Molecular mechanisms for the evolution of multicellular complexity in social amoebas

Lead Research Organisation: University of Dundee
Department Name: College of Life Sciences

Abstract

Biologists want to understand how complex multicellular organisms like ourselves have evolved from their simple single-celled ancestors. We know in theory how this happened: Spontaneous mutations in the genes of earlier organisms caused small changes in the developmental program of their offspring. This sometimes resulted in an improved adult that more successfully reproduced, and therefore gradually replaced the earlier form. However, to really understand this process and prove that it actually occurred, we have to trace back which genes were mutated and how this mutation changed gene function. We also need to know which developmental mechanisms were regulated by the mutated genes and how the altered developmental mechanism eventually produced the improved adult form. Because it is not possible to obtain such detailed information for highly evolved animals like ourselves, we investigate this problem in the social amoebas. These organisms live as single cells when they are feeding. However, when starved, they come together and form a multicellular fruiting body, in which a proportion of cells is preserved as spores. The other cells form a stalk and other structures to support the spore mass. This life style depends on mutual collaboration and specialization of cells. In the course of evolution the social amoebae have progressed from basal species that formed structures with 10-100 cells and only two cell-types, to species that form large complex structures with over 1 million cells and up to five cell types. One species, D.discoideum, is used by many laboratories as a model system to understand how cells move, eat, propagate and communicate with each other. Over a 100 known social amoeba species have been isolated worldwide. To understand how these species gradually became more complex and different from each other, we first used DNA data to construct a family tree of the social amoebas. This tree showed that there are four major groups of social amoebas and that D.discoideum is a member of the group that was formed most recently. We next measured a large number of characters that determine the typical size and form of all 75 species. By plotting these characters on the family tree we can trace back which character came first and how it gradually changed into greater complexity. Most recently we were involved in sequencing the genomes of species that represent each of the four groups. These project are almost completed and offer us enormous opportunities to study how genes have changed during evolution. In this study we will combine a detailed analysis of changes in genes with our earlier analysis of the changes in form that occurred during evolution. This should give us indications which changes in the genes might have been responsible for the appearance of novel forms. By manipulating the gene in question and observing its effect on the form of the species, we will be able to prove that a particular genetic change was the actual cause for a specific change in form. In this manner we will be able to unravel the genetic mechanisms that have been used by evolution to generate the enormous variety of forms that we see in modern multicellular organisms.

Technical Summary

A major goal of biology is to understand how complex multicellular organisms evolved from unicellular life forms. This is ultimately caused by natural selection acting on genetic variation, but it has proven to be difficult to identify the gene modifications that actually caused the evolution of novel multicellular forms. Dictyostelid social amoebas or are uniquely suited to resolve this problem. They display conditional multicellularity, where cells aggregate to form motile slugs and architecturally complex fruiting structures. Several Dictyostelia show excellent experimental and genetic tractability and one species, D.discoideum, is a widely used model for studying problems in cell- and developmental biology. In previous research we constructed a robust molecular phylogeny of all Dictyostelia. We plotted an extensive range of species traits to the phylogeny, providing information about the order in which these traits evolved. Most recently we participated in an international effort to sequence the genome of at least one species in each of the four major groups of Dictyostelia. In addition to the completed D.discoideum genome, the genomes of D.fasciculatum and P.pallidum are now almost completely assembled, while draft sequences of two more genomes are being finalized. Combined with the map of trait evolution, the completed genomes offer a tremendous opportunity to understand how changes in genes and genomes caused the appearance of novel phenotypes. We will firstly identify genes with core developmental roles in all social amoebas and when possible to retrace the original function of these genes to their solitary ancestors. Secondly, we will map how key regulatory genes have changed during evolution and correlate these changes with the evolution of morphological features. Selected genes will be subjected to allelic replacement with ancestral orthologs to confirm that the genetic change caused the phenotypic innovation.

