1
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Dai J, Wilhelm KB, Bischoff AJ, Pereira JH, Dedeo MT, García-Almedina DM, Adams PD, Groves JT, Francis MB. A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins. Small 2023; 19:e2207805. [PMID: 36811150 DOI: 10.1002/smll.202207805] [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: 12/13/2022] [Revised: 01/26/2023] [Indexed: 05/18/2023]
Abstract
Photosynthetic light harvesting requires efficient energy transfer within dynamic networks of light-harvesting complexes embedded within phospholipid membranes. Artificial light-harvesting models are valuable tools for understanding the structural features underpinning energy absorption and transfer within chromophore arrays. Here, a method for attaching a protein-based light-harvesting model to a planar, fluid supported lipid bilayer (SLB) is developed. The protein model consists of the tobacco mosaic viral capsid proteins that are gene-doubled to create a tandem dimer (dTMV). Assemblies of dTMV break the facial symmetry of the double disk to allow for differentiation between the disk faces. A single reactive lysine residue is incorporated into the dTMV assemblies for the site-selective attachment of chromophores for light absorption. On the opposing dTMV face, a cysteine residue is incorporated for the bioconjugation of a peptide containing a polyhistidine tag for association with SLBs. The dual-modified dTMV complexes show significant association with SLBs and exhibit mobility on the bilayer. The techniques used herein offer a new method for protein-surface attachment and provide a platform for evaluating excited state energy transfer events in a dynamic, fully synthetic artificial light-harvesting system.
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Affiliation(s)
- Jing Dai
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kiera B Wilhelm
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Amanda J Bischoff
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jose H Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michel T Dedeo
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Paul D Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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2
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Bloomer BJ, Natoli SN, Garcia-Borràs M, Pereira JH, Hu DB, Adams PD, Houk KN, Clark DS, Hartwig JF. Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics. Nat Catal 2023. [DOI: 10.1038/s41929-022-00899-9] [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: 01/13/2023]
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3
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Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. Structural plasticity enables evolution and innovation of RuBisCO assemblies. Sci Adv 2022; 8:eadc9440. [PMID: 36026446 PMCID: PMC9417184 DOI: 10.1126/sciadv.adc9440] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.
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Affiliation(s)
- Albert K. Liu
- 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
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Jose H. Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alexander J. Kehl
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Daniel J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Simon K. S. Chu
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Douglas M. Banda
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D. Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, CA 95616, USA
- Chemistry Department, University of California, Davis, Davis, CA 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Sacramento, Sacramento, CA 95616, USA
| | - Patrick M. Shih
- 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
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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4
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Macdonald S, Pereira JH, Liu F, Tegl G, DeGiovanni A, Wardman JF, Deutsch S, Yoshikuni Y, Adams PD, Withers SG. A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides. ACS Cent Sci 2022; 8:430-440. [PMID: 35505869 PMCID: PMC9052796 DOI: 10.1021/acscentsci.1c01570] [Citation(s) in RCA: 2] [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] [Received: 12/22/2021] [Indexed: 05/14/2023]
Abstract
The considerable utility of glycoside phosphorylases (GPs) has led to substantial efforts over the past two decades to expand the breadth of known GP activities. Driven largely by the increase of available genomic DNA sequence data, the gap between the number of sequences in the carbohydrate active enzyme database (CAZy DB) and its functionally characterized members continues to grow. This wealth of sequence data presented an exciting opportunity to explore the ever-expanding CAZy DB to discover new GPs with never-before-described functionalities. Utilizing an in silico sequence analysis of CAZy family GH94, we discovered and then functionally and structurally characterized the new GP β-1,3-N-acetylglucosaminide phosphorylase. This new GP was sourced from the genome of the cell-wall-less Mollicute bacterium, Acholeplasma laidlawii and was found to synthesize β-1,3-linked N-acetylglucosaminide linkages. The resulting poly-β-1,3-N-acetylglucosamine represents a new, previously undescribed biopolymer that completes the set of possible β-linked GlcNAc homopolysaccharides together with chitin (β-1,4) and PNAG (poly-β-1,6-N-acetylglucosamine). The new biopolymer was denoted acholetin, a combination of the genus Acholeplasma and the polysaccharide chitin, and the new GP was thus denoted acholetin phosphorylase (AchP). Use of the reverse phosphorolysis action of AchP provides an efficient method to enzymatically synthesize acholetin, which is a new biodegradable polymeric material.
