Introns Flashcards
Give examples of genes that have arisen by intron gain
Rice catalaseA gene
Midge globin genes
What does an introns early model suggest happened with introns?
Loss of introns in many lineages
What does an introns late model suggest happened with introns?
Sporadical transposition of introns into few lineages
What do functional introns contain?
snoRNAs or miRNAs
When do phylogenetic analyses suggest that functional introns were present?
In early metazoans
What does snoRNAs stand for?
Small nucleolar RNAs
Do bacteria contain snoRNAs?
Not found (yet)
Are introns junk?
Maybe, but also have enhancer sequences determining when and where a gene is expressed
Have other properties apart from abilities to splice themselves out of genes, e.g. Tetrahymena group 1 intron
What types of introns are there?
Group I introns Group II introns Spliceosomal introns tRNA Group III twintrons
What are group III twintrons?
Introns within introns
Give examples of group III twintrons
Chloroplasts
Euglena
RNA splicing is catalysed by a spliceosome formed from the assembly of what?
U1, U2, U5 and U4/U6 snRNPs plus other components
> 150 proteins > ribosome
When were introns discovered?
1977
What did Gilbert propose about introns in 1978?
Proposed ‘exon shuffling’ for protein evolution
Introns EARLY
What do Go plots define?
A compact protein module
What gave rise to mitochondria?
Purple bacteria
Describe group I introns
Self splicers
In rRNA of lower eukaryotes, e.g. Tetrahymena
Also tRNA, rRNA and mRNA genes of bacteria and higher plants
In eukaryotes found in mitochondria and chloroplasts
Describe group II introns
Mitochondrial and chloroplasts reverse transcriptase ORF, self-splicers, different splice mechanism from eukaryote pre-mRNAs (5’ GU, 3’ A- any purine, AG)
Describe spliceosomal introns
5’ GU, 3’ AG
Describe tRNA introns
Any base for donors/acceptors
What did Blake suggest about introns in 1978?
Exon = globular protein domain with compact structure.
Shuffling domains to make new proteins helped by introns which separate domains.
What are introns more common in, eukaryotes or prokaryotes?
Introns are more common in higher eukaryotes
Rare in lower eukaryotes and prokaryotes
What do Go domains define?
Exons
What does the limited intron distribution suggest about introns?
It is much more likely that they came in later sporadically
What did further analysis into introns and compact domains by Gilbert in 1998 reveal?
That there is a correlation between intron position and protein domain only for introns in phase zero, i.e. between codons ~40% introns
What percentage of introns are ancient compared to those due to later insertions?
~40% introns are ancient whereas ~60% might be due to later insertions
Are phase zero introns in more ancient or recent parts of genes?
More ancient
Is there any correlation for introns that fall within codon, phase 1 and 2?
No correlation
Which introns would be lost more readily, functional or non-functional?
Non-functional
What is the function of snoRNAs?
To methylate rRNA
What does each individual gene in split tRNA genes encode?
A hairpin
Recent phylogenetic analysis reveals several split tRNA genes sporadically in archaeobacteria. What does sequence analysis suggest about this?
Arisen through recent acquisition through mobile elements
What is the take home message about introns?
Introns may have provided an ancient mechanism for bringing sequences together, so intron/exon boundaries could be a very early evolutionary development
What do other complex features of the split genes also suggest?
An ancient origin
What is Carpediemonas?
A free living soil anaerobic eukaryote
Does Carpediemonas have identifiable mitochondria?
No
What does Carpediemonas have in its carbamate kinase genes? And what is the significance of this?
A splicesomal intron
Pushes back origins of introns even earlier but still after eukaryotic evolution
What was discovered about Trichomonas in 2005?
It has spliceosomal introns
Were introns and spliceosomal proteins present in the earliest eukaryotes?
Yes, but as the spliceosome is very complex is must have evolved much earlier
How many species revealed positional conservation in functional versus non-functional introns?
28 species
Was introns late before or after protein synthesis was established?
After
Was introns early before or after protein synthesis was established?
Before
Is the intron early view intron loss or intron gain?
Intron loss
Is the intron late view intron loss or intron gain?
