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Kaçar, Betül

Publications and source records attributed to Kaçar, Betül.

4 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molybdenum in basalt-hosted seafloor hydrothermal systems: Experimental, theoretical, and field sampling approaches

Here, seafloor hydrothermal vents represent potential sources of Mo and other biologically relevant transition metals to the global ocean, complementing continental runoff. Here, we use a combination of experimental, theoretical, and field-sampling approaches to investigate the behavior of Mo in basalt-hosted seafloor hydrothermal systems to provide insight into the processes controlling Mo concentrations in hydrothermal fluids and to derive estimates of vent fluid Mo concentrations and fluxes. Results of this study demonstrate that reaction fluids generated from 350°C, 500 bar hydrothermal basalt alteration experiments contain 775–801 nmol/kg Mo and are thus comparable to a recently collected time series of natural seafloor vent fluids that contained 200–220 nmol/kg Mo at 302°C and 29–30 nmol/kg at 281–282°C (Evans et al., 2023). Synchrotron-based analyses of experimentally altered basalt produced in this study and additional natural samples of altered oceanic crust originally collected from Pito Deep Rift reveal the presence of Mo-rich particles consistent with trace molybdenite. Comparisons of Mo:Cu ratios in natural vent fluids and near-vent sediment trap samples from Main Endeavour Field indicate that vent fluid Mo is readily incorporated into buoyant plume particles and advected out of the near-vent field, analogous to previous mass balance studies of Cu in this region. Thermodynamic calculations of molybdenite solubility in the context of mineral-buffered hydrothermal fluids and comparisons with natural and experimental hydrothermal fluids suggest that high-temperature vent fluids contain 30–1500 nmol/kg Mo. While a minor component of the modern Mo budget, hydrothermal Mo fluxes are estimated to have constituted 0.3–200× the contemporaneous continental weathering fluxes prior to the ~2.4 Ga ago “Great Oxidation Event” and widespread oxidative continental weathering. Overall, identification of hydrothermal vents as a source of Mo-rich plume particles with potential for dispersal into the wider marine environment has significant implications for hypotheses regarding the co-evolution of Life and Earth’s environments, specifically the form and availability of Mo in anoxic Archean-Eon oceans, where Mo-dependent enzymatic pathways are thought to have emerged and subsequently evolved.

58 GEOSCIENCES↗