Self-nonself recognition: genomic and transcriptomic insights from the sponge aggregation factors

Abstract

The multicellular condition cannot be maintained without safeguards protecting the integrity of the individual. Tissue contact and fusion with other conspecific individuals may threaten this integrity, as genetically non-identical cells may shirk their somatic duties and gain disproportionate access to the germ line. As sessile invertebrates that commonly inhabit crowded benthic environments, sponges are particularly reliant on a molecular self-nonself defense system in order to resist loss of habitat space, chimerism and possible germ line parasitism by neighbouring conspecific sponges. Sponge allorecognition appears to be, at least in part, under the control of extracellular proteoglycans called aggregation factors (AFs), which were first discovered based on their role in the species-specific reaggregation of dissociated sponge cells. Although the AFs have been extensively studied for over fifty years, the majority of this work has involved biochemical, rather than genetic approaches, and has focussed on the role of the glycan subunits associated with the AFs. In the present work, I investigate the genetic properties underlying the AF protein backbone, to better understand the functions and evolution of these putative allorecognition molecules.Using newly-available genomic and transcriptomic data, I surveyed the phylum Porifera for novel putative AF sequences, to explore the evolutionary origins of this gene family. I conclude that the AFs are a demosponge and hexactinellid-specific innovation. I then performed an in-depth characterisation of the six AF genes from the model demosponge species, Amphimedon queenslandica. The six genes display a highly modular intron/exon organisation. However, as expected of putative allorecognition genes, the AFs are greatly diversified between individuals, with nucleotide polymorphism (and possible positive selection) and intron retention events distributed across the six genes. The AFs are very highly expressed across sponge development and in response to alloimmune challenge, and undergo a particular spike in gene expression levels after the onset of sponge metamorphosis. The AF genes also exhibit expression patterns across development that are significantly correlated with those of other, developmentally important genes with roles in various cell signalling pathways. I conclude that the AFs play a novel developmental role, in addition to their putative allorecognition capabilities.iii S e l f -N o N S e l f R e c o g N i t i o N : S p o N g e ag g R e g at i o N f a c t o R S Declaration by authorThis thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis.I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial ...

The biology of choanocytes and choanocyte chambers and their role in the sponge stem cell system

“…Principal component analysis within choanocyte samples revealed a large proportion of the differences found correlated with the individuals they were isolated from (Appendix 4.4), as observed in previous studies (Grice, 2015). To eliminate the effect of individual variation, another choanocyte CEL-Seq dataset was generated, using 10 whole choanocyte chambers, individually isolated from a single adult sponge.…”