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Prywes N, Philips NR, Oltrogge LM, Lindner S, Candace Tsai YC, de Pins B, Cowan AE, Taylor-Kearney LJ, Chang HA, Hall LN, Bellieny-Rabelo D, Nisonoff HM, Weissman RF, Flamholz AI, Ding D, Bhatt AY, Shih PM, Mueller-Cajar O, Milo R, Savage DF. A map of the rubisco biochemical landscape. bioRxiv 2024:2023.09.27.559826. [PMID: 38645011 PMCID: PMC11030240 DOI: 10.1101/2023.09.27.559826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Rubisco is the primary CO2 fixing enzyme of the biosphere yet has slow kinetics. The roles of evolution and chemical mechanism in constraining the sequence landscape of rubisco remain debated. In order to map sequence to function, we developed a massively parallel assay for rubisco using an engineered E. coli where enzyme function is coupled to growth. By assaying >99% of single amino acid mutants across CO2 concentrations, we inferred enzyme velocity and CO2 affinity for thousands of substitutions. We identified many highly conserved positions that tolerate mutation and rare mutations that improve CO2 affinity. These data suggest that non-trivial kinetic improvements are readily accessible and provide a comprehensive sequence-to-function mapping for enzyme engineering efforts.
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Affiliation(s)
- Noam Prywes
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
| | - Naiya R. Philips
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
| | - Luke M. Oltrogge
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
| | | | - Yi-Chin Candace Tsai
- School of Biological Sciences, Nanyang Technological University; Singapore 637551, Singapore
| | - Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of Science; Rehovot 76100, Israel
| | - Aidan E. Cowan
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory; Emeryville, CA 94608, USA
| | - Leah J. Taylor-Kearney
- Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Hana A. Chang
- Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Laina N. Hall
- Biophysics, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California; Berkeley, CA 94720, USA
| | - Hunter M. Nisonoff
- Center for Computational Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Rachel F. Weissman
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
| | - Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
| | - David Ding
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
| | - Abhishek Y. Bhatt
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
- School of Medicine, University of California, San Diego; La Jolla, CA 92092, USA
| | - Patrick M. Shih
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory; Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute; Emeryville, CA 94608, USA
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University; Singapore 637551, Singapore
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science; Rehovot 76100, Israel
| | - David F. Savage
- Innovative Genomics Institute, University of California; Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California; Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California; Berkeley, California 94720, USA
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2
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Ding D, Shaw AY, Sinai S, Rollins N, Prywes N, Savage DF, Laub MT, Marks DS. Protein design using structure-based residue preferences. Nat Commun 2024; 15:1639. [PMID: 38388493 PMCID: PMC10884402 DOI: 10.1038/s41467-024-45621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at individual residues-without accounting for mutation interactions-explain much and sometimes virtually all of the combinatorial mutation effects across 8 datasets (R2 ~ 78-98%). Hence, few observations (~100 times the number of mutated residues) enable accurate prediction of held-out variant effects (Pearson r > 0.80). We hypothesized that the local structural contexts around a residue could be sufficient to predict mutation preferences, and develop an unsupervised approach termed CoVES (Combinatorial Variant Effects from Structure). Our results suggest that CoVES outperforms not just model-free methods but also similarly to complex models for creating functional and diverse protein variants. CoVES offers an effective alternative to complicated models for identifying functional protein mutations.
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Affiliation(s)
- David Ding
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
| | - Ada Y Shaw
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sam Sinai
- Dyno Therapeutics, Watertown, MA, 02472, USA
| | - Nathan Rollins
- Seismic Therapeutics, Lab Central, Cambridge, MA, 02142, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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3
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Valentin-Alvarado LE, Fakra SC, Probst AJ, Giska JR, Jaffe AL, Oltrogge LM, West-Roberts J, Rowland J, Manga M, Savage DF, Greening C, Baker BJ, Banfield JF. Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism. Microbiome 2024; 12:15. [PMID: 38273328 PMCID: PMC10811913 DOI: 10.1186/s40168-023-01704-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/18/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. RESULTS Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. CONCLUSIONS Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.
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Affiliation(s)
- Luis E Valentin-Alvarado
- Graduate Group in Microbiology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexander J Probst
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry,, University of Duisburg-Essen, Essen, Essen, Germany
| | - Jonathan R Giska
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Cleaner Air Oregon Program, Oregon Department of Environmental Quality, Portland, USA
| | - Alexander L Jaffe
- Graduate Group in Microbiology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Joel Rowland
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Earth and Env. Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Michael Manga
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Brett J Baker
- Department of Integrative Biology, University of Texas, Austin, USA
- Department of Marine Science, University of Texas, Austin, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Marine Science, University of Texas, Austin, USA.
- Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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4
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Oltrogge LM, Chen AW, Chaijarasphong T, Turnšek JB, Savage DF. α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2. Biochemistry 2024; 63:219-229. [PMID: 38085650 PMCID: PMC10795168 DOI: 10.1021/acs.biochem.3c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Carboxysomes are protein microcompartments that function in the bacterial CO2 concentrating mechanism (CCM) to facilitate CO2 assimilation. To do so, carboxysomes assemble from thousands of constituent proteins into an icosahedral shell, which encapsulates the enzymes Rubisco and carbonic anhydrase to form structures typically > 100 nm and > 300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here, we show that the size of α-carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats that bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of α-carboxysomes.
