ISALAN - gene & genome duplication

Question 1

Ways for a genome to acquire new genes:

Answer 1

• Horizontal gene transfer – recombination between DNA allows genetic material to be transferred from one species to another (Ex. from virus to bacteria by integrases)
• Exon Shuffling
• Duplication & Divergence (1% chance for 1 gene in 1 million years)
  -Originally 1 gene, but is duplicated and diverges to obtain a different function
  -Ex. protease genes that have the same underlying proteolytic reaction but diverges to have different protein recognition site

Question 2

Gene Duplication can occur by:

Answer 2

1. Unequal crossing over
2. Unequal sister chromatid exchange
3. DNA Amplification during replication
4. Replication Slippage
5. Retrotransposition

Question 3

Unequal crossing over

Answer 3

• Recombination is initiated by similar sequences that are not in identical places on homologous chromosome pair
• During meiotic recombination, repeated sequences flanking a gene are misaligned between homologous chromosomes, resulting in gene duplication in on one of the chromosomes, and gene deletion in another.
• The resulting daughter gamete will then have a gene duplicate, in which if an evolutionary advantage exists, the duplicate will also get passed on over generations

Question 4

Unequal sister chromatid exchange

Answer 4

• During meiotic or mitotic recombination, repeated sequences flanking a gene are misaligned between sister chromatids, resulting in gene duplication in on one of the sister chromatids, and gene deletion in another.
• Depending on the species, the duplication may or may not be passed down on to the progeny.
  o if duplication happens in mitosis of human somatic kidney cell, will not be inherited (because duplication is not in gametes)
  o but if in single-cell species ex. amoeba, mitosis (binary fission) can lead to gene
  duplication in an evolutionary context.

Question 5

DNA Amplification during replication

Answer 5

• An unequal recombination during replication which can occur in haploid organisms that do not have polyploid chromosomes ex. bacteria
• At replication bubble, homologous DNA can exist as polymerases replicate each template strands and form daughter strands in opposite directions. Inappropriate line up of the repeated sequences flanking the gene in the replication bubble can result in gene duplication on one DNA and a deletion in the other.

Question 6

Replication Slippage

Answer 6

• not common for genes, mostly for short DNA sequences (ex. micro,minisatellites)
• Short repeat sequences’ ability to form hairpin structure during replication can cause some repeat units to be replicated.

Question 7

Retrotransposition

Answer 7

Certain sequences (Ex. LINES, SINES) can utilize Reverse Transcriptase to revert their RNA back to cDNA which can then be inserted back into the genome at a different position

Question 8

Outcomes of Gene Duplication

Answer 8

1. Conserved Gene duplication
2. Pseudogene formation
3. Gene Neofunctionalization

Question 9

Conserved Gene duplication

Answer 9

• If an increased synthesis of the gene (due to its duplication) is beneficial, the duplicated
  gene will continue to be synthesized and remain in the genome
• lead to formation of multigene family, gene superfamilies

Question 10

Multi gene family

Answer 10

• a group of similar genes that appear multiple times in the genome due to replication events. The genes can be near each other or spread out among the same or different chromosomes

Ex. RNA genes
Cells have to optimize number of RNA to match the metabolic requirements of different cell types – different cell types = different number of copies (due to different numbers of duplicated copies kept)
i.e. Mycoplasma genitalium: 2 copies;
Xenopus laevis ≥ 500 copies

Question 11

Gene superfamilies

Answer 11

Large multigene families (more nearly identical copies of the genes)
* ex. Zinc finger domains (400 different locations)
* ex. The Globin Superfamily
o Carry out different functions in different tissues (carry O2 vs carry CO2 in different tissues) – shows how each gene in the superfamily has evolved/ diverged to specialize in different functions for the organism to survive
o Duplications are retained due to Globin’s importance:
-Present in all 3 domains of life
-Used for O2 transport, storage, sensing, detoxification
-Members in humans:
* Members have different structures (duplication patterns)
-Hemoglobin = ⍺2β2 tetramer
-Myoglobin = monomer allow for the differing O2 loading on/off properties required in
different environments they are expressed in

