Molecular and genetic mechanisms of evolution 529 - Development.

Molecular and genetic mechanisms of evolution

529 - Development

Study of evolution on molecular level

Study of mutations in DNA and RNA

and changes in amino acids sequences.

Comparison of genomes, comparison of

chromosomal segments and structural parts of

DNA or proteins between species.

Study and comparisons of genome‘s sizes

RNA as the first NA molecule

The first molecules formed abiotically.

Some RNA are able to replicate autonomously.

Some have catalytic properties

Errors in replication form different sequences, differentiation of RNA

molecules, origin of family with closely related RNA molecules.

Ribosyms

• have auto-replication activity

• ribosome, spliceosome have enzymatic properties

Coenzyms

are non-protein parts of some enzymes. Some are derived from

nucleotides.

Genetic code

is nearly universal with small exceptions. Codons have the

same sense in all living organisms, from viruses to humans.

The most important exception is in mitochondria of mammals, yeast and

other species:

4 different codons (stop codons), further 60 codons in mammalian

mitochondria have the same meaning as in the nuclear mRNA.

70-75% genes of mice have equivalents in humans. 96% to 98% of

genome is identical between human and chimpanzee.

Comparison of genes, genomes

Many different types of organisms used the same proteins with small

changes in amino acids sequences.

Many proteins in human and chimp are similar, 99% percent of their

amino acids are identical.

Two strongly preserved proteins are cytochrome C and

proteins of homeobox, histons, globins.

CYTOCHROME C - Cytochrome C occur in all eukaryotes.

20 of 104 amino acids in the molecule of protein occupy the

identical positions.

Comparison of protein sequences

Proteins of Homeobox

occur in all multicellular species.

Sequence of 60 amino acids = homeodomain is highly

preserved part of proteins that are encoded by homeobox

genes. They are mostly genes for transcription factors.

Mechanisms of evolutional changes of genome:

1. Intragenic combinations

2. Duplication

3. Structural chromosomal aberrations

4. Horizontal transfer – parasexual mechanisms

5. Recombination

6. Mutations

1. Intragene combination- exons, introns combination

- Insertion of transposons – mobile DNA elements in the

genome. They can cause reconstructions, breaks, mutations

„jumping genes“

Types: 1. "cut and paste" transposons

2. transposons replicative

3. retrotransposons - similar to retroviruses, mobility based on

reverse transcriptase.

LTR retrotransposons consist of central coding region for enzymes,

bounded by long terminal repeats - LTRs

NON-LTR retrotransposons:

human LINE, SINE

LINE "long interspersed nuclear element

about 1kb long, original transposons, encode enzymes, proliferate and

migrate

SINE "short interspersed nuclear element"

less than 400 bp long – inactive, no code for protein

44-45% od human genome derived from the trans. elements

Heterochromatin, repetitive DNA is a cemetery of inactive transposons.

2. Gene duplication

Caused by unequal crossing-over

Duplication of chromosome parts leads to:

• degradation of gene, origin of pseudogene

• new function

• same or similar function - become a member of gene

family

Strachan and Read: Human genetics ,2. edition

Consequences of duplication

Types of sequential duplicates:

Partial gene duplication internal duplication

Exons duplication and exon shuffling

Complete gene duplication - gene families

Partial or complete duplication of chromosomes - very rare

Polyploidy - duplication of entire genome - general

mechanism in plants, animals (beetles, fish, amphibian)

Gene families occur is Eukaryotic genomes.

They have similar nucleotide sequence and encode very similar proteins -

isoforms with the same or overlapping functions.

They could occur in one chromosome or scattered over the genome.

Pseudogenes - a secondary non-active product of evolution.

Superfamily

-immunoglobulin gene family, HLA (MHC) genes, TCR genes

on chromosomes 2, 14, 22, 6, 7

- genes for LDL receptor

- alpha, beta-globin family on chromosomes 16, 11

evolution of globin family

Globin family on 11 a 16 chromosome

Density of coding genes relates to the number of duplicated

genes. Eukaryotic genomes have a lower density of

coding genes as these genomes contain a considerable

amount of repetitive DNA.