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Affiliation(s)
- Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Allen W. Chen
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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5
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Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon P, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert R, Knott GJ, Lapinaite A, Pausch P, Cofsky J, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res 2024; 52:D590-D596. [PMID: 37889041 PMCID: PMC10767948 DOI: 10.1093/nar/gkad890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
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Affiliation(s)
- Benjamin A Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elaine Zhang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Hannah M Karp
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Rachel F Weissman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
| | - Tomas Hessler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Colognori
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ron Boger
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Connor A Tsuchida
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan V Tran
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Laura Hofman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Graduate School of Life Sciences, Utrecht University, 3584 CS Utrecht, UT, The Netherlands
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Kevin M Wasko
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Zehan Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Chenglong Xia
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Muntathar J Al-Shimary
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jaymin R Patel
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Vienna C J X Thomas
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Rithu Pattali
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew J Kan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, CA 94158, USA
| | - Anna Vardapetyan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Alana Yang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Micaela F Maxwell
- Department of Chemistry and Biochemistry, Hampton University, Hampton, VA 23668, USA
| | - Andrew G Murdock
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Glenn C Ramit
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Hope R Henderson
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Roland W Calvert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rebecca S Bamert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Patrick Pausch
- LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Joshua C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Genetics Otago, University of Otago, Dunedin 9016, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9016, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, 2629 HZ Delft, The Netherlands
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | | | | | | | - Rodolphe Barrangou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Virginius Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The University of Melbourne, Parkville, VIC 3052, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94158, USA
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6
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Blikstad C, Dugan EJ, Laughlin TG, Turnšek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc Natl Acad Sci U S A 2023; 120:e2308600120. [PMID: 37862384 PMCID: PMC10614612 DOI: 10.1073/pnas.2308600120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/22/2023] Open
Abstract
Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation-Rubisco and carbonic anhydrase-and are the centerpiece of the bacterial CO2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO2 by carbonic anhydrase, producing a high CO2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus. We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Thomas G. Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Julia B. Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Mira D. Liu
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sophie R. Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Nikoleta Vogiatzi
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Jonathan P. Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
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7
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Armbruster EG, Lee J, Hutchings J, VanderWal AR, Enustun E, Adler BA, Aindow A, Deep A, Rodriguez ZK, Morgan CJ, Ghassemian M, Charles E, Cress BF, Savage DF, Doudna JA, Pogliano K, Corbett KD, Villa E, Pogliano J. Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection. bioRxiv 2023:2023.09.20.558163. [PMID: 37781618 PMCID: PMC10541120 DOI: 10.1101/2023.09.20.558163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Eukaryotic viruses assemble compartments required for genome replication, but no such organelles are known to be essential for prokaryotic viruses. Bacteriophages of the family Chimalliviridae sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of viral protein ChmA. Using the dRfxCas13d-based knockdown system CRISPRi-ART, we show that ChmA is essential for the E. coli phage Goslar life cycle. Without ChmA, infections are arrested at an early stage in which the injected phage genome is enclosed in a membrane-bound vesicle capable of gene expression but not DNA replication. Not only do we demonstrate that the phage nucleus is essential for genome replication, but we also show that the Chimalliviridae early phage infection (EPI) vesicle is a transcriptionally active, phage-generated organelle.
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Affiliation(s)
- Emily G. Armbruster
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Arica R. VanderWal
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Eray Enustun
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Benjamin A. Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Ann Aindow
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Zaida K. Rodriguez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Chase J. Morgan
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Emeric Charles
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - David F. Savage
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D. Corbett
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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8
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Stahl EC, Sabo JK, Kang MH, Allen R, Applegate E, Kim SE, Kwon Y, Seth A, Lemus N, Salinas-Rios V, Soczek KM, Trinidad M, Vo LT, Jeans C, Wozniak A, Morris T, Kimberlin A, Foti T, Savage DF, Doudna JA. Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs. Mol Ther 2023; 31:2422-2438. [PMID: 37403358 PMCID: PMC10422012 DOI: 10.1016/j.ymthe.2023.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
Transient delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) into the central nervous system (CNS) for therapeutic genome editing could avoid limitations of viral vector-based delivery including cargo capacity, immunogenicity, and cost. Here, we tested the ability of cell-penetrant Cas9 RNPs to edit the mouse striatum when introduced using a convection-enhanced delivery system. These transient Cas9 RNPs showed comparable editing of neurons and reduced adaptive immune responses relative to one formulation of Cas9 delivered using AAV serotype 9. The production of ultra-low endotoxin Cas9 protein manufactured at scale further improved innate immunity. We conclude that injection-based delivery of minimally immunogenic CRISPR genome editing RNPs into the CNS provides a valuable alternative to virus-mediated genome editing.
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Affiliation(s)
- Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer K Sabo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Min Hyung Kang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Allen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth Applegate
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shin Eui Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yoonjin Kwon
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anmol Seth
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Lemus
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Viviana Salinas-Rios
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Linda T Vo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chris Jeans
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | | | | | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, Berkeley, San Francisco, CA 94114, USA.
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9
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Wang RZ, Nichols RJ, Liu AK, Flamholz AI, Artier J, Banda DM, Savage DF, Eiler JM, Shih PM, Fischer WW. Carbon isotope fractionation by an ancestral rubisco suggests that biological proxies for CO 2 through geologic time should be reevaluated. Proc Natl Acad Sci U S A 2023; 120:e2300466120. [PMID: 37155899 DOI: 10.1073/pnas.2300466120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
The history of Earth's carbon cycle reflects trends in atmospheric composition convolved with the evolution of photosynthesis. Fortunately, key parts of the carbon cycle have been recorded in the carbon isotope ratios of sedimentary rocks. The dominant model used to interpret this record as a proxy for ancient atmospheric CO2 is based on carbon isotope fractionations of modern photoautotrophs, and longstanding questions remain about how their evolution might have impacted the record. Therefore, we measured both biomass (εp) and enzymatic (εRubisco) carbon isotope fractionations of a cyanobacterial strain (Synechococcus elongatus PCC 7942) solely expressing a putative ancestral Form 1B rubisco dating to ≫1 Ga. This strain, nicknamed ANC, grows in ambient pCO2 and displays larger εp values than WT, despite having a much smaller εRubisco (17.23 ± 0.61‰ vs. 25.18 ± 0.31‰, respectively). Surprisingly, ANC εp exceeded ANC εRubisco in all conditions tested, contradicting prevailing models of cyanobacterial carbon isotope fractionation. Such models can be rectified by introducing additional isotopic fractionation associated with powered inorganic carbon uptake mechanisms present in Cyanobacteria, but this amendment hinders the ability to accurately estimate historical pCO2 from geological data. Understanding the evolution of rubisco and the CO2 concentrating mechanism is therefore critical for interpreting the carbon isotope record, and fluctuations in the record may reflect the evolving efficiency of carbon fixing metabolisms in addition to changes in atmospheric CO2.
