Genome organization in
prokaryotes and eukaryotes
Prof. Marcos De Donato, PhD
DBI, Tecnológico de Monterrey
Campus Querétaro
Genome organization in
prokaryotes and eukaryotes
Prokaryotic Genomes
1. Genomes sequenced
2. Genome size and structure
3. Mobile elements
Eukaryotic Genomes
1. Genome structure
2. Repetitive elements
3. Chromatin structure
Prokaryotic
Genomes
Bacterial Cell Size
Tree of Life
Animals
Plants
The first phylogenetic tree based on rRNA data, emphasizing the separation of
bacteria, archaea, and eukaryotes, as proposed by Woese et al. in 1990.
Woese et al. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria,
and Eucarya. PNAS, 1990; 87(12), 4576-4579.
Tree of Life
Animals
Plants
Pace NR. A molecular view of microbial diversity and the biosphere. Science, 1997; 276(5313):734-40.
Modern Version of the Tree of Life
A current view of the tree of life, encompassing the total
diversity represented by sequenced genomes. The tree
includes 92 named bacterial
phyla, 26 archaeal phyla and all five of the Eukaryotic
supergroups. Lineages lacking an isolated representative
are shown with red dots.
http://geschwindlab.neurology.ucla.edu/protocols/next-generation-sequencing
Hug, Laura A., et al. A new view of the tree of life. Nature microbiology 1.5 (2016): 16048.
All
Known
Animals
All
Known
Plants
Bacterial DNA
http://myhome.sunyocc.edu/~weiskirl/parts_of_all_cells.htm
http://fbio.uh.cu/sites/genmol/confs/conf1/p1.htm
Bacterial Cell
Viral Genome Sizes are Non-Randomly Distributed in the Tree of Life
Campillo-Balderas et al. Frontiers in Ecology and Evolution. 2015 Dec 23;3:143.
Core genome: Contains the genes that are
essential to the basic functions of the species.
These genes are called the housekeeping
genes.
Pangenome: Contains all the genes that can be
found in any strain of the species (including
those in the core genome). Strain specific
genes are part of the pangenome, which can
provide different functions that help the
bacteria to adapt to different environments.
Core vs Pangenomes
Core vs Pangenomes
There is a very large number of
genes in the pan genome,
compared to the number
in the core genome of
E. coli
Core vs Pangenomes
https://tel.archives-ouvertes.fr/tel-01599361/document
Bacterial DNA Structure
Prokaryotic Cell
Plasmids
Bacterial Chromosome
https://www.shmoop.com/biology-cells/prokaryotic-cells.html
Bacterial DNA Structure
http://biology.kenyon.edu/courses/biol114/Chap01/chrom_struct.html
Bacterial DNA Structure
http://biology.kenyon.edu/courses/biol114/Chap01/chrom_struct.html
Bacterial DNA Structure
http://biology.kenyon.edu/courses/biol114/Chap01/chrom_struct.html
Bacterial Mobile Elements
Frost et al. Nature Reviews Microbiology. 2005; 3(9):722.
Bacterial Mobile Elements
Finan TM. Microbiol. Mol. Biol. Rev. 2017; 81(3):e00019-17.
Eukaryotic
Genomes
Mitochondrial and Plastid Endosymbiosis
Schematic tree of newer
hypotheses for phylogenetic
relationships among major
groups of eukaryotes.
Martin, W. & Mentel, M. (2010) The Origin of Mitochondria. Nature Education 3(9):58.
Mitochondrial and Plastid Endosymbiosis
Figure 1. Mitochondrion-late and
mitochondrion-early models for
the origin of eukaryotes. Fossil
evidence has it that eukaryotes
are 1.5 billion to 1.8 billion years
old. All current models for the
origin of eukaryotes have
mitochondria in the eukaryote
common ancestor. (A) In
mitochondrion-late models, an
archaeon (red) becomes a
complex protoeukaryote, evolves
phagocytosis, and acquires the
proteobacterium (blue). (B) In
mitochondrion-early models,
phagocytosis came after the
mitochondrion. Mitochondrionearly models typically start with
metabolic interactions between
an archaeon and the
proteobacterial ancestor of
mitochondria.