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Affiliation(s)
- Spencer
S. Macdonald
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jose H. Pereira
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Feng Liu
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Gregor Tegl
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Andy DeGiovanni
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob F. Wardman
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Biochemistry & Molecular Biology, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Samuel Deutsch
- The US Department
of Energy Joint Genome Institute, Lawrence
Berkley National Laboratory, Berkeley, California 94720, United States
| | - Yasuo Yoshikuni
- The US Department
of Energy Joint Genome Institute, Lawrence
Berkley National Laboratory, Berkeley, California 94720, United States
| | - Paul D. Adams
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California
Berkeley, Berkeley, California 94720, United States
| | - Stephen G. Withers
- Michael
Smith Laboratories, University of British
Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department
of Biochemistry & Molecular Biology, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
- E-mail:
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5
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Wagschal K, Chan VJ, Pereira JH, Zwart PH, Sankaran B. Chromohalobacter salixigens Uronate Dehydrogenase: Directed Evolution for Improved Thermal Stability and Mutant CsUDH-inc X-ray Crystal Structure. Process Biochem 2022; 114:185-192. [PMID: 35462854 PMCID: PMC9031460 DOI: 10.1016/j.procbio.2020.02.013] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chromohalobacter salixigens contains a uronate dehydrogenase termed CsUDH that can convert uronic acids to their corresponding C1,C6-dicarboxy aldaric acids, an important enzyme reaction applicable for biotechnological use of sugar acids. To increase the thermal stability of this enzyme for biotechnological processes, directed evolution using gene family shuffling was applied, and the hits selected from 2-tier screening of a shuffled gene family library contained in total 16 mutations, only some of which when examined individually appreciably increased thermal stability. Most mutations, while having minimal or no effect on thermal stability when tested in isolation, were found to exhibit synergy when combined; CsUDH-inc containing all 16 mutations had ΔK t 0.5 +18 °C, such that k cat was unaffected by incubation for 1 hr at ~70 °C. X-ray crystal structure of CsUDH-inc showed tight packing of the mutated residue side-chains, and comparison of rescaled B-values showed no obvious differences between wild type and mutant structures. Activity of CsUDH-inc was severely depressed on glucuronic and galacturonic acids. Combining select combinations of only three mutations resulted in good or comparable activity on these uronic acids, while maintaining some improved thermostability with ΔK t 0.5 ~+ 10 °C, indicating potential to further thermally optimize CsUDH for hyperthermophilic reaction environments.
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Affiliation(s)
- Kurt Wagschal
- USDA Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA,Corresponding Authors: ,
| | - Victor J. Chan
- USDA Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA
| | - Jose H. Pereira
- Molecular Biophysics and Integrated Bioimaging, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Peter H. Zwart
- Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratories,1 Cyclotron Road, Berkeley, CA, 94703, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA,Corresponding Authors: ,
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6
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Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, Pereira JH, Rodrigues AV, van Dijk AA, Ebrecht AC, Opperman DJ, Sagmeister T, Buhlheller C, Pavkov-Keller T, Rathinaswamy MK, Dalwadi U, Yip CK, Burke JE, Garcia KC, Grishin NV, Adams PD, Read RJ, Baker D. Accurate prediction of protein structures and interactions using a three-track neural network. Science 2021; 373:871-876. [PMID: 34282049 PMCID: PMC7612213 DOI: 10.1126/science.abj8754] [Citation(s) in RCA: 2062] [Impact Index Per Article: 687.3] [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: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 01/17/2023]
Abstract
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.
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Affiliation(s)
- Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sergey Ovchinnikov
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA 02138, USA
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Claudia Millán
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Carson Adams
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Caleb R Glassman
- Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andy DeGiovanni
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jose H Pereira
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andria V Rodrigues
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alberdina A van Dijk
- Department of Biochemistry, Focus Area Human Metabolomics, North-West University, 2531 Potchefstroom, South Africa
| | - Ana C Ebrecht
- Department of Biochemistry, Focus Area Human Metabolomics, North-West University, 2531 Potchefstroom, South Africa
| | - Diederik J Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein 9300, South Africa
| | - Theo Sagmeister
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Christoph Buhlheller
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- Medical University of Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - K Christopher Garcia
- Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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7
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Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. Novel bacterial clade reveals origin of form I Rubisco. Nat Plants 2020; 6:1158-1166. [PMID: 32868887 DOI: 10.1038/s41477-020-00762-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Rubisco sustains the biosphere through the fixation of CO2 into biomass. In plants and cyanobacteria, form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco forms lack small subunits. The rise of the form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco's evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to form I Rubisco that evolved without small subunits. This clade diverged before the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.
