Recent Development of Genetic Code Expansion for Posttranslational Modification Studies

Overview

Journal Molecules

Publisher MDPI

Specialty Biology

Date 2018 Jul 11

PMID 29986538

Citations 23

Authors

Hao Chen

Sumana Venkat

Paige McGuire

Qinglei Gan

Chenguang Fan

Affiliations

Soon will be listed here.

Abstract

Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs. However, only limited studies have been performed to validate or characterize those identified modification targets, mostly because PTMs are very dynamic, undergoing large changes in different growth stages or conditions. To overcome this issue, the genetic code expansion strategy has been introduced into PTM studies to genetically incorporate modified amino acids directly into desired positions of target proteins. Without using modifying enzymes, the genetic code expansion strategy could generate homogeneously modified proteins, thus providing powerful tools for PTM studies. In this review, we summarized recent development of genetic code expansion in PTM studies for research groups in this field.

Citing Articles

Genetic Code Expansion Approaches to Decipher the Ubiquitin Code.

Wanka V, Fottner M, Cigler M, Lang K Chem Rev. 2024; 124(20):11544-11584.

PMID: 39311880 PMC: 11503651. DOI: 10.1021/acs.chemrev.4c00375.

Lactylation Modification in Cardiometabolic Disorders: Function and Mechanism.

Li X, Cai P, Tang X, Wu Y, Zhang Y, Rong X Metabolites. 2024; 14(4).

PMID: 38668345 PMC: 11052226. DOI: 10.3390/metabo14040217.

Orthogonal Translation for Site-Specific Installation of Post-translational Modifications.

Gan Q, Fan C Chem Rev. 2024; 124(5):2805-2838.

PMID: 38373737 PMC: 11230630. DOI: 10.1021/acs.chemrev.3c00850.

Modulation of plant acetyl-CoA synthetase activity by post-translational lysine acetylation.

Sofeo N, Winkelman D, Leung K, Nikolau B Front Mol Biosci. 2023; 10:1117921.

PMID: 37006614 PMC: 10062202. DOI: 10.3389/fmolb.2023.1117921.

Functional analysis of protein post-translational modifications using genetic codon expansion.

Peng T, Das T, Ding K, Hang H Protein Sci. 2023; 32(4):e4618.

PMID: 36883310 PMC: 10031814. DOI: 10.1002/pro.4618.

References

Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C . Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev. 2015; 40(1):41-56. DOI: 10.1093/femsre/fuv041. View

Hauf M, Richter F, Schneider T, Faidt T, Martins B, Baumann T . Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code. Chembiochem. 2017; 18(18):1819-1823. DOI: 10.1002/cbic.201700327. View

Wang L, Brock A, Herberich B, Schultz P . Expanding the genetic code of Escherichia coli. Science. 2001; 292(5516):498-500. DOI: 10.1126/science.1060077. View

Xie J, Supekova L, Schultz P . A genetically encoded metabolically stable analogue of phosphotyrosine in Escherichia coli. ACS Chem Biol. 2007; 2(7):474-8. DOI: 10.1021/cb700083w. View

Choudhary C, Weinert B, Nishida Y, Verdin E, Mann M . The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol. 2014; 15(8):536-50. DOI: 10.1038/nrm3841. View

Kim S, Lee K, Kim S, Kim J, Cho K, Ro H . Genetic incorporation of N-acetyllysine reveals a novel acetylation-sumoylation switch in yeast. Biochim Biophys Acta Gen Subj. 2017; 1861(11 Pt B):3030-3037. DOI: 10.1016/j.bbagen.2017.02.002. View

Witze E, Old W, Resing K, Ahn N . Mapping protein post-translational modifications with mass spectrometry. Nat Methods. 2007; 4(10):798-806. DOI: 10.1038/nmeth1100. View

Gattner M, Vrabel M, Carell T . Synthesis of ε-N-propionyl-, ε-N-butyryl-, and ε-N-crotonyl-lysine containing histone H3 using the pyrrolysine system. Chem Commun (Camb). 2012; 49(4):379-81. DOI: 10.1039/c2cc37836a. View

Elsasser S, Ernst R, Walker O, Chin J . Genetic code expansion in stable cell lines enables encoded chromatin modification. Nat Methods. 2016; 13(2):158-64. PMC: 4888942. DOI: 10.1038/nmeth.3701. View

10.

Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T . Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Sci Rep. 2015; 5:17204. PMC: 4660432. DOI: 10.1038/srep17204. View

11.

Kehoe J, Bertozzi C . Tyrosine sulfation: a modulator of extracellular protein-protein interactions. Chem Biol. 2000; 7(3):R57-61. DOI: 10.1016/s1074-5521(00)00093-4. View

12.

Lothrop A, Torres M, Fuchs S . Deciphering post-translational modification codes. FEBS Lett. 2013; 587(8):1247-57. PMC: 3888991. DOI: 10.1016/j.febslet.2013.01.047. View

13.

Wan W, Tharp J, Liu W . Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool. Biochim Biophys Acta. 2014; 1844(6):1059-70. PMC: 4016821. DOI: 10.1016/j.bbapap.2014.03.002. View

14.

Neumann H, Peak-Chew S, Chin J . Genetically encoding N(epsilon)-acetyllysine in recombinant proteins. Nat Chem Biol. 2008; 4(4):232-4. DOI: 10.1038/nchembio.73. View

15.

Gary J, Clarke S . RNA and protein interactions modulated by protein arginine methylation. Prog Nucleic Acid Res Mol Biol. 1998; 61:65-131. DOI: 10.1016/s0079-6603(08)60825-9. View

16.

Grunstein M . Histone acetylation in chromatin structure and transcription. Nature. 1997; 389(6649):349-52. DOI: 10.1038/38664. View

17.

Cohen S, Arbely E . Single-Plasmid-Based System for Efficient Noncanonical Amino Acid Mutagenesis in Cultured Mammalian Cells. Chembiochem. 2016; 17(11):1008-11. DOI: 10.1002/cbic.201500681. View

18.

Groff D, Chen P, Peters F, Schultz P . A genetically encoded epsilon-N-methyl lysine in mammalian cells. Chembiochem. 2010; 11(8):1066-8. PMC: 2882943. DOI: 10.1002/cbic.200900690. View

19.

Sterner D, Berger S . Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev. 2000; 64(2):435-59. PMC: 98999. DOI: 10.1128/MMBR.64.2.435-459.2000. View

20.

Lee S, Oh S, Yang A, Kim J, Soll D, Lee D . A facile strategy for selective incorporation of phosphoserine into histones. Angew Chem Int Ed Engl. 2013; 52(22):5771-5. PMC: 3775851. DOI: 10.1002/anie.201300531. View