Week 2 => introns/inteins, and prokaryotic genomes Flashcards
Mobile genetic elements
- DNA elements that encode proteins that mediate the moment of the element within a genome and between genomes
- AUNDANT and highly DYNAMIC
- “Parasitic” or “selfish” genetic elements
Alu
primate-specific 300 bp elements (10% of the genome)
Mobile introns
(Group I and II introns) intervening sequences that are capable of self-splicing and moving themselves withing and between genomes
Inteins
Are mobile genetic elements capable of self-splicing post-translationally. Inteins remove themselves from a precursor protein and ligate the flanking sequences with a peptide bond.
Group I introns
mobile self-splicing ribozymes that catalyze their own removal from RNA
How are introns removed/spliced?
via two transesterification reaction
Where are group I introns found?
They exists in protein, rRNA and tRNA genes in diverse eukaryotic nuclear, mitochondria, and plastid genomes, as well as in bacteria
What do group II introns look like and how do they work?
- 200-500 nt in length with complex secondary/tertiary structure
*some contains an ORF encoding a ‘homing endonuclease” (HE) - Intron removed by two transesterification reactions
Homing
The lateral (or horizontal) transfer of an intervening sequence to an intron-lacking version of the gen
Homing endonuclease (HEs)
- Recognize and cleave 12 to 40 bp DNA sequence motifs
- Some also have a ‘maturase’ function, whereby they help the intron fold into the proper 3D shape required for splicing
Ectopic transportation
movement of intron to new genomic sites
How do group I introns spread to new locations?
Ectopic transposition (also known as reverse splicing)
Group II introns
like group I introns, group II introns are mobile genetic elements capable of self splicing
Where are group II introns found?
- Group II introns exist in protein genes in many bacteria, a few archaea, and mitochondrial and plastid genomes
- are thought to be the progenitors of nuclear spliceosomal introns
What do group II introns look like and how do they work?
- 400-800 nt in length with complex secondary/tertiary structure
- Some (nut not all) group II introns contain an ORF encoding a multifunctional intron-encoding protein (IEP) that includes a reverse transcriptase domain
- Like group I introns, group II splicing occurs via two transesterification reactions (first initiated by a ‘bulging A’ residue within the intron)
IEP features
reverse transcriptase (RT), endonuclease (E), and ‘maturase’ (M) domains => forms RNP complex
What does RNP (like IEP) mediate?
Mediates homing of introns to intron-minus locations (exact mechanism is somewhat different than for Group I intron homing)
Twintrons
introns-within-introns
Where are inteins found?
- First discovered in 1990 in yeast (in vacuolar ATP synthase A subunit)
- Inteins are found in protein-coding genes in all domains of life, as well as in viruses
- Inteins are particularly common in cyanobacteria, proteobacteria, and archea
What do inteins look like?
- 100-800 amino acids long
- C, S, or T residues at the amino- and C-Terminal junctions (essential for splicing)
- Internal homing endonucleases (can be present of absent) as in group I introns
Minimal (“mini”) intein
Lack homing endonuclease
Slit intein
splicing done in trans (separation between amino-terminal splicing domain and carboxyl-terminal splicing domain)
Splicing
A complex multistep process that involves successive peptide bond modifications and transient formation of a ‘branched intermediate’ at the C- terminal intein/extein junction
What inadvertently duplicates intervening sequences of Group I introns, Group II introns, and inteins?
Cellular double-strand break repair mechanisms using homologous recombination
Three or two domains of life?
Three domains: eukaryotes are sisters to archaea, thus three branches in tree
Two domains: eukaryotes are nested withing archaea
Possible forms of chromosomes
- Circular
- Linear
- Circular and linear
- ‘Megaplasmids’
Why are plasmids not considered ‘chromosomes’?
Because they are not essential
What do bacteria have instead of histones?
Nucleoid-Associated proteins (NAPs)
Genome length of Ktedonobacter (a soil bacterium)
13.7 mb
Gene density
number of genes per units of DNA length (e.g., x genes per kilobase)
Genome length of Nasuia deltocephalinicola (a bacterial endosymbiont)
112 kb
Clonal model
novelty comes from mutations arising within asexual populations
What domain exhibit a highly uniform gene density?
