Biology subjects

Schittenhelm, R. B.

Publications and source records attributed to Schittenhelm, R. B..

3 recordsLinked to original sources

bioRxiv2019

Carbon monoxide dehydrogenases enhance bacterial survival by respiring atmospheric CO

Carbon monoxide (CO) is a ubiquitous atmospheric trace gas produced by natural and anthropogenic sources. Some aerobic bacteria can oxidize atmospheric CO and, collectively, they account for the net loss of ~250 teragrams of CO from the atmosphere each year. However, the physiological role, genetic basis, and ecological distribution of this process remain incompletely resolved. In this work, we addressed these knowledge gaps through culture-based and culture-independent work. We confirmed through shotgun proteomic and transcriptional analysis that the genetically tractable aerobic soil actinobacterium Mycobacterium smegmatis upregulates expression of a carbon monoxide dehydrogenase by 50-fold when exhausted for organic carbon substrates. Whole-cell biochemical assays in wild-type and mutant backgrounds confirmed that this organism aerobically respires CO, including at sub-atmospheric concentrations, using the enzyme. Contrary to current paradigms on CO oxidation, the enzyme did not support chemolithoautotrophic growth and was dispensable for CO detoxification. However, it significantly enhanced long-term survival, suggesting that atmospheric CO serves a supplemental energy source during organic carbon starvation. Phylogenetic analysis indicated that atmospheric CO oxidation is widespread and an ancestral trait of CO dehydrogenases. Homologous enzymes are encoded by 685 sequenced species of bacteria and archaea, including from seven dominant soil phyla, and we confirmed genes encoding this enzyme are abundant and expressed in terrestrial and marine environments. On this basis, we propose a new survival-centric model for the evolution of CO oxidation and conclude that, like atmospheric H2, atmospheric CO is a major energy source supporting persistence of aerobic heterotrophic bacteria in deprived or changeable environments.

microbiology↗

bioRxiv2019

The diversity of the immunogenic components of the melanoma immunopeptidome.

Antigen-recognition by CD8+ T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Recent studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of non-contiguous regions of proteins to form novel peptide antigens. Here we used high-resolution mass-spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of interferon-{gamma}. In total, we identified more than 60,000 peptides from a single patient derived cell line (LM-MEL-44) and demonstrated that interferon-{gamma} induced marked changes in the peptidome with an overlap of only [~]50% between basal and treated cells. Around 6-8% of the peptides were identified as cis-spliced peptides, and 2213 peptides (1827 linear, 386 cis-spliced peptides) were derived from known melanoma-associated antigens. These peptide antigens were equally distributed between the constitutive and interferon-{gamma} induced peptidome. We next examined additional HLA-matched patient derived cell lines to investigate how frequently these peptides were identified and found that a high proportion of both linear and spliced peptides were conserved between individual patient tumors, drawing on data amassing to over 100,000 peptide sequences from these extended data sets. Moreover, several of these peptides showed in vitro immunogenicity across multiple melanoma patients. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that can be exploited therapeutically and suggest that spliced peptides are a major new class of tumor antigens.

immunology↗

bioRxiv2019

Interaction of Plasmodium falciparum Casein kinase 1 (PfCK1) with components of host cell protein trafficking machinery.

During infection, the Plasmodium falciparum casein kinase 1 (PfCK1) is secreted to the extracellular medium and appears on the RBC membrane during trophozoite stage of development. We attempted to identify a mechanism that describes the secretion of PfCK1 and its appearance on the RBC membrane and suspected a mechanism involving multiple host proteins may be utilised. Indeed, we found that the host proteins GTPase-activating protein and Vps9 domain-containing protein (GAPVD1) and Sorting nexin 22 (SNX22), which have described functions in membrane trafficking in higher eukaryotes, consistently co-purify with PfCK1 suggesting the parasite utilises trafficking pathways previously thought to be inactive in RBCs. Further, reciprocal immunoprecipitation experiments with GAPVD1 identified parasite proteins suggestive of a recycling pathway hitherto only described in higher eukaryotes to recycle membrane proteins. Thus, we have identified components of a trafficking pathway involving parasite proteins that act in concert with host proteins which we hypothesise coordinate the trafficking of PfCK1 during infection.

microbiology↗