Recombination-induced Tag Exchange to Track Old and New Proteins

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2009 Dec 19

PMID 20018668

Citations 59

Authors

Kitty F Verzijlbergen

Victoria Menendez-Benito

Tibor van Welsem

Sjoerd J van Deventer

Derek L Lindstrom

Huib Ovaa

Jacques Neefjes

Daniel E Gottschling

Fred van Leeuwen

Affiliations

Soon will be listed here.

Abstract

The dynamic behavior of proteins is critical for cellular homeostasis. However, analyzing dynamics of proteins and protein complexes in vivo has been difficult. Here we describe recombination-induced tag exchange (RITE), a genetic method that induces a permanent epitope-tag switch in the coding sequence after a hormone-induced activation of Cre recombinase. The time-controlled tag switch provides a unique ability to detect and separate old and new proteins in time and space, which opens up opportunities to investigate the dynamic behavior of proteins. We validated the technology by determining exchange of endogenous histones in chromatin by biochemical methods and by visualizing and quantifying replacement of old by new proteasomes in single cells by microscopy. RITE is widely applicable and allows probing spatiotemporal changes in protein properties by multiple methods.

Citing Articles

CHMP2B promotes CHMP7 mediated nuclear pore complex injury in sporadic ALS.

Keeley O, Mendoza E, Menon D, Coyne A Acta Neuropathol Commun. 2024; 12(1):199.

PMID: 39709457 PMC: 11662732. DOI: 10.1186/s40478-024-01916-7.

Nuclear pore complexes undergo Nup221 exchange during blood-stage asexual replication of parasites.

Blauwkamp J, Ambekar S, Hussain T, Mair G, Beck J, Absalon S mSphere. 2024; 9(12):e0075024.

PMID: 39526784 PMC: 11656741. DOI: 10.1128/msphere.00750-24.

Nuclear basket proteins regulate the distribution and mobility of nuclear pore complexes in budding yeast.

Zsok J, Simon F, Bayrak G, Isaki L, Kerff N, Kicheva Y Mol Biol Cell. 2024; 35(11):ar143.

PMID: 39320946 PMC: 11617099. DOI: 10.1091/mbc.E24-08-0371.

DNA polymerase delta governs parental histone transfer to DNA replication lagging strand.

Tian C, Zhang Q, Jia J, Zhou J, Zhang Z, Karri S Proc Natl Acad Sci U S A. 2024; 121(20):e2400610121.

PMID: 38713623 PMC: 11098083. DOI: 10.1073/pnas.2400610121.

Heterogeneous non-canonical nucleosomes predominate in yeast cells .

Tan Z, Cai S, Noble A, Chen J, Shi J, Gan L Elife. 2023; 12.

PMID: 37503920 PMC: 10382156. DOI: 10.7554/eLife.87672.

References

Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velazquez-Muriel J, Sali A . The structural dynamics of macromolecular processes. Curr Opin Cell Biol. 2009; 21(1):97-108. PMC: 2774249. DOI: 10.1016/j.ceb.2009.01.022. View

Subach F, Subach O, Gundorov I, Morozova K, Piatkevich K, Cuervo A . Monomeric fluorescent timers that change color from blue to red report on cellular trafficking. Nat Chem Biol. 2009; 5(2):118-26. PMC: 2662996. DOI: 10.1038/nchembio.138. View

Dion M, Kaplan T, Kim M, Buratowski S, Friedman N, Rando O . Dynamics of replication-independent histone turnover in budding yeast. Science. 2007; 315(5817):1405-8. DOI: 10.1126/science.1134053. View

Reits E, Benham A, Plougastel B, Neefjes J, Trowsdale J . Dynamics of proteasome distribution in living cells. EMBO J. 1997; 16(20):6087-94. PMC: 1326292. DOI: 10.1093/emboj/16.20.6087. View

Mann M . Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol. 2006; 7(12):952-8. DOI: 10.1038/nrm2067. View

Rufiange A, Jacques P, Bhat W, Robert F, Nourani A . Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol Cell. 2007; 27(3):393-405. DOI: 10.1016/j.molcel.2007.07.011. View

Jamai A, Imoberdorf R, Strubin M . Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol Cell. 2007; 25(3):345-55. DOI: 10.1016/j.molcel.2007.01.019. View

Logie C, Stewart A . Ligand-regulated site-specific recombination. Proc Natl Acad Sci U S A. 1995; 92(13):5940-4. PMC: 41617. DOI: 10.1073/pnas.92.13.5940. View

Adams S, Tsien R . Preparation of the membrane-permeant biarsenicals FlAsH-EDT2 and ReAsH-EDT2 for fluorescent labeling of tetracysteine-tagged proteins. Nat Protoc. 2008; 3(9):1527-34. PMC: 2843588. DOI: 10.1038/nprot.2008.144. View

10.

Reits E, Neefjes J . From fixed to FRAP: measuring protein mobility and activity in living cells. Nat Cell Biol. 2001; 3(6):E145-7. DOI: 10.1038/35078615. View

11.

Linger J, Tyler J . Global replication-independent histone H4 exchange in budding yeast. Eukaryot Cell. 2006; 5(10):1780-7. PMC: 1595336. DOI: 10.1128/EC.00202-06. View

12.

Gunjan A, Verreault A . A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell. 2003; 115(5):537-49. DOI: 10.1016/s0092-8674(03)00896-1. View

13.

Kim H, Seol J, Han J, Youn H, Cho E . Histone chaperones regulate histone exchange during transcription. EMBO J. 2007; 26(21):4467-74. PMC: 2063486. DOI: 10.1038/sj.emboj.7601870. View

14.

DAngelo M, Hetzer M . Structure, dynamics and function of nuclear pore complexes. Trends Cell Biol. 2008; 18(10):456-66. PMC: 2697926. DOI: 10.1016/j.tcb.2008.07.009. View

15.

Choi E, Shin J, Kim H, Jang Y . Dynamic regulation of replication independent deposition of histone H3 in fission yeast. Nucleic Acids Res. 2005; 33(22):7102-10. PMC: 1316113. DOI: 10.1093/nar/gki1011. View

16.

Gorski S, Dundr M, Misteli T . The road much traveled: trafficking in the cell nucleus. Curr Opin Cell Biol. 2006; 18(3):284-90. DOI: 10.1016/j.ceb.2006.03.002. View

17.

Chow C, Georgiou A, Szutorisz H, Maia E Silva A, Pombo A, Barahona I . Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division. EMBO Rep. 2005; 6(4):354-60. PMC: 1299280. DOI: 10.1038/sj.embor.7400366. View

18.

Schermer U, Korber P, Horz W . Histones are incorporated in trans during reassembly of the yeast PHO5 promoter. Mol Cell. 2005; 19(2):279-85. DOI: 10.1016/j.molcel.2005.05.028. View

19.

Mito Y, Henikoff J, Henikoff S . Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet. 2005; 37(10):1090-7. DOI: 10.1038/ng1637. View

20.

Henikoff S . Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet. 2007; 9(1):15-26. DOI: 10.1038/nrg2206. View