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At least 253 records · Page 14

The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure

Aggregation of α-synuclein is a defining molecular feature of Parkinson’s disease, Lewy body dementia, and multiple systems atrophy. Hereditary mutations in α-synuclein are linked to both Parkinson’s disease and Lewy body dementia; in particular, patients bearing the E46K disease mutation manifest a clinical picture of parkinsonism and Lewy body dementia, and E46K creates more pathogenic fibrils in vitro. Understanding the effect of these hereditary mutations on α-synuclein fibril structure is fundamental to α-synuclein biology. We therefore determined the cryo-electron microscopy (cryo-EM) structure of α-synuclein fibrils containing the hereditary E46K mutation. The 2.5-Å structure reveals a symmetric double protofilament in which the molecules adopt a vastly rearranged, lower energy fold compared to wild-type fibrils. We propose that the E46K misfolding pathway avoids electrostatic repulsion between K46 and K80, a residue pair which form the E46-K80 salt bridge in the wild-type fibril structure. We hypothesize that, under our conditions, the wild-type fold does not reach this deeper energy well of the E46K fold because the E46-K80 salt bridge diverts α-synuclein into a kinetic trap—a shallower, more accessible energy minimum. The E46K mutation apparently unlocks a more stable and pathogenic fibril structure.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering a universal and efficient platform for terpenoid synthesis in yeast

Engineering microbes for the production of valuable natural products is often hindered by the regulation of native competing metabolic networks in host. This is particularly evident in the case of terpenoid synthesis in yeast, where the canonical terpenoid precursors are tightly coupled to the biosynthesis of sterols essential for yeast viability. One way to circumvent this limitation is by engineering product pathways less connected to the host native metabolism. Here, we introduce a two-step isopentenol utilization pathway (IUP) in Saccharomyces cerevisiae to augment the native mevalonate pathway by providing a shortcut to the synthesis of the common terpenoid precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). As such, the IUP was capable of elevating the IPP/DMAPP pool by 147-fold compared with the native pathway. We further demonstrate that cofeeding isoprenol and prenol enhances geranyl diphosphate (GPP) content for monoterpene biosynthesis. More importantly, we established a synthetic three-step route for efficient synthesis of di-and tetraterpene precursor geranylgeranyl diphosphate (GGPP), circumventing the competition with farnesyl diphosphate (FPP) for sterol biosynthesis and elevating the GGPP level by 374-fold. We combine these IUP-supported precursor-forming platforms with downstream terpene synthases to harness their potential and improve the production of industrially relevant terpenoids by several fold. In conclusion, our exploration provides a universal and effective platform for supporting terpenoid synthesis in yeast.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits

Dynamic, multi-input gene regulatory networks (GRNs) are ubiquitous in nature. Multilayer CRISPR-based genetic circuits hold great promise for building GRNs akin to those found in naturally occurring biological systems. We develop an approach for creating high-performing activatable promoters that can be assembled into deep, wide, and multi-input CRISPR-activation and -interference (CRISPRa/i) GRNs. By integrating sequence-based design and in vivo screening, we engineer activatable promoters that achieve up to 1,000-fold dynamic range in an Escherichia coli-based cell-free system. These components enable CRISPRa GRNs that are six layers deep and four branches wide. We show the generalizability of the promoter engineering workflow by improving the dynamic range of the light-dependent EL222 optogenetic system from 6-fold to 34-fold. Additionally, high dynamic range promoters enable CRISPRa systems mediated by small molecules and protein–protein interactions. We apply these tools to build input-responsive CRISPRa/i GRNs, including feedback loops, logic gates, multilayer cascades, and dynamic pulse modulators. Our work provides a generalizable approach for the design of high dynamic range activatable promoters and enables classes of gene regulatory functions in cell-free systems.