Yeast ........... 30% of duplicated genes

Cenorhabditis ..... 10% of medium repetetive DNA

Mammalian DNA genomes .. 45% of medium repetetive DNA

sequences - most derived from transposons

Density of coding genes

Translocation, inversion, duplication, fusion

Synteny - co-localization of genetic loci within individuals or

species, based on preservation, conservation of segments

and blocks of genes. There wasn‘t recombination in time,

also because of incomplete gene linkage.

Comparison of chromosomes:

human chromosome 17, bovine chromosome 19, pig chromosome 12.

Large chromosome segments - chromosome 2

Combination of chromosome segments - chromosome 3, 21

3. Structural chromosomal aberration

Karyotype of human (left)

and karyotype of

chimpanzee (right)

Differences: fusion

between chromosomes 15

and 17 with origin of

chromosome 2, also

inversions and

duplications.

http://www.riverapes.com/Me/Work/HumanHybridisationTheory.htm

Human chromosome banding patterns compared to the great apes (From Strachan & Dean 1998 p 344)

Notes H, C, G, O for Human, Chimpanzee, Gorilla and Orang-utan respectively. Chromosomes 2, 5 & 6 shown only.

High resolution chromosome banding

Sexual chromosomes developed from a pair of

homologous autosomes by mutation, deletions,

translocation and unequal crossing over.

Lower vertebrates (fish, amphibians, reptiles) - is no morphological

differentiation from gonosomes

Higher vertebrates – shape of chromosome Y is different -

only a small part are homologous = pseudoautosomal

area

Gonosomes

4. Horizontal transfers of NA between speciesprovide recombination of genomes predominantly of prokaryotic organisms;

bacteria could developed in time, adapt to new environment and become

resistant to changes and to new conditions.

endosymbiosis

somatic hybridization – fusion of cells

parasexual processes:

transformation – free income of DNA

conjugation - direct transfer of DNA

transduction - transfer of DNA by virus

transfer of plasmids

Bacterial transformation

= free intake of DNA into bacterial cells. Only

competent bacteria with relevant enzymes are

capable of transformation (not Escherichia coli)

Proof that DNA carries genetic information:

Griffith (1928) 1. Experiment with S. pneumoniae

Avery, McLeod, McCarthy (1944) - the same effect with an isolated DNA

Exchange,

recombination of

homologous parts

after transfer

Bacterial conjugation

= direct transfer of DNA

The F+ plasmid of donor cell is transferred to the

acceptor F- by conjugation bridge

F pilli on the surface of F+ bacteria

(encoded by F plasmid)

Hfr strain „High frequency of recombination“

is strain with the F plasmid integrated

into genomic DNA (episom)

Conjugation F+ into F- bacteria

Conjugation Hfr into F- bacteria

= when bacteriophages spontaneously transmit bacterial genes

It comes to pass for all bacteria.

Specialized = incorrect cut out of the genome of bacteriophage from the bacterial genome during the transition from lysogenic to lytic cycle

General = into small number of phage particles are packaged molecules of bacterial DNA instead of phage‘s DNA molecules

Application in history - mapping of DNA: How often the genes are transmitted together in the general transduction, more about that are localized closer.

Transduction

General transduction

5. Recombination – sexual reproduction

evolutionary significance of diploidy - masking of recessive

alleles

evolutionary significance of sexual reproduction – origin of

new combinations and genetic variants due to combination of parental

genomes in offspring and alternation of haploid and diploid phase of their

cells

Variability is done by

•a combination of genomes in zygotes

•a combination of chromosomes in the gametes

•crossing-over in meiosis

6. Mutation - origin of alleles

Mutations are sources of new genetic variations. More

variants of one locus is called polymorphism.

Polymorphism of standard alleles – caused by neutral

mutations

pathologic alleles – caused by negative mutations

Mutations positive - advantageous

negative - disadvantageous, losing

neutral

Selection, genetic drift, migration, non-random mating

Genetika, D P. SnustadM.J. Simmons, 5. edition, 2009

Human genetics, Ricki Lewis, 5. vydání, 2003

Thank you for your attention