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Affiliation(s)
- Douglas M Banda
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jose H Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Albert K Liu
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | | | - Paul D Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
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8
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Curran SC, Pereira JH, Baluyot MJ, Lake J, Puetz H, Rosenburg DJ, Adams P, Keasling JD. Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Biochemistry 2020; 59:1630-1639. [PMID: 32250597 DOI: 10.1021/acs.biochem.0c00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
α/β hydrolases make up a large and diverse protein superfamily. In natural product biosynthesis, cis-acting thioesterase α/β hydrolases can terminate biosynthetic assembly lines and release products by hydrolyzing or cyclizing the biosynthetic intermediate. Thioesterases can also act in trans, removing aberrant intermediates and restarting stalled biosynthesis. Knockout of this "editing" function leads to reduced product titers. The borrelidin biosynthetic gene cluster from Streptomyces parvulus Tü4055 contains a hitherto uncharacterized stand-alone thioesterase, borB. In this work, we demonstrate that purified BorB cleaves acyl substrates with a preference for propionate, which supports the hypothesis that it is also an editing thioesterase. The crystal structure of BorB shows a wedgelike hydrophobic substrate binding crevice that limits substrate length. To investigate the structure-function relationship, we made chimeric BorB variants using loop regions from characterized homologues with different specificities. BorB chimeras slightly reduced activity, arguing that the modified region is a not major determinant of substrate preference. The structure-function relationships described here contribute to the process of elimination for understanding thioesterase specificity and, ultimately, engineering and applying trans-acting thioesterases in biosynthetic assembly lines.
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Affiliation(s)
- Samuel C Curran
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jose H Pereira
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Marian-Joy Baluyot
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Julie Lake
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Hendrik Puetz
- Department of Biochemistry, University of Cologne, 50923 Albertus-Magnus-Platz, Cologne 51149, Germany.,Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | | | - Paul Adams
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
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9
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Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Jungle Express is a versatile repressor system for tight transcriptional control. Nat Commun 2018; 9:3617. [PMID: 30190458 PMCID: PMC6127294 DOI: 10.1038/s41467-018-05857-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 08/30/2017] [Accepted: 07/30/2018] [Indexed: 11/09/2022] Open
Abstract
Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of 'Jungle Express', an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.
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Affiliation(s)
- Thomas L Ruegg
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Institute of Botany, University of Basel, 4001, Basel, Switzerland
| | - Jose H Pereira
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joseph C Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Andy DeGiovanni
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Pavel Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Giovani P Tomaleri
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Michael P Thelen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
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10
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Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD. Engineering glycoside hydrolase stability by the introduction of zinc binding. Acta Crystallogr D Struct Biol 2018; 74:702-710. [PMID: 29968680 PMCID: PMC6038386 DOI: 10.1107/s2059798318006678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/31/2018] [Accepted: 05/01/2018] [Indexed: 02/04/2023] Open
Abstract
The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance. The amino-acid sequence of J30 shows comparably low identity to those of previously analyzed enzymes. As an enzyme that combines a well measurable activity with a relatively low optimal temperature (50°C) and a modest thermal tolerance, it offers the potential for structural optimization aimed at increased stability. Here, the crystal structure of wild-type J30 is presented along with that of a designed triple-mutant variant with improved characteristics for industrial applications. Through the introduction of a structural Zn2+ site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C.
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Affiliation(s)
- Thomas L. Ellinghaus
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jose H. Pereira
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan P. McAndrew
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ditte H. Welner
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andy M. DeGiovanni
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joel M. Guenther
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Huu M. Tran
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Taya Feldman
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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11
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Pereira JH, McAndrew RP, Tomaleri GP, Adams PD. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. J Appl Crystallogr 2017; 50:1352-1358. [PMID: 29021733 PMCID: PMC5627680 DOI: 10.1107/s1600576717011347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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] [Received: 06/27/2017] [Accepted: 08/01/2017] [Indexed: 01/29/2023] Open
Abstract
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.