42 ENGINEERING↗

Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus

Mycobacterium abscessus (Mab), a nontuberculous mycobacterial (NTM) species, is an emerging pathogen with high intrinsic drug resistance. Current standard-of-care therapy results in poor outcomes, demonstrating the urgent need to develop effective antimycobacterial regimens. Through synthetic modification of spectinomycin (SPC), we have identified a distinct structural subclass of N-ethylene linked aminomethyl SPCs (eAmSPCs) that are up to 64-fold more potent against Mab over the parent SPC. Mechanism of action and crystallography studies demonstrate that the eAmSPCs display a mode of ribosomal inhibition consistent with SPC. However, they exert their increased antimicrobial activity through enhanced accumulation, largely by circumventing efflux mechanisms. The N-ethylene linkage within this series plays a critical role in avoiding TetV-mediated efflux, as lead eAmSPC 2593 displays a mere fourfold susceptibility improvement against Mab ΔtetV, in contrast to the 64-fold increase for SPC. Even a minor shortening of the linkage by a single carbon, akin to 1st generation AmSPC 1950, results in a substantial increase in MICs and a 16-fold rise in susceptibility against Mab ΔtetV. These shifts suggest that longer linkages might modify the kinetics of drug expulsion by TetV, ultimately shifting the equilibrium towards heightened intracellular concentrations and enhanced antimicrobial efficacy. Furthermore, lead eAmSPCs were also shown to synergize with various classes of anti-Mab antibiotics and retain activity against clinical isolates and other mycobacterial strains. Encouraging pharmacokinetic profiles coupled with robust efficacy in Mab murine infection models suggest that eAmSPCs hold the potential to be developed into treatments for Mab and other NTM infections.

59 BASIC BIOLOGICAL SCIENCES↗

Partial PdAu nanoparticle embedding into TiO 2 support accentuates catalytic contributions from the Au/TiO 2 interface

Despite the broad catalytic relevance of metal–support interfaces, controlling their chemical nature, the interfacial contact perimeter (exposed to reactants), and consequently, their contributions to overall catalytic reactivity, remains challenging, as the nanoparticle and support characteristics are interdependent when catalysts are prepared by impregnation. Here, we decoupled both characteristics by using a raspberry-colloid-templating strategy that yields partially embedded PdAu nanoparticles within well-defined SiO 2 or TiO 2 supports, thereby increasing the metal–support interfacial contact compared to nonembedded catalysts that we prepared by attaching the same nanoparticles onto support surfaces. Between nonembedded PdAu/SiO 2 and PdAu/TiO 2 , we identified a support effect resulting in a 1.4-fold higher activity of PdAu/TiO 2 than PdAu/SiO 2 for benzaldehyde hydrogenation. Notably, partial nanoparticle embedding in the TiO 2 raspberry-colloid-templated support increased the metal–support interfacial perimeter and consequently, the number of Au/TiO 2 interfacial sites by 5.4-fold, which further enhanced the activity of PdAu/TiO 2 by an additional 4.1-fold. Theoretical calculations and in situ surface-sensitive desorption analyses reveal facile benzaldehyde binding at the Au/TiO 2 interface and at Pd ensembles on the nanoparticle surface, explaining the connection between the number of Au/TiO 2 interfacial sites (via the metal–support interfacial perimeter) and catalytic activity. Our results demonstrate partial nanoparticle embedding as a synthetic strategy to produce thermocatalytically stable catalysts and increase the number of catalytically active Au/TiO 2 interfacial sites to augment catalytic contributions arising from metal–support interfaces.

Lim, Kang Rui Garrick (ORCID:0000000321599844)↗

A riboswitch separated from its ribosome-binding site still regulates translation

Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.

59 BASIC BIOLOGICAL SCIENCES↗

Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene

Abstract Left-handed G-quadruplexes (LHG4s) belong to a class of recently discovered noncanonical DNA structures under the larger umbrella of G-quadruplex DNAs (G4s). The biological relevance of these structures and their ability to be targeted with classical G4 ligands is underexplored. Here, we explore whether the putative LHG4 DNA sequence from the SLC2A1 oncogene promoter maintains its left-handed characteristics upon addition of nucleotides in the 5′- and 3′-direction from its genomic context. We also investigate whether this sequence interacts with a well-established G4 binder, N-methylmesoporphyrin IX (NMM). We employed biophysical and X-ray structural studies to address these questions. Our results indicate that the sequence d[G(TGG)3TGA(TGG)4] (termed here as SLC) adopts a two-subunit, four-tetrad hybrid left-/right-handed G4 (LH/RHG4) topology. Addition of 5′-G or 5′-GG abolishes the left-handed fold in one subunit, while the addition of 3′-C or 3′-CA maintains the original fold. X-ray crystal structure analyses show that SLC maintains the same hybrid LH/RHG4 fold in the solid state and that NMM stacks onto the right-handed subunit of SLC. NMM binds to SLC with a 1:1 stoichiometry and a moderate-to-tight binding constant of 15 μM−1. This work deepens our understanding of LHG4 structures and their binding with traditional G4 ligands.

