ZIF-1-mediated Degradation of Zinc Finger Proteins in the Caenorhabditis Elegans Germ Line

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2023 Aug 30

PMID 37647858

Authors

Aaron Z A Schwartz

Yusuff Abdu

Jeremy Nance

Affiliations

Soon will be listed here.

Abstract

Rapid and conditional protein depletion is the gold standard genetic tool for deciphering the molecular basis of developmental processes. Previously, we showed that by conditionally expressing the E3 ligase substrate adaptor ZIF-1 in Caenorhabditis elegans somatic cells, proteins tagged with the first CCCH Zn finger 1 (ZF1) domain from the germline regulator PIE-1 degrade rapidly, resulting in loss-of-function phenotypes. The described role of ZIF-1 is to clear PIE-1 and several other CCCH Zn finger proteins from early somatic cells, helping to enrich them in germline precursor cells. Here, we show that proteins tagged with the PIE-1 ZF1 domain are subsequently cleared from primordial germ cells (PGCs) in embryos and from undifferentiated germ cells in larvae and adults by ZIF-1. We harness germline ZIF-1 activity to degrade a ZF1-tagged fusion protein from PGCs and show that its depletion produces phenotypes equivalent to those of a null mutation. Our findings reveal that ZIF-1 transitions from degrading CCCH Zn finger proteins in somatic cells to clearing them from undifferentiated germ cells, and that ZIF-1 activity can be harnessed as a new genetic tool to study the early germline.

References

Negishi T, Kitagawa S, Horii N, Tanaka Y, Haruta N, Sugimoto A . The auxin-inducible degron 2 (AID2) system enables controlled protein knockdown during embryogenesis and development in Caenorhabditis elegans. Genetics. 2021; 220(2). PMC: 9208642. DOI: 10.1093/genetics/iyab218. View

Guven-Ozkan T, Robertson S, Nishi Y, Lin R . zif-1 translational repression defines a second, mutually exclusive OMA function in germline transcriptional repression. Development. 2010; 137(20):3373-82. PMC: 2947753. DOI: 10.1242/dev.055327. View

Martinez M, Kinney B, Medwig-Kinney T, Ashley G, Ragle J, Johnson L . Rapid Degradation of Proteins at Single-Cell Resolution with a Synthetic Auxin. G3 (Bethesda). 2019; 10(1):267-280. PMC: 6945041. DOI: 10.1534/g3.119.400781. View

Mainpal R, Nance J, Yanowitz J . A germ cell determinant reveals parallel pathways for germ line development in Caenorhabditis elegans. Development. 2015; 142(20):3571-82. PMC: 6514396. DOI: 10.1242/dev.125732. View

Brenner S . The genetics of Caenorhabditis elegans. Genetics. 1974; 77(1):71-94. PMC: 1213120. DOI: 10.1093/genetics/77.1.71. View

Pepper A, Lo T, Killian D, Hall D, Hubbard E . The establishment of Caenorhabditis elegans germline pattern is controlled by overlapping proximal and distal somatic gonad signals. Dev Biol. 2003; 259(2):336-50. DOI: 10.1016/s0012-1606(03)00203-3. View

Dickinson D, Ward J, Reiner D, Goldstein B . Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods. 2013; 10(10):1028-34. PMC: 3905680. DOI: 10.1038/nmeth.2641. View

Hubbard E, Schedl T . Biology of the Germline Stem Cell System. Genetics. 2019; 213(4):1145-1188. PMC: 6893382. DOI: 10.1534/genetics.119.300238. View

Belew M, Chien E, Wong M, Michael W . A global chromatin compaction pathway that represses germline gene expression during starvation. J Cell Biol. 2021; 220(9). PMC: 8210574. DOI: 10.1083/jcb.202009197. View

10.

Tabara H, Hill R, Mello C, Priess J, Kohara Y . pos-1 encodes a cytoplasmic zinc-finger protein essential for germline specification in C. elegans. Development. 1998; 126(1):1-11. DOI: 10.1242/dev.126.1.1. View

11.

Mello C, Schubert C, Draper B, Zhang W, LOBEL R, Priess J . The PIE-1 protein and germline specification in C. elegans embryos. Nature. 1996; 382(6593):710-2. DOI: 10.1038/382710a0. View

12.

Tenlen J, Molk J, London N, Page B, Priess J . MEX-5 asymmetry in one-cell C. elegans embryos requires PAR-4- and PAR-1-dependent phosphorylation. Development. 2008; 135(22):3665-75. DOI: 10.1242/dev.027060. View

13.

Subramaniam K, Seydoux G . nos-1 and nos-2, two genes related to Drosophila nanos, regulate primordial germ cell development and survival in Caenorhabditis elegans. Development. 1999; 126(21):4861-71. DOI: 10.1242/dev.126.21.4861. View

14.

Zhang L, Ward J, Cheng Z, Dernburg A . The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans. Development. 2015; 142(24):4374-84. PMC: 4689222. DOI: 10.1242/dev.129635. View

15.

Hills-Muckey K, Martinez M, Stec N, Hebbar S, Saldanha J, Medwig-Kinney T . An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans. Genetics. 2021; 220(2). PMC: 9097248. DOI: 10.1093/genetics/iyab174. View

16.

Seydoux G, Dunn M . Transcriptionally repressed germ cells lack a subpopulation of phosphorylated RNA polymerase II in early embryos of Caenorhabditis elegans and Drosophila melanogaster. Development. 1997; 124(11):2191-201. DOI: 10.1242/dev.124.11.2191. View

17.

Reese K, Dunn M, Waddle J, Seydoux G . Asymmetric segregation of PIE-1 in C. elegans is mediated by two complementary mechanisms that act through separate PIE-1 protein domains. Mol Cell. 2000; 6(2):445-55. DOI: 10.1016/s1097-2765(00)00043-5. View

18.

Armenti S, Lohmer L, Sherwood D, Nance J . Repurposing an endogenous degradation system for rapid and targeted depletion of C. elegans proteins. Development. 2014; 141(23):4640-7. PMC: 4302935. DOI: 10.1242/dev.115048. View

19.

Kimble J, White J . On the control of germ cell development in Caenorhabditis elegans. Dev Biol. 1981; 81(2):208-19. DOI: 10.1016/0012-1606(81)90284-0. View

20.

Oyewale T, Eckmann C . Germline immortality relies on TRIM32-mediated turnover of a maternal mRNA activator in . Sci Adv. 2022; 8(41):eabn0897. PMC: 9565796. DOI: 10.1126/sciadv.abn0897. View