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Affiliation(s)
- Jose H. Pereira
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Ryan P. McAndrew
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | | | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
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12
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Eudes A, Pereira JH, Yogiswara S, Wang G, Teixeira Benites V, Baidoo EEK, Lee TS, Adams PD, Keasling JD, Loqué D. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin. Plant Cell Physiol 2016; 57:568-79. [PMID: 26858288 PMCID: PMC4790474 DOI: 10.1093/pcp/pcw016] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/13/2016] [Indexed: 05/19/2023]
Abstract
Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity to acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jose H Pereira
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Bioengineering & Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - George Wang
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Graduate Program, San Francisco State University, San Francisco, CA 94132, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Bioengineering & Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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13
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Pereira JH, Petchprayoon C, Hoepker AC, Moriarty NW, Fink SJ, Cecere G, Paterson I, Adams PD, Marriott G. Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues. ChemMedChem 2014; 9:2286-93. [PMID: 25047814 DOI: 10.1002/cmdc.201402150] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 04/28/2014] [Indexed: 11/12/2022]
Abstract
The actin filament-binding and filament-severing activities of the aplyronine, kabiramide, and reidispongiolide families of marine macrolides are located within the hydrophobic tail region of the molecule. Two synthetic tail analogues of aplyronine C (SF-01 and GC-04) are shown to bind to G-actin with dissociation constants of (285±33) and (132±13) nM, respectively. The crystal structures of actin complexes with GC-04, SF-01, and kabiramide C reveal a conserved mode of tail binding within the cleft that forms between subdomains (SD) 1 and 3. Our studies support the view that filament severing is brought about by specific binding of the tail region to the SD1/SD3 cleft on the upper protomer, which displaces loop-D from the lower protomer on the same half-filament. With previous studies showing that the GC-04 analogue can sever actin filaments, it is argued that the shorter complex lifetime of tail analogues with F-actin would make them more effective at severing filaments compared with plasma gelsolin. Structure-based analyses are used to suggest more reactive or targetable forms of GC-04 and SF-01, which may serve to boost the capacity of the serum actin scavenging system, to generate antibody conjugates against tumor cell antigens, and to decrease sputum viscosity in children with cystic fibrosis.
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Affiliation(s)
- Jose H Pereira
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA)
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14
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Chen Z, Pereira JH, Liu H, Tran HM, Hsu NSY, Dibble D, Singh S, Adams PD, Sapra R, Hadi MZ, Simmons BA, Sale KL. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass. PLoS One 2013; 8:e79725. [PMID: 24244549 PMCID: PMC3828181 DOI: 10.1371/journal.pone.0079725] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
Ionic liquid pretreatment of biomass has been shown to greatly reduce the recalcitrance of lignocellulosic biomass, resulting in improved sugar yields after enzymatic saccharification. However, even under these improved saccharification conditions the cost of enzymes still represents a significant proportion of the total cost of producing sugars and ultimately fuels from lignocellulosic biomass. Much of the high cost of enzymes is due to the low catalytic efficiency and stability of lignocellulolytic enzymes, especially cellulases, under conditions that include high temperatures and the presence of residual pretreatment chemicals, such as acids, organic solvents, bases, or ionic liquids. Improving the efficiency of the saccharification process on ionic liquid pretreated biomass will facilitate reduced enzyme loading and cost. Thermophilic cellulases have been shown to be stable and active in ionic liquids but their activity is typically at lower levels. Cel5A_Tma, a thermophilic endoglucanase from Thermotoga maritima, is highly active on cellulosic substrates and is stable in ionic liquid environments. Here, our motivation was to engineer mutants of Cel5A_Tma with higher activity on 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) pretreated biomass. We developed a robotic platform to screen a random mutagenesis library of Cel5A_Tma. Twelve mutants with 25–42% improvement in specific activity on carboxymethyl cellulose and up to 30% improvement on ionic-liquid pretreated switchgrass were successfully isolated and characterized from a library of twenty thousand variants. Interestingly, most of the mutations in the improved variants are located distally to the active site on the protein surface and are not directly involved with substrate binding.
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Affiliation(s)
- Zhiwei Chen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Jose H. Pereira
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hanbin Liu
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Huu M. Tran
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Nathan S. Y. Hsu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dean Dibble
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Paul D. Adams
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Rajat Sapra
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Masood Z. Hadi
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Blake A. Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
| | - Kenneth L. Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
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15
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Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams PD. Mechanism of nucleotide sensing in group II chaperonins. EMBO J 2012. [DOI: 10.1038/emboj.2012.245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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16
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Pereira JH, Goh EB, Keasling JD, Beller HR, Adams PD. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus. Acta Crystallogr D Biol Crystallogr 2012; 68:1320-8. [PMID: 22993086 PMCID: PMC3447401 DOI: 10.1107/s0907444912028351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/22/2012] [Indexed: 11/11/2022]
Abstract
Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.
