Mapping Microhabitats: Metabolome Informed Proteome Imaging of Lignocellulose Decomposition by a Naturally Evolved Microbial Consortium
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ABSTRACT:
INSTRUMENT(S): Q Exactive Plus
ORGANISM(S): Environmental Samples <bacteria> (ncbitaxon:48479)
SUBMITTER: 
Kristin E. Burnum-Johnson
PROVIDER: MSV000091701 | MassIVE | Wed Apr 12 20:33:00 BST 2023
REPOSITORIES: MassIVE
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Project description:Lignocellulose Biomass Degradation by microbial consortium
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Project description:Spatial omics are increasingly "fused" with classical biomedical imaging modalities to complement them with spatially-resolved molecular profiling, enabling deeper understanding of the biochemical basis of health and diesease. Before the multimodal information can be fused, all contributing imaging data must be spatially aligned through a process called coregistration, which remains a challenge. Here we present a multimodal coregistration framework with great genericity and accuracy for spatial omics data. Specifically, an original dimension reduction algorithm "PseudoRep" is used to bridge cross-modal gaps: PseudoRep can generate a single-channel representation of the highly multiplexed molecular image from spatial omics and ensure that the resulting representation appears "pseudo-unimodal" to the image from the other modality. Then, a Deep Learning-based transformation algorithm "DeepReg" is adopted to accurately model nonlinear tissue deformations due to anatomical variations or sample manipulations. Our method demonstrated its versatility by coregistering mass spectrometry imaging-mediated spatial metabolomics data with diverse modalities (magnetic resonance imaging, brain atlas, microscopy, and spatial transcriptomics) and reduced 38\%\textemdash69\% of coregistration errors compared to existing methods. Notably, we open-source a toolbox to implement both the coregistration and its downstream tasks (co-expression analysis, anatomical annotation, and pansharpening), which is expected to greatly facilitate the democratization of multimodal fusion studies in the spatial omics community.
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Project description:BackgroundThe biomanufacturing of D-glucaric acid has attracted increasing interest because it is one of the top value-added chemicals produced from biomass. Saccharomyces cerevisiae is regarded as an excellent host for D-glucaric acid production.ResultsThe opi1 gene was knocked out because of its negative regulation on myo-inositol synthesis, which is the limiting step of D-glucaric acid production by S. cerevisiae. We then constructed the biosynthesis pathway of D-glucaric acid in S. cerevisiae INVSc1 opi1Δ and obtained two engineered strains, LGA-1 and LGA-C, producing record-breaking titers of D-glucaric acid: 9.53 ± 0.46 g/L and 11.21 ± 0.63 g/L D-glucaric acid from 30 g/L glucose and 10.8 g/L myo-inositol in fed-batch fermentation mode, respectively. However, LGA-1 was preferable because of its genetic stability and its superior performance in practical applications. There have been no reports on D-glucaric acid production from lignocellulose. Therefore, the biorefinery processes, including separated hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF) and consolidated bioprocessing (CBP) were investigated and compared. CBP using an artificial microbial consortium composed of Trichoderma reesei (T. reesei) Rut-C30 and S. cerevisiae LGA-1 was found to have relatively high D-glucaric acid titers and yields after 7 d of fermentation, 0.54 ± 0.12 g/L D-glucaric acid from 15 g/L Avicel and 0.45 ± 0.06 g/L D-glucaric acid from 15 g/L steam-exploded corn stover (SECS), respectively. In an attempt to design the microbial consortium for more efficient CBP, the team consisting of T. reesei Rut-C30 and S. cerevisiae LGA-1 was found to be the best, with excellent work distribution and collaboration.ConclusionsTwo engineered S. cerevisiae strains, LGA-1 and LGA-C, with high titers of D-glucaric acid were obtained. This indicated that S. cerevisiae INVSc1 is an excellent host for D-glucaric acid production. Lignocellulose is a preferable substrate over myo-inositol. SHF, SSF, and CBP were studied, and CBP using an artificial microbial consortium of T. reesei Rut-C30 and S. cerevisiae LGA-1 was found to be promising because of its relatively high titer and yield. T. reesei Rut-C30 and S. cerevisiae LGA-1were proven to be the best teammates for CBP. Further work should be done to improve the efficiency of this microbial consortium for D-glucaric acid production from lignocellulose.
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2019-11-18 | PXD015234 | Pride
Project description:BackgroundLactobacillus plantarum is an attractive candidate for metabolic engineering towards bioprocessing of lignocellulosic biomass to ethanol or polylactic acid, as its natural characteristics include high ethanol and acid tolerance and the ability to metabolize the two major polysaccharide constituents of lignocellulolytic biomass (pentoses and hexoses). We recently engineered L. plantarum via separate introduction of a potent cellulase and xylanase, thereby creating two different L. plantarum strains. We used these strains as a combined cell-consortium for synergistic degradation of cellulosic biomass.ResultsTo optimize enzymatic degradation, we applied the cell-consortium approach to assess the significance of enzyme localization by comparing three enzymatic paradigms prevalent in nature: (i) a secreted enzymes system, (ii) enzymes anchored to the bacterial cell surface and (iii) enzymes integrated into cellulosome complexes. The construction of the three paradigmatic systems involved the division of the production and organization of the enzymes and scaffold proteins into different strains of L. plantarum. The spatial differentiation of the components of the enzymatic systems alleviated the load on the cell machinery of the different bacterial strains. Active designer cellulosomes containing a xylanase and a cellulase were thus assembled on L. plantarum cells by co-culturing three distinct engineered strains of the bacterium: two helper strains for enzyme secretion and one producing only the anchored scaffoldin. Alternatively, the two enzymes were anchored separately to the cell wall. The secreted enzyme consortium appeared to have a slight advantage over the designer cellulosome system in degrading the hypochlorite pretreated wheat straw substrate, and both exhibited significantly higher levels of activity compared to the anchored enzyme consortium. However, the secreted enzymes appeared to be less stable than the enzymes integrated into designer cellulosomes, suggesting an advantage of the latter over longer time periods.ConclusionsBy developing the potential of L. plantarum to express lignocellulolytic enzymes and to control their functional combination and stoichiometry on the cell wall, this study provides a step forward towards optimal biomass bioprocessing and soluble fermentable sugar production. Future expansion of the preferred secreted-enzyme and designer-cellulosome systems to include additional types of enzymes will promote enhanced deconstruction of cellulosic feedstocks.
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