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Affiliation(s)
- Renée Z Wang
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Robert J Nichols
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Albert K Liu
- Plant Biosystems Design, Lawrence Berkeley National Lab, Joint Bioenergy Institute, Emeryville, CA 94608
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616
| | - Avi I Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Juliana Artier
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Doug M Banda
- Department of Plant Biology, University of California, Davis, CA 95616
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720
| | - John M Eiler
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Patrick M Shih
- Plant Biosystems Design, Lawrence Berkeley National Lab, Joint Bioenergy Institute, Emeryville, CA 94608
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Woodward W Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
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10
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Abstract
Carbon fixation is the process by which CO2 is converted from a gas into biomass. The Calvin-Benson-Bassham cycle (CBB) is the dominant carbon-consuming pathway on Earth, driving >99.5% of the ∼120 billion tons of carbon that are converted to sugar by plants, algae, and cyanobacteria. The carboxylase enzyme in the CBB, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), fixes one CO2 molecule per turn of the cycle into bioavailable sugars. Despite being critical to the assimilation of carbon, rubisco's kinetic rate is not very fast, limiting flux through the pathway. This bottleneck presents a paradox: Why has rubisco not evolved to be a better catalyst? Many hypothesize that the catalytic mechanism of rubisco is subject to one or more trade-offs and that rubisco variants have been optimized for their native physiological environment. Here, we review the evolution and biochemistry of rubisco through the lens of structure and mechanism in order to understand what trade-offs limit its improvement. We also review the many attempts to improve rubisco itself and thereby promote plant growth. Expected final online publication date for the Annual Review of Biochemistry, Volume 92 is June 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, California, USA;
| | - Naiya R Phillips
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Owen T Tuck
- Department of Chemistry, University of California, Berkeley, California, USA
| | | | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Graduate Group in Microbiology, University of California, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, USA
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11
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Carpenter WB, Lavania AA, Turnšek JB, Perez D, Oltrogge LM, Dahlberg PD, Savage DF, Moerner WE. Ratiometric sensing of redox environments inside individual carboxysomes trapped in solution. Biophys J 2023; 122:304a. [PMID: 36783520 DOI: 10.1016/j.bpj.2022.11.1712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Abhijit A Lavania
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Julia B Turnšek
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Davis Perez
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Peter D Dahlberg
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - William E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA
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12
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Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J. Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries. Glob Health Action 2022; 15:2062175. [PMID: 35730550 PMCID: PMC9225690 DOI: 10.1080/16549716.2022.2062175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Science education and research have the potential to drive profound change in low- and middle-income countries (LMICs) through encouraging innovation, attracting industry, and creating job opportunities. However, in LMICs, research capacity is often limited, and acquisition of funding and access to state-of-the-art technologies is challenging. The Alliance for Global Health and Science (the Alliance) was founded as a partnership between the University of California, Berkeley (USA) and Makerere University (Uganda), with the goal of strengthening Makerere University’s capacity for bioscience research. The flagship program of the Alliance partnership is the MU/UCB Biosciences Training Program, an in-country, hands-on workshop model that trains a large number of students from Makerere University in infectious disease and molecular biology research. This approach nucleates training of larger and more diverse groups of students, development of mentoring and bi-directional research partnerships, and support of the local economy. Here, we describe the project, its conception, implementation, challenges, and outcomes of bioscience research workshops. We aim to provide a blueprint for workshop implementation, and create a valuable resource for bioscience research capacity strengthening in LMICs.
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Affiliation(s)
- Celine Perier
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Isabelle Charles
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Derek Bangs
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - P Robert Beatty
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Amy Diallo
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Hildy Fong Baker
- School of Public Health, Center for Global Public Health (CGPH), University of California, Berkeley, CA, USA
| | - Jackson Gardner
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Birungi Joanah
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | - David Kateete
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Matt Knight
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Maria Krasilnikov
- Department of Molecular Biology and Microbiology, Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | | | - Eric Lee
- Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Daniel Licht
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Katie Lien
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Zilose Lyons
- California China Climate Institute, University of California, Berkeley, CA, USA
| | - Gerald Mboowa
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Ivan Mwebaza
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | | | - Robert Nichols
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Sarah Petnic
- Quality and Clinical Excellence Department, Providence Queen of the Valley Medical Center, Napa, CA, USA
| | | | - Stephen J Popper
- Sustainable Sciences Institute, San Francisco, CA, USA.,School of Public Health, Department of Infectious Disease and Vaccinology, University of California, Berkeley, CA, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Arthur Reingold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | | | - Oren S Rosenberg
- Department of Medicine, University of California, San Francisco, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | | | - Ivan Sserwadda
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Sarah Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | | | | | - Erik Van Dis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Joanna Vinden
- Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Jeffery S Cox
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Moses L Joloba
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Julia Schaletzky
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
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13
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Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell 2022; 185:4574-4586.e16. [PMID: 36423580 DOI: 10.1016/j.cell.2022.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/10/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022]
Abstract
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 that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells.
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Affiliation(s)
- Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Zheng Li
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Evan Groover
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Dylan Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Patrick Pausch
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Carolyn J Huang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA; Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA.