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Affiliation(s)
- Jose H. Pereira
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ee-Been Goh
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Harry R. Beller
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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17
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Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin AP, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem 2012; 287:25335-43. [PMID: 22645145 DOI: 10.1074/jbc.m112.362640] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymes are traditionally viewed as having exquisite substrate specificity; however, recent evidence supports the notion that many enzymes have evolved activities against a range of substrates. The diversity of activities across glycoside hydrolase family 5 (GH5) suggests that this family of enzymes may contain numerous members with activities on multiple substrates. In this study, we combined structure- and sequence-based phylogenetic analysis with biochemical characterization to survey the prevalence of dual specificity for glucan- and mannan-based substrates in the GH5 family. Examination of amino acid profile differences between the subfamilies led to the identification and subsequent experimental confirmation of an active site motif indicative of dual specificity. The motif enabled us to successfully discover several new dually specific members of GH5, and this pattern is present in over 70 other enzymes, strongly suggesting that dual endoglucanase-mannanase activity is widespread in this family. In addition, reinstatement of the conserved motif in a wild type member of GH5 enhanced its catalytic efficiency on glucan and mannan substrates by 175 and 1,600%, respectively. Phylogenetic examination of other GH families further indicates that the prevalence of enzyme multispecificity in GHs may be greater than has been experimentally characterized. Single domain multispecific GHs may be exploited for developing improved enzyme cocktails or facile engineering of microbial hosts for consolidated bioprocessing of lignocellulose.
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Affiliation(s)
- Zhiwei Chen
- Joint BioEnergy Institute, Emeryville, California 94608, USA
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18
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McAndrew RP, Peralta-Yahya PP, DeGiovanni A, Pereira JH, Hadi MZ, Keasling JD, Adams PD. Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production. Structure 2012; 19:1876-84. [PMID: 22153510 DOI: 10.1016/j.str.2011.09.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 09/09/2011] [Accepted: 09/12/2011] [Indexed: 11/30/2022]
Abstract
The sesquiterpene bisabolene was recently identified as a biosynthetic precursor to bisabolane, an advanced biofuel with physicochemical properties similar to those of D2 diesel. High-titer microbial bisabolene production was achieved using Abies grandis α-bisabolene synthase (AgBIS). Here, we report the structure of AgBIS, a three-domain plant sesquiterpene synthase, crystallized in its apo form and bound to five different inhibitors. Structural and biochemical characterization of the AgBIS terpene synthase Class I active site leads us to propose a catalytic mechanism for the cyclization of farnesyl diphosphate into bisabolene via a bisabolyl cation intermediate. Further, we describe the nonfunctional AgBIS Class II active site whose high similarity to bifunctional diterpene synthases makes it an important link in understanding terpene synthase evolution. Practically, the AgBIS crystal structure is important in future protein engineering efforts to increase the microbial production of bisabolene.
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Affiliation(s)
- Ryan P McAndrew
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA 94608, USA
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19
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Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams PD. Mechanism of nucleotide sensing in group II chaperonins. EMBO J 2011; 31:731-40. [PMID: 22193720 DOI: 10.1038/emboj.2011.468] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 11/28/2011] [Indexed: 11/09/2022] Open
Abstract
Group II chaperonins mediate protein folding in an ATP-dependent manner in eukaryotes and archaea. The binding of ATP and subsequent hydrolysis promotes the closure of the multi-subunit rings where protein folding occurs. The mechanism by which local changes in the nucleotide-binding site are communicated between individual subunits is unknown. The crystal structure of the archaeal chaperonin from Methanococcus maripaludis in several nucleotides bound states reveals the local conformational changes associated with ATP hydrolysis. Residue Lys-161, which is extremely conserved among group II chaperonins, forms interactions with the γ-phosphate of ATP but shows a different orientation in the presence of ADP. The loss of the ATP γ-phosphate interaction with Lys-161 in the ADP state promotes a significant rearrangement of a loop consisting of residues 160-169. We propose that Lys-161 functions as an ATP sensor and that 160-169 constitutes a nucleotide-sensing loop (NSL) that monitors the presence of the γ-phosphate. Functional analysis using NSL mutants shows a significant decrease in ATPase activity, suggesting that the NSL is involved in timing of the protein folding cycle.
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Affiliation(s)
- Jose H Pereira
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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20
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Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol 2010; 172:372-9. [DOI: 10.1016/j.jsb.2010.06.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/16/2010] [Accepted: 06/23/2010] [Indexed: 11/29/2022]
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Pereira JH, Ralston CY, Douglas NR, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams PD. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem 2010; 285:27958-66. [PMID: 20573955 PMCID: PMC2934662 DOI: 10.1074/jbc.m110.125344] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [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: 03/19/2010] [Revised: 06/02/2010] [Indexed: 11/06/2022] Open
Abstract
Chaperonins are large protein complexes consisting of two stacked multisubunit rings, which open and close in an ATP-dependent manner to create a protected environment for protein folding. Here, we describe the first crystal structure of a group II chaperonin in an open conformation. We have obtained structures of the archaeal chaperonin from Methanococcus maripaludis in both a peptide acceptor (open) state and a protein folding (closed) state. In contrast with group I chaperonins, in which the equatorial domains share a similar conformation between the open and closed states and the largest motions occurs at the intermediate and apical domains, the three domains of the archaeal chaperonin subunit reorient as a single rigid body. The large rotation observed from the open state to the closed state results in a 65% decrease of the folding chamber volume and creates a highly hydrophilic surface inside the cage. These results suggest a completely distinct closing mechanism in the group II chaperonins as compared with the group I chaperonins.
