Understanding Genetic Variation and Horizontal Gene Transfer in Evolution

1. Lecture 8Mechanisms of Evolution: Genetic Variation - Horizontal Gene Transfer October 1, 2019 Jeremy Glasner PhD

2. Science, 1997

3. Variation among genomes arises as they diverge from a common ancestor • Point mutations introduce small changes in one or the other lineages (SNPs, small insertions and deletions). • Recombination during meiosis leads to new combinations of alleles from different loci. • Rearrangements introduce inversions and translocations of segments of DNA within or between chromosomes. This can include changes in chromosome number. • Duplications of whole genomes, segments, or genes generate new genome content. Deletions remove genome content. • Transposable elements can lead to duplications of themselves, and disruption of other features/genes. • Horizontal gene transfer (and hybridization in eukaryotes) can replace segments of a genome with a homologous copy from another species. HGT can also introduce entirely new content from another species.

4. Impacts of Variation • Gain and Loss of Content • Changes in gene/feature function • Changes in Regulation • Gene expression turned on or off • Gene expression at a different times • Gene expression in different places • Gene expression in response to different cues

5. Cell Division Occurs by Binary Fission in Bacteria and Other Single Celled Organisms Bacteria/Archea Unicellular Eukaryotic Cell Division In Binary Fission, the cell divides itself into two, equal, identical parts with the same DNA Mutations can occur in the DNA sequences and can be passed on to daughter cells The variation between genome sequences is inherited VERTICALLY from parent cell to daughter cells

6. Vertical Evolution of Genomes as Species Diverge mutation mutation mutation mutation mutation mutation species1 genome1 species2 genome2 species3 genome3 species4 genome4 species5 genome5 species6 genome6 Time Mutations occur over time, but are only inherited from a common ancestor

7. Vertical Evolution of DNA sequences as Species Diverge Species Tree DNA sequences Time Mutations occur over time, but are only inherited from a common ancestor

8. Rates of Nucleotide Substitution Vary Dramatically in Different Genomes Figure 5-34

9. Vertical Evolution of Genetic Variation in Diploid Eukaryotes (like us) Variation occurs between the sequences of chromosomes from different individuals but are always inherited directly from parents to offspring Recombination and chromosome segregation create new combinations of variable sequences in parental chromosomes during meiosis

10. Horizontal Gene Transfer (HGT, aka Lateral Gene Transfer (LGT) Horizontal gene transfer refers to the acquisition of DNA sequences through mechanisms other than inheritance from a common ancestor (vertical transfer). It occurs across all domains of life but appears most commonly in bacterial and archaeal genomes. It can result in recombination of alleles across lineages or introduction of new sequences from other organisms.

11. Small subunit rDNA perspective The branching patterns observed in the tree reflect common ancestry and assume vertical inheritance of sequences (and bifurcation) The species tree can be useful for detecting horizontally transferred sequences when a “gene tree” differs from the species tree DNA (or protein) sequences that are conserved across different organisms (such as ribosomal RNA encoding genes) can be used to infer the “species tree” that describes the ancestry of the different groups Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese CR, Kandler O, Wheelis ML. Proc NatlAcadSci U S A. 1990 Jun;87(12):4576-9.

12. Incongruence between gene trees and species trees can indicate horizontal transfer (species tree)

13. Two Types of Horizontal Gene Transfer • Introduce genes from one lineage into another lineage • Replace an existing gene with a copy from a different lineage Inferring Horizontal Gene Transfer. Matt Ravenhall, NivesŠkunca, Florent Lassalle, Christophe Dessimoz. PLoSComput Biol. 2015 May; 11(5): e1004095. PMCID: PMC4462595

14. G+C Content can highlight HGT sequences • DNA is double stranded, G pairing with C • Measure the amount of G+C content in regions • If one region varies significantly from most of the genome, more than likely HGT HGT 52% 43% 52%

