sulfur starvation-induced proteins

The application of environmentally friendly biological desulfurization (BDS) methods for treating organic sulfur offers significant potential to enhance the utilization of organic sulfur, reduce waste generation, and mitigate environmental harm. Several strains, including Escherichia coli, Rhodococcus erythropolis, and Mycobacterium tuberculosis, have been studied for their sulfur metabolic pathways and regulatory proteins involved in BDS. However, the current understanding of these regulatory mechanisms remains limited. This review outlines the role played by sulfur transport, acquisition and assimilation during sulfur metabolism and biosulfuration in response to sulfur starvation. In addition, we outline the involvement of sulfur starvation-inducible proteins in the L-methionine biosynthetic system. We hope to provide initial insights into the regulation of sulfur starvation-induced proteins. By exploring sulfur metabolism regulatory proteins, this review aims to offer valuable insights for the industrial application of biodesulfurization and unlock new possibilities for future research in this field.

Biodesulfurization enhancement via targeted re-insertion of the flavin reductase dszD in the genome of the model strain Rhodococcus qingshengii IGTS8

Biodesulfurization (BDS) has emerged as an alternative to the excessively costly hydrodesulfurization of recalcitrant heterocyclic sulfur compounds, such as dibenzothiophene (DBT) and its derivatives. The model desulfurizing strain Rhodococcus qingshengii IGTS8 is responsible for the removal of sulfur through the 4S metabolic pathway, operating through a plasmid-borne dszABC operon, as well as the chromosomal gene for the flavin reductase, d szD. However, naturally occurring biocatalysts do not exhibit the required BDS activity to be useful for industrial applications and for this reason, genetic modifications are currently being explored. Here, we constructed a genetically modified R. qingshengii IGTS8 strain, which carries an additional copy of the flavin reductase gene dszD under the control of the rhodococcal promoter P kap1 , inserted in the neutral chromosomal genetic locus crtI. We conducted a comparative study of the growth and biodesulfurization capabilities of P kap1 -dszD, wild-type and crtIΔ strains, grown on different types and concentrations of carbon and sulfur sources. A significant enhancement of biodesulfurization activity, maximum calculated biomass, and dszD transcript levels in the presence of DBT as the sole sulfur source was achieved for the P kap1 -dszD strain paving the way for further studies that could lead to a more viable commercial biodesulfurization process.

Genetic and metabolic engineering approaches for enhanced biodesulfurization of petroleum fractions

Sulfur, an abundant component of crude oil, causes severe damage to the environment, poses risks to human health, and poisons the catalysts used in combustion engines. Hydrodesulfurization, the conventionally used method, is not sufficient to remove thiophenes like dibenzothiophene (DBT) and other aromatic heterocyclic compounds. The push for "ultra-clean" fuels, with sulfur content less than 15 ppm, drives the need for deep desulfurization. Thus, in conjunction with hydrodesulfurization, efficient and eco-friendly methods of deep desulfurization, like biodesulfurization, are desirable. In biodesulfurization, naturally desulfurizing microorganisms are used, with genetic engineering and biotechnology, to reduce the sulfur content of crude oil to below 15 ppm. In this review, we describe genetic and metabolic engineering approaches reported to date to develop more efficient methods to carry out biodesulfurization, making it a practically applicable reality.

Interplay between Sulfur Assimilation and Biodesulfurization Activity in Rhodococcus qingshengii IGTS8: Insights into a Regulatory Role of the Reverse Transsulfuration Pathway

Biodesulfurization is a process that selectively removes sulfur from dibenzothiophene and its derivatives. Several natural biocatalysts harboring the highly conserved desulfurization operon dszABC, which is significantly repressed by methionine, cysteine, and inorganic sulfate, have been isolated. However, the available information on the metabolic regulation of gene expression is still limited. In this study, scarless knockouts of the reverse transsulfuration pathway enzyme genes cbs and metB were constructed in the desulfurizing strain Rhodococcus sp. strain IGTS8. We provide sequence analyses and report the enzymes' involvement in the sulfate- and methionine-dependent repression of biodesulfurization activity. Sulfate addition in the bacterial culture did not repress the desulfurization activity of the Δcbs strain, whereas deletion of metB promoted a significant biodesulfurization activity for sulfate-based growth and an even higher desulfurization activity for methionine-grown cells. In contrast, growth on cysteine completely repressed the desulfurization activity of all strains. Transcript level comparison uncovered a positive effect of cbs and metB gene deletions on dsz gene expression in the presence of sulfate and methionine, but not cysteine, offering insights into a critical role of cystathionine β-synthase (CβS) and MetB in desulfurization activity regulation. IMPORTANCE Precise genome editing of the model biocatalyst Rhodococcus qingshengii IGTS8 was performed for the first time, more than 3 decades after its initial discovery. We thus gained insight into the regulation of dsz gene expression and biocatalyst activity, depending on the presence of two reverse transsulfuration enzymes, CβS and MetB. Moreover, we observed an enhancement of biodesulfurization capability in the presence of otherwise repressive sulfur sources, such as sulfate and l-methionine. The interconnection of cellular sulfur assimilation strategies was revealed and validated.

Characterization of a dszEABC operon providing fast growth on dibenzothiophene and construction of broad-host-range biodesulfurization catalysts

A new operon for biodesulfurization (BDS) of dibenzothiophene and derivatives has been isolated from a metagenomic library made from oil-contaminated soil, by selecting growth of E. coli on DBT as the sulfur source. This operon is similar to a dszEABC operon also isolated by metagenomic functional screening but exhibited substantial differences: (i) the new fosmid provides much faster growth on DBT; (ii) associated dszEABC genes can be expressed without the need of heterologous expression from the vector promoter; and (iii) monooxygenases encoded in the fosmid cannot oxidize indole to produce indigo. We show how expression of the new dszEABC operon is regulated by the sulfur source, being induced under sulfur-limiting conditions. Its transcription is activated by DszR, a type IV activator οf σ^N -dependent promoters. DszR is coded in a dszHR operon, whose transcription is in turn regulated by sulfur and presumably activated by the global regulator of sulfur metabolism CysB. Expression of dszH is essential for production of active DszR, although it is not involved in sulfur sensing or regulation. Two broad-host-range DBT biodesulfurization catalysts have been constructed and shown to provide DBT biodesulfurization capability to three Pseudomonas strains, displaying desirable characteristics for biocatalysts to be used in BDS processes.