RuBisCO in the CPR bacteria and DPANN archaea
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ABSTRACT:
PROVIDER: PRJEB29721 | ENA |
REPOSITORIES: ENA
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Project description:Multiple studies have shown Rubisco to be subject to Lys-acetylation at various residues; however, conflicting reports exist about the biological significance of these post-translational modifications. One aspect of the Lys-acetylation that has not been addressed in plants generally, or with Rubisco specifically, is the stoichiometry at which these Lys-acetylation events occur. As a method to ascertain which Lys-acetylation sites on Arabidopsis Rubisco might be of regulatory importance, we purified Rubisco from leaves in both the day and night-time and performed independent mass-spectrometry based methods to determine the stoichiometry of Rubisco Lys-acetylation events.
2020-09-28 | PXD019268 | Pride
Project description:Chromosome segregation is a vital process for all organisms. The mechanisms underpinning chromosomal partitioning in the archaeal domain remain elusive. Our group has identified the first chromosome segregation system in thermophilic archaea. Sulfolobus solfataricus partition system consists of SegA, an orthologue of bacterial Walker-type ParA proteins; SegB, an archaea-specific DNA binding protein and a cis-acting DNA region. ChIP-seq experiments disclosed multiple SegB binding sites scattered over the chromosome and revealed a novel DNA binding motif.
2025-06-25 | GSE169604 | GEO
Project description:Rubisco is the main entry point of inorganic carbon into the biosphere and a central player in the global carbon system. Its relatively low catalytic constant as well as its tendency to also accept O2 as a substrate have made it a common target of enzyme engineering. We have developed an enzyme engineering and screening platform for Rubisco using the model cyanobacterium Synechocystis sp. PCC 6803. Starting with the Form II Rubisco from Gallionella, we first show that the enzyme can replace the native Form I Rubisco in Synechocystis and that growth rates become sensitive to CO2 and O2 levels. We address the challenge of designing a zero-shot input library, without prior experimental knowledge, by coupling the phylogenetically-guided model EVmutation with “in silico evolution”. Starting with this targeted mutagenesis library, we used competitive growth coupled to deep sequencing to compare the properties of Rubisco protein variants under different cultivation conditions. We identified an amino acid exchange which increased the thermostability of Gallionella Rubisco and conveyed resilience to detrimental exchanges. The establishment of this platform is a first step towards high-throughput screening of Rubisco variants in Synechocystis and creating optimized enzyme variants to accelerate the Calvin-Benson-Bassham cycle in cyanobacteria and possibly chloroplasts. DIA proteomics was used to compare relative quantities of the native and heterologous RuBisCO, as well as the proteome at large at different gas conditions and with or without the heterologous enzyme.
2025-08-04 | PXD059631 | Pride
Project description:Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Though recently discovered, trace gas oxidation is now recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. While trace gas oxidation has been reported in nine phyla of bacteria, it was not known whether archaea also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurred during both growth and survival across a wide range of temperatures (10 to 70°C). Genomic analysis demonstrated that A. brierleyi encodes a canonical carbon monoxide dehydrogenase and, unexpectedly, four distinct [NiFe]-hydrogenases from subgroups not known to mediate aerobic H2 uptake. Quantitative proteomic analyses showed that A. brierleyi differentially produced these enzymes in response to electron donor and acceptor availability. A previously unidentified group 1 [NiFe]-hydrogenase, with a unique genetic arrangement, is constitutively expressed and upregulated during stationary phase and aerobic hydrogenotrophic growth. Another archaeon, Metallosphaera sedula, was also found to oxidize atmospheric H2. These results suggest that trace gas oxidation is a common trait of aerobic archaea, which likely plays a role in their survival and niche expansion, including during dispersal through temperate environments. These findings also demonstrate that atmospheric H2 consumption is a cross-domain phenomenon, suggesting an ancient origin of this trait, and identify previously unknown microbial and enzymatic sinks of atmospheric H2 and CO.
2024-02-26 | PXD040286 | Pride