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Affiliation(s)
- Jose H. Pereira
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Corie Y. Ralston
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Nicholai R. Douglas
- the Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305
| | - Daniel Meyer
- the Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305
| | - Kelly M. Knee
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Daniel R. Goulet
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Jonathan A. King
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Judith Frydman
- the Department of Biological Sciences and BioX Program, Stanford University, Stanford, California 94305
| | - Paul D. Adams
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- the Department of Bioengineering, University of California, Berkeley, California 94720
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Pereira JH, Palande DD, Narayanakumar TS, Subramanian AS, Gschmeissner S, Wilkinson M. Nerve repair by denatured muscle autografts promotes sustained sensory recovery in leprosy. ACTA ACUST UNITED AC 2008; 90:220-4. [PMID: 18256092 DOI: 10.1302/0301-620x.90b2.19586] [Citation(s) in RCA: 10] [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: 11/05/2022]
Abstract
A total of 38 patients with leprosy and localised nerve damage (11 median at the wrist and 37 posterior tibial at the ankle) were treated by 48 freeze-thawed skeletal muscle autografts ranging between 2.5 cm and 14 cm in length. Sensory recovery was noted in 34 patients (89%) and was maintained during a mean period of follow-up of 12.6 years (4 to 14). After grafting the median nerve all patients remained free of ulcers and blisters, ten demonstrated perception of texture and eight recognised weighted pins. In the posterior tibial nerve group, 24 of 30 repairs (80%) resulted in improved healing of the ulcers and 26 (87%) demonstrated discrimination of texture. Quality of life and hand and foot questionnaires showed improvement; the activities of daily living scores improved in six of seven after operations on the hand, and in 14 of 22 after procedures on the foot. Another benefit was subjective improvement in the opposite limb, probably because of the protective effect of better function in the operated side. This study demonstrates that nerve/muscle interposition grafting in leprosy results in consistent sensory recovery and high levels of patient satisfaction. Ten of 11 patients with hand operations and 22 of 25 with procedures to the foot showed sensory recovery in at least one modality.
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Affiliation(s)
- J H Pereira
- James Paget University Hospital NHS Foundation Trust, Lowestoft Road, Gorleston, Great Yarmouth, Norfolk NR31 6LA, UK.
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Groneberg DA, Tai YF, Almari AF, Pereira JH. Gastrointestinal: diaphragmatic hernia. J Gastroenterol Hepatol 2001; 16:1305. [PMID: 11903752 DOI: 10.1046/j.1440-1746.2001.02524.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- D A Groneberg
- Department of Surgery, James Paget Hospital, Gorleston, Norfolk, United Kingdom
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Canduri F, Delatorre P, Fadel V, Lorenzi CC, Pereira JH, Olivieri JR, Ruggiero Neto J, Konno K, Palma MS, Yamane T, de Azevedo WF. Crystallization and preliminary X-ray diffraction analysis of a eumenine mastoparan toxin: a new class of mast-cell degranulating peptide in the wasp venom. Acta Crystallogr D Biol Crystallogr 2000; 56:1434-6. [PMID: 11053843 DOI: 10.1107/s0907444900009719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/1999] [Accepted: 07/11/2000] [Indexed: 11/10/2022]
Abstract
Mastoparans are tetradecapeptides found to be the major component of vespid venoms. A mastoparan toxin isolated from the venom of Anterhynchium flavomarginatum micado has been crystallized and X-ray diffraction data collected to 2.7 A resolution using a synchrotron-radiation source. Crystals were determined to belong to the space group P6(2)22 (P6(4)22). This is the first mastoparan to be crystallized and will provide further insights into the conformational significance of mastoparan toxins with respect to their potency and activity in G-protein regulation.
