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Zhao X, Zhao Y, Zeng QY, Liu CJ. Cytochrome b5 diversity in green lineages preceded the evolution of syringyl lignin biosynthesis. THE PLANT CELL 2024; 36:2709-2728. [PMID: 38657101 PMCID: PMC11218783 DOI: 10.1093/plcell/koae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Lignin production marked a milestone in vascular plant evolution, and the emergence of syringyl (S) lignin is lineage specific. S-lignin biosynthesis in angiosperms, mediated by ferulate 5-hydroxylase (F5H, CYP84A1), has been considered a recent evolutionary event. F5H uniquely requires the cytochrome b5 protein CB5D as an obligatory redox partner for catalysis. However, it remains unclear how CB5D functionality originated and whether it coevolved with F5H. We reveal here the ancient evolution of CB5D-type function supporting F5H-catalyzed S-lignin biosynthesis. CB5D emerged in charophyte algae, the closest relatives of land plants, and is conserved and proliferated in embryophytes, especially in angiosperms, suggesting functional diversification of the CB5 family before terrestrialization. A sequence motif containing acidic amino residues in Helix 5 of the CB5 heme-binding domain contributes to the retention of CB5D function in land plants but not in algae. Notably, CB5s in the S-lignin-producing lycophyte Selaginella lack these residues, resulting in no CB5D-type function. An independently evolved S-lignin biosynthetic F5H (CYP788A1) in Selaginella relies on NADPH-dependent cytochrome P450 reductase as sole redox partner, distinct from angiosperms. These results suggest that angiosperm F5Hs coopted the ancient CB5D, forming a modern cytochrome P450 monooxygenase system for aromatic ring meta-hydroxylation, enabling the reemergence of S-lignin biosynthesis in angiosperms.
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Affiliation(s)
- Xianhai Zhao
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yunjun Zhao
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qing-yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry and Northeast Forestry University, Beijing 100091, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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Osgerby A, Overton TW. Approaches for high-throughput quantification of periplasmic recombinant proteins. N Biotechnol 2023; 77:149-160. [PMID: 37708933 DOI: 10.1016/j.nbt.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The Gram-negative periplasm is a convenient location for the accumulation of many recombinant proteins including biopharmaceutical products. It is the site of disulphide bond formation, required by some proteins (such as antibody fragments) for correct folding and function. It also permits simpler protein release and downstream processing than cytoplasmic accumulation. As such, targeting of recombinant proteins to the E. coli periplasm is a key strategy in biologic manufacture. However, expression and translocation of each recombinant protein requires optimisation including selection of the best signal peptide and growth and production conditions. Traditional methods require separation and analysis of protein compositions of periplasmic and cytoplasmic fractions, a time- and labour-intensive method that is difficult to parallelise. Therefore, approaches for high throughput quantification of periplasmic protein accumulation offer advantages in rapid process development.
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Affiliation(s)
- Alexander Osgerby
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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3
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Yantsevich AV, Dzichenka YV, Ivanchik AV, Shapiro MA, Trawkina M, Shkel TV, Gilep AA, Sergeev GV, Usanov SA. [Proteomic analysis of contaminants in recombinant membrane hemeproteins expressed in E. coli and isolated by metal affinity chromatography]. APPL BIOCHEM MICRO+ 2018; 53:173-87. [PMID: 29508978 DOI: 10.1134/s000368381702017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Contaminating proteins have been identified by “shotgun” proteomic analysis in 14 recombinant preparations of human membrane heme- and flavoproteins expressed in Escherichia coli and purified by immobilized metal ion affinity chromatography. Immobilized metal ion affinity chromatography of ten proteins was performed on Ni2+-NTA-sepharose 6B, and the remaining four proteins were purified by ligand affinity chromatography on 2',5'-ADP-sepharose 4B. Proteomic analysis allowed to detect 50 protein impurities from E. coli. The most common contaminant was Elongation factor Tu2. It is characterized by a large dipole moment and a cluster arrangement of acidic amino acid residues that mediate the specific interaction with the sorbent. Peptidyl prolyl-cis-trans isomerase SlyD, glutamine-fructose-6-phosphate aminotransferase, and catalase HPII that contained repeating HxH, QxQ, and RxR fragments capable of specific interaction with the sorbent were identified among the protein contaminants as well. GroL/GroS chaperonins were probably copurified due to the formation of complexes with the target proteins. The Ni2+ cations leakage from the sorbent during lead to formation of free carboxyl groups that is the reason of cation exchanger properties of the sorbent. This was the putative reason for the copurification of basic proteins, such as the ribosomal proteins of E. coli and the widely occurring uncharacterized protein YqjD. The results of the analysis revealed variation in the contaminant composition related to the type of protein expressed. This is probably related to the reaction of E. coli cell proteome to the expression of a foreign protein. We concluded that the nature of the protein contaminants in a preparation of a recombinant protein purified by immobilized metal ion affinity chromatography on a certain sorbent could be predicted if information on the host cell proteome were available.
