1
|
Aarthy M, George A, Ayyadurai N. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review. Int J Biol Macromol 2021; 191:840-851. [PMID: 34560154 DOI: 10.1016/j.ijbiomac.2021.09.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022]
Abstract
Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.
Collapse
Affiliation(s)
- Mayilvahanan Aarthy
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Augustine George
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India
| | - Niraikulam Ayyadurai
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Chennai 600020, India.
| |
Collapse
|
2
|
Jiang HK, Wang YH, Weng JH, Kurkute P, Li CL, Lee MN, Chen PJ, Tseng HW, Tsai MD, Wang YS. Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues. Biochemistry 2020; 59:2205-2209. [PMID: 32484330 DOI: 10.1021/acs.biochem.0c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited. Herein, we report the application of an evolved PylRS, FOWRS2, for efficient incorporation of five Trp analogues into the deubiquitinase USP30 to decipher the role of W475 for diubiquitin selectivity. Structures of the five FOWRS-C/Trp analogue complexes at 1.7-2.5 Å resolution showed multiple ncAA binding modes. The W475 near the USP30 active site was replaced with Trp analogues, and the effect on the activity as well as the selectivity toward diubiquitin linkage types was examined. It was found that the Trp analogue with a formyl group attached to the nitrogen atom of the indole ring led to an improved activity of USP30 likely due to enhanced polar interactions and that another Trp analogue, 3-benzothienyl-l-alanine, induced a unique K6-specificity. Collectively, genetically encoded noncanonical Trp analogues by evolved PylRS·tRNACUAPyl pair unravel the spatial role of USP30-W475 in its diubiquitin selectivity.
Collapse
Affiliation(s)
- Han-Kai Jiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Yi-Hui Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Prashant Kurkute
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Lung Li
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Man-Nee Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Pei-Jung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hsueh-Wei Tseng
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
3
|
Cavaco M, Castanho MARB, Neves V. Peptibodies: An elegant solution for a long-standing problem. Biopolymers 2017; 110. [PMID: 29266205 DOI: 10.1002/bip.23095] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 01/09/2023]
Abstract
Chimeric proteins composed of a biologically active peptide and a fragment crystallizable (Fc) domain of immunoglobulin G (IgG) are known as peptibodies. They present an extended half-life due to neonatal Fc receptor (FcRn) salvage pathway, a decreased renal clearance rate owing to its increased size (≈70 kDa) and, depending on the peptide used in the design of the peptibody, an active-targeting moiety. Also, the peptides therapeutic activity is boosted by the number of peptides in the fusion protein (at least two peptides) and to some peptides' alterations. Peptibodies are mainly obtained through recombinant DNA technology. However, to improve peptide properties, "unnatural" changes have been introduced to the original peptides' sequence, for instance, the incorporation of D- or non-natural amino acid residues or even cyclization thus, limiting the application of genetic engineering in the production of peptibodies, since these peptides must be obtained via chemical synthesis. This constrains prompted the development of new methods for conjugation of peptides to Fc domains. Another challenge, subject of intense research, relates to the large-scale production of such peptibodies using these new techniques, which can be minimized by their proved value. To date, two peptibodies, romiplostim and dulaglutide, have been approved and stay as the standard of care in their areas of action. Furthermore, a considerable number of peptibodies are currently in preclinical and clinical development.
Collapse
Affiliation(s)
- Marco Cavaco
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal
| | - Miguel A R B Castanho
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal
| | - Vera Neves
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal
| |
Collapse
|
4
|
Melo Czekster C, Robertson WE, Walker AS, Söll D, Schepartz A. In Vivo Biosynthesis of a β-Amino Acid-Containing Protein. J Am Chem Soc 2016; 138:5194-7. [PMID: 27086674 DOI: 10.1021/jacs.6b01023] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
It has recently been reported that ribosomes from erythromycin-resistant Escherichia coli strains, when isolated in S30 extracts and incubated with chemically mis-acylated tRNA, can incorporate certain β-amino acids into full length DHFR in vitro. Here we report that wild-type E. coli EF-Tu and phenylalanyl-tRNA synthetase collaborate with these mutant ribosomes and others to incorporate β(3)-Phe analogs into full length DHFR in vivo. E. coli harboring the most active mutant ribosomes are robust, with a doubling time only 14% longer than wild-type. These results reveal the unexpected tolerance of E. coli and its translation machinery to the β(3)-amino acid backbone and should embolden in vivo selections for orthogonal translational machinery components that incorporate diverse β-amino acids into proteins and peptides. E. coli harboring mutant ribosomes may possess the capacity to incorporate many non-natural, non-α-amino acids into proteins and other sequence-programmed polymeric materials.
Collapse
Affiliation(s)
- Clarissa Melo Czekster
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Wesley E Robertson
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Allison S Walker
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Dieter Söll
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry, ‡Department of Molecular, Cellular, and Developmental Biology, and §Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| |
Collapse
|