Research

Novel genes dramatically alter regulatory network topology in amphioxus

Qing Zhang^1* , Christian M Zmasek^1* , Larry J Dishaw^2,3 , M Gail Mueller² , Yuzhen Ye⁴ , Gary W Litman^2,3,5 and Adam Godzik^1,6

¹  Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA

²  Department of Molecular Genetics, All Children's Hospital, 6th Street South, St. Petersburg, FL 33701, USA

³  H Lee Moffitt Cancer Center and Research Institute, Magnolia Drive, Tampa, FL 33612, USA

⁴  School of Informatics, Indiana University, E. 10th Street, Bloomington, IN 47408, USA

⁵  Department of Pediatrics, University of South Florida, Children's Research Institute, First Street South, St. Petersburg, FL 33701, USA

⁶  Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, Gilman Drive, La Jolla, CA 92093, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R123doi:10.1186/gb-2008-9-8-r123

Published:	4 August 2008

Subject areas: Immunology, Evolution, Genome studies

Abstract

Background

Regulation in protein networks often utilizes specialized domains that 'join' (or 'connect') the network through specific protein-protein interactions. The innate immune system, which provides a first and, in many species, the only line of defense against microbial and viral pathogens, is regulated in this way. Amphioxus (Branchiostoma floridae), whose genome was recently sequenced, occupies a unique position in the evolution of innate immunity, having diverged within the chordate lineage prior to the emergence of the adaptive immune system in vertebrates.

Results

The repertoire of several families of innate immunity proteins is expanded in amphioxus compared to both vertebrates and protostome invertebrates. Part of this expansion consists of genes encoding proteins with unusual domain architectures, which often contain both upstream receptor and downstream activator domains, suggesting a potential role for direct connections (shortcuts) that bypass usual signal transduction pathways.

Conclusion

Domain rearrangements can potentially alter the topology of protein-protein interaction (and regulatory) networks. The extent of such arrangements in the innate immune network of amphioxus suggests that domain shuffling, which is an important mechanism in the evolution of multidomain proteins, has also shaped the development of immune systems.