[YBI-37806] SAMENVATTING
Lecture 3 [Archaea]
- A protist (/ˈproʊtɪst/) is any eukaryotic organism (that is, an organism whose cells
contain a cell nucleus) that is not an animal, plant, or fungus.
- 16S gene commonly used to construct the Tree of Life by sequencing the genes.
Trees reflected those based on 16S rNA genes, but are they actually really suitable to
reconstruct the Tree of Life?
- The genome of micro-organisms can be divided into roughly three functional
‘classes’ of genes:
These flexible shell genes are not always present in all organisms and are lifestyle-specific,
thus it may vary from species to species (particularly further apart).
,Each circle represents an e. coli
genome (three different strains).
If looking at genes, you see that
they share all less then 40% of
genes. Many genes in each genome
are specific to certain strain
(unique). So even at species level a
genome content can be very
different. Micro-organisms often
obtain and exchange genes through
horizontal gene transfer. If genes
are being exchanged, these genes
do not reflect evolutionary history.
So these genes are not suitable for constructing Tree of Life. Beste genes would be the core
genes, as they are universally present in all lifeforms, they are slow-evolving and not
subjected to horizontal gene transfer. It should evolve, but very slowly. From the core genes
there are only 100 genes that have really not been subjected to horizontal gene transfer,
mostly genes involved in translation (ribosomal proteins).
In their field they don’t work with DNA or RNA sequences, but use amino-acid sequences of
proteins, these are better conserved:
The mismatches are where we have interesting information, gaps are often deleted from
the data. They do same trick for all universal genes that code for proteins.
,Eukaryotes and bacteria share some features, like membrane and lipids (and mitochondria,
which are developed through endosymbiosis), whilst those differ very much from archeae.
Whilst archaea also have features like transcription, translation, etc. like in bacteria and
eukaryotes.
Genome study with lot of markers
resulted in this tree. Hundreds of
types of alphaproteobacteria, show
that endosymbiont theory holds up.
Mitochondria don’t only produce
ATP, but also citric acid cycle in
mitochondria, redox reactions and
enzymes. Mitochondria do a lot more
than just energy production. Many of
mitochondria genomes still encode
the proteins necessary for these
actions, BUT following
endosymbiosis, many of the
mitochondria genes from the
ancestor alphaproteabacterium were
lost or transferred to nuclear genome
, Human genome, on the far right, only has 13 original mitochondrial genes that encode for
proteins. So part of the chimeric nature of eukaryotes can be explained by horizontal
transfer of genes.
Archezoa hypothesis
Model based on part of the tree of life with only eukaryotes, right are eukaryotes with
mitochondria, and on the left some eukaryotes without mitochondria. So group on the left
(archezoa) split off from eukaryotic tree of life BEFORE endosymbiosis. HOWEVER, this was
done on little amount of data and there were observations made later that this theory was
false. Many lineages did not indeed contain classic mitochondria, but they did contain some
organelles that were shown to be derived from mitochondria, they were reduced
(mitizomes). The could also show that they actually contained genes of mitochondrial
descend.
Lecture 3 [Archaea]
- A protist (/ˈproʊtɪst/) is any eukaryotic organism (that is, an organism whose cells
contain a cell nucleus) that is not an animal, plant, or fungus.
- 16S gene commonly used to construct the Tree of Life by sequencing the genes.
Trees reflected those based on 16S rNA genes, but are they actually really suitable to
reconstruct the Tree of Life?
- The genome of micro-organisms can be divided into roughly three functional
‘classes’ of genes:
These flexible shell genes are not always present in all organisms and are lifestyle-specific,
thus it may vary from species to species (particularly further apart).
,Each circle represents an e. coli
genome (three different strains).
If looking at genes, you see that
they share all less then 40% of
genes. Many genes in each genome
are specific to certain strain
(unique). So even at species level a
genome content can be very
different. Micro-organisms often
obtain and exchange genes through
horizontal gene transfer. If genes
are being exchanged, these genes
do not reflect evolutionary history.
So these genes are not suitable for constructing Tree of Life. Beste genes would be the core
genes, as they are universally present in all lifeforms, they are slow-evolving and not
subjected to horizontal gene transfer. It should evolve, but very slowly. From the core genes
there are only 100 genes that have really not been subjected to horizontal gene transfer,
mostly genes involved in translation (ribosomal proteins).
In their field they don’t work with DNA or RNA sequences, but use amino-acid sequences of
proteins, these are better conserved:
The mismatches are where we have interesting information, gaps are often deleted from
the data. They do same trick for all universal genes that code for proteins.
,Eukaryotes and bacteria share some features, like membrane and lipids (and mitochondria,
which are developed through endosymbiosis), whilst those differ very much from archeae.
Whilst archaea also have features like transcription, translation, etc. like in bacteria and
eukaryotes.
Genome study with lot of markers
resulted in this tree. Hundreds of
types of alphaproteobacteria, show
that endosymbiont theory holds up.
Mitochondria don’t only produce
ATP, but also citric acid cycle in
mitochondria, redox reactions and
enzymes. Mitochondria do a lot more
than just energy production. Many of
mitochondria genomes still encode
the proteins necessary for these
actions, BUT following
endosymbiosis, many of the
mitochondria genes from the
ancestor alphaproteabacterium were
lost or transferred to nuclear genome
, Human genome, on the far right, only has 13 original mitochondrial genes that encode for
proteins. So part of the chimeric nature of eukaryotes can be explained by horizontal
transfer of genes.
Archezoa hypothesis
Model based on part of the tree of life with only eukaryotes, right are eukaryotes with
mitochondria, and on the left some eukaryotes without mitochondria. So group on the left
(archezoa) split off from eukaryotic tree of life BEFORE endosymbiosis. HOWEVER, this was
done on little amount of data and there were observations made later that this theory was
false. Many lineages did not indeed contain classic mitochondria, but they did contain some
organelles that were shown to be derived from mitochondria, they were reduced
(mitizomes). The could also show that they actually contained genes of mitochondrial
descend.
