Abstract
DNA N6-methyladenine (6mA) modification is widespread in organisms and plays an important functional role in the regulation of cellular processes. As a model organism in biohydrometallurgy, Acidithiobacillus ferrooxidans can obtain energy from the oxidation of ferrous iron (Fe2+) and various reduced inorganic sulfides (RISCs) under acidic conditions. To determine the linkage between genomic DNA methylation and the switching between the two oxidative metabolic pathways in A. ferrooxidans, the 6mA landscape in the genome of A. ferrooxidans cultured under different conditions was evaluated by using 6mA-IP-seq. A total of 214 and 47 high-confidence peaks of 6mA were identified under the Fe2+ and RISCs oxidizing conditions, respectively (P<10−5), suggesting that genomic methylation was greater under Fe2+ oxidizing conditions. 6mA experienced a decline at the transcription start site (TSS) and occurs frequently in gene bodies under both oxidizing conditions. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that 7 KEGG pathways were mapped into and most of the differentially methylated genes were enriched in oxidative phosphorylation and metabolic pathways. Fourteen genes were selected for studying the effect of differences in methylation on mRNA expression. Thirteen genes, excluding petA-1, demonstrated a decrease in mRNA expression as methylation levels increased. Overall, the 6mA methylation enrichment patterns are similar under two conditions but show differences in the enriched pathways. The phenomenon of upregulated gene methylation levels coupled with downregulated expression suggests a potential association between the regulation mechanisms of 6mA and the Fe2+ and RISCs oxidation pathways.
Funder
National Key Research and Development program Foundation of China
National Natural Science Foundation of China
Publisher
Public Library of Science (PLoS)
Reference45 articles.
1. Acidithiobacillus ferrooxidans.;R Quatrini;Trends in Microbiology,2019
2. Preservation of Acidithiobacillus ferrooxidans;Y Yang;Journal of Central South University (Science and Technology),2006
3. Bioleaching of rare-earth elements from phosphate rock using Acidithiobacillus ferrooxidans;Y Tian;Letters in Applied Microbiology,2022
4. Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans;R Quatrini;Bmc Genomics,2009
5. Differential expression of two bc1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation.;P Bruscella;Microbiology-Sgm,2007