Diversification of Transcription Factor NF-κB in Protists

Abstract

Abstract

In this report, we investigate the evolution of transcription factor NF-κB by examining its structure, activity, and regulation in two protists using phylogenetic, cellular, and biochemical techniques. In Capsaspora owczarzaki (Co), we find that full-length NF-κB has an N-terminal DNA-binding domain and a C-terminal Ankyrin (ANK) repeat inhibitory domain, and its DNA-binding activity is more similar to metazoan NF-κB rather than Rel proteins. As with mammalian NF-κB proteins, removal of the ANK repeats is required for Co-NF-κB to enter the nucleus, bind DNA, and activate transcription. However, C-terminal processing of Co-NF-κB is not induced by co-expression of IKK in human cells. Exogenously expressed Co-NF-κB localizes to the nucleus in Co cells. NF-κB mRNA and DNA-binding levels differ across three life stages of Capsaspora, suggesting distinct roles for NF-κB in these life stages. RNA-seq and GO analyses identify possible gene targets and biological functions of Co-NF-κB. We also show that three NF-κB-like proteins from the choanoflagellate Acanthoeca spectabilis (As) all consist of primarily the N-terminal conserved Rel Homology domain sequences of NF-κB, and lack C-terminal ANK repeats. All three As-NF-κB proteins constitutively enter the nucleus of human and Co cells, but differ in their DNA-binding and transcriptional activation activities. Furthermore, all three As-NF-κB proteins can form heterodimers, indicating that NF-κB diversified into multi-subunit families at least two times during evolution. Overall, these results present the first functional characterization of NF-κB in a taxonomic kingdom other than Animalia and provide information about the evolution and diversification of this biologically important transcription factor.

Significance These results represent the first functional characterization of the biologically important transcription factor NF-κB in a taxonomic kingdom other than Animalia. As such, they provide information on the evolutionary origins and basal diversification of NF-κB outside of metazoans. These results suggest that NF-κB plays life stage-specific roles in Capsaspora, the closest unicellular ancestor to all metazoans. Finally, the analysis of three NF-κB proteins in a single choanoflagellate indicates that choanoflagellates have subclasses of NF-κBs, which can form heterodimers, suggesting that NF-κB subunit expansion and diversification has occurred at least twice in evolution.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

* ↵* Dr. Thomas D. Gilmore, Biology Department, Boston University, 5 Cummington Mall, Boston, MA 02215, USA; 617-353-5444 (phone); 617-353-6340 (fax); email: gilmore{at}bu.edu

* ↵1 BB522 Molecular Biology Laboratory: Dana H.M. Alburi, Ludmila Anisimov, Aria Y. Armstrong, Sydney J. Badger, Elham Banaie, Joana A. Barbosa Teixeira, Madeleine T. Billingsley, Anoush Calikyan, Yinxing Chen, Aidan B. Coia, Daniel Cutillo, Breanna R. Dooling, Parth P. Doshi, Kyra R. Dubinsky, Berta Escude Velasco, Jabari R. Evans, Jasmine Gordon, Huibo Guan, Spiro N. Haliotis, Niccolas T. Hood, Yen-Chun Huang, Wenjing Jiang, Isabelle C. Kreber, Ekin B. Kurak, Cheng-Che Lee, Tanner M. Lehmann, Savina J.W. Lin, Edward Liu, Kevin Liu, Yen-Yu Liu, Alexandra L. Luther, Alexa A. Macgranaky-Quaye, Daniel J. Magat, Lauren E. Malsick, Parmida Masoudi, Parsida Masoudi, Chad R.H. Max, Ethan Z. McCaslin, Eleanor T. McGeary, Kathleen M. McLaughlin, Victoria S.A. Momyer, Lake D. Murphy, Sonny V. Nguyen, Kareemah Ni, Leon Novak, Roberto Nunes Campos E Santos, Yemi D. Osayame, Jun Bai Park Chang, Harshal M. Patel, Tony V. Pham, Sheila M. Phillips, Jhonathan Perea Piedrahita, Tricia L. Post, Rebecca A. Prather, Pauline I. Reck, Jaime A. Rodriguez, Kirquenique A. Rolle, Joseph A. Salzo, Kathryn M. Satko, Davis G. Settipane, Kara J. Sevola, Mithil V. Shah, Viktoriya Skidanova, Georgia M. Snyder, Rebecca J. Sprague, Ryan A. Stagg, Danielle Tong, Andreas A. Towers, Nicholas W. Turgiss, Natalie S. Wheeler, Ann S. Yung

* Two Supplemental Videos have been added, which were overlooked on the first submission.