Abstract
The microbial production of methane, methanogenesis, utilizes simple carbon substrates (1 to 2 carbons) and metabolizes them through a series of redox reactions to generate energy and assimilate carbon. Hydrogenotrophic methanogenesis uses CO2 and H2 as substrates, with many of the key enzymes in the pathway relying on nickel as a cofactor, including the protein that extracts reducing equivalents from H2, [NiFe]-hydrogenase. However, transition metals are cytotoxic at high concentrations, and cellular uptake and regulation of nickel is poorly understood in methanogens. In order to investigate which proteins may be involved in nickel transport and regulation in Methanococcus maripaludis, a model methanogen, we performed quantitative proteomics on cells grown in varying nickel concentrations. Additionally, we investigated a mutant deleted of the hypB2 gene, which has an unclear function but was hypothesized to have a role in [NiFe] hydrogenase maturation. Several proteins were identified with distinct responses to the varying nickel concentrations, as well as responding to the deletion of hypB2. Notable responses include differential abundance of transporters that are likely involved in transporting metal across the cell membrane and the S-layer protein that constitutes the S- layer (the cell envelope), during limited nickel availability, while simultaneously altering formate dehydrogenase activity in metabolic pathways and a ribosomal component potentially involved in translational processes to compensate for changing nutrient and substrate availability. Together, these responses represent an adaptive response to environmental stress (nickel limitation) and demonstrate that, the microbe can adjust its metabolism meet its bioenergetic needs.
Publication Date
8-7-2026
Document Type
Thesis
Student Type
Graduate
Degree Name
Bioinformatics (MS)
College
College of Science
Advisor
Stefan Schulze
Advisor/Committee Member
Kylie Allen
Advisor/Committee Member
Paul Craig
Recommended Citation
Thompson, Nathan, "Quantitative Proteomics of Nickel-Dependent Methanogenesis" (2026). Thesis. Rochester Institute of Technology. Accessed from
https://repository.rit.edu/theses/12753
Thompson_Nathan_Methods_supplementary_file_1.docx (16 kB)
Thompson_Nathan_Methods_supplentary_file_2.pdf (26629 kB)
Thompson_Nathan_MSFragger_MSstats_comparisons.csv (2487 kB)
Thompson_Nathan_MSstats_PTM_comparison.csv (78 kB)
Thompson_Nathan_Ursgal2_IonQuant.csv (100200 kB)
Thompson_Nathan_Ursgal2_MSstats_no100.csv (1659 kB)
Campus
RIT – Main Campus
