A5015752296- Photosynthetic Processes and Mechanisms
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced biosensing and bioanalysis techniques
- Algal biology and biofuel production
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Photoreceptor and optogenetics research
- Microfluidic and Bio-sensing Technologies
- ATP Synthase and ATPases Research
- Ion Transport and Channel Regulation
- Enzyme Catalysis and Immobilization
- Nanopore and Nanochannel Transport Studies
- Microbial Fuel Cells and Bioremediation
- Metalloenzymes and iron-sulfur proteins
- RNA modifications and cancer
- Microfluidic and Capillary Electrophoresis Applications
- Hemoglobin structure and function
- Membrane-based Ion Separation Techniques
- Advanced Electron Microscopy Techniques and Applications
University of California, Berkeley
2016-2025
Howard Hughes Medical Institute
2022-2025
Innovative Genomics Institute
2021-2025
QB3
2023
Energy Biosciences Institute
2013-2016
University of California, San Francisco
2003-2010
Harvard University
2008-2010
Center for Systems Biology
2008-2010
Harvard University Press
2009
Cyanobacterial carbon fixation is a major component of the global cycle. This process requires carboxysome, an organelle-like proteinaceous microcompartment that sequesters enzymes from cytoplasm. Here, fluorescently tagged carboxysomes were found to be spatially ordered in linear fashion. As consequence, cells undergoing division evenly segregated nonrandom process. Mutation cytoskeletal protein ParA specifically disrupted carboxysome order, promoted random segregation during cell division,...
Bacterial microcompartments are proteinaceous complexes that catalyze metabolic pathways in a manner reminiscent of organelles. Although microcompartment structure is well understood, much less known about their assembly and function vivo. We show here carboxysomes, CO(2)-fixing encoded by 10 genes, can be heterologously produced Escherichia coli. Expression carboxysomes E. coli resulted the production icosahedral similar to those from native host. In vivo, were capable both assembling with...
Many carbon-fixing bacteria rely on a CO2 concentrating mechanism (CCM) to elevate the concentration around carboxylating enzyme ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The CCM is postulated simultaneously enhance rate of carboxylation and minimize oxygenation, competitive reaction with O2 also catalyzed by RuBisCO. To achieve this effect, combines two features: active transport inorganic carbon into cell colocalization carbonic anhydrase RuBisCO inside proteinaceous...
Rubisco is the primary carboxylase of Calvin cycle, most abundant enzyme in biosphere, and one best-characterized enzymes. On basis correlations between kinetic parameters, it widely posited that constraints embedded catalytic mechanism enforce trade-offs CO2 specificity, SC/O, maximum carboxylation rate, kcat,C. However, reasoning established this view was based on data from ≈20 organisms. Here, we re-examine models catalysis using a set ≈300 Correlations parameters are substantially...
Abstract The CRISPR-Cas9 system provides the ability to edit, repress, activate, or mark any gene (or DNA element) by pairing of a programmable single guide RNA (sgRNA) with complementary sequence on target. Here we present new method for small-molecule control function through insertion aptamers into sgRNA. We show that CRISPR-Cas9-based repression (CRISPRi) can be either activated deactivated in dose-dependent fashion over >10-fold dynamic range response two different ligands. Since our...
CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find CRISPR also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded belong to all six known types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins 44 families...
Recent developments in protein design rely on large neural networks with up to 100s of millions parameters, yet it is unclear which residue dependencies are critical for determining function. Here, we show that amino acid preferences at individual residues-without accounting mutation interactions-explain much and sometimes virtually all the combinatorial effects across 8 datasets (R
Abstract Rubisco is the primary CO 2 -fixing enzyme of biosphere 1 , yet it has slow kinetics . The roles evolution and chemical mechanism in constraining its biochemical function remain debated 3,4 Engineering efforts aimed at adjusting parameters rubisco have largely failed 5 although recent results indicate that functional potential a wider scope than previously known 6 Here we developed massively parallel assay, using an engineered Escherichia coli 7 which activity coupled to growth,...
Abstract Bacteriophages constitute one of the largest reservoirs genes unknown function in biosphere. Even well-characterized phages, functions most remain unknown. Experimental approaches to study phage gene fitness and at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d selectively interfere with protein translation measure a transcriptome-wide scale. We find CRISPR Interference through Antisense...
Aquaporins are a family of water and small molecule channels found in organisms ranging from bacteria to animals. One these channels, the E. coli protein aquaporin Z (AqpZ), has been shown selectively conduct only at high rates. We have expressed, purified, crystallized, solved X-ray structure AqpZ. The 2.5 Å resolution AqpZ suggests selectivity results both steric mechanism due pore size specific amino acid substitutions that regulate preference for hydrophobic or hydrophilic substrate....
ABSTRACT Metabolic engineering of cyanobacteria has the advantage that sunlight and CO 2 are sole source energy carbon for these organisms. However, as photoautotrophs, generally lack transporters to move hydrophilic primary metabolites across membranes. To address whether could be engineered produce secrete organic metabolites, Synechococcus elongatus PCC7942 was express genes encoding an invertase a glucose facilitator, which mediated secretion fructose. Similarly, expression lactate...
Background Cyanobacteria play a significant role in the global carbon cycle. In Synechococcus elongatus, carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is concentrated into polyhedral, proteinaceous compartments called carboxysomes. Methodology/Principal Findings Using live cell fluorescence microscopy, we show that carboxysomes are first detected as small seeds of RuBisCO colocalize with existing These contain little or no shell protein, but increase content...
Abstract In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact optogenetics has been limited by a lack user-friendly, flexible, accessible hardware. Here, we engineer Light Plate Apparatus (LPA), device that can deliver two independent 310 1550 nm signals each well 24-well plate intensity over three orders magnitude millisecond resolution. Signals are programmed...
Abstract Single-fluorescent protein biosensors (SFPBs) are an important class of probes that enable the single-cell quantification analytes in vivo . Despite advantages over other detection technologies, their use has been limited by inherent challenges construction. Specifically, rational design green fluorescent (GFP) insertion into a ligand-binding domain, generating requisite allosteric coupling, remains rate-limiting step. Here, we describe unbiased approach, termed domain-insertion...
The encapsulation of enzymes and other proteins within a proteinaceous shell has been observed in many bacteria archaea, but the function utility such compartments are enigmatic. Efforts to study these functions have complicated by size complexity traditional protein compartments. One potential system for investigating effect compartmentalization is encapsulin, large newly discovered class shells that typically composed two proteins: protomer assembles into icosahedral cargo packaged inside....
Many photosynthetic organisms employ a CO 2 concentrating mechanism (CCM) to increase the rate of fixation via Calvin cycle. CCMs catalyze ≈50% global photosynthesis, yet it remains unclear which genes and proteins are required produce this complex adaptation. We describe construction functional CCM in non-native host, achieved by expressing from an autotrophic bacterium Escherichia coli strain engineered depend on rubisco carboxylation for growth. Expression 20 enabled E. grow fixing...