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14
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Lavania A, Carpenter WB, Oltrogge LM, Perez D, Turnšek JB, Savage DF, Moerner WE. Exploring Masses and Internal Mass Distributions of Single Carboxysomes in Free Solution Using Fluorescence and Interferometric Scattering in an Anti-Brownian Trap. J Phys Chem B 2022; 126:8747-8759. [PMID: 36282790 PMCID: PMC9639131 DOI: 10.1021/acs.jpcb.2c05939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Carboxysomes are self-assembled bacterial microcompartments that facilitate carbon assimilation by colocalizing the enzymes of CO2 fixation within a protein shell. These microcompartments can be highly heterogeneous in their composition and filling, so measuring the mass and loading of an individual carboxysome would allow for better characterization of its assembly and function. To enable detailed and extended characterizations of single nanoparticles in solution, we recently demonstrated an improved interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which tracks the position of a single nanoparticle via its scattering of a near-infrared beam and applies feedback to counteract its Brownian motion. Importantly, the scattering signal can be related to the mass of nanoscale proteinaceous objects, whose refractive indices are well-characterized. We calibrate single-particle scattering cross-section measurements in the ISABEL trap and determine individual carboxysome masses in the 50-400 MDa range by analyzing their scattering cross sections with a core-shell model. We further investigate carboxysome loading by combining mass measurements with simultaneous fluorescence reporting from labeled internal components. This method may be extended to other biological objects, such as viruses or extracellular vesicles, and can be combined with orthogonal fluorescence reporters to achieve precise physical and chemical characterization of individual nanoscale biological objects.
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Affiliation(s)
- Abhijit
A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California94305, United States,Department
of Applied Physics, Stanford University, Stanford, California94305, United States
| | - William B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California94305, United States,Department
of Applied Physics, Stanford University, Stanford, California94305, United States,
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15
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Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng 2022; 6:944-956. [PMID: 35953650 PMCID: PMC10367768 DOI: 10.1038/s41551-022-00917-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/30/2022] [Indexed: 11/10/2022]
Abstract
Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies μl-1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13-35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23-31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.
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Affiliation(s)
- Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Aditya R Jangid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tina Y Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine Kogut
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA. .,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Patrick D Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. .,Arc Institute, Palo Alto, CA, USA.
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16
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Carpenter W, Lavania AA, Borden JS, Oltrogge LM, Perez D, Dahlberg PD, Savage DF, Moerner WE. Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. J Phys Chem Lett 2022; 13:4455-4462. [PMID: 35549289 PMCID: PMC9150107 DOI: 10.1021/acs.jpclett.2c00782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diffusion of biological nanoparticles in solution impedes our ability to continuously monitor individual particles and measure their physical and chemical properties. To overcome this, we previously developed the interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which uses scattering to localize a particle and applies electrokinetic forces that counteract Brownian motion, thus enabling extended observation. Here we present an improved ISABEL trap that incorporates a near-infrared scatter illumination beam and rapidly interleaves 405 and 488 nm fluorescence excitation reporter beams. With the ISABEL trap, we monitored the internal redox environment of individual carboxysomes labeled with the ratiometric redox reporter roGFP2. Carboxysomes widely vary in scattering contrast (reporting on size) and redox-dependent ratiometric fluorescence. Furthermore, we used redox sensing to explore the chemical kinetics within intact carboxysomes, where bulk measurements may contain unwanted contributions from aggregates or interfering fluorescent proteins. Overall, we demonstrate the ISABEL trap's ability to sensitively monitor nanoscale biological objects, enabling new experiments on these systems.
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Affiliation(s)
- William
B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Julia S. Borden
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National
Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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17
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Lavania AA, Carpenter WB, Oltrogge LM, Borden J, Perez DD, Squires AH, Dahlberg PD, Savage DF, Moerner WE. Characterizing physical properties of single carboxysomes in the Interferometric Scattering Anti-Brownian ELectrokinetic trap. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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18
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LaFrance BJ, Cassidy-Amstutz C, Nichols RJ, Oltrogge LM, Nogales E, Savage DF. The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein. Sci Rep 2021; 11:22810. [PMID: 34815415 PMCID: PMC8610991 DOI: 10.1038/s41598-021-01932-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/29/2021] [Indexed: 11/09/2022] Open
Abstract
Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based 'organelles' found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~ 25-50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure-function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model Thermotoga maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryo-EM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the Thermotoga maritima encapsulin, the decameric cargo protein with fivefold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier-it also plays a significant role in the structure and function of the cargo enzyme.
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Affiliation(s)
- Benjamin J LaFrance
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Robert J Nichols
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
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19
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Lien KA, Dinshaw K, Nichols RJ, Cassidy-Amstutz C, Knight M, Singh R, Eltis LD, Savage DF, Stanley SA. A nanocompartment system contributes to defense against oxidative stress in Mycobacterium tuberculosis. eLife 2021; 10:e74358. [PMID: 34751132 PMCID: PMC8635971 DOI: 10.7554/elife.74358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/06/2021] [Indexed: 01/18/2023] Open
Abstract
Encapsulin nanocompartments are an emerging class of prokaryotic protein-based organelle consisting of an encapsulin protein shell that encloses a protein cargo. Genes encoding nanocompartments are widespread in bacteria and archaea, and recent works have characterized the biochemical function of several cargo enzymes. However, the importance of these organelles to host physiology is poorly understood. Here, we report that the human pathogen Mycobacterium tuberculosis (Mtb) produces a nanocompartment that contains the dye-decolorizing peroxidase DyP. We show that this nanocompartment is important for the ability of Mtb to resist oxidative stress in low pH environments, including during infection of host cells and upon treatment with a clinically relevant antibiotic. Our findings are the first to implicate a nanocompartment in bacterial pathogenesis and reveal a new mechanism that Mtb uses to combat oxidative stress.
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Affiliation(s)
- Katie A Lien
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Kayla Dinshaw
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
| | - Robert J Nichols
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Caleb Cassidy-Amstutz
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Matthew Knight
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Rahul Singh
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, The University of British ColumbiaVancouverCanada
| | - David F Savage
- Department of Molecular and Cell Biology, Division of Biochemistry, Biophysics and Structural Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, BerkeleyBerkeleyUnited States
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, BerkeleyBerkeleyUnited States
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20
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Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nat Commun 2021; 12:5664. [PMID: 34580310 PMCID: PMC8476515 DOI: 10.1038/s41467-021-25992-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 09/10/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
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Affiliation(s)
- Arik Shams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sean A Higgins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, 92093, USA
| | - Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Rachel Lew
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Shin Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Maria Lukarska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Madeline Arnold
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brett T Staahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA.