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Affiliation(s)
- F Canduri
- Departamento de Física, IBILCE, UNESP, CP 136, CEP 15054-000, São José Rio Preto, SP, Brazil
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Pereira JH, Bowden RE, Narayanakumar TS, Gschmeissner SE. Peripheral nerve reconstruction using denatured muscle autografts for restoring protective sensation in hands and feet of leprosy patients. Indian J Lepr 1996; 68:83-91. [PMID: 8727118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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de Blaquière GE, Curtis J, Pereira JH, Turk JL. Denatured muscle grafts for nerve repair in an experimental model of nerve damage in leprosy. 1. A functional and morphometric study. Int J Lepr Other Mycobact Dis 1994; 62:55-63. [PMID: 8189090] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The effectiveness of denatured autologous muscle grafts for nerve repair in an experimental model of leprosy was assessed. Nerve damage resembling that caused by Mycobacterium leprae in humans was induced by the injection of cobalt-irradiated M. leprae into the tibial nerve of guinea pigs. At the time of maximum functional loss, caused by the formation of a granuloma within the nerve, the area of damage was excised and a denatured autologous muscle graft was used to repair the nerve. Assessment of nerve regeneration through the graft was made using clinical, electrophysiological and microscopic morphometric analysis at intervals up to 20 weeks. The results were compared with regeneration after grafting of a normal nerve. Clinically, some motor and sensory recovery occurred in all of the graft recipients in the normal nerve by 8 weeks, and by 11 weeks in the recipients of grafts in the granulomatous nerve. Full sensory recovery occurred in all but one animal by 20 weeks. Motor function recovered to near normal levels at 14 weeks after repair of the normal nerve but, at 20 weeks, there was variation in motor recovery after repair of the granulomatous nerve. Electrophysiology showed increased conduction velocity of the nerve fibers at each time-point. The conduction velocity at 8 weeks after grafting of the normal nerve was similar to that at 12 weeks after grafting of the granulomatous nerve. Morphometry showed an increasing number of myelinated fibers repopulating the distal nerve up to 20 weeks. Myelin fiber numbers, at this time, were one third of normal after repair of the granulomatous nerve and two thirds after repair of the normal nerve.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- G E de Blaquière
- Department of Pathology, Royal College of Surgeons of England, London, U.K
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Santamaria L, Terenghi G, Curtis J, de Blaquière GE, Pereira JH, Turk JL, Polak JM. Denatured muscle grafts for nerve repair in an experimental model of nerve damage in leprosy. 2. Recovery of peripheral peptide-containing nerves assessed by quantitative immunohistochemical study. Int J Lepr Other Mycobact Dis 1994; 62:64-74. [PMID: 7514642] [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] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A marked depletion of neuropeptide-immunoreactive nerves, a consequence of the nerve damage which is commonly found in leprosy, has been reported in peripheral tissues of leprosy patients and of a leprosy animal model. The aim of this study was to investigate peripheral reinnervation following a denatured autologous muscle graft in an animal model of leprosy nerve damage. Possible reinnervation of the foot-pad skin was studied by immunohistochemistry using antisera to the neuronal marker protein gene product 9.5 (PGP), the neuropeptides calcitonin gene-related peptide (CGRP), substance P (SP), vasoactive intestinal peptide (VIP), and the C-flanking peptide of neuropeptide Y (CPON). The extent of the reinnervation process was assessed by image analysis quantification at different time points. At 8 weeks after muscle grafting, there were small numbers of immunoreactive nerves (p < 0.05). At 12, 16, and 20 weeks postoperatively there was a gradual increase in all immunostaining. At 20 weeks, no significant difference was found for PGP-, CGRP-, and SP-immunoreactive nerves in the epidermal and subepidermal layers compared to control (contralateral) tissue. In experimental tissue the recovery of immunoreactive nerves around sweat glands took longer (up to 12 weeks) than in other skin compartments, but after that time the recovery was rapid and at 20 weeks no difference was measured for VIP-immunoreactive nerves in comparison with controls. Around blood vessels, the recovery of CGRP- and CPON-immunoreactive fibers was slow, and at 20 weeks a difference with control samples (p < 0.01) was noted. In the same area, there was no significant difference for PGP immunoreactivity between controls and tissues at 20 weeks. In contrast, the immunoreactive nerve bundles in the dermis showed a faster recovery than nerves in other skin areas, with amounts similar to controls at 20 weeks. The significant recovery of immunoreactive nerves, in particular of those containing sensory neuropeptide, is consistent with the described functional recovery.