Prokaryotes
Homologous recombiantion
novelty comes from recombination of existing alleles
Relationship of recombination and sequence divergence
Rate of recombination drops exponentially as sequences diverge
Transposition
movement in the genome
Insertion sequence (IS) elements
small DNA segments that are capable of transposition and mediating recombination (within and between genomes)
Non-replicative (IS element)
IS element is excised from donor site and inserted into a new site
Replicative (IS element)
IS element excised and inserted into multiple sites at the time of DNA replication
Inverted repeats (IR)
left and right, with signals for recognition by the transposase and for the DNA cleavage needed for IS displacement
Plasmids are hotbeds of ___ activity
IS
Meaning of “IS elements are highly promiscuous”
they spread within and between a wide variety of different types of organisms, even between archaea and bacterial genomes
Genomic islands
‘Large’ (5 to 100+ kb) regions of a genome that exhibit a ‘patchy’ distribution (found in some strains of a given species, but not others) and show evidence of having been acquired by lateral gene transfer (LGT)
Alternate name for ‘genomic islands’
pathogenicity islands and resistance islands
Genomic islands are often enriched in:
- mobile genetic elements
- ‘mobile genes’ such as transposases and integrases
- Insertion sequence (IS) elements
- tRNA genes (are known as phage integration sites)
- repetitive sequences
Virulence factors (VFs)
allow a pathogenic organism to replicate and disseminate by subverting or eluding the defense systems of the host. They include adhesins, invasions, endotoxins, hemolysins, proteases, etc.
Genomic islands (GIs) are enriched in____
Virulence factors
Lateral (or horizontal) gene transfer (LGT/HGT)
The movement of genetic material between different species in a manner often than ‘traditional’ reproduction (to be contrasted with vertical transfer of genes from parents to offspring via sexual or clonal reproduction)
Mechanisms of LGT
- Transformation
- Transduction
- Conjugation => integrative and conjugative elements (ICEs)
How do we detect ‘foreign’ genes in a genome? And how we we determine where they come from?
- Gene presence/absence
- compositional a anomalies/genomic landscape
- phylogenetic incongruence
Transformation
a bacterium takes up a piece of DNA floating in its environment
Transduction
Transduction involves the transfer of a DNA fragment from one bacterium to another by a bacteriophage. There are two forms of transduction: generalized transduction and specialized transduction.
Conjugation
Genetic recombination in which there is a transfer of DNA from a living donor bacterium to a living recipient bacterium by cell-to-cell contact. In Gram-negative bacteria it typically involves a conjugation or sex pilus.
Integrative and conjugative elements (ICEs)
Bacterial mobile genetic elements that primarily reside in the host chromosome, but can excise and be transferred to other cell by conjugation
What mediates integration/excision?
Integrase and excisionase proteins
What secretion system does conjugative transfer typically occur?
Typically occurs via assembly of a “type IV secretion system”, through which DNA passes by rolling circle replication
Example of ICEs in class
SXT family of ICEs, found in Vibrio cholera and related bacteria. 52 genes in total. Confer multi-drug resistance and other adaptive features to their bacterial hosts
Where do genomic islands come from?
Many genomic islands are ICEs that have lost the ability to mediate excision and/or conjugation.
Gene presence/absence
*Deciding between gene gain or loss often involves parsimony
* Need to have a reasonably good understanding of the relationship between the organism under consideration
Pasimony
In biology, parsimony is the principle that the simplest explanation is most likely to be true. In phylogenetics, the principle of parsimony is used to construct evolutionary trees that minimize the number of changes required to explain the data.
Synteny
gene order conservation
Yersinia pestis
causative agent of plague
Amelioration
A change in the nucleotide composition of a laterally transferred gene (or group of genes) towards that of its current genomic context. Acquired genes resemble their donor genomes in G+G content and codon bias at the time of transfer; over time they come to resemble their recipient genome
Phylogenetic incongruence
If you know (or have a good idea of) the relationship between the organisms of interest, you can make and alignment of the DNA and/or protein and build a phylogenetic tree. If the resulting topology is incongruent with known/predicted relationships, then LGT can reasonably inferred
Example of phylogenic incongruence and LGT discussed in class?
- The phylogenetic tree of bacterial threonyl tRNA synthases suggesting that some cyanobacteria obtained this gene from gamma-proteobacteria, as they are embedded inside the gamma-proteobacterial clade
LGT-Factors influencing frequency of successful transfer between organisms
- Physical proximity
- Gene-transfer mechanisms
- Metabolic compatibility
- Gene expression systems
Pan-genome
The collection of genes shared among members of the same ‘species’
* branches into variable-genome and core-genome
Prokaryotic genomes are highly dynamic entities comprising of ______
- A relatively stable (albeit unexpectedly small) “core” of genes
- Variable ‘accessory’ genes, which come and go via LGT, facilitating rapid adaptation of the organisms to new environments
