De novo creation of new genes

De novo creation of new genes

1. Retrotransposition (+/- cooption of other sequences)

AAAAA Pre-mRNA

AAAAA Splicing to remove intron

Reverse transcription by TE polymerases(in CYTOSOL)

Integration into the genome (in NUCLEUS)

Often see short flanking repeats due to mechanism of TE integration

1

De novo creation of new genes

1. Retrotransposition (+/- cooption of other sequences)

AAAAA Pre-mRNA

AAAAA Splicing to remove intron

Reverse transcription by TE polymerases(in CYTOSOL)

Integration into the genome (in NUCLEUS)

Often see short flanking repeats due to mechanism of TE integration

2

De novo creation of new genes

1. Retrotransposition (+/- cooption of other sequences)

2. Gene duplication into other sequences = chimeric structure/regulation

3

De novo creation of new genes

1. Retrotransposition (+/- cooption of other sequences)

2. Gene duplication into other sequences = chimeric structure/regulation

3. Cooption of non-coding DNA (from introns, intergenic sequence)

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De novo creation of new genes

Challenge in distinguishing Novel Gene vs. missed orthology due to rapid evolution

1. Retrotransposition (+/- cooption of other sequences)

2. Gene duplication into other sequences = chimeric structure/regulation

3. Cooption of non-coding DNA (from introns, intergenic sequence)

4. Horizontal gene transfer (very prevalent in bacteria)- also observed from bacterial parasites to insect hosts

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Horizontal (or Lateral) Gene Transfer

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Vertical Transfer (e.g. along species tree)

Horizontal Transfer

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Mechanisms of HGTSteps 1-3: DNA TransferStep 4: Persistence (replication) in RecipientStep 5: Selection to maintain sequence

From Thomas & Nielsen. Nat Rev Microbiol. 2005

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Mechanisms of HGT:DNA Transfer

A. Transformation: direct uptake of naked DNA

• Donor and recipient do NOT need to co-exist in the same time/space• Can occur across distantly related species• Efficiency depends on ‘competency’ of recipient

Some species readily take up DNA Other species have transient (e.g. stress/starvation) competency

B. Transduction via bacteriophages

• Phage can package random or adjacent donor DNA• DNA size limited by capsid packaging (but still can be 100 kb)• Recipient must be able to take up phage (through specific receptors, etc)

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Mechanisms of HGT:DNA Transfer

C. Conjugation: direct connection between two bacteria

• Species need to co-exist in the same environment• Need pairs of species that can conjugate• DNA transferred as mobile element or plasmid

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Mobile (Transposable) Elements & Bacteriophages are a

major force of HGT

Transposase

Antibiotic resistance genes

IR(inverted repeat)

IR(inverted repeat)

Some mobile elements excise and reintegrate,others are replicative.

Some integrate at specific sites (“att” sites) & often adjacent to tRNAs.

Many can excise or replicate neighboring DNA

Many triggered to move upon environmental stress

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Mechanisms of HGT:DNA Stabilization

Transferred DNA needs to replicate & get passed on

• Episomal replication (e.g. plasmid)• Integration along with phage genome or mobile element• Homologous recombination• Non-homologous (“illegitimate”) recombination

Benefit of transferred DNA needs to outweigh its cost

• Burden of extra DNA and/or protein synthesis• Famous cases of HGT involve antibiotic resistance or pathogenicity

New DNA needs to be expressed to provide beneficial functions

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Question: How does the prevalence of operons in bacteriainfluence evolution by Horizontal Gene Transfer?

Having suites of functionally related genes linked and co-expressed = easy to transfer whole pathways

13From Juhas et al. 2009. FEMS Micro

Genomic Islands: families of horizontally transferred genes

Often near tRNAOften contain own mobility genes

& sequencesEvolve through gene acquisition & loss

14From Juhas et al. 2009. FEMS Micro

Grey = sequence homology around 4 genomic islands (2 related to pathogenicityand 2 related to environmental responses); black = Genomic Islands

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Detecting HGT sequences

1. Often have unusual sequence characteristics (GC content, codon usage, di-nt frequencies) compared to the rest of the genome

Signatures of other genomes speckled in the host.

2. Often flanked by repeat elements (from phage or mobile element insertion)or tRNAs (since integration often near tRNAs)

3. Gene tree is very different from the species tree

1. These days, easily detected by sequencing many isolates of the same ‘species’and detecting variable gene sequences

16From Tenaillon et al. Nat Revs Micro 2010

17From Keeling & Palmer Nat Rev Genetics 2008

Effects of HGT on Gene Trees

Best evidence for HGT: sequencing of many strains of the same ‘species’

… but What is a bacterial species?? No sex, lots of HGT across species …

the idea of the Pan Genome: the total gene pool represented within a ‘species’

Core Genome: genes common to ALL isolates of a given species

Accessory Genome: variable parts found in subsets of isolates

Bacterial Pan Genomes

In study of 8 E. coli genomes:

Only 40% of the Pan Genome was madeup of the Core Genes

But extrapolation suggests many more accessory genes in E. coli (but not all species … why?)

From Mira et al. 2010. Internat. Micro

From Mira et al. 2010. Internat. Micro

Mobile elements more prominent for some species

Some species more readily take up DNA;others do not do homologousrecombination well

Some species occupy very narrow niche – little exposure to other DNA, etc

Bacterial Pan Genomes

In study of 8 E. coli genomes:

Only 40% of the Pan Genome was madeup of the Core Genes

But extrapolation suggests many more accessory genes in E. coli (but not all species … why?)

Different genes enriched in the Core vs. Accessory Genomes

Core Genomes: ‘Housekeeping’ functions

Accessory Genomes:* Environmental genes* Poorly characterized genes* Orphan genes (no homology to any known gene)* More mobile elements, phage sequences, repeats

Orphan genes:Considerably shorter than normal genesSome are fragments of other genesSome may be non-functionalMay original from poorly sampled world of phage genes

Metagenomics: uncovering the world of new bacterial/phage genes

Metagenomics: sequencing the entire pool of DNA found in environmental sample

* Done without cloning or culturing (most bacteria cannot be cultured!)* Computational methods of linking sequence back to particular species

* Work to try to assemble genomes* Most analysis to date done on pools of sequences, not

genomes assembled from those sequences

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Ed DeLong: 3:30 pm Thursday, February 12: Microbial Sciences Seminar Series