15. Codon Bias Varies Along the Chromosome Blattner et al. Science, 1997 Regions of the chromosome that show atypical codon bias may represent HGT sequences

16. Prokaryotic Genome • Haemophilus influenzae Prokaryotic Genomes often consist of one or a few circular chromosome(s)

17. Distribution of Genome Sizes Among Diverse Groups of Organisms "Genome Sizes" by Abizar at English Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Genome_Sizes.png#mediaviewer/File:Genome_Sizes.png

18. Most bacteria and archaea have pretty small genomes but exhibit extraordinary metabolic and ecological diversity

19. Number of genes as a function of Genome Size "Genome Sizes" by Abizar at English Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Genome_Sizes.png#mediaviewer/File:Genome_Sizes.png

20. Smaller Population Size • Differences in genome architecture (noncoding, nonfunctional) (regulatory sequence) (transcribed sequence)

21. FIGURE 21.2 Isolated bacterial chromosome. Electron micrograph of a purified, surface-spread E. coli chromosome. Photograph prepared by R. Kavenoff and O. Ryder; reprinted from Chromosoma by permission of the publisher. Bar represents 1 ^m

22. The question: how much HGT really goes on? • Rare going from prokaryotes into multi-celled eukaryotes because must go into egg/sperm • Exception is mitochondria, plastids • Instances of Euks ->Proks ?!?! • How often does it happen in proks?

23. Lateral Gene Transfer and the nature of bacterial innovationOchman, Lawrence, and Groisman, Nature 405:299-304 • Single celled organism, genome varies only by an order of magnitude. • Narrow taxonomic groups, phenotypic diversity is remarkable. • Usually have a unique set of physiological characters to define its particular ecological niche.

24. Even “closely related” bacterial species can show tremendous variability in metabolic capabilities and lifestyles

25. Prokaryotic Operons • The organization of genes into an operon allows for simultaneous expression of multiple genes that are located next to each other in the operon • It also enables the set of genes to undergo horizontal gene transfer as a single unit • One transfer can move several genes encoding proteins with related functions together as a unit

27. So, Most Prokaryotic mRNA is Polycistronic • Most of the mRNA found in bacteria and archaea is polycistronic, havinga single mRNA that encodes for multiple different polypeptides • Bacterial Operons Produce Polycistronic mRNAs: Polycistronic mRNA carries the information of several genes, which are translated into several proteins. These proteins usually have a related function and are grouped and regulated together in an operon • (most eukaryotic mRNA is monocistronic) Having suites of functionally related genes linked and co-expressed = easy to transfer whole pathways

28. Loss of syntenywithin bacterial species illustrated using a DotPlot Sharma et al. 2013 AMB Express

29. Synteny among Drosophila species on a genomic scale Bhutkar et al. 2008 Genetics

30. Science, 1997

31. How can you detect HGT’s? • DNA sequence information • Phylogenetic trees • G+C Content • Codon bias • Sequences new to a genome will retain (for a while) the signatures of the donor genome and distinguished from ancestral DNA

32. Mechanisms of HGT Transformation Conjugation Vesicle-mediated Transduction

33. We’ve known about mechanisms of HGT in bacteria for a long time. But it was thought to have relatively little impact on evolution

34. Horizontal Transfer Mediated by Transformation Some bacteria can directly uptake DNA from the environment and incorporate the sequences into their own genome. These could be autonomously replicating sequences like plasmids or recombination of the donor DNA into the recipient chromosome https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Kaiser)/Unit_2%3A_Bacterial_Genetics_and_the_Chemical_Control_of_Bacteria/3%3A_Bacterial_Genetics/3.1%3A_Horizontal_Gene_Transfer_in_Bacteria