Martin et al. Microbiol Mol Biol Rev. 2017;81(3). pii: e00008-17.
Secondary Endosymbiosis
Martin et al. Microbiol Mol Biol Rev. 2017;81(3). pii: e00008-17.
Evolution of the Domains of Life
López-García P, Eme L, Moreira D. J Theor Biol. 2017 Dec 7;434:20-33.
C-Value Paradox
https://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-18/CB18.html
Genome Sizes in Viruses, Bacteria, Archaea and Eukaryotes
Koonin, EV. 2011. The Logic of Chance: The Nature and Origin of Biological Evolution. FT Press.
Relation between Gene Fraction & Genome Size in Eukaryotes
Drosohila
A. thaliana
https://slideplayer.com/slide/8850552/
Genome Size Variation in Amniotes
Kapusta A, Suh A, Feschotte C. Dynamics of genome size evolution in birds and mammals. PNAS. 2017;
114(8):E1460-9.
Different Components Making up the Human Genome
About 1.5% of the genome consists of the ≈20,000 protein-coding sequences which are
interspersed by the non coding introns, making up about 26%. Transposable elements are the
largest fraction (40-50%) including for example long interspersed nuclear elements (LINEs),
and short interspersed nuclear elements (SINEs). Most transposable elements are genomic
remnants, which are currently defunct. (Gregory TR. Nat Rev Genet. 9:699-708, 2005)
Barbara McClintock and Her Jumping Genes
 1940s, Barbara McClintock discovered the first transposable
element in maize, earned a Nobel prize in 1983.
 Late 1960s, transposition was also found in Bacteria.
http://newshub.agilent.com/2015/06/16/barbara-mcclintock-and-her-jumping-genes/
Aleurone Color in Maize
Aleurone is a layer surrounding the maize seed and the color is
determined by several genes. Only when the aleurone has no
color (transparent), the color of the endosperm can be seen.
Colorless
Substance
c/c
C2
X
Colorless
Substance 2
pr1/pr1
Pr1
X
Red
Pigment
Bz1
X
bz1/bz1
Purple
Pigment
Ds/Ac Mobile Elements in Maize
The movement of mobile
elements can induce
mutations including
chromosome brakage. This
is how McClintock found
out about these elements
in maize.
The excision of the mobile
element from the gene
makes it functional again,
allowing the production of
pigment, but only in the
cells that have inherited the
functional copy (purple
patches). Those cells where
the gene is still disrupted by
Ds will show the yellow
background).
http://www.bio.miami.edu/dana/250/250S12_17print.html
Ds/Ac Mobile Elements in Maize
Normal gene producing
pigment
Disrupted gene not
producing pigment
Cells where Ds have
excise out of the gene,
cells resume pigment
production
Ac can also disrupt the
gene and when it excise
out of the gene, cells
resume pigment
production
http://www.bio.miami.edu/dana/250/250S12_17print.html
Disruption of gene function by Mobile Elements
Transposable elements
can be inserted in
different places within a
gene, causing different
effects.
http://www.bx.psu.edu/~ross/workmg/TranspositionCh9.htm
P Element in Drosophila
P element in drosophila
is a mobile element
causing sterility when
they become active.
http://www.bio.miami.edu/dana/250/250S12_17print.html
P Element in Drosophila
In the fly gametes, the P
element can become
active, inserting into many
places and causing
disruption in several
important genes, resulting
in sterility. Only when the P
element is inherited from
the mother, the individuals
also get suppressors of the
P element movement, not
allowing them to move.
http://www.bio.miami.edu/dana/250/250S12_17print.html
Types of Transposable Elements
Sampath & Yang. Plant Breeding and
Biotechnology. 2014; 2(4):322-33.
Transposition in Transposable Elements (TEs)
Levin & Moran. Nature Reviews Genetics, 2011; 12(9):615-627.