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Affiliation(s)
- L Santamaria
- Department of Histochemistry, Royal Postgraduate Medical School, Hammersmith Hospital, London, U.K
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Miko TL, Gschmeissner SE, le Maitre C, Kinfu Y, Kazen R, Pereira JH. Regeneration at the predilective damage sites of nerve trunks in treated leprosy. LEPROSY REV 1993; 64:330-7. [PMID: 8127220 DOI: 10.5935/0305-7518.19930038] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Superficially located large and medium sized mixed peripheral limb nerves in active leprosy have previously been shown to have well-recognized fusiform swellings. It is generally agreed that these are the sites of predilective nerve involvement where the severest degeneration and fibrosis occur. A semiquantitative histopathological study on one of these sites, the flexor retinaculum region of the posterior tibial nerve, has been carried out on 14 treated leprosy patients who suffered from total sensory loss to the foot for between 2 and 40 years. The following observations were made: (1) large-scale nerve regeneration was present as characterized by numerous Schwann cells and unmyelinated axons which formed regeneration clusters; (2) thick myelinated axons were either absent or present only in very low numbers; (3) the intraneural fibrosis was usually not severe; (4) the presence of active inflammation probably interfered with nerve regeneration; (5) it appeared that this regeneration started shortly after the onset of therapy and persisted for decades; (6) lepromatous cases were characterized by evenly distributed pathology, whereas borderline tuberculoid cases had an unevenly distributed pathology; (7) the massive nerve regeneration observed was functionally ineffective--these findings indicate that the total nerve damage may affect the more peripheral nerve branches.
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Affiliation(s)
- T L Miko
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Pereira JH, Bowden RE, Gattuso JM, Norris RW. Comparison of results of repair of digital nerves by denatured muscle grafts and end-to-end sutures. J Hand Surg Br 1991; 16:519-23. [PMID: 1791363 DOI: 10.1016/0266-7681(91)90107-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A further report is made on patients with primary and delayed repair of digital nerves with autogenous denatured muscle grafts. There was evidence of continued improvement in threshold response to tactile stimuli, and discriminative function. These results were superior to those in 24 patients with conventional end-to-end sutures on clinical testing.
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Affiliation(s)
- J H Pereira
- Department of Anatomy, Royal College of Surgeons of England, East Grinstead
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Abstract
Autologous muscle grafts were used to repair 12 mixed peripheral nerves (9 posterior tibial, 3 median) in 10 patients with leprosy who had total anaesthesia and analgesia of the area supplied by the nerve. Postoperatively, 7 patients reported improved sensation in the foot or hand, with a return of vibration sense and joint position sense in 11 and of perception of a 10 g pin in 5; the ability to sweat in the affected area was also restored in 7.
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Affiliation(s)
- J H Pereira
- Royal College of Surgeons of England, London, UK
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Affiliation(s)
- S E Gschmeissner
- Electronmicroscopic Unit, Imperial Cancer Research Fund, London, England
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Abstract
Mycobacteria were present in 4 out of 8 mixed peripheral nerve trunks from patients (3 BT and 1 BL) treated with DDS and/or MDT for periods ranging from 21 months to 8 years. Most of the bacilli appeared to be 'whole'. Nerve destruction with areas of granulomatous infiltration appeared more active than expected. Possible reasons for a continued presence of bacilli in treated nerves and its implications in 'relapse' are discussed.
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Affiliation(s)
- J H Pereira
- Department of Anatomy, Royal College of Surgeons of England, East Grinstead
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Abstract
A review was carried out on 10 patients with superficial transitional cell carcinoma of the bladder (Ta lesions) that were causing ureteric obstruction. Evidence of upper tract obstruction did not necessarily indicate deep invasion.
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Affiliation(s)
- J H Pereira
- Department of General Surgery, Luton and Dunstable Hospital
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Pereira JH, Cowley SA, Gschmeissner SE, Bowden RE, Turk JL. Denatured muscle grafts for nerve repair. An experimental model of nerve damage in leprosy. J Bone Joint Surg Br 1990; 72:874-80. [PMID: 2170419 DOI: 10.1302/0301-620x.72b5.2170419] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
About 20% of patients with leprosy develop localised granulomatous lesions in peripheral nerves. We report experiments in guinea-pigs in which freeze-thawed autogenous muscle grafts were used for the treatment of such mycobacterial granulomas. Granulomas were induced in guinea-pig tibial nerves and the animals were left for 7 to 100 days in order to assess maximal damage. The local area of nerve damage was then excised and the gap filled with denatured muscle grafts. Clinical assessment after periods up to 150 days showed good sensory and motor recovery which correlated well with the histological findings. The muscle graft technique may be of value for the treatment of chronic nerve lesions in selected cases of leprosy.
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Affiliation(s)
- J H Pereira
- Department of Anatomy, Royal College of Surgeons, London, England
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