36. Can transfer DNA from donor cell to recipient cell e.g. in E. coli a plasmid called “F” for fertility contains genes encoding a structure called a pilus that can transfer the plasmid, and occasionally large pieces of the E. coli chromosome to cells that lack the F plasmid. The transferred DNA can sometimes recombine into the recipient’s genome Bacterial Conjugation So even traditionally “asexually” reproducing organisms do exchange genetic material and undergo recombination, “sex”, but it is often called “lateral gene transfer” since it mechanistically somewhat different from sex in most eukaryotes that involves meiosis and recombination http://okanogan1.com/wp/wp-content/uploads/2011/02/brinton_conjugation_small.gif

37. Transduction of DNA is mediated by bacteriophage (bacterial viruses) that can pick up DNA from a donor genome and deliver it to the recipient organism Specialized transduction -the bacteriophage DNA has integrated into the bacterial chromosome (lysogeny)

38. 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

39. Mechanisms of HGT: Stabilization of Transferred DNA • 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 The expectation is that most horizontally transferred sequences will be non-functional or deleterious and rapidly deleted from the recipient genome (bacteria tend to have high rates of deletion of sequences) New DNA needs to be expressed to provide beneficial functions!

40. Requirements for Transfer Proximity to donor DNA Stability of DNA in environment Vector transmission Uptake and insertion Sequence similarity (for homologous recombination) Maintenance Stabilization Selection Important determinants in the likelihood of horizontal transfer of sequences What Limits/Prevents Transfer Instability in new host Restriction systems GC/Codon usage incompatibility Splicing and other signals incorrect RNA editing Lack of appropriate interacting genes

41. 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) • C. Transfer of DNA by bacterial mating (conjugation) • Transfer sequences encode structures like pili that facilitate DNA exchange • DNA transfer size can be very large (entire bacterial chromosome) • The recipient genome may now encode transfer functions • Recipient must be able to mate with donor organism

42. Horizontal transfer of DNA sequences requires two distinct events -Introduction of the donor DNA into the recipient cell transformation transduction conjugation -Incorporation of the donor DNA into the recipient cell plasmid –extrachromosomal replicating element (with its own origin of replication) recombination into recipient chromosome homologous recombination illegitimo

43. HGT is much more common between closely related species Strong correlation between sequence similarity and rates or horizontal gene transfer. This is because homologous recombination is much more likely to occur between highly similar sequences.

44. A newly inserted segment can spread rapidly within a species or population through recombination in conserved flanking sequences The initial insertion of a new piece of DNA from another organism into a genome is thought to usually be a very rare event. Once the DNA has inserted into the recipient chromosome it is now flanked by sequences that are homologous to those of other members of the species and the new piece of DNAS can move rapidly through the population by homologous recombination in those conserved flanking sequences From Tenaillon et al. Nat Revs Micro 2010

45. How much HGT is there in the species E. coli? The 2ndE. coli genome Perna et al. 2001, Nature

46. The 2ndE. coli genome Where the two genomes match, they are nearly identical and in the same order Regions where the two genomes don’t match are distributed throughout the genome. Frequently, there is strain-specific content at the same sites. Perna et al. 2001, Nature

47. The 2ndE. coli genome Where the two genomes match, they are nearly identical and in the same order Regions where the two genomes don’t match are distributed throughout the genome. MORE THAN 20% OF THE GENOME, 20% OF THE GENES, ARE NOT CONSERVED BETWEEN TWO MEMBERS OF THE SAME SPECIES Frequently, there is strain-specific content at the same sites. Perna et al. 2001, Nature

48. A 3rdE. coli genome Welch et al. 2002, PNAS

49. Pan-genome = all the distinct genes found in the population/species/unit as a whole Genome of any one organism Genome of the species Core Core Variable Variable

50. Core and Pan Genomes • The Core Genome consists of genes shared by all the strains studied and probably encode functions related to the basic biology and phenotypes of the species • The Pan-Genome is the sum of the above core genome and the dispensable genome • The dispensable genome contributes to the species’diversity and probably provides functions that are not essential to its basic lifestyle but confer selective advantages including niche adaptation, antibiotic resistance, and the ability to colonize new hosts. • The Pan-Genome tends to be much much larger than the Core Genome of a prokaryotic “species”