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21
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. Nat Chem Biol 2021; 17:982-988. [PMID: 34354262 PMCID: PMC10184463 DOI: 10.1038/s41589-021-00842-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided RNA recognition that triggers cleavage and release of a fluorescent reporter molecule, but long reaction times hamper their detection sensitivity and speed. Here, we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 molecules per µl of RNA in 20 min. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA extracted from respiratory swab samples with quantitative reverse transcriptase PCR (qRT-PCR)-derived cycle threshold (Ct) values up to 33, using a compact detector. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables sensitive, direct RNA detection in a format that is amenable to point-of-care infection diagnosis as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria, Australia
| | - Dylan C J Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Emeric J Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Brittney W Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Stephanie I Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shineui Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Berkeley Stem Cell Center, University of California, Berkeley, Berkeley, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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22
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Nichols RJ, LaFrance B, Phillips NR, Radford DR, Oltrogge LM, Valentin-Alvarado LE, Bischoff AJ, Nogales E, Savage DF. Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism. eLife 2021; 10:e59288. [PMID: 33821786 PMCID: PMC8049743 DOI: 10.7554/elife.59288] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 04/04/2021] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle-like compartment in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryo-electron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.
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Affiliation(s)
- Robert J Nichols
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Benjamin LaFrance
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Naiya R Phillips
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Devon R Radford
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Luis E Valentin-Alvarado
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Amanda J Bischoff
- Department of Chemistry, University of California BerkeleyBerkeleyUnited States
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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23
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Agrawal S, Fanton A, Chandrasekaran SS, Charrez B, Escajeda AM, Son S, Mcintosh R, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid, point-of-care molecular diagnostics with Cas13. medRxiv 2021:2020.12.14.20247874. [PMID: 33354689 PMCID: PMC7755151 DOI: 10.1101/2020.12.14.20247874] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/μL of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.
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Affiliation(s)
- Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Sita S. Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C. J. Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tina Y. Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- School of Public Health, University of California, Berkeley, CA, USA
| | - Liana F. Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
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24
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Borden JS, Savage DF. New discoveries expand possibilities for carboxysome engineering. Curr Opin Microbiol 2021; 61:58-66. [PMID: 33798818 DOI: 10.1016/j.mib.2021.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022]
Abstract
Carboxysomes are CO2-fixing protein compartments present in all cyanobacteria and some proteobacteria. These structures are attractive candidates for carbon assimilation bioengineering because they concentrate carbon, allowing the fixation reaction to occur near its maximum rate, and because they self-assemble in diverse organisms with a set of standard biological parts. Recent discoveries have expanded our understanding of how the carboxysome assembles, distributes itself, and sustains its metabolism. These studies have already led to substantial advances in engineering the carboxysome and carbon concentrating mechanism into recombinant organisms, with an eye towards establishing the system in industrial microbes and plants. Future studies may also consider the potential of in vitro carboxysomes for both discovery and applied science.
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Affiliation(s)
- Julia S Borden
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA.
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25
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim SE, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. medRxiv 2021:2021.03.19.21253328. [PMID: 33791736 PMCID: PMC8010768 DOI: 10.1101/2021.03.19.21253328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y. Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Dylan C. J. Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J. Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Emeric J. Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brittney W. Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I. Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shin E. Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Katherine S. Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Liana F. Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
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26
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Flamholz AI, Dugan E, Blikstad C, Gleizer S, Ben-Nissan R, Amram S, Antonovsky N, Ravishankar S, Noor E, Bar-Even A, Milo R, Savage DF. Functional reconstitution of a bacterial CO 2 concentrating mechanism in Escherichia coli. eLife 2020; 9:59882. [PMID: 33084575 PMCID: PMC7714395 DOI: 10.7554/elife.59882] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an Escherichia coli strain engineered to depend on rubisco carboxylation for growth. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth in ambient air depending on the components of the CCM. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Sumedha Ravishankar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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27
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Laughlin TG, Savage DF, Davies KM. Recent advances on the structure and function of NDH-1: The complex I of oxygenic photosynthesis. Biochim Biophys Acta Bioenerg 2020; 1861:148254. [PMID: 32645407 DOI: 10.1016/j.bbabio.2020.148254] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/07/2020] [Accepted: 06/22/2020] [Indexed: 12/29/2022]
Abstract
Photosynthetic NADH dehydrogenase-like complex type-1 (a.k.a, NDH, NDH-1, or NDH-1L) is a multi-subunit, membrane-bound oxidoreductase related to the respiratory complex I. Although originally discovered 30 years ago, a number of recent advances have revealed significant insight into the structure, function, and physiology of NDH-1. Here, we highlight progress in understanding the function of NDH-1 in the photosynthetic light reactions of both cyanobacteria and chloroplasts from biochemical and structural perspectives. We further examine the cyanobacterial-specific forms of NDH-1 that possess vectorial carbonic anhydrase (vCA) activity and function in the CO2-concentrating mechanism (CCM). We compare the proposed mechanism for the cyanobacterial NDH-1 vCA-activity to that of the DAB (DABs accumulates bicarbonate) complex, another putative vCA. Finally, we discuss both new and remaining questions pertaining to the mechanisms of NDH-1 complexes in light of these recent advances.
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Affiliation(s)
- Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Karen M Davies
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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28
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Oltrogge LM, Chaijarasphong T, Chen AW, Bolin ER, Marqusee S, Savage DF. Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nat Struct Mol Biol 2020; 27:281-287. [PMID: 32123388 PMCID: PMC7337323 DOI: 10.1038/s41594-020-0387-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022]
Abstract
Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO2-concentrating mechanism by facilitating high CO2 concentrations near the carboxylase Rubisco. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the α-carboxysome, there is little molecular insight into protein-protein interactions that drive the assembly process. Here, studies on the α-carboxysome from Halothiobacillus neapolitanus demonstrate that Rubisco interacts with the N-terminus of CsoS2, a multivalent, intrinsically disordered protein. X-ray structural analysis of the CsoS2 interaction motif bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate CsoS2 acts as an interaction hub to condense Rubisco and enable efficient α-carboxysome formation.