Intron gain
What type of intron does the Giardia lamblia ferrodoxin gene have?
Spliceosomal introns
What type of organism is the Giardia lamblia?
A primitive gut eukaryote
Describe the metabolism of Giardia lamblia
Anaerobic, does not have identifiable mitochondria
What does the finding of the spliceosomal protein genes Sm (Prp8p, Prp11p) suggest about Giardia lamblia?
It has deep phylogenetic roots
If introns added late, then date is pushed back to earliest common eukaryotic ancestor
Describe what is meant by intron conservation
Different lineages show different rate of gain and loss but ancestor was intron rich irrespective of phylogeny
What was the rate of intron loss 1.5-2 billion years ago?
2E-9 to 2E-10 per year
What was the rate of intron gain 1.5-2 billion years ago?
6E-13 to 4E-12 per year
When scientists took 450 human genes that have snoRNAs or miRNAs containing introns, they found orthologues in how many other species?
27
It is thought that introns could be functional or non-functional, true or false?
True
According to the introns first theory, if the spliceosome was found in early eukaryotes, and took a long time to evolve, what must there have been?
A lot of introns in the earliest eukaryotic ancestors.. prokaryotes?
Are spliceosomal proteins ancient or modern?
Ancient and found in the most primitive eukaryotes
Are spliceosomes small or large?
Huge! - took a long time to evolve
Have U1-6snRNAs, but >150 other proteins
Where are snoRNAs preferentially encoded?
Within spliceosomal introns of genes encoding chaperones (heat shock proteins) and ribosomal proteins
Why must introns be older than the exons surrounding them?
Because they are critical to maturing the ribosome: must be older than the origin of proteins
What kingdom, other than eukaryotes, are snoRNAs found in and what does this mean about its ancestry?
Found in archaea! (no nucleolus, no introns, no spliceosome)
Thus must have been in eukaryotic/archaen ancestor
If introns predate proteins, the spliceosome must have been around in ancestors of archaea/eukaryotes, therefore archaea must have lost..
The spliceosome
Why would you need spliceosomal sno/RNAs in archaea if you do not have introns or a spliceosome?
Back to RNA world. Maybe as replicators became more efficient, longer RNA molecules would be generated. Need to keep the catalytic part and remove the junk RNA
When not in chaperone/ribosomal protein genes, where are snoRNAs often found?
In introns where exons are non-coding, i.e. exon is junk
What is the suggested theory for the origin of translation?
Maybe unused junk RNA became exons?
What is the smallest microorganism known (1% volume of E. coli)?
Nanoarchaeum equitans
What is the genome size of Nanoarchaeum equitans?
0.5Mb
Where are Nanoarchaeum equitans found and with what other hyperthermophile?
Found in submarine Icelandic hot geysers (100 degrees centigrade) with Ignicoccus hospitalis
Why has Nanoarchaeum equitans been studied?
To investigate other roles for introns, particularly the function of ancient introns
Where is the split of the tRNA split gene?
After position 37, one nucleotide downstream of anticodon, and in position of tRNA intron
Do tRNA split genes have the same or different promoters?
Same promoter (for RNA polymerase III) found in 5’ half and 3’ half
For tRNA split genes, sequences upstream of 3’ half (GC rich) are the reverse complement of sequences found..
Downstream of 5’ half
Which type of introns are mobile?
Group III
Which is more complicated, the ribosome or the spliceosome?
The spliceosome
Introns must have evolved early as without recombination there would be..
Phase issues
When was the eukaryotic/prokaryotic split?
Very early, around 2-3 billion years
Which is the more accepted theory, introns early or introns late? Why?
Introns early
Common ancestors are intron rich
More evidence
Which is the more accepted idea, RNA life started before chemical life, or chemical life started before RNA life?
RNA life started before chemical life
Where is an intronic sequence normally located?
Just downstream of the anticodon site
What are the three theories for introns?
Introns late
Introns early
Introns first
Briefly describe what a cladogram shows
No time on it
Lengths of branches don’t reflect time
Briefly describe what a phylogenetic tree shows
Time associated with branches
What can bias the view of evolution?
Natural selection