• Hemoglobin’s tetrameric structure allows for allosteric regulation, thus co-operative binding of O2
  -At low O2 conc, hemoglobin has difficulty binding to O2, but at a higher O2 conc, each subsequent O2 binding allows for a higher binding affinity of O2 to hemoglobin – results in a sigmoidal curve
  -Allows it to readily bind O2 where O2 is in excess, and to readily release O2 where O2 conc. is low
• Myoglobin’s monomeric structure does not allow for cooperative binding of O2, so it has a higher affinity for O2 overall
• Hemoglobin is in red blood cells which are used to carry and supply O2 for different tissues while myoglobin is in muscle which allows it to readily load on O2 when hemoglobin reaches the muscle

Question 12

Formation of pseudogenes

Answer 12

• If an increased synthesis of the gene (due to its duplication) is NOT beneficial, random
  mutations can occur within the second copy and inactivate it. As a result, broken genes
  or “pseudogenes” exist throughout the genome
  (Pseudogene: A DNA sequence that resembles a gene but has been mutated into an inactive form over the course of evolution)

Question 13

Types of pseudogenes:

Answer 13

• Non-processed pseudogenes:
  -Does not go through the processing step of becoming RNA before they were replicated. Duplication happens during DNA replication, resulting in tandem duplication of genomic region only
  -Inactivated due to mutations/ incomplete duplication
  -Could miss regulatory regions ex. distal enhancers, promotors, but still contains ALL the intron and exon structures
• Processed pseudogenes:
  -Duplication occurs after the DNA has been processed into mRNA, so the mRNA has to undergo reverse transcription back into cDNA. cDNA then undergoes genome integration in order to make the second duplicated gene copy. (pseudogene as a result of retrotransposition)
  -Lacks regulatory regions AND INTRONS, and can also have different exon combinations
  -Can contain polyA tail and flanking repeats (UTRs)
  -Can integrate into the same or different chromosomes (more spread out)

Question 14

Gene Neofunctionalization

Answer 14

• Mutations in the duplicated gene can result in gaining of a new function or a sub function (a specialized function) apart from the original gene
• Ex. proteases: trypsin and chymotrypsin (duplicated ~ 1500 million years ago)
  >Mutations following duplication result in a different specialized function
  between the 2 proteases:
  -Trypsin: cuts at arginine & lysine (small, neg charged side chains)
  -Chymotrypsin: cuts at phenylalanines, tryptophans & tyrosines (bulky
  side chains)

Question 15

Genome Duplication

Answer 15

• There can be larger duplications than of genes/ segments ex. whole chromosome duplications.
• This will cause gene product imbalance which reduces life expectancies of the affected cell/ individuals
  ex. Down syndrome – whole chromosome duplication of human chromosome 21

Question 16

Whole Genome Duplication (WGD):

Answer 16

duplication of the entire genome (ex. from 2n to 4n) which causes polyploidy – multiple copies of the same set of chromosomes

Question 17

Polyploidy

Answer 17

Polyploidy is common in plants. Polyploidy (more genomic content) results in a bigger cell size.
* ≤ 80% of flowering plants species likely originated via recent polyploidy ex. oats, cotton, potatoes, bananas, coffee, sugar cane, peanut, apples etc.
-Polyploidy is also possible to occur in vertebrates/ animals.
-Common in invertebrates, fish & amphibians, rare in mammals

Question 18

Mechanisms of polyploidy formation:

Answer 18

• Autopolyploidy – polyploidy formation involving a single species
• Allopolyploidy -polyploidy formation due to crossing between 2 reproductively compatible species

Question 19

Autopolyploidy

Answer 19

• Occurs due to meiosis error within a single species, resulting in the accidental production of unreduced gametes (not rare: 1-40% frequency depending on organisms & their genetic control)
• Fertilization by unreduced gametes from both parents result in multiple copies of the genome present in the offspring which will now be a new sub-species
• Issues: cause genomic shock (due to unfamiliar dosage of gene products) which can trigger global changes in gene expression, activation of transposons, recombination
• Autopolyploids can reproduce successfully among themselves, but not with parental species (only produce unviable offsprings when crossed with parents – chromosomes are unpaired during mitosis)
  o This is because the number of chromosomes must be even for proper alignment during metaphase of mitosis or else the mitotic cycle is going to crash
  o The successful internal reproduction and barrier between the autopolyploid and their parental species can permit speciation ex: (evening primrose)

Question 20

Allopolyploidy

Answer 20

Can occur via:
* One-step model: 2 unreduced gametes from 2 reproductively compatible species
fertilize, resulting directly in a polyploid species
* Two-step model: 2 normal reduced gametes of 2 reproductively compatible species fertilize, and polyploidy occurs at the level of the offspring by somatic doubling or formation of offspring’s unreduced gametes
-Ex. in plant: Pollen from 1 species germinates on stigma of 2nd which is followed by endoreduplication in the zygote