Seth, Paul↗

Formation of a simple cubic antiferromagnet through charge ordering in a double Dirac material

Following the topological classification of electronic phases, interest has grown in materials with unique electronic or magnetic properties driven by topology and interactions. Here, in this study, we report that the topologically nontrivial mixed valent intermetalllic EuPd 3 S 4 undergoes long-range charge ordering at 𝑇 𝐶⁢𝑂 = 340 K wherein 𝐽 = 7/2 Eu 2+ and Van Vleck 𝐽 = 0 Eu 3+ ions on a body-centered-cubic lattice separate into two interpenetrating simple cubic sublattices. The reduced symmetry transmutes 8-fold double Dirac states into 4-fold Dirac states and leads to a simple cubic Heisenberg antiferromagnet with G-type antiferromagnetic order for 𝑇 <⁢ 𝑇 𝑁 = 2.85⁢(6) K. While time reversal symmetry is broken, its combination with nearest neighbor lattice translation can form a nonsymmorphic symmetry preserving the 4-fold Dirac point. The application of a magnetic field yields a spin flop transition at the lowest temperatures but, as a consequence of the extreme isotropy of Eu, that phase transition turns into a cross-over at higher temperatures. Our work demonstrates how charge order modifies topology in EuPd 3 S 4 and exposes an archetypal simple cubic Heisenberg antiferromagnet.

Berry, Tanya [Johns Hopkins Univ., Baltimore, MD (↗

Towards a Deeper Fundamental Understanding of (Al,Sc)N Ferroelectric Nitrides

Density functional theory (DFT) calculations, within the virtual crystal alloy approximation, are performed, along with the development of a Landau-type model employing a symmetry-allowed analytical expression of the internal energy and having parameters determined from first principles, to investigate properties and energetics of Al1-xScxN ferroelectric nitrides in their hexagonal forms. These DFT computations and this model predict the existence of two different types of minima, namely, the fourfold-coordinated wurtzite (WZ) polar structure and a five-fold coordinated paraelectric hexagonal phase (denoted as H5), for any Sc composition up to 40%. The H5 minimum progressively becomes the lowest-energy state within hexagonal symmetry as the Sc concentration increases from 0 to 0.4. Furthermore, the model points to several key findings. Examples include the crucial role of the coupling between polarization and strains to create the WZ minimum, in addition to polar and elastic energies, and that the origin of the H5 state overcoming the WZ phase as the global minimum within hexagonal symmetry when increasing the Sc composition mostly lies in the compositional dependency of only two parameters-one linked to the polarization and another one being purely elastic in nature. Other examples are that forcing Al1-xScxN systems to have no or a weak change in lattice parameters when heating them allows us to reproduce their finite-temperature polar properties well and that a value of the axial ratio close to that of the ideal WZ structure implies a large polarization at low temperatures but not necessarily at high temperatures because of the ordered-disordered character of the temperature-induced formation of the WZ state. Such findings should allow for a better fundamental understanding of (Al,Sc)N ferroelectric nitrides, which may be used to design efficient devices having, e.g., low operating voltages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cross-Cap Defects and Fault-Tolerant Logical Gates in the Surface Code and the Honeycomb Floquet Code

We consider the Z 2 toric code, surface code, and Floquet code defined on a nonorientable surface, which can be considered as families of codes extending Shor’s nine-qubit code. We investigate the fault-tolerant logical gates of the Z 2 toric code in this setup, which corresponds to e ↔ m exchanging symmetry of the underlying Z 2 gauge theory. We find that nonorientable geometry provides a new way for the emergent symmetry to act on the code space, and discover the new realization of the fault-tolerant Hadamard gate of the two-dimensional surface code with a single cross cap connecting the vertices nonlocally along a slit, dubbed a nonorientable surface code. This Hadamard gate can be realized by a constant-depth local unitary circuit modulo nonlocality caused by a cross cap. Via folding, the nonorientable surface code can be turned into a bilayer local quantum code, where the folded cross cap is equivalent to a bilayer twist terminated on a gapped boundary and the logical Hadamard only contains local gates with intralayer couplings when being away from the cross cap, as opposed to the interlayer couplings on each site needed in the case of the folded surface code. We further obtain the complete logical Clifford gate set for a stack of nonorientable surface codes and similarly for codes defined on Klein-bottle geometries. We then construct the honeycomb Floquet code in the presence of a single cross cap, and find that the period of the sequential Pauli measurements acts as a H Z logical gate on the single logical qubit, where the cross cap enriches the dynamics compared with the orientable case. We find that the dynamics of the honeycomb Floquet code is precisely described by a condensation operator of the Z 2 gauge theory, and illustrate the exotic dynamics of our code in terms of a condensation operator supported at a nonorientable surface. Published by the American Physical Society 2024

