1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
6
|
Shyntum DY, Nkomo NP, Shingange NL, Gricia AR, Bellieny-Rabelo D, Moleleki LN. The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator. Front Microbiol 2019; 10:2379. [PMID: 31681235 PMCID: PMC6813493 DOI: 10.3389/fmicb.2019.02379] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Received: 08/05/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022] Open
Abstract
The complexity of plant microbial communities provides a rich model for investigating biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) represents an emerging group of plant-pathogens causing soft rot/blackleg diseases resulting in economic losses worldwide in a variety of crops. A preliminary screening using next-generation sequencing of 16S rRNA comparatively analyzing healthy and diseased potato tubers, identified several taxa from Proteobacteria to Firmicutes as potential potato endophytes/plant pathogens. Subsequent to this, a range of molecular and computational techniques were used to determine the contribution of antimicrobial factors such as bacteriocins, carbapenem and type VI secretion system (T6SS), found in an aggressive SRE (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692) against these endophytes/plant pathogens. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only the Pcb1692 pyocin seems to play a role in growth inhibition. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Finally, the results demonstrated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta. IMPORTANCE Soft rot Enterobacteriaceae (SRE) represents important phytopathogens causing soft rot/blackleg diseases in a variety of crops leading to huge economic losses worldwide. These pathogens have been isolated alongside other bacteria from different environments such as potato tubers, stems, roots and from the soil. In these environments, SREs coexist with other bacteria where they have to compete for scarce nutrients and other resources. In this report, we show that Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692, which represents one of the SREs, inhibits growth of several different bacteria by producing different antimicrobial compounds. These antimicrobial compounds can be secreted inside or outside the plant host, allowing Pcb1692 to effectively colonize different types of ecological niches. By analyzing the genome sequences of several SREs, we show that other SREs likely deploy similar antimicrobials to target other bacteria.
Collapse
Affiliation(s)
- Divine Yufetar Shyntum
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntombikayise Precious Nkomo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ntwanano Luann Shingange
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Alessandro Rino Gricia
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Daniel Bellieny-Rabelo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry, Agriculture and Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| |
Collapse
|