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Affiliation(s)
- Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Thawatchai Chaijarasphong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Allen W Chen
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Eric R Bolin
- Biophysics Graduate Program, University of California Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.,Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
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29
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Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF. DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nat Microbiol 2019; 4:2204-2215. [PMID: 31406332 PMCID: PMC10184468 DOI: 10.1038/s41564-019-0520-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 12/30/2022]
Abstract
Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, a systematic screen of the components of CCMs is lacking. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the γ-proteobacterium Halothiobacillus neapolitanus. Screening revealed that the CCM comprises at least 17 and probably no more than 25 genes, most of which are encoded in 3 operons. Two of these operons (DAB1 and DAB2) contain a two-gene locus that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam: PF00361). Physiological and biochemical assays demonstrated that these proteins-which we name DabA and DabB, for DABs accumulate bicarbonate-assemble into a heterodimeric complex, which contains a putative β-carbonic anhydrase-like active site and functions as an energy-coupled inorganic carbon (Ci) pump. Interestingly, DAB operons are found in a diverse range of bacteria and archaea. We demonstrate that functional DABs are present in the human pathogens Bacillus anthracis and Vibrio cholerae. On the basis of these results, we propose that DABs constitute a class of energized Ci pumps and play a critical role in the metabolism of Ci throughout prokaryotic phyla.
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Affiliation(s)
- John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Allen W Chen
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Kelly Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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30
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Lee TH, Carpenter TS, D'haeseleer P, Savage DF, Yung MC. Encapsulin carrier proteins for enhanced expression of antimicrobial peptides. Biotechnol Bioeng 2019; 117:603-613. [PMID: 31709513 DOI: 10.1002/bit.27222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. To address these limitations, we have developed a novel AMP fusion protein system based on an encapsulin nanocompartment protein and have demonstrated its utility in enhancing expression of HBCM2, an AMP with activity against Gram-negative bacteria. Here, HBCM2 was fused to the N-terminus of several Encapsulin monomer (Enc) variants engineered with multiple TEV protease recognition site insertions to facilitate proteolytic release of the fused HBCM2. Fusion of HBCM2 to the Enc variants, but not other common carrier proteins, enabled robust overexpression in Escherichia coli C43(DE3) cells. Interestingly, variants with a TEV site insertion following residue K71 in Enc exhibited the highest overexpression and HBCM2 release efficiencies compared to other variants but were deficient in cage formation. HBCM2 was purified from the highest expressing variant following TEV protease digestion and was found to be highly active in inhibiting E. coli growth (MIC = 5 μg/ml). Our study demonstrates the potential use of the Enc system to enhance expression of AMPs for biomanufacturing and therapeutic applications.
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Affiliation(s)
- Tek-Hyung Lee
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - Timothy S Carpenter
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - Patrik D'haeseleer
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, California
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Livermore, California
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31
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Huang TP, Zhao KT, Miller SM, Gaudelli NM, Oakes BL, Fellmann C, Savage DF, Liu DR. Author Correction: Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat Biotechnol 2019; 37:820. [PMID: 31182863 DOI: 10.1038/s41587-019-0168-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kevin T Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Nicole M Gaudelli
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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32
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Harper CC, Elliott AG, Oltrogge LM, Savage DF, Williams ER. Multiplexed Charge Detection Mass Spectrometry for High-Throughput Single Ion Analysis of Large Molecules. Anal Chem 2019; 91:7458-7465. [PMID: 31082222 DOI: 10.1021/acs.analchem.9b01669] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Applications of charge detection mass spectrometry (CDMS) for measuring the masses of large molecules, macromolecular complexes, and synthetic polymers that are too large or heterogeneous for conventional mass spectrometry measurements are made possible by weighing individual ions in order to avoid interferences between ions. Here, a new multiplexing method that makes it possible to measure the masses of many ions simultaneously in CDMS is demonstrated. Ions with a broad range of kinetic energies are trapped. The energy of each ion is obtained from the ratio of the intensity of the fundamental to the second harmonic frequencies of the periodic trapping motion making it possible to measure both the m/ z and charge of each ion. Because ions with the exact same m/ z but with different energies appear at different frequencies, the probability of ion-ion interference is significantly reduced. We show that the measured mass of a protein complex consisting of 16 protomers, RuBisCO (517 kDa), is not affected by the number of trapped ions with up to 21 ions trapped simultaneously in these experiments. Ion-ion interactions do not affect the ion trapping lifetime up to 1 s, and there is no influence of the number of ions on the measured charge-state distribution of bovine serum albumin (66.5 kDa), indicating that ion-ion interactions do not adversely affect any of these measurements. Over an order of magnitude gain in measurement speed over single ion analysis is demonstrated, and significant additional gains are expected with this multi-ion measurement method.
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33
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Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun 2019; 10:2127. [PMID: 31073154 PMCID: PMC6509140 DOI: 10.1038/s41467-019-09985-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 04/10/2019] [Indexed: 12/26/2022] Open
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 a complementary sequence on the DNA target. Here we present a new method for small-molecule control of CRISPR-Cas9 function through insertion of RNA aptamers into the sgRNA. We show that CRISPR-Cas9-based gene repression (CRISPRi) can be either activated or deactivated in a dose-dependent fashion over a >10-fold dynamic range in response to two different small-molecule ligands. Since our system acts directly on each target-specific sgRNA, it enables new applications that require differential and opposing temporal control of multiple genes.
