Download Questions for Lecture 16 Genomics and Evolution

Essentials of Glycobiology
Lecture 16
Genomics and Evolution
Chapters 7 and 19
May 19, 2008
Pascal Gagneux
Questions for Lecture 16 Genomics and Evolution, Monday, May 19. 2008
1. Explain what is a sequence-based classification of
glycosyltransferases.
2. Describe the ways that gene sequence predicts or fails to
predict functionality in transferases, hydrolases, and glycanbinding proteins.
3. Give examples of bifunctional enzymes involved in
glycosylation. Suggest the driving force for the evolution of
bifunctional transferases?
4. What can you learn about the way of life of an organism
(“ecology”) based on the relative number of glycosyl
hydrolases and glycosyltransferase
5. How could an organism effectively augment the number of
glycosyl hydrolasesand or glycosyltransferases at its disposal.
6. Do viruses entirely rely on their host cells for glycosylation?
Questions for Lecture 16 Genomics and Evolution, Monday, May 19. 2008
7. Discuss the concept of "glycan genes.”
8. What processes could be responsible for maintaining glycan
polymorphisms (i.e., structural heterogeneity) within
populations?
9. What changes in sialic acid biology occurred during human
evolution?
10. Can you think of evolutionary trends in glycosylation?
11. What are the problems in using “comparative glycobiology”
for determining evolutionary relationships (phylogeny)?
12. How could glycans on mammalian red blood cells protect
against viral infection?
The universal tree of cellular life
You are here
Viruses
Olson & Woese 1993
16s rRNA based phylogeny
Replicator (Genome) Sizes:
C-values, bases in haploid genome complement
mycoplasma E.coli
BACTERIA
yeast
FUNGI
bean
lily
PLANTS
Drosophila
INSECTS
MOLLUSKS
shark
CARTILAGINOUS FISH
BONY FISH
frog
newt
AMPHIBIANS
Viruses
REPTILES
BIRDS
human
MAMMALS
105
106
107
108
109
1010
1011
Genetic vocabulary:
“genome, gene, allele, haplotype”
• Genome
X
• Gene, Locus
Chromosome
(ADN)
Locus 1
Locus 1
Allele 1*01’
• Allele
Locus2
Locus 3
Chromosome 1
Intron 1
Locus 4
Intron 2
Chromosome 1’
• Haplotype
Allele 1*02’
Locus 1
Exon 1
Locus 1
Locus 2
Locus 3
Allele 1*01’ Allele 2*01’ Allele 1*01’
Haplotype 1
Haplotype 2
Allele 1*02’ Allele2*02’ Allele 3*02’
Locus 1
Locus 2
Locus 3
Primary
transcript
mRNA
GLYCOSYLATION
Glycoprotein
Glycosyl
Transferase
Protein
Exon 2
Exon 3
100 million years of:
Translocations, duplications, rearrangements
Genomics
• 500 genomes fully sequenced
• Ranging in sizes:
– 450 Kb archea, 3 Gb primate, some plants and amphibians 100 Gb
• Number of genes:
– a few hundred (Mycoplasma) to ~20 500 (H.sap). Making up ~
1.5% of total genome.
• Comparative genomics:
– 5% of mammalian genome under evolutionary constraint.
• ENCODE Project Consortium for comparative mammalian
genomics:
– Many novel non-protein coding transscripts
– Many novel transcription start sites
– Regulatory regions symmetrically distributed upstream and down
stream from start sites.
– Many functional elements are surprisingly unconstrained. Large
pool of neutral elements with biological activity
– “warehouse for natural selection”?
– Source of lineage-specific elements and functionally conserved but
non-orthologous elements between species.
Genomics of Glycosylation
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Glycosyl transferases GT, Glycosyl hydrolases GH (glycosidases) and
glycan binding proteins GBP (lectins).
Prediction of function based on sequence similarity often limited.
Carbohydrate Active enZymes, www.cazy.org
Listing candidate enzymes based on genomic sequence and predicted
folding pattern of proteins.
5% of the vertebrate genome encoding genes involved in
glycan synthesis – degradation – recognition
In H. sapiens: ~250 GTs, ~250 GHs, and 100-200 GBP. Jointly
comparable to the number of Kinase genes.
Reduction in symbionts and parasites.
But, B. thetaiotaomicron has 2.3 times more GH than humans!
Increase of GT’s in plants (450in A. thaliana, 560 in rice, and 800 in
poplar.
