D. F. Savage

Genetic elements and defense systems drive diversification and evolution in Asgard archaea

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

Asgard archaea modulate potential methanogenesis substrates in wetland soil

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.

A map of the rubisco biochemical landscape

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.

A transcriptionally active lipid vesicle encloses theinjected Chimalliviridae genome in early infection

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.

Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi

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

α-carboxysome size is controlled by the disordered scaffold protein CsoS2

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.

Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs

This study demonstrates that minimally immunogenic Cas9 RNPs delivered via convection enhanced delivery can edit mouse striatal neurons with reduced immune responses compared to AAV-delivered Cas9.

Autotrophic biofilms sustained by deeply-sourced groundwater host diverse CPR bacteria implicated in sulfur and hydrogen metabolism

The paper identifies CPR bacteria in sulfide-rich biofilms, linking them to sulfur and hydrogen metabolism through genomic and spectroscopic analyses.

Exploring masses and internal mass distributions of single carboxysomes in free solution using fluorescence and interferometric scattering in an anti-Brownian trap

Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2 through geologic time should be re-evaluated

The paper measures carbon isotope fractionation of an ancestral rubisco in cyanobacteria, showing that evolutionary changes in photosynthesis physiology, not just atmospheric CO2, affect the carbon isotope record.

Trajectories for the evolution of bacterial CO2-concentrating mechanisms

This paper studies the evolution of bacterial CO2-concentrating mechanisms by engineering E. coli to express ancestral forms of these systems and testing their growth under varying CO2 concentrations.

Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution

The paper improves the ISABEL trap to monitor redox environments inside individual carboxysomes using ratiometric fluorescence.

Discovery of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome

This study identifies the structural basis of carbonic anhydrase incorporation into carboxysomes by showing direct interaction with Rubisco via an N-terminal domain.

Engineering improved Cas13 effectors for targeted post-transcriptional regulation of gene expression

This paper engineers improved Cas13 effectors for targeted post-transcriptional regulation, showing efficient translational repression in bacteria and exon skipping in human cells.

The encapsulin from Thermatoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein

This study investigates the structure and function of the T. maritima encapsulin, revealing its role in cargo protein encapsulation and enzymatic activity through symmetry-matching and flavin binding.

A nanocompartment containing the peroxidase DypB contributes to defense against oxidative stress in M. tuberculosis

This study identifies a nanocompartment in M. tuberculosis containing DypB that enhances resistance to oxidative stress during infection and antibiotic treatment.

α-carboxysome formation is mediated by the multivalent and disordered protein CsoS2

The paper identifies CsoS2's N-terminal peptide as a multivalent interaction hub that binds Rubisco through electrostatic interactions, enabling efficient α-carboxysome formation via avidity.