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Affiliation(s)
- Kale Kundert
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - James E Lucas
- UC Berkeley - UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kyle E Watters
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94704, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94704, USA
| | - Andrew H Ng
- UC Berkeley - UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Benjamin M Heineike
- Bioinformatics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christina M Fitzsimmons
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94704, USA
| | - Jiuxin Qu
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Neha Prasad
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Oren S Rosenberg
- Department of Medicine, University of California San Francisco, San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94704, USA
| | - Hana El-Samad
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94704, USA
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, 94704, USA
| | - Tanja Kortemme
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
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34
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Avi I Flamholz
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
| | - David F Savage
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
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35
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Welkie DG, Rubin BE, Diamond S, Hood RD, Savage DF, Golden SS. A Hard Day's Night: Cyanobacteria in Diel Cycles. Trends Microbiol 2019; 27:231-242. [PMID: 30527541 PMCID: PMC6377297 DOI: 10.1016/j.tim.2018.11.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are influential in global geochemistry and are promising candidates for industrial applications. Because the livelihood of cyanobacteria is directly dependent upon light, a comprehensive understanding of metabolism in these organisms requires taking into account the effects of day-night transitions and circadian regulation. These events synchronize intracellular processes with the solar day. Accordingly, metabolism is controlled and structured differently in cyanobacteria than in heterotrophic bacteria. Thus, the approaches applied to engineering heterotrophic bacteria will need to be revised for the cyanobacterial chassis. Here, we summarize important findings related to diurnal metabolism in cyanobacteria and present open questions in the field.
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Affiliation(s)
- David G Welkie
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA 94720, USA
| | - Rachel D Hood
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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36
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Affiliation(s)
- David F Savage
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , United States
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37
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Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell 2019; 176:254-267.e16. [PMID: 30633905 PMCID: PMC6414052 DOI: 10.1016/j.cell.2018.11.052] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022]
Abstract
The ability to engineer natural proteins is pivotal to a future, pragmatic biology. CRISPR proteins have revolutionized genome modification, yet the CRISPR-Cas9 scaffold is not ideal for fusions or activation by cellular triggers. Here, we show that a topological rearrangement of Cas9 using circular permutation provides an advanced platform for RNA-guided genome modification and protection. Through systematic interrogation, we find that protein termini can be positioned adjacent to bound DNA, offering a straightforward mechanism for strategically fusing functional domains. Additionally, circular permutation enabled protease-sensing Cas9s (ProCas9s), a unique class of single-molecule effectors possessing programmable inputs and outputs. ProCas9s can sense a wide range of proteases, and we demonstrate that ProCas9 can orchestrate a cellular response to pathogen-associated protease activity. Together, these results provide a toolkit of safer and more efficient genome-modifying enzymes and molecular recorders for the advancement of precision genome engineering in research, agriculture, and biomedicine.
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Affiliation(s)
- Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Harneet Rishi
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kian L Taylor
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shawn M Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana C Nadler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rayka Yokoo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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38
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Affiliation(s)
- Thawatchai Chaijarasphong
- Mahidol University; Faculty of Science, Department of Biotechnology; Rama VI Rd. Bangkok 10400 Thailand
| | - David F. Savage
- University of California; Department of Molecular and Cell Biology; 2151 Berkeley Way, Berkeley CA 94720 USA
- University of California; Department of Chemistry; 2151 Berkeley Way, Berkeley CA 94720 USA
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39
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Laughlin TG, Savage DF, Davies KM. Revealing the Subunit Architecture of NAD(P)H Dehydrogenase Type-1 from Cyanobacteria through Cryo-EM. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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40
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Oltrogge LM, Chaijarasphong T, Savage DF. Molecular Self-Assembly of the α-Carboxysome. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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41
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Affiliation(s)
- Sean A. Higgins
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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42
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Abstract
Comprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. There is thus a need for robust and unbiased molecular biological approaches for the construction of the requisite comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space. Using the fluorescent protein iLOV as a model target, we build a complete mutagenesis library and find it to be specific and comprehensive, detecting 99.8% of our intended mutations. We then develop a thermostability screen and utilize our comprehensive mutation data to rapidly construct a targeted and multiplexed library that identifies significantly improved variants, thus demonstrating rapid protein engineering in a simple protocol.
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Affiliation(s)
- Sean A. Higgins
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| | - Sorel V. Y. Ouonkap
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, and ‡Department of Chemistry, UC Berkeley, Berkeley, California 94720, United States
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43
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Affiliation(s)
- Robert J. Nichols
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
| | | | | | - David F. Savage
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
- Department of Chemistry, UC Berkeley, Berkeley, CA, USA
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44
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Cassidy-Amstutz C, Oltrogge L, Going CC, Lee A, Teng P, Quintanilla D, East-Seletsky A, Williams ER, Savage DF. Identification of a Minimal Peptide Tag for in Vivo and in Vitro Loading of Encapsulin. Biochemistry 2016; 55:3461-8. [DOI: 10.1021/acs.biochem.6b00294] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Caleb Cassidy-Amstutz
- Department
of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
| | - Luke Oltrogge
- Department
of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
| | - Catherine C. Going
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Antony Lee
- Department
of Physics, University of California at Berkeley, Berkeley, California 94720, United States
| | - Poh Teng
- Department
of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
| | - David Quintanilla
- Department
of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
| | - Alexandra East-Seletsky
- Department
of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
| | - Evan R. Williams
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
- Department
of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Energy
Biosciences Institute, University of California at Berkeley, Berkeley, California 94720, United States
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45
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Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. Programmed Ribosomal Frameshifting Mediates Expression of the α-Carboxysome. J Mol Biol 2016; 428:153-164. [DOI: 10.1016/j.jmb.2015.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/04/2015] [Accepted: 11/12/2015] [Indexed: 01/24/2023]
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Abstract
Cyanobacteria are a diverse bacterial phylum whose members possess a high degree of ultrastructural organization and unique gene regulatory mechanisms. Unraveling this complexity will require the use of live-cell fluorescence microscopy, but is impeded by the inherent fluorescent background associated with light-harvesting pigments and the need to feed photosynthetic cells light. Here, we outline a roadmap for overcoming these challenges. Specifically, we show that although basic cyanobacterial biology creates challenging experimental constraints, these restrictions can be mitigated by the careful choice of fluorophores and microscope instrumentation. Many of these choices are motivated by recent successful live-cell studies. We therefore also highlight how live-cell imaging has advanced our understanding of bacterial microcompartments, circadian rhythm, and the organization and segregation of the bacterial nucleoid.