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Sergeev GV, Gilep AA, Usanov SA. The role of cytochrome b5 structural domains in interaction with cytochromes P450. BIOCHEMISTRY (MOSCOW) 2015; 79:406-16. [PMID: 24954591 DOI: 10.1134/s0006297914050046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To understand the role of the structural elements of cytochrome b5 in its interaction with cytochrome P450 and the catalysis performed by this heme protein, we carried out comparative structural and functional analysis of the two major mammalian forms of membrane-bound cytochrome b5 - microsomal and mitochondrial, designed chimeric forms of the heme proteins in which the hydrophilic domain of one heme protein is replaced by the hydrophilic domain of another one, and investigated the effect of the highly purified native and chimeric heme proteins on the enzymatic activity of recombinant cytochromes P4503A4 and P45017A1 (CYP3A4 and CYP17A1). We show that the presence of a hydrophobic domain in the structure of cytochrome b5 is necessary for its effective interaction with its redox partners, while the nature of the hydrophobic domain has no significant effect on the ability of cytochrome b5 to stimulate the activity of cytochrome P450-catalyzed reactions. Thus, the functional properties of cytochrome b5 are mainly determined by the structure of the heme-binding domain.
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Affiliation(s)
- G V Sergeev
- Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Minsk, 220141, Belarus.
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6
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Gnedenko O, Yablokov E, Usanov S, Mukha D, Sergeev G, Bulko T, Kuzikov A, Moskaleva N, Shumyantseva V, Ivanov A, Archakov A. SPR and electrochemical analyses of interactions between CYP3A4 or 3A5 and cytochrome b5. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gruenewald S, Wahl B, Bittner F, Hungeling H, Kanzow S, Kotthaus J, Schwering U, Mendel RR, Clement B. The Fourth Molybdenum Containing Enzyme mARC: Cloning and Involvement in the Activation of N-Hydroxylated Prodrugs. J Med Chem 2008; 51:8173-7. [DOI: 10.1021/jm8010417] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanja Gruenewald
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Bettina Wahl
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Florian Bittner
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Helen Hungeling
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Stephanie Kanzow
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Joscha Kotthaus
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Ulrike Schwering
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Ralf R. Mendel
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
| | - Bernd Clement
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, D-24118 Kiel, Germany, Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, D-38106 Braunschweig, Germany
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Sobrado P, Goren MA, James D, Amundson CK, Fox BG. A Protein Structure Initiative approach to expression, purification, and in situ delivery of human cytochrome b5 to membrane vesicles. Protein Expr Purif 2007; 58:229-41. [PMID: 18226920 DOI: 10.1016/j.pep.2007.11.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 11/26/2007] [Accepted: 11/30/2007] [Indexed: 11/18/2022]
Abstract
A specialized vector backbone from the Protein Structure Initiative was used to express full-length human cytochrome b5 as a C-terminal fusion to His8-maltose binding protein in Escherichia coli. The fusion protein could be completely cleaved by tobacco etch virus protease, and a yield of approximately 18 mg of purified full-length human cytochrome b5 per liter of culture medium was obtained (2.3mg per g of wet weight bacterial cells). In situ proteolysis of the fusion protein in the presence of chemically defined synthetic liposomes allowed facile spontaneous delivery of the functional peripheral membrane protein into a defined membrane environment without prior exposure to detergents or other lipids. The utility of this approach as a delivery method for production and incorporation of monotopic (peripheral) membrane proteins is discussed.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Room 141B, 433 Babcock Drive, Madison, WI 53706, USA
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