David F. Savage

This study uses CRISPR-Cas9 to knockout CYP79A1 in sorghum, reducing cyanogenic potential and providing a method for low-cyanogenic crop development.

The paper determines the structure of the DAB1 complex from Thermocrinis albus using cryo-EM, revealing how proton translocation couples to active-site remodeling for directional CO2 hydration.

This study shows polyphosphate regulates carbon fixation and nucleoid structure in cyanobacteria by organizing spatial relationships between carboxysomes and the nucleoid.

This paper develops yeast-selected SpCas9 variants with re-specified PAM recognition to enable allele-specific editing, demonstrating improved specificity and catalytic efficiency compared to PAM-broadened variants.

Ymu1 TnpB unwinds DNA via a long-lived partially unwound intermediate before a rarely stable open state; the WFR triple variant stabilizes both, boosting plant editing.

This study investigates the trade-off between activity and specificity in adenine base editors using machine learning and high-throughput screening, finding that activity is the primary determinant of editing outcomes.

This paper uses cryoET to determine Rubisco polymerization constants in α-carboxysomes by converting tomography data into binding curves.

Tobacco rattle virus delivery of engineered ISDra2 variant eTnpBc and its guide RNA as a single transcript achieves up to 90% somatic and 100% heritable editing in Nicotiana benthamiana.

PEINT simulates realistic protein evolution by modeling sequence changes over time, generating functional proteins that retain enzymatic activity.

The paper develops a high-throughput MPRA to map cis-regulatory elements in cereal promoters, identifying mutations that significantly increase gene expression.

This study uses random barcode transposon-site sequencing in Mycobacterium tuberculosis to identify gene functions, revealing novel phenotypes and metabolic pathways.

The paper introduces SABER, a method to efficiently map tolerated deletions in SaCas9, enabling the design of minimal CRISPRi effectors.

The paper shows that Chimalliviridae form a lipid membrane-bound EPI vesicle during early infection, which hosts transcription of the phage genome, and demonstrates the necessity of a second compartment, the phage nucleus, for genome replication.

The paper develops a CRISPRi-ART system to knock down protein expression in diverse bacteriophages and identifies essential genes, including many with unknown functions.

This study identifies activating mutations in TnpB enzymes that enhance genome editing activity across multiple species.

The paper maps the sequence-to-function relationship of rubisco by assaying single amino acid mutants in E. coli, identifying conserved positions and mutations that improve CO2 affinity.

This paper develops a high-efficiency sorghum transformation toolkit using CRISPR/Cas9 and SpRY to improve genome editing efficiency and expand promoter-editing capabilities.

The paper reconstructs genomes of soil-associated Asgard archaea and uses metatranscriptomics to show their role in carbon compound metabolism relevant to methane production in wetlands.

This study identifies conserved and repetitive motifs in CsoS2 that drive α-carboxysome assembly and demonstrates in vitro reconstitution of carboxysomes.

This paper introduces a translation-independent method to engineer aminoacyl-tRNA synthetases that can incorporate noncanonical amino acids into proteins.

This study investigates the functional plasticity of HCO3- uptake and CO2 fixation in C. necator H16 by testing endogenous and heterologous genes, showing that DIC transporters can support autotrophic growth and higher cell densities.

This study identifies mobile genetic elements and defense systems in Asgard archaea, revealing their role in shaping genetic diversity and evolution.

This study identifies CsoS2 as the protein controlling α-carboxysome size through its interactions with the shell, proposing a model based on repeat classes and curvature preferences.

The paper uses a genetic minimization technique to identify minimal DNA-binding modules in Cas9, showing that large domain deletions can retain function.

The paper demonstrates that a bacterial CO2 concentrating mechanism enables E. coli to fix CO2 from ambient air using 20 CCM genes.

The paper re-examines tradeoffs between Rubisco kinetic parameters using data from ~300 organisms, finding that most correlations are attenuated and only one tradeoff model remains.

Inserting theophylline aptamers into the sgRNA yields ligand-activated and ligand-deactivated guides that tune CRISPRi in E. coli over 11x to 13x dynamic ranges, enabling two-ligand multiplexing.

The paper identifies a novel class of inorganic carbon transporters in chemoautotrophic bacteria through a genome-wide screen and characterizes their function as energy-coupled bicarbonate pumps.

This paper demonstrates plasmid recombineering as a method for rapid and programmable protein mutagenesis, showing it can generate comprehensive libraries and identify improved variants.