Biology subjects

Pian, B.

Publications and source records attributed to Pian, B..

6 recordsLinked to original sources

bioRxiv2024

Bio-Accelerated Weathering of Ultramafic Minerals with Gluconobacter oxydans

Ultramafic rocks are an abundant source of cations for CO2 mineralization (e.g., Mg) and elements for sustainability technologies (e.g., Ni, Cr, Mn, Co, Al). However, there is no industrially useful process for dissolving ultramafic materials to release cations for CO2 sequestration or mining them for energy-critical elements. Weathering of ultramafic rocks by rainwater, release of metal cations, and subsequent CO2 mineralization already naturally sequesters CO2 from the atmosphere, but this natural process will take thousands to hundreds of thousands of years to remove excess anthropogenic CO2, far too late to deal with global warming that will happen over the next century. Mechanical acceleration of weathering by grinding can accelerate cation release but is prohibitively expensive. In this article we show that gluconic acid-based lixiviants produced by the mineral-dissolving microbe Gluconobacter oxydans accelerate leaching of Mg2+ by 20x over deionized water, and that leaching of Mg, Mn, Fe, Co, and Ni further improves by 73% from 24 to 96 hours. At low pulp density (1%) the G. oxydans biolixiviant is only 6% more effective than gluconic acid. But, at 60% pulp density the G. oxydans biolixiviant is 3.2x more effective than just gluconic acid. We demonstrate that biolixiviants made with cellulosic hydrolysate are not significantly worse than biolixiviants made with glucose, dramatically improving the feedstock available for bioleaching. Finally, we demonstrate that we can reduce the number of carbon atoms in the biolixiviant feedstock (e.g., glucose or cellulosic hydrolysate) needed to release one Mg2+ ion and mineralize one atom of carbon from CO2 from 525 to 1.

bioengineering↗

bioRxiv2024

Direct Genome-Scale Screening of Gluconobacter oxydans B58 for Rare Earth Element Bioleaching

The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REE). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole genome knockout collection for the bioleaching microbe Gluconobacter oxydans B58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in bioleaching by up to 111% (G. oxydans {delta}GO_1598, a disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% ({delta}GO_1096, a disruption of the gene encoding the GTP-binding protein TypA). Notable changes in biolixiviant pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching by G. oxydans through targeted genetic engineering.

synthetic biology↗

bioRxiv2023

Unusual 1-3 peptidoglycan cross-links in Acetobacteriaceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains

Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position 4 of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software which can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a Sudoku transposon library, we identified a G. oxydans mutant with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.

microbiology↗

bioRxiv2023

High Efficiency Rare Earth Element Biomining with Systems Biology Guided Engineering of Gluconobacter oxydans

The global demand for critical rare earth elements (REE) is rising1 with the increase in demand for sustainable energy technologies like wind turbines2,3, electric vehicles2,3, and high efficiency lighting4. Current processes for producing REE require high energy inputs and can produce disproportionate amounts of hazardous waste. Biological methods for REE production are a promising solution to this problem. In earlier work we identified the most important genetic mechanisms contributing to the REE-bioleaching capability of Gluconobacter oxydans B585. Here we have targeted two of these mechanisms to generate a high-efficiency bio-mining strain of G. oxydans. Disruption of the phosphate-specific transport system through a clean deletion of pstS constitutively turns on the phosphate starvation response, yielding a much more acidic biolixiviant, and increasing bioleaching by up to 30%. Coupling knockout of pstS with the over-expression of the mgdh membrane-bound glucose dehydrogenase gene, results in up to 73% improvement of REE-bioleaching.

synthetic biology↗

bioRxiv2022

Genomic Characterization of Rare Earth Binding by Shewanella oneidensis

Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today1. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions2, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-13,4. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We found, among other things, that disruptions of a key regulatory component of the arc system (hptA), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes (wbpQ, wbnJ, SO_3183) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685--a capsular polysaccharide (CPS) synthesis gene--disruption which results in an up to 79% increase in biosorption and nusA--a regulatory protein--disruption which results in an up to 35% decrease in biosorption. Knockouts of glnA, pyrD, and SO_3183 increase relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Taken together, these results begin to elucidate how various genes affect the membrane chemistry of S. oneidensis and offer potential targets for improving biosorption and separation of REE.

systems biology↗

bioRxiv2021

Gluconobacter oxydans Knockout Collection Finds Improved Rare Earth Element Extraction

Rare earth elements (REE) are critical components of our technological society and essential for renewable energy technologies. Traditional thermochemical processes to extract REE from mineral ores or recycled materials are costly and environmentally harmful1, and thus more sustainable extraction methods require exploration. Bioleaching offers a promising alternative to conventional REE extraction2-4, and is already used to extract 5% of the worlds gold, and {approx} 15% of the worlds copper supply5,6. However, the performance of REE bioleaching lags far behind thermochemical processes2,7-9. Despite this, to the best of our knowledge no genetic engineering strategies have yet been used to enhance REE bioleaching, and little is known of the genetics that confer this capability. Here we build a whole genome knockout collection for Gluconobacter oxydans B58, one of the most promising organisms for REE bioleaching10, and use it to comprehensively characterize the genomics of REE bioleaching. In total, we find 304 genes that notably alter production of G. oxydans acidic biolixiviant, including 165 that hold up under statistical comparison with wild-type. The two most impactful groups of genes involved in REE bioleaching have opposing influences on acid production and REE bioleaching. Disruption of genes underlying synthesis of the cofactor pyrroloquinoline quinone (PQQ) and the PQQ-dependent membrane-bound glucose dehydrogenase all but eliminates bioleaching. In contrast, disruption of the phosphate-specific transport system accelerates acid production and enhances bioleaching. We identified 6 disruption mutants, that increase bioleaching by at least 11%. Most significantly, disruption of pstC, encoding part of the phosphate-specific transporter, pstSCAB, enhances bioleaching by 18%. Taken together, these results give a comprehensive roadmap for engineering multiple sites in the genome of G. oxydans to further increase its bioleaching efficiency.

genomics↗