Physics↗

Triacylglycerol, total fatty acid, and biomass accumulation of metabolically engineered energycane grown under field conditions confirms its potential as feedstock for drop‐in fuel production

Abstract Metabolic engineering for hyperaccumulation of lipids in vegetative tissues of high biomass crops promises a step change in oil yields for the production of advanced biofuels. Energycane is the ideal feedstock for this approach due to its exceptional biomass production and persistence under marginal conditions. Here, we evaluated metabolically engineered energycane with constitutive expression of the lipogenic factors WRINKLED 1 ( WRI 1), DIACYLGLYCEROL ACYLTRANSFERASE 1 ( DGAT 1), and OLEOSIN 1 ( OLE 1) for the accumulation of triacylglycerol (TAG), total fatty acid (TFA), and biomass under field conditions at the University of Florida‐IFAS experiment station near Citra, Florida. TAG and TFA accumulation were highest in leaves (up to 9.9% and 12.9% of DW, respectively), followed by juice from crushed stems, stems, and roots. TAG and TFA accumulation increased up to harvest time and correlated highest with OLE 1 and DGAT 1 expression. Biomass dry weight, TAG, and TFA content differed greatly depending on DGAT 1 and OLE 1 expression in transgenic lines with similar WRI 1 expression. Biomass did not significantly differ between WT and line L2 with DAGT 1 and OLE 1 expressed at low levels and TAG and TFA accumulating to 12‐ and 1.6‐fold that of WT leaves, respectively. In contrast, line L13, with intron‐mediated enhancement of DGAT 1 expression, displayed a 245‐ to 330‐fold increase in TAG and a 4.75‐ to 6.45‐fold increase in TFA content compared with WT leaves and a biomass reduction of 52%. These results provide the basis for developing novel feedstocks for expanding plant lipid production and point to new prospects for advanced biofuels.

59 BASIC BIOLOGICAL SCIENCES↗

Multisite Field Evaluation of Oil Accumulation and Agronomic Performance in Grain and Sweet Sorghums Engineered for Lipid Hyperaccumulation

Oil sorghum (OS) has been developed by engineering grain (TX430) and sweet (Ramada) genetic backgrounds to accumulate triacylglycerols (TAG) in vegetative tissues as an energy-dense feedstock for sustainable aviation fuel (SAF) and other biofuels. This study evaluated two TX430 OS lines (TxHO-2, TxHO-3) and two Ramada OS lines (RmHO-1, RmHO-2) alongside wild-type (WT) lines in NE and IL over 2 years (2023–2024) to quantify genotype × environment effects on agronomic performance and TAG accumulation. Across four environments, TX430 OS lines showed average TAG concentrations of 15.0 g kg −1 in leaves and 12.8 g kg −1 in stems, approximately 19-fold higher than WT. Ramada OS lines accumulated 26.1 g kg −1 in leaves and 12.3 g kg −1 in stems, approximately 25-fold and 13-fold increases over WT, respectively. OS lines in TX430 exhibited an 18% reduction in biomass (8.4 vs. 9.9 Mg ha −1 for WT), while Ramada OS lines had similar WT biomass (18.3 vs. 19.9 Mg ha −1 for WT). Among TX430 OS lines, TxHO-2 achieved the highest TAG yield (190 kg ha −1 ), while RmHO-1 led the Ramada lines (335 kg ha −1 ) due to higher biomass and similar TAG concentration. Enhanced TAG accumulation increased N, P, and K removal in TX430 lines but not in Ramada lines. Structural carbohydrate and ash concentration were unaffected. Overall, results confirm vegetative lipid accumulation as a viable strategy for high-biomass sorghum, supporting its potential as a dual-purpose feedstock for SAF. Future work should focus on minimizing biomass yield penalties and improving nutrient use efficiency in oil sorghum systems.