Publications

10 25 50
 
Description We aim to understand how genetic changes caused the evolution of multicellularity. To achieve this we seek correlations between genome evolution and the emergence of multicellular complexity. We use the Dictyostelid social amoebas to study this problem, because they can be genetically modified to prove that the genetic change caused the increased complexity.
1. Comparative analysis of multicellular complexity.
We measured 30 phenotypic characters across 99 Dictyostelium species and analysed group-specific trends in character evolution. The analysis showed that the last common ancestor (LCA) of Dictyostelia erected small fruiting structures directly from aggregates. It secreted cAMP pulses to coordinate fruiting body formation, and another compound to mediate aggregation. This phenotype persisted up to the LCAs of groups 1-3. The group 4 LCA started to use cAMP pulses for aggregation and evolved much larger fruiting bodies and a migrating "slug" stage. However, it lost encystation, the survival strategy of solitary amoebas. 2. Evolution of cAMP signalling
We used genome information to study the evolution of cAMP signalling genes. The
cAMP phosphodiesterase PdsA is essential to degrade secreted cAMP between pulses and is regulated by a secreted inhibitor PdiA. We found that the PdsA genes in groups 1-3 have a 200-fold lower affinity for cAMP than the group 4 PdsA, while PdiA was only present in group 4. PdiA is essential for initiation of spiral cAMP waves, which, by organizing large territories, generate the large fruiting structures that characterize group 4. Studies in which we replaced a group 4 PdsA with a group 2 PdsA showed that the high affinity PdsA was essential for efficient cAMP mediated aggregation.
Intracellular cAMP, produced by the adenylate cyclase ACG and ACR and degraded by the cAMP phosphodiesterase RegA, was known to be essential for induction of spore differentiation in group 4. These genes are conserved in all Dictyostelia. We found that deletion of the RegA gene from the group 2 species P.pallidum caused precocious fruiting body formation as is also the case in the group 4 species D.discoideum. More remarkable, deletion of RegA inhibited growth, because the amoebas encysted while they were still feeding. This finding is medically important, because encystation of pathogenic amoebas renders them resistant to antibiotics.
Exploitation Route By sequencing group-representative genomes and preparing a detailed map of phenotypic evolution in Dictyostelia, we prepared the way for others to firstly identify the core components in their cell- or developmental problem of interest and to secondly assess the phenotypic consequences of evolutionary changes in the core pathway
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description ERC Advanced Grant
Amount € 2,128,602 (EUR)
Funding ID 742288 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 04/2017 
End 03/2022
 
Description Comparative genome sequencing of Dictyostelia 
Organisation Friedrich Schiller University Jena (FSU)
Country Germany 
Sector Academic/University 
PI Contribution Comparative genome sequencing of three Dictyostelid species. Genome sequencing, fosmid mapping and gene annotation of three Dictyostelium genomes Continued with comparative transcriptome analysis and sequencing of Protostelium genomes
Collaborator Contribution The Jena team performed most of the genome and transcriptome sequencing, sequence assembly and gene model prediction. The Jena and Cologne also contributed to protein annotation.
Impact The sequences of two genomes have been published doi:10.1101/gr.121137.111. The publication of sequence of the third Dictyostelium genome was incorporated into a broader evolutionary analysis of multicellularity genes (doi: 10.1038/ncomms12085). The comparative transcriptomic analysis was also published (DOI: 10.1186/s12864-016-3223-z) and the data were also used for improved gene model annotation (doi: 10.1186/s12864-017-3505-0) A manuscript for one Protostelium genome is in preparation. The available genome sequences form a cornerstone of our evolutionary work and are also widely used by the Dictyostelium community.
Start Year 2013
 
Description Comparative genome sequencing of Dictyostelia 
Organisation University of Cologne
Country Germany 
Sector Academic/University 
PI Contribution Comparative genome sequencing of three Dictyostelid species. Genome sequencing, fosmid mapping and gene annotation of three Dictyostelium genomes Continued with comparative transcriptome analysis and sequencing of Protostelium genomes
Collaborator Contribution The Jena team performed most of the genome and transcriptome sequencing, sequence assembly and gene model prediction. The Jena and Cologne also contributed to protein annotation.
Impact The sequences of two genomes have been published doi:10.1101/gr.121137.111. The publication of sequence of the third Dictyostelium genome was incorporated into a broader evolutionary analysis of multicellularity genes (doi: 10.1038/ncomms12085). The comparative transcriptomic analysis was also published (DOI: 10.1186/s12864-016-3223-z) and the data were also used for improved gene model annotation (doi: 10.1186/s12864-017-3505-0) A manuscript for one Protostelium genome is in preparation. The available genome sequences form a cornerstone of our evolutionary work and are also widely used by the Dictyostelium community.
Start Year 2013
 
Description cAMP signalling in presenilin null mutants 
Organisation Royal Holloway, University of London
Country United Kingdom 
Sector Academic/University 
PI Contribution Christina Schilde and Zhi-hui Chen, two postdocs in my lab performed cAMP measurements in presenilin null mutants
Collaborator Contribution Prepared the presenilin null mutants and examined other aspects of its phenotype
Impact The work was published doi: 10.1242/jcs.140939
Start Year 2012
 
Description cAMP signalling in steelyA null mutants 
Organisation Sophia University Japan
Country Japan 
Sector Academic/University 
PI Contribution We hosted and supervised a Ph.D. student from Sophia University for 2 months to perform various cAMP signal transduction assays for this work
Collaborator Contribution Prepared the steelyA mutant and examined all other aspects of its phenotype
Impact The work was published in PlosOne 4. doi:10.1371/journal.pone.010
Start Year 2012
 
Description Open doors day College of Life Sciences Dundee 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Members of the public participated enthousiastically in hands-on experiments and gained information on the life cycles of social and pathogenic amoebas

Increased understanding of science in the general public
Year(s) Of Engagement Activity 2012,2014,2015
URL http://www.dundee.ac.uk/revealingresearch/newsandevents/dod/
 
Description RSE Masterclass 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Schools
Results and Impact High school pupils participated with enthousiasm and obtained a certificate for successfully completing experiments

The Masterclasses continue to be highly popular with schools in the regions
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,2009,2010,2012
URL http://www.royalsoced.org.uk/cms//files/youngpeople/sciencemasterclass/DundeeAutum14flyer.pdf