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Affiliation(s)
- Rayka Yokoo
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Rachel D Hood
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - David F Savage
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA.
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47
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Abstract
CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is easily targeted to bind and cleave a DNA sequence via a complementary RNA; this straightforward programmability has gained Cas9 rapid acceptance in the field of genetic engineering. While this technology has developed quickly, a number of challenges regarding Cas9 specificity, efficiency, fusion protein function, and spatiotemporal control within the cell remain. In this work, we develop a platform for constructing novel proteins to address these open questions. We demonstrate methods to either screen or select active Cas9 mutants and use the screening technique to isolate functional Cas9 variants with a heterologous PDZ domain inserted within the protein. As a proof of concept, these methods lay the groundwork for the future construction of diverse Cas9 proteins. Straightforward and accessible techniques for genetic editing are helping to elucidate biology in new and exciting ways; a platform to engineer new functionalities into Cas9 will help forge the next generation of genome-modifying tools.
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Affiliation(s)
- Benjamin L Oakes
- Department of Molecular & Cell Biology, University of California, Berkeley, California, USA
| | - Dana C Nadler
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - David F Savage
- Department of Molecular & Cell Biology, University of California, Berkeley, California, USA; Department of Chemistry, University of California, Berkeley, California, USA; Energy Biosciences Institute, University of California, Berkeley, California, USA.
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48
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Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS One 2013; 8:e76127. [PMID: 24023971 PMCID: PMC3762834 DOI: 10.1371/journal.pone.0076127] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 08/23/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Cyanobacteria play a significant role in the global carbon cycle. In Synechococcuselongatus, the 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 that colocalize with existing carboxysomes. These seeds contain little or no shell protein, but increase in RuBisCO content over several hours, during which time they are exposed to the solvent. The maturing seed is then enclosed by shell proteins, a rapid process that seals RuBisCO from the cytosol to establish a distinct, solvent-protected microenvironment that is oxidizing relative to the cytosol. These closure events can be spatially and temporally coincident with the appearance of a nascent daughter RuBisCO seed. CONCLUSIONS/SIGNIFICANCE Carboxysomes assemble in a stepwise fashion, inside-to-outside, revealing that cargo is the principle organizer of this compartment's biogenesis. Our observations of the spatial relationship of seeds to previously formed carboxysomes lead us to propose a model for carboxysome replication via sequential fission, polymerization, and encapsulation of their internal cargo.
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Affiliation(s)
- Anna H. Chen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Avi Robinson-Mosher
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - David F. Savage
- Department of Molecular and Cell Biology, Department of Chemistry and Energy Biosciences Institute, University of California, Berkeley, California, United States of America
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Jessica K. Polka
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
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Chen AH, Afonso B, Silver PA, Savage DF. Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. PLoS One 2012; 7:e47837. [PMID: 23112856 PMCID: PMC3480399 DOI: 10.1371/journal.pone.0047837] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 09/21/2012] [Indexed: 01/02/2023] Open
Abstract
The spatial and temporal control of chromosome duplication and segregation is crucial for proper cell division. While this process is well studied in eukaryotic and some prokaryotic organisms, relatively little is known about it in prokaryotic polyploids such as Synechococcus elongatus PCC 7942, which is known to possess one to eight copies of its single chromosome. Using a fluorescent repressor-operator system, S. elongatus chromosomes and chromosome replication forks were tagged and visualized. We found that chromosomal duplication is asynchronous and that the total number of chromosomes is correlated with cell length. Thus, replication is independent of cell cycle and coupled to cell growth. Replication events occur in a spatially random fashion. However, once assembled, replisomes move in a constrained manner. On the other hand, we found that segregation displays a striking spatial organization in some cells. Chromosomes transiently align along the major axis of the cell and timing of alignment was correlated to cell division. This mechanism likely contributes to the non-random segregation of chromosome copies to daughter cells.
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Affiliation(s)
- Anna H. Chen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bruno Afonso
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - David F. Savage
- Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, California, United States of America
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Abstract
Aquaporins are transmembrane channels that facilitate the permeation of water and small, uncharged amphipathic molecules across cellular membranes. One distinct aquaporin subfamily contains pure water channels, whereas a second subfamily contains channels that conduct small alditols such as glycerol, in addition to water. Distinction between these substrates is central to aquaporin function, though the contributions of protein structural motifs required for selectivity are not yet fully characterized. To address this question, we sequentially engineered three signature amino acids of the glycerol-conducting subfamily into the Escherichia coli water channel aquaporin Z (AqpZ). Functional analysis of these mutant channels showed a decrease in water permeability but not the expected increase in glycerol conduction. Using X-ray crystallography, we determined the atomic resolution structures of the mutant channels. The structures revealed a channel surprisingly similar in size to the wild-type AqpZ pore. Comparison with measured rates of transport showed that, as the size of the selectivity filter region of the channel approaches that of water, channel hydrophilicity dominated water conduction energetics. In contrast, the major determinant of selectivity for larger amphipathic molecules such as glycerol was channel cross-section size. Finally, we find that, although the selectivity filter region is indeed central to substrate transport, other structural elements that do not directly interact with the substrates, such as the loop connecting helices M6 and M7, and the C loop between helices C4 and C5, play an essential role in facilitating selectivity.
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Affiliation(s)
- David F. Savage
- Graduate Group in Biophysics, and
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Joseph D. O’Connell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Larry J. W. Miercke
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Janet Finer-Moore
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
| | - Robert M. Stroud
- Graduate Group in Biophysics, and
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517
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