60 APPLIED LIFE SCIENCES↗

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing

CRISPR-associated transposases (CASTs) hold tremendous potential for microbial genome editing because of their ability to integrate large DNA cargos in a programmable, site-specific manner. However, their widespread application has been hindered by poorly understood host factor requirements for transposition. To address this gap, we conducted the first genome-wide screen for host factors affecting Vibrio cholerae CAST (VchCAST) activity using an Escherichia coli RB-TnSeq library and identified 15 genes affecting VchCAST transposition. Of these, seven factors were validated to improve VchCAST activity, and two were inhibitory. Guided by the identification of homologous recombination effectors, RecD and RecA, we tested the λ-Red recombineering system in our VchCAST editing vectors and increased editing efficiency by 55.2-fold in E. coli, 5.6-fold in Pseudomonas putida, and 10.8-fold in Klebsiella michiganensis while maintaining high target specificity and similar insertion arrangements. This study improves the understanding of factors affecting VchCAST activity and enhances its efficiency as a bacterial genome editor.

Song, Leo C T↗

Tools for genetic engineering and gene expression control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides

ABSTRACT Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts that have the potential to contribute to the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans , Rhodobacter sphaeroides , and Zymomonas mobilis show promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis , N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn 7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides . We screen a synthetic promoter library to identify isopropyl β-D-1-thiogalactopyranoside-inducible promoters with regulated activity in both organisms (up to ~15-fold induction in N. aromaticivorans and ~5-fold induction in R. sphaeroides ). Combining Tn 7 integration with promoters from our library, we establish CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference systems for N. aromaticivorans and R. sphaeroides (up to ~10-fold knockdown in N. aromaticivorans and R. sphaeroides ) that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these species and other Alphaproteobacteria. IMPORTANCE It is important to increase our understanding of the microbial world to improve health, agriculture, the environment, and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise promising properties for conversion are challenging to genetically engineer. Here we report genetic tools for Novosphingobium aromaticivorans and Rhodobacter sphaeroides that add to the burgeoning set of tools available for genome engineering and gene expression in Alphaproteobacteria. Our approaches allow straightforward insertion of engineered pathways into the N. aromaticivorans or R. sphaeroides genome and control of gene expression by inducing genes with synthetic promoters or repressing genes using CRISPR interference. These tools can be used in future work to gain additional insight into these and other Alphaproteobacteria and to aid in optimizing yield of biofuels and bioproducts.

Hall, Ashley N.↗

Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms

ABSTRACT Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications. IMPORTANCE Although soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction—less than 1%—can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from anin situsoil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.

Biotechnology & Applied Microbiology↗

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

Background: G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies. Results: G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R 2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion: G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans.

59 BASIC BIOLOGICAL SCIENCES↗

Field evaluation of transgenic hybrid poplars with desirable wood properties and enhanced growth for biofuel production by bicistronic expression of PdGA20ox1 and PtrMYB3 in wood-forming tissue

Background: To create an ideotype woody bioenergy crop with desirable growth and biomass properties, we utilized the viral 2A-meidated bicistronic expression strategy to express both PtrMYB3 ( MYB46 ortholog of Populus trichocarpa , a master regulator of secondary wall biosynthesis) and PdGA20ox1 (a GA20-oxidase from Pinus densiflora that produces gibberellins) in wood-forming tissue (i.e., developing xylem). Results: Transgenic Arabidopsis plants expressing the gene construct DX15::PdGA20ox1-2A-PtrMYB3 showed a significant increase in both stem fresh weight (threefold) and secondary wall thickening (1.27-fold) relative to wild-type (WT) plants. Transgenic poplars harboring the same gene construct grown in a greenhouse for 60 days had a stem fresh weight up to 2.6-fold greater than that of WT plants. In a living modified organism (LMO) field test conducted for 3 months of active growing season, the stem height and diameter growth of the transgenic poplars were 1.7- and 1.6-fold higher than those of WT plants, respectively, with minimal adverse growth defects. Although no significant changes in secondary wall thickening of the stem tissue of the transgenic poplars were observed, cellulose content was increased up to 14.4 wt% compared to WT, resulting in improved saccharification efficiency of the transgenic poplars. Moreover, enhanced woody biomass production by the transgenic poplars was further validated by re-planting in the same LMO field for additional two growing seasons. Conclusions: Taken together, these results show considerably enhanced wood formation of our transgenic poplars, with improved wood quality for biofuel production.

09 BIOMASS FUELS↗