Mobile DNA Elements
https://openi.nlm.nih.gov/detailedresult.php?img=PMC3386198_ppat.1002790.g003&req=4
SINEs
Short interspersed elements (SINEs) are defined as
relatively short (< 700 bp) nonautonomous
retroposons transcribed by the cellular RNA
polymerase III (pol III) from an internal promoter, while
their reverse transcription depends on the RT of
partner LINEs.
• Most are tRNA derived; Alu is 7SL-RNA
• Nonautonomous
• Dependent on other machinery- genome “parasite”
• RNA Pol III
• Needs LINE Endonuclease and Reverse
Transcriptase for activity
• Composed of 3 parts: 5’ head, Body, 3’ tail
Average size ~200 base pairs
Vassetzky & Kramerov. Nucleic acids research. 2012; 41(D1):D83-9:
http://sines.eimb.ru/
Polymorphism of Alu Insertion
The ancestral human population is shown
at the top, and two separate
subpopulations as shown here. A
monomorphic Alu insertion (red) is
shared by all members of the population.
Several Alu insertion polymorphisms are
also shown, including an intermediatefrequency Alu insertion polymorphism in
the ancestral and subpopulations (green),
a population-specific element (blue) and
a de novo insert in subpopulation B
(mauve).
Batzer MA, Deininger PL. Alu repeats and human genomic
diversity. Nature reviews genetics. 2002 May;3(5):370.
The Impact of TEs on Mammalian Genomes
Garcia-Perez JL, Widmann TJ, Adams IR. The impact of
transposable elements on mammalian development.
Development. 2016; 143(22):4101-14.
Silencing Mechanisms Controlling TE Activity
Horváth V, Merenciano M, González J. Revisiting the relationship between transposable
elements and the eukaryotic stress response. Trends in Genetics. 2017; 33(11)832-41.
Effect of Stress on TEs
Horváth V, Merenciano M, González J. Revisiting the relationship between transposable
elements and the eukaryotic stress response. Trends in Genetics. 2017; 33(11)832-41.
TEs Can Alter Expression and Structure of Nearby Genes
Horváth V, Merenciano M, González J. Revisiting the relationship between transposable
elements and the eukaryotic stress response. Trends in Genetics. 2017; 33(11)832-41.
Repetitive Elements
Most of the human genome is made of repetitive elements, with the largest fraction
originated from transposable and retrotransposable elements. LINEs and SINEs (Alus) are
the most frequent retrotransposons.
Exon Shuffling by Homologous Recombination
Repetitive elements, like Alu elements can
participate in a process called exon shuffling,
where genes can exchange exons, changing the
proteins they code, allowing for the creation of
new functions.
Exon Shuffling by Transposition
Exon Shuffling
Exon Shuffling can produce new genes with novel functions
that can help the individual to adapt to new environmental
conditions or niches.
This is especially important when the genes have been
previously duplicated, allowing for the original gene to
conserve the original function and the duplicated gene to
acquire the new function.
Processed pseudogenes can re-acquire a function if they are
inserted next to a promoter of another gene.
DNA Organization in Eukaryotes
DNA Organization in Eukaryotes
CHROMOSOME
STRUCTURE
CHROMOSOME
Telomeres
STRUCTURE
Arms
Centromere
Chromatids
Telomeres
"SMC" proteins- structural maintenance of chromosomes
https://www.studyblue.com/notes/note/n/chapter-4-dna-chromosomes-and-genomes/deck/8763553
Telomeres
http://www.sens.org/research/research-blog/2013-research-report-part-3-12-cancerous-cells
Neumann & Reddel. Nature Rev Cancer. 2:879-884, 2002
Centromere
Centromere structure and
organization.
(A) Centromeric chromatin underlies
the kinetochore, which contains inner
and outer plates that form
microtubule-attachment sites.
Pericentromeric heterochromatin
flanks centromeric chromatin, and
contains a high density of cohesin,
which mediates sister-chromatid
cohesion. (B) Schematic depiction of
centromeric DNA in humans and
mice, Drosophila,
Schizosaccharomyces pombe, Candida
albicans and Saccharomyces
cerevisiae.
Allshire & Karpen. Nature Rev Genet, 9:923-937, 2008