Question 21

Resulting in triploid organisms…

Answer 21

Allopolyploidy where diploid gametes fertilize with haploid gametes, can result in triploids organisms which will have problems in gamete formation (infertile):
* Triploids from allopolyploidy can be a viable organism because chromosomes are paired during mitosis
* But in meiosis, homologous chromosomes do not evenly pair up, resulting in unbalanced gametes
* The gametes then become non-viable and the species will have difficulties in reproduction

Question 22

Allopolyploidy from wheat-rye hybrid:

Answer 22

• Want the high-yield of wheat and the disease-tolerance property of rye
• Problem: wheat is tetraploid (diploid gametes) and rye is diploid (haploid gametes), so their hybrid (triticale) is a triploid which initially is not fertile

Question 23

Biotechnological solution to triploid infertility:

Answer 23

• Utilize colchicine which interferes with the spindle machinery of cells, changing the way chromosomes are separated during mitosis/ meiosis
• Colchicine treatment of sterile triticale germ line cells prevent the separation of chromosomes during meiosis1, resulting in chromosome doubling. Meiosis2 then produce doubled gametes. Fertilization of doubled triticale gametes will result in a new generation of triticale with an even number of chromosomes, which are thus fertile.

Question 24

Effects of Whole Genome Duplication (WGD)

Answer 24

• Multivalent formation: during meiosis, association of multiple homologous chromosomes can result in complex recombination events, generating more diversity and/or more local gene duplication.
  o From observing the multivalent formation – difficult to discern if it happens from auto or alloploidy due to complex structures
  o Ex. very likely to have occurred in Saccharomyces cerevisiae: brewers’ yeast
  -Contain many duplicated sets of genes - 800 gene pairs (55 duplicate sets of at least 3 genes in same order)
  -Detected even in ancestors or related yeast species
  -10 % of genes in S. cerevisiae likely derive from WGD

Question 25

Benefits of WGD

Answer 25

In short term, can cause genomic shock, so the fact that the duplication is preserved means that there must be a competitive advantage against non-polyploid progenitor

1. Provide raw material for evolutionary diversification – has many duplicated genes that can undergo neofunctionalization, sub-functionalization
   * This can allow adaptation and colonisation of new environments, preventing extinction
   or allow the new subspecies to outcompete the other organisms the parental species has not been able to overcome before
2. Defence against mutation (because have a spare copy of every gene)
3. Fitness consequences:
   * Increased cell size, organ size
   * Faster growth – more metabolic components per cell
   * Evolved dosage regulation of gene expression to control the large number of genes
   * In alloploidy, “Hybrid vigour” (‘Heterosis’) can occur – combination of unrelated sets of
   genes often give healthier, longer-living, more robust offspring because there are more
   recombination of beneficial animal-specialized genes

Question 26

Effects of Whole Genome Duplication (WGD) - HOX genes

Answer 26

• Provides a basis for an organism’s increase in organisational “complexity”
  Ex. Hox gene family (Homeobox genes – 60 aa)
  o Code for homeodomains – gene-specific transcription factors – each different homeodomain binds specific target genes in developmental pathways of organisms
  o Order of Hox genes is important due to 2 properties:
  -‘spatial colinearity’: order of gene reflects order of expression from head to tail in an organism (order specifies body segment structures)
  -‘temporal colinearity’: order of gene reflects order of expression in time as the embryo develops

Therefore, Mutations or shuffling of the Hox genes will result in rearrangement of body patterns (ex. in drosophila: bithorax– number of wings double or antennapedia – legs grown in place of head)

WGD, increasing the number and/or components of Hox gene clusters correlate to higher complexity and developmental patterns :
-Insects + Cephalochordates = 1 Hox cluster
-Vertebrates = 4 clusters (usually) with up to 13 genes
* Marine fish-like chordate: 1 cluster
* Sea lamprey (Petromyzon marinus): 4 clusters
* Hagfish (Eptatretus stoutii): 4 Hox clusters
o Start to have Spinal chord, chordate, produces slime in response to attack.
* As move up to bony fish, sharks, and eventually humans, duplication, leading to more components of Hox gene clusters are present fish = more duplication resulting in more complicated body parts than humans