comparative genomics and structural proteomics:...

COMPARATIVE GENOMICS AND STRUCTURAL PROTEOMICS:

SEQUENCE AND STRUCTURAL HOMOLOGY TO UNRAVEL BIOLOGICAL

HIDDEN FEATURES

Luca Ambrosino, PhD

Topics

• Comparative genomics: orthologs/paralogs prediction

• Comparative genomics: functional annotation

• Structural proteomics: 3D-modeling of protein structures

Comparative genomics studies the differences and similarities in genomic features of different organisms

Comparative Genomics

Ancestor

A B

A1

B1

A2

B2

Duplication

Speciation

paralogs paralogs

orthologs

The detection of ortholog genes is one of the key approaches

Comparative Genomics

A

A1

A2

A1A

A2B

A2C

A2D

ORIGINAL FUNCTION

NEW FUNCTION

NO FUNCTION

SUBFUNCTIONALIZATION

Gene duplication

GENETICNOVELTY

PROTEIN

AT1G07600

PROTEIN

AT5G56795

5’-UTR Coding region

mRNA

AT5G56795

3’-UTR 5’-UTR Coding region

mRNA

AT1G07600

3’-UTR

X

ORF misassignment of AT5G56795 gene

NO SIMILARITY

PARALOGS

Multilevel analysis

5’-UTR Coding region 3’-UTR

mRNA

5’-UTR 3’-UTRCoding regionIntron Intron

GENE

PROTEIN

Multilevel analysis

23

4 5

B

CD

E

1 AXSpecies Xgene collection

Species Ygene collection

Higher score

Lower score

67 F

G

Orthologs definition

23

4 5

B

CD

E

Species Xgene collection


67 F

G

1 A

Lower e-value

Higher e-value

Paralogs definition

Lower e-value

Higher e-value

23

4 5 BCD

E

Species Xgene collection


67 F

G

1 A

Networks construction

0

1

2

3

4

5

6

7

8

9

0 1 2 3 4 5 6 7 8 9

3-9 gene networks

0

5

10

15

20

25

30

0 5 10 15 20 25 30

10+ gene networks

Spec

ies

y ge

nes

Species x genes

2143

1356

102

0 500 1000 1500 2000 2500

2

3-9

10+

N

Net

wo

rk S

ize

Paralog/ortholog networks

0

1

2

3

4

5

6

7

8

9

0 1 2 3 4 5 6 7 8 9

3-9 gene networks

0

5

10

15

20

25

30

0 5 10 15 20 25 30

10+ gene networks

Spec

ies

y ge

nes

Species x genes

2143

1356

102

0 500 1000 1500 2000 2500

2

3-9

10+

N

Net

wo

rk S

ize

Auxin responsive proteins


0

1

2

3

4

5

6

7

8

9

0 1 2 3 4 5 6 7 8 9

3-9 gene networks

0

5

10

15

20

25

30

0 5 10 15 20 25 30

10+ gene networks

Spec

ies

y ge

nes

Species x genes

2143

1356

102

0 500 1000 1500 2000 2500

2

3-9

10+

N

Net

wo

rk S

ize


0

1

2

3

4

5

6

7

8

9

0 1 2 3 4 5 6 7 8 9

3-9 gene networks

0

5

10

15

20

25

30

0 5 10 15 20 25 30

10+ gene networks

V. v

inif

era

gen

es

S. lycopersicum genes

2143

1356

102

0 500 1000 1500 2000 2500

2

3-9

10+

N

Net

wo

rk S

ize

Glutaredoxin

Acetolactate synthase


16454 15631

11093 11477

4786 1828

PARALOGS E-50

BBHs

PARALOGS E-3

SPECIES-SPECIFIC

2394 1035

SINGLETONS

PARALOGS

SINGLETONS

PARALOGS

545

1849 928

107

Multilevel comparison

Species x Species y

• Orthologs• Paralogs• Networks of orthologs and paralogs• Multilevel approach

COMparative for PARalog and Ortolog genes

COMPARO

Input files

Sequence comparisons

Ortholgs preprocessing

BBHs detection


Alignments reconstruction

Paralogs preprocessingExtraction of .fasta files

Threshold assessment

COMPARO

Input files

Extraction of .fasta files

Sequence comparisons

Ortholgs preprocessing

BBHs detection


Alignments reconstruction

Paralogs preprocessing

Threshold assessmentGenomic.fasta

Genomic.gff

COMPARO

Topics




Functional annotation


X

The GENOMA platform

Species x Species y


16454 15631

11093 11477

4786 1828

PARALOGS E-50

BBHs

PARALOGS E-3

SPECIES-SPECIFIC

2394 1035

SINGLETONS

PARALOGS

SINGLETONS

PARALOGS

545

1849 928

107

Ribosomal protein L5

metallocarboxypeptidase inhibitor (fruit-specific protein)

Transcriptional regulator LysR family

Nuclear pore complex protein (different types)

ATP-dependent DNA helicase (different types)

E3 ubiquitin-protein ligase (different types)

Ethylene-responsive transcription factor (different types)Zinc finger domains (different

types)peptidylprolyl isomerase

EC: 5.2.1.8

Agglutinin

Fanconi anaemia protein FANCD2

GPI ethanolamine phosphate transferase 2

Immediate early response 3-interacting protein 1

DNA repair protein RAD50

Metallothionein-like protein type 3

Rubredoxin-type fold domain


0

300

600

900

1200

1500

0 300 600 900 1200 1500

P-loop containing nucleoside triphosphate hydrolase

Protein kinase-like domain

Protein kinase domain

Inte

rPro

Do

mai

ns

occ

urr

ence

s(S

pe

cies

2)

InterPro Domains occurrences (Species 1)

0

300

600

900

1200

1500

0 300 600 900 1200 1500

0

50

100

150

200

250

300

0 50 100 150 200 250 300


Chalcone/stilbene synthase

Germin, manganese binding site

Transposase, MuDR, plant

Ribonuclease III domain

Protein family Ycf2, chloroplast

InterPro Domains occurrences (Species 1)

Inte

rPro

Do

mai

ns

occ

urr

ence

s(S

pec

ies

2)

SPECIES-SPECIFIC DOMAINS


Species 1 Species 2

21731 17

Carbapenem biosynthesis

Ethylbenzene degradation

Nicotinate and nicotinamide metabolism

Aflatoxin biosynthesis

Monoterpenoid biosynthesis

Glycosaminoglycan biosynthesis

(heparan sulfate / heparin)


Species 1 Species 2

Topics




Homology modeling

Homology modeling

TemplateTarget sequence

Sequence alignment

Homology modeling

Target sequenceTemplate sequence

Homology modeling

Conclusions

Orthologs, paralogs and species-specific genes

Functional annotations

3-D modeling

• COMPARO: COMparative for PARalog and Ortolog genes

• Molecular dynamics simulations

Already available services

Soon available

comparative genomics and structural proteomics:...

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