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Regulatory response of methanogen cells to different forms of iron and sulfur

ABSTRACT: We used comparative transcriptomics to explore cellular responses to growth on pyrite (FeS2) or aqueous iron (Fe(II)) and sulfur (cysteine or sulfide). Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study. Transcriptomic data from wild type M. barkeri identified subset of genes that was significantly upregulated during grown on FeS2 versus ferrous iron and cysteine or sulfide. Several of these genes, including a membrane-bound hydrolase, alpha-keto reductases, and flavin mononucleotide-dependent flavodoxin reductases were highly conserved among known FeS2-reducing methanogens and were located in a single gene cassette. Putative enzymatically catalyzed mechanisms of FeS2 reduction are proposed for each of these enzyme systems to guide their future biochemical and biophysical study.

ORGANISM(S): Methanosarcina barkeri

PROVIDER: GSE168895 | GEO | 2022/03/13

REPOSITORIES: GEO

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Project description:(from abstract): Iron oxidation is a desirable trait of biomining microorganisms, although the mechanism is not well-understood in extreme thermoacidophiles. The complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ~2300 ORFs) provides insights into biologically catalyzed metal sulfide oxidation. Comparative genomics was used to identify pathways and proteins (in)directly involved with bioleaching. As expected, the M. sedula genome encodes genes related to autotrophic carbon fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence of hybrid quinol-cytochrome oxidase complexes. Comparisons with the mesophilic biomining bacterium Acidithiobacillus ferrooxidans ATCC 23270 indicate that the M. sedula genome encodes at least one putative rusticyanin, involved in iron oxidation. The fox gene cluster, involved in iron oxidation in the thermoacidophilic archaeon Sulfolobus metallicus, could also be identified. These iron-oxidizing components are missing from genomes of non-leaching Sulfolobales like Sulfolobus solfataricus P2 and Sulfolobus acidocaldarius DSM 639. Whole genome transcriptional response analysis showed that 88 ORFs were up-regulated 2-fold or more in M. sedula upon addition of ferrous sulfate to yeast extract-based medium; these included components of terminal oxidase clusters predicted to be involved with iron oxidation, as well as genes predicted to be involved with sulfur metabolism. Many hypothetical proteins were also differentially transcribed, indicating that aspects of the iron and sulfur metabolism of M. sedula remain to be identified and characterized. Dye flip of Mse cells includes two samples, yeast exact (YE) and yeast extract + ferrous sulfate (YEF). The first slide, Y3F5, has YE RNA labeled with cy3 and YEF RNA labeled with cy5, while the second slide, F3Y5, has YEF RNA labeled with cy3 and YE RNA labeled with cy5. YE serves as the reference condition, with the expectation that ORFs involved with Fe2+ oxidation (and SO4 metabolism) will be upregulated on YEF (log2 fold change of YE-YEF < -1).

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Regulatory response of methanogen cells to different forms of iron and sulfur

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