Transcriptomic Analysis Reveals Reduced Inorganic Sulfur Compound Oxidation Mechanism in Acidithiobacillus ferriphilus

Abstract

A new Acidithiobacillus sp. strain Acidithiobacillus ferriphilus (A. ferriphilus) SCUT-1 was identified, which belongs to the group IV Fe(II)-oxidizing acidithiobacilli. The genome of A. ferriphilus SCUT-1 was sequenced and assembled, and the genes related to sulfur metabolism were identified. Gene expression profiles of the strain cultured in Fe²⁺, S⁰, and FeS₂ medium were compared (FeS₂/Fe²⁺, S⁰/Fe²⁺, and FeS₂/S⁰) in order to identify the genes involved in RISC (reduced inorganic sulfur compound) and ferrous iron (Fe²⁺) oxidation in A. ferriphilus SCUT-1, with the method of transcriptome reconstruction based on RNA-Seq and genome-guided transcriptome assembly. The soxY-Z-B genes encoding sulfur oxidation proteins, the soe gene cluster encoding sulfite oxidation complex, the hdr gene cluster involved in encoding HDR complex and sulfur transfer proteins, and the cyoA-B-C-D gene cluster encoding bo₃ oxidase were were significantly up-regulated in sulfur-containing media, suggesting their engagement in reduced sulfur oxidation in A. ferriphilus SCUT-1. Based on the differentially expressed genes and the putative genes predicted from the genome sequence, the RISC oxidation model and the genes involved in ferrous iron oxidation in A. ferriphilus SCUT-1 were preliminarily elucidated, which helps to interpret the oxidation mechanism of RISC and Fe²⁺ in acidithiobacilli.