Increase of GHs in fungi
Some large viruses e.g. mimivirus: 12 putative GTs., Bacteriophage T4
glycosylates its DNA with Glucose.
http://www.cazy.org/
http://www.cazy.org/
TAXONOMY OF GT ENZYMES:
Two basic different topologies
B. subtilis SpsA
phage T4 b-glucosylT
Journal of Molecular Biology
Volume 328, Issue 2, 25 April 2003, Pages 307-317
An Evolving Hierarchical Family Classification for Glycosyltransferases
Pedro M. Coutinho1, Emeline Deleury1, Gideon J. Davies2 and Bernard Henrissat1, Corresponding Author Contact Information
Rates of Evolution
• Extremely conserved:
• think signalling in development
• Fucosyl Transferase:
– Fucosylates the cell signal molecule Notch and modifies its
interactions with ligands serrate and delta conserved
between insects and Primates.
• Much less conserved:
• think blood groups in primates
• Fucosyl Transferase IV
– Secretor only in primates
• Under strong adaptive selection:
• Xylosyl Transferase 1 in humans…..
– Initiates GAG synthesis on proteoglycan core peptides.
Ortholog or Paralog ?
Or Both?
Speciation
Xie et al. Genome Biology 2003 4:R14
Duplication
Partial gene conversion in
Human Siglec 11
Hayakawa et al. Science 2005
Genomic Evolution of Hox Gene Clusters
Derek Lemons and William McGinnis
Science 29 September 2006
Comparisons of the Siglec gene cluster
in human, dog, and mouse
Angata, Takashi 2006, MolecularDiversity10:555–566
Genomics of Glycosylation
• Evolving by expanding and modifying glycan
modifying tool kits:
• Gene numbers, gene families:
• Analogies from non glycan related genes:
– G-coupled proteins, such as OR, >1000 loci in many
mammals.
– Kinases, 500 functional genes, plus many pseudogenes,
many of these possibly functional.
• GH gene copy number variation as mechanism for
dosage and functional adaptation:
– Salivary amylase genes in humans: agriculture vs foraging.
• Polyploidy, i.e. gain of additional gene copies
– (plants, fish e.g. salmon).
• Symbionts and contribution of their combined glycan
modifying genomes.
Modularity of GTs:
• monocatalytic appended with non-catalytic module (A), tandem GTs
on same polypeptide (B), GT with appended trans glycosidase
module (C).
Journal of Molecular Biology
Volume 328, Issue 2, 25 April 2003, Pages 307-317
An Evolving Hierarchical Family Classification for Glycosyltransferases
Pedro M. Coutinho1, Emeline Deleury1, Gideon J. Davies2 and Bernard Henrissat1, Corresponding Author Contact Information
Carbohydrate active Enzymes and total gene number
in the three kingdoms
Distribution of various glycan types in nature
Lineage effects in the three domains
Specific: GPI anchors
Bishop & Gagneux, Glycobiology, 2007
Glycans and recognition phenomena
exogenous
endogenous
Phylogenetic distribution of Sialic acids
Archaea
EuryarchaeotaCrenarchaeota
PATHOGENS
Bacteria
Gram-positive
Low G+C
Gram-negative
Protozoa
Eukarya
Gram-positive
High G+C
Protostomes
Chlamydia
Thermus/
Deinococcus
Deuterostomes
Cyanobacteria
Aquifex
Common ancestor
of cellular life
Plants
Fungi
Spirochetes
Angata &Varki 2002 Chem. Rev.
present
possibly present
HOSTS
Mimicry
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Hyaluronan in pathogenic bacteria (Pasteurella multicoda)
Polysialic acid in Neisseria meningitidis and E. coli K1.
Disialylated gangliosides on LOS of H. influenzae
Sialylated Siglec ligands by Group B Streptococcus
Gullain Barré Syndrome: associated with central nervous system
glycan bearing pathogens and resulting anti-GM1 , Gd1a, GT1a, GQ1a
autoantibodies: Campylobacter jejuni, cytomegalovirus , Epstein-Barr
virus , Mycoplasma pneumoniae, Brucella melitensis. All these
pathogens carry ganglioside-like glycans.
Fucosylation of Bacteroides fragilis capsular glycans and induction of
hosts gut epithelial fucose expression.
freshwater snail Biomphalaria glabrata host N-glycans mimicked by
helminth parasite Schistosoma mansoni.
Questions:
– Parasites with multiple hosts belonging to very different animal lineages
face spectacular challenges in adapting to glycans in each of their hosts
and vectors e.g. Plasmodium in insect and vertebrate host, Schistosomes in
mollusk and mammalian hosts!
