Lecture 13 - Homeotic genes in development and the ABC model (2) Flashcards
What experiment was done to identify the molecular basics of ple mutations (looking for c function genes)?
- Used AGAMOUS in arabidopsis (Ag) as a probe to identify the equivilent gene in antirrhinum
- > Plena (antirrhinum)
- transposon tagging showed that the transposon insertion with the PLENA gene is linked to the mutant phenotype (loss of c function, conversion of stamens and carpels to petals and sepals)
- but did not explain why the Ag probe at low stingency identifies other sequences that do not correlate with the c function
What did evolutionary analysis show about the other genes picked up in the southern blot hybridisation to look for AGAMOUS in antirrinum (PLENA)?
- FARINELLA (from antirrhinium) is more closely related to AGAMOUS than PLENA is to AGAMOUS
- would expect Far and Ag to have the same function
- but Ple has the c function (unexpected)
- Far mutants in antirrhinium: do not cause homeotic transformations
- in whorls 3 and 4 stay as stamen and carpels, but if male they are sterile
How can related genes be generated?
Gene duplication event
What are the three possible outcomes of a gene duolication event?
- Selective pressure on both genes -> genes similar and maintain functions
- Selective pressure on just one -> 1 copy degrades
- Selective pressure on just one -> 1 copy allowed to aquire a new function
What are the two different possiblities that can occur when a gene duplication event results in the second gene aquiring a new function?
Subfuntionalisation
-duplicated genes perform different aspects of the original gene’s function
e.g. if a gene was used for transcriptional regulators, perhaps the new gene binds to only some of the areas the original did, so that regulation is changed
Neofunctionalisation
-one of the duplicated genes aquires a new function
What are the feautures of the MADS box genes?
-inc:
MCM1
AGAMOUS
DEFICIENS
Serum response factor
-different number in different organisms means that gene duplications have occured at different frequencies in the the different organisms->
107 in arabidopsis
71 in rice
4 in yeast
2 in mice, flies and humans (MEF2 and SRF)
-in plants this molecular switch is clearly used more often so the gene family has more oppourtunity to expand in plants
What is synteny?
conservation of gene order
- if order is conserved, you are likely looking at equivilent sequence in the genome in a different organism
- doesn’t tell you how close organisms are, but does tell you how close sequences are related
- can use to tell which are the equivelent genes in different organisms e.g. in Arabidopsis and Antirrhinium
How did synteny help to identify the plena equivilent gene in arabidopsis?
- look at antirrhinium sequence that contains plena
- line up the equivilent rows in arabidopsis
- based on sequence conservation believe that SNP genes are equivulent to plena
What was shown through comparing Ag in arabidopsis with antirrhinium?
- in arabidopsis GDSI gene hasn’t been duplicated
- believe that Far shares a common ancester with Agamous based on this
- Ple shown to share a common ancester with SNP1 and 2
What are teh SHATTERPROOF genes?
- shp1 and shp2
- equivilent of plena in arabidopsis
- expressed in the carpels
- required at valve margin and in ovules (shown from evidence of shp1 and shp2 mutants)
- associated with explosive seed dispersal
- closely related to agamous but perform only a subset of the ancestral gene functions (more specific)
Why are there two sph genes?
- arabisposis is a member of the brassica family
- these are not teraploid -> they have reduced genes themselves but lots have two copies of shp
- whole genome duplications produced 2 shp genes which were both retained
- 1 each on chr 2 and 3 (found through related sequences form synteny of chrs and same functions)
- only 1 Ag gene present (chrm 4, the part of the chromosome that had been duplicated) but there was once probably another that didn’t survive gene duplication
How has a hypothesis been built to explain the presence of Ag and Shp in Arabidopsis and Antihinnium?
- through comparison of lots of sequences
- confirmed that the duplication of the c function ancestor gene gave rise to Ag and plena ancestors
- both antirrhinium and arabidopsis have ancestral copies of Ag and Ple but:
- in antirrhinium Ag has evolved to Far (stamen function only) and Ple has maintained (c function, reproductive organ identity)
- in arabidopsis another genome duplication led to the maintenance of one Ag gene (c function, reproductive organ identity) and Ple has evolved to 2 Shp genes (carpel function only)
- As ag and Ple have c function this has allowed Far and Shp to adopt different functions
How can the evolution of Ple and Far in arabidopsis and antirrhinium been proven experimentally?
-take Far and Ple organ (both originally c function genes)
-express in whole plant via the 35s promoter
-do this in separate plants but for both antirrhinium and arabidopsis
Ple over expression
Arabidopsis - whorls 1 and 2 express the c function gene, so would expect them to be converted to stamen and carpels
-> get partial sepals, but carpels and petals replaced by stamen (almost as expected)
Same in Antirrhinium
Far over expression
Antirrhinium - get partial stamen -> would not do this normally, therefore must be showing some of its ancestral function of specifying the sex organ
-Same in arabidopsis
However we know that the networks these proteins operate within are different in the different species
What are the functions of Far and Ple in antirrhinium and arabidopsis?
- Far and Ple have Ag-like function in arabidopsis
- not in antirrhinium - have a differential ability to promote male and female organogenesis (subfunctionalisation), Far hardly influences sepal identity
- Ag and Sph show to be functionally equivilent when ectopically expressed in arabidopsis (both direct male and female organogenesis) although Shp only required in the carpels
What conclusions have been drawn about these genes? (sorry)
- clear evidence for random evolutionary trajectory of gene functions after duplication event
- different members of a duplicated gene pair have retained the primary homeotic function in different lineages
- this illustrates the role of chance in evolution
- differential ability of antirrhinium to promote ale and female development provides an example of subfunctionalisation at the protein level
