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Analysis of the domain superfamily composition in unicellular and multicellular fungi

Wilhelmsson, Per (2013) BINP31 20131
Degree Projects in Bioinformatics
Abstract
Abstract

It has been shown that the super kingdoms of Bacteria and Archaea are under the influence of reductive evolution compared to Eukaryotes. Reductive evolution, the strive towards increased mass-normalized efficiency, favoured by growth optimized cells does not have to be excluded from Eukaryotes. The kingdom of fungi has been vastly investigated and contains species with a broad variety of morphologies. This project set out to investigate if the same reductive relations between Bacteria/Archaea and Eukaryotes could be found between unicellular and multicellular fungi. Using SCOP (Structural classification of proteins) domain super families, and a function annotation scheme, sensu stricto yeasts (unicellular) and filaments... (More)
Abstract

It has been shown that the super kingdoms of Bacteria and Archaea are under the influence of reductive evolution compared to Eukaryotes. Reductive evolution, the strive towards increased mass-normalized efficiency, favoured by growth optimized cells does not have to be excluded from Eukaryotes. The kingdom of fungi has been vastly investigated and contains species with a broad variety of morphologies. This project set out to investigate if the same reductive relations between Bacteria/Archaea and Eukaryotes could be found between unicellular and multicellular fungi. Using SCOP (Structural classification of proteins) domain super families, and a function annotation scheme, sensu stricto yeasts (unicellular) and filaments (multicellular) were compared on the basis of their super family composition. The analysis was narrowed down to the subphylum Saccharomycotina containing 15 sensu stricto yeasts and 11 filaments. Except for the increased amount of classified domains amongst the filaments there were also a bias towards functions related to morphology e.g. cell-adhesion compared to the sensu stricto yeasts. The amount of unique super families were fewer amongst the sensu stricto yeasts (777) compared to the filaments (790). Adding to this there was a tendency towards shorter linker lengths amongst the sensu stricto yeasts which together with the other results might point towards a reductive evolution amongst fungi. (Less)
Abstract
Popular science summary

Reductive evolution in fungi?

It has been shown that the super kingdoms of Bacteria and Archaea are under the influence of reductive evolution compared to Eukaryotes. Even if the process of reductive evolution is not the predominant mode of evolution amongst Eukaryotes, since the majority of species are not growth optimized, the process may still be present.

It has been shown that Bacteria and Archaea posses a reduced functional repertoire compared to Eukaryotes. This reductive trajectory is thought to be the result of growth-rate optimization being favoured by Bacteria and Archaea since the three super kingdoms diverged. “Linkers”, functioning as connective links in proteins, has also been affected. They... (More)
Popular science summary

Reductive evolution in fungi?

It has been shown that the super kingdoms of Bacteria and Archaea are under the influence of reductive evolution compared to Eukaryotes. Even if the process of reductive evolution is not the predominant mode of evolution amongst Eukaryotes, since the majority of species are not growth optimized, the process may still be present.

It has been shown that Bacteria and Archaea posses a reduced functional repertoire compared to Eukaryotes. This reductive trajectory is thought to be the result of growth-rate optimization being favoured by Bacteria and Archaea since the three super kingdoms diverged. “Linkers”, functioning as connective links in proteins, has also been affected. They have been shown to be shortened amongst Bacteria and Archaea. These changes are thought to increase the mass efficiency of proteins and protein synthesis which is highly preferred by growth-rate optimized cells (Archaea and Bacteria). Growth-rate optimized cells can still be found throughout Eukaryota e. g. among algae and fungi. Yeasts represent unicellular growth-rate optimized fungi and are widely distributed within the fungi kingdom.

Within the subphylum of Saccharomycotina there is a split, thought to have occurred ~175 My ago, that divides yeasts and filamentous fungi. Presupposing that this low level of morphological transition is coupled to growth-rate optimization, clonal expanding yeasts being more growth optimized, reductive evolution might have influenced these yeasts compared to the filaments since the divergence.

The functional repertoire were found to be slightly reduced amongst the yeasts compared to the filaments. Also though the total amount of functional units were more abundant amongst the filament there was a bias towards functions related to a more complex morphology e. g. cell-adhesion. The linker lengths were also found to be shorter amongst the yeasts compared to the filaments of Saccharomycotina.

The smaller functional repertoire and the shorter linker lengths amongst the yeasts of Saccaromycotina might indicate that the yeast branch has been more influenced by reductive evolution then their neighbouring filamentous branch. This brings up the general question of how big the overall influence of reductive evolution is amongst different Eukaryote lineages. Adding more data, sequencing more genomes, will contribute to further clarifying this potential reductive influence.

Advisor: Björn Canbäck
Master's Degree Project, 45 credits in Bioinformatics 2013
Department of Biology, Lund university (Less)
Please use this url to cite or link to this publication:
author
Wilhelmsson, Per
supervisor
organization
course
BINP31 20131
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
4194645
date added to LUP
2013-12-11 15:20:35
date last changed
2013-12-11 15:20:35
@misc{4194645,
  abstract     = {Popular science summary

Reductive evolution in fungi?

It has been shown that the super kingdoms of Bacteria and Archaea are under the influence of reductive evolution compared to Eukaryotes. Even if the process of reductive evolution is not the predominant mode of evolution amongst Eukaryotes, since the majority of species are not growth optimized, the process may still be present.

It has been shown that Bacteria and Archaea posses a reduced functional repertoire compared to Eukaryotes. This reductive trajectory is thought to be the result of growth-rate optimization being favoured by Bacteria and Archaea since the three super kingdoms diverged. “Linkers”, functioning as connective links in proteins, has also been affected. They have been shown to be shortened amongst Bacteria and Archaea. These changes are thought to increase the mass efficiency of proteins and protein synthesis which is highly preferred by growth-rate optimized cells (Archaea and Bacteria). Growth-rate optimized cells can still be found throughout Eukaryota e. g. among algae and fungi. Yeasts represent unicellular growth-rate optimized fungi and are widely distributed within the fungi kingdom.

Within the subphylum of Saccharomycotina there is a split, thought to have occurred ~175 My ago, that divides yeasts and filamentous fungi. Presupposing that this low level of morphological transition is coupled to growth-rate optimization, clonal expanding yeasts being more growth optimized, reductive evolution might have influenced these yeasts compared to the filaments since the divergence. 

The functional repertoire were found to be slightly reduced amongst the yeasts compared to the filaments. Also though the total amount of functional units were more abundant amongst the filament there was a bias towards functions related to a more complex morphology e. g. cell-adhesion. The linker lengths were also found to be shorter amongst the yeasts compared to the filaments of Saccharomycotina. 

The smaller functional repertoire and the shorter linker lengths amongst the yeasts of Saccaromycotina might indicate that the yeast branch has been more influenced by reductive evolution then their neighbouring filamentous branch. This brings up the general question of how big the overall influence of reductive evolution is amongst different Eukaryote lineages. Adding more data, sequencing more genomes, will contribute to further clarifying this potential reductive influence.

Advisor: Björn Canbäck
Master's Degree Project, 45 credits in Bioinformatics 2013
Department of Biology, Lund university},
  author       = {Wilhelmsson, Per},
  language     = {eng},
  note         = {Student Paper},
  title        = {Analysis of the domain superfamily composition in unicellular and multicellular fungi},
  year         = {2013},
}