– Anisakis simplex (herring worm) nematodes in marine mammals,
curstaceans and herring/cod.
Convergent Evolution or Mimicry?
• Gangliosides in octopus and squid?
• Ganglioside-like structures in vertebrate
pathogens?
Distribution of various glycan types in nature
Bishop & Gagneux, Glycobiology, 2007
Distribution of various glycan types in nature
Bishop & Gagneux, Glycobiology, 2007
Discrete Domains of Life?
• Pick your ploysaccharide:
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Plants: cellulose and pectins,
Vertebrates hyaluronan, GAGs and polysialic acids,
insects chitin,
fungi chitin,
bacteria peptidoglycans and LOS
• Polysaccharides were likely among the first cell
constituents for structural roles and biochemical
properties?
• How did different lineages get stuck with different
types?
Nature of constraints
Internal Constraints
• Once a lineage has elaborated upon a set of glycan
types, change may become more difficult.
• No radical re-design possible for living organisms!
• Both because of:
– the integration of the glycan in important features
– Irreversible loss of enzymatic machinery. (“Use it or lose it”).
External Constraints
• The use of non-self glycan types for innate and
adaptive immunity, tends to rule out the use of the
same glycan types in the future.
Functions for Discrete Domains of Life?
Viruses are classified by the type of organism they
infect:
– Plant viruses almost never infect animals
– Bacterial viruses (phages) do not infect animals or plants
– Fungal viruses semm highly specialized on fungi.
• Unlike bacteriophages and animal viruses, plant
viruses do not seem to exploit host cell membrane
surface glycans,
• rather plant viruses carry characteristic movement
protein, which interact with plasmodesmata of plants
and allow entry.
• Most plant viruses are non-enveloped, most animal
viruses are enveloped (I.e. the latter inherit cell
membrane characteristics including certain glycans
from their animal host cells).
• Discrete glycan types as “firewalls” for horizontal
infection?
Evolutionary trends?
• Galactosylceramide and its derivatives in deuterostome
animals versus glucocerebrosides in protostomes.
• Loose to structured myelin?
• Increase in sialic acid content of gangliosides between
reptiles, fish and mammals.
• Cold blooded animals express many polysialylated
gangliosides in the brain.
• N-glycans Trends: core relatively conserved but
trimming and extension is key feature of vetrebrate and
plant N-glycans.
• GPI-anchors as eukaryotic invention?
Eukaryotic N-Glycan trends?
Glycan phylogenetic “watershed”?
e.g. ßGalNAc-T1
Ramakrishnan & Qasba
J Mol Biol. 2007 365(3): 570–576.
Herd immunity through glycan polymorphisms?
Gagneux & Varki 1999 Glycobiology 9:747-755
RBC’s as viral traps?
350 X 350 Å
of the Human Red Blood Cell Surface
Glycophorin
(Missing in some healthy humans!)
Sialic Acid
Sugar chains
=“Glycan”
Protein
Cell Membrane
(Lipids)
Modified from Viitala & Järnefelt, 1985
Non-nucleated RBC in most mammals
Viral Traps – Smoke Screens – Decoys?
NO
NO
NO
NO
NUCLEUS
GENOME
TRANSCRIPTION
TRANSLATION
POLYMORPHIC GLYCANS
Contingency and
the primate hand
With very few exceptions
(colobus and spider
monkeys), all primates
have five digits on all four
limbs.
Analogy:
Once you use sialic acid as
a common terminal
monosaccharide, it may be
virtually impossible to
abolish it.
The SO4-GalNAcß14GlcNAcß1- terminal unit
on pituitary glycproteins,
conserved throughout
vertebrate evolution.
The search for the essential glycan…
Are there selectively neutral glycans?
Gagneux & Varki 1999 Glycobiology 9:747-755
Roles of endogenous lectin - glycan recognition
throughout life
Exogenous Recognition:
Infection
Vaccines
Allergy
Microbiome
Cancer
Xenotransplantation
Any change selected for under one process is
likely to affect many unrelated processes!
Agenda for Research
• How much neutral glycan variationis there?
• How rapid is glycan evolution and how much time is needed for
targeting innate immunity to novel non-self glycans?
• What is the scope of intrinsic constraints on glycan-mediated
escape options from pathogens?
• What is the cost of a successful escape?
– E.g. loss of Neu5Gc in humans?
– Both in terms of functional consequences and future evolution.
• What are the constraints on pathogens?
– A master of all trades is a master of none?
• Why are there not more pathogens pretending to be symbionts?
Current State of Glycomics:
Ursus Wehrli