Comparative Genomics

Perspectives and Current Trends in Bioinformatics Dr.
Lalitha Guruprasad
Lessons Learnt From Comparative Genomics

Dr. Lalitha Guruprasad
Email: lgpsc@uohyd.ernet.in
Perspectives and Current Trends in Bioinformatics

CCMB, 13th September, 2007
Perspectives and Current Trends in Bioinformatics Dr. Lalitha Guruprasad
What is comparative genomics?
What are the goals of comparative

genomics?
Why carry out comparative genomics?
• Analyse and compare genomic information from

different species
• Understand the similarities and differences
between different species
• To understand the uniqueness of a species
• To compare species across the evolution
• in silico analysis reduces the time taken to get the
results as compared to experimental methods
What is compared?
At the proteome level
- number and sequence
At the genome level length of proteins
- number of chromosomes - extent of similarity
- number of genes - number and nature of
- position of genes domains
- SNP positions - sequence motifs and
- EST database searches patterns
- codon usage - post translational
- splice sites modifications
- number of exons - secondary structure
- number of introns similarity
- alternate splicing - tertiary structure
- sequence similarity similarity
- functional similarity
What is the reference?

Depends upon the quest
- all representative genome comparison (the

evolution of organisms)
- human versus chimpanzee (speech, recognition,
movement)
- virulent strain vs avirulent strain (same organism
for disease specific genes)
- protein in the disease state vs normal protein
(mutations, structure and function loss?)
- isoforms in the same species (duplication events)
Of mice and men

Analysis of genes in microbial genomes

Comparison of M. tuberculosis complex

members
recent
deletion
ancient
deletion
PE, PPE protein family

analysis
- The pair-wise sequence identity is greater than

18%
-Conservation of 15 amino acid residues is

distributed over whole length of the domain.
-α-helices and β-strands arranged in the order H1-

E1-H2-E2-E3-E4-E5-H3-E6-E7-H4 at aligned
positions in the multiple sequence alignment.
-Therefore this domain is likely to have a compact

fold.
(accession number: PF08237), ‘PE-PPE domain’
Rv2608
MT2683
Rv1430
MT1474
Rv1800
MT1849
Rv0151
MT0160 PE and PPE proteins
Rv0152
MT0162
Rv0159
MT0168
Rv0160
MT0169
Rv3539
MT3643
Rv3822
MT3930 Hypothetical proteins
ML1232
Q49633
Rv1184
MT1121
Propose a cell
surface antigenic
role for the PE
family proteins
- The sequence of archaeal genome, M. acetivorans
C2A was reported by Galagan et al., 2002 and shown to
comprise 5,751,492 bp with 4,524 proteins.
-Cell surface proteins (CSPs) make up the surface layer

(S-layer), the outer most envelope of most of the
archaeal and eubacterial organisms.
- These are multi-domain proteins.
- Responsible for various functions.
- They are responsible for the cell shape and contribute

to virulence when present in pathogens.
RIVW 42 aa repeat.
DNRLRE 200 aa domain
LGxL 42 aa repeat
PEGA 70 aa domain
LGFP 54 aa repeat
LVIVD 42 aa repeat
Repeats
identified by
TRUST program
SMART entry present

SMART
database
searches
No SMART entry
No Repeats
PSI-BLAST
submission
Repeats
Offline Interpro and Pfam Yes

searches
No
Yes
Online Interpro and Pfam
No
Discarded
Novel Repeats or
Domains
Systematic analysis of Repeats
identification
Protein structure modeling
comparative modeling: To predict the

probable three - dimensional structure of
a protein given its amino acid sequence
and the 3-D structure co-ordinates of
another protein with which it shares
sequence homology.
- Ag85A, B and C (PDB_ID;
1SVR, 1F0N, 1DQZ) structures
were used as templates for
building the models. Comprise
α/β hydrolase fold and have
catalytic triad similar to that of
serine proteases, (Ser 124, Glu
228 and His 260).
-Two trehalose substrate
binding pockets are present one
closer to the active site.
-Pairwise sequence identity Overall fold of
among mycobacteria 67-82% mycolyltransferases
and among corynebacteria is
29-44%.
Shorter loop length proteins:
CGL2878, CGL2875,
CE2709, CE2710
Long loop length proteins:

CGL1031, CE1488,
CGL2181, CGL0922,
CE0984 and CGL0343,
CE0356
We observed mutations in
key trehalose substrate
binding residues in some
corynebacterium proteins.
40 43 12 22 26 26 26 154 15 15 23 23 23 23 23
D* R* 6S 3N 2H 3S 4W D# 7Q 9M 1N 2F 5S 6S 9K
* * # * * # # # # * * *
1F0N
D R S N H S W D Q M N F S S K
ML2028
D R S N H S W D Q I N F G S K
1DQZ
D R S N H S W N E W G L R T T
ML2655
D R S N H S W N E W S L S T I
RV3804
D R S N H S W D Q M G F T S K
ML0097
D R S N H S W D N M G L T S K
CGL2875
D R S N H S W D S G V I M T T
CE2709
D R S N H A W D S G L I M T T
CGL2878
D R S R H G W N A G F V T S I
CE2710
D R S R H S W T A G A V A T A
CGL1031
D G S L H N W S L P R G S C A
CE1488
D G S L H N W S L P R G S C A
CGL0922
G D S V H A W E N W A M T C N
CE0984
G D S I H A W E N W A L T C N
CGL2181
G D S V H A W E N W A M T C N
CGL0343
N D S V H S W A S L A A K C D
CE0356
N D S I H S W S S P A A K C D
From the binding pocket specificities and loop

length, - it is clear that
-CGL2875, CGL2878, CE2710, CE2710 exhibit
high affinity for trehalose.
-CGL1031, CE1488, CGL0922,
CE0984,CGL2181 – low affinity for trehalose
-CGL0343, CE0356 no affinity for the
trehalose.
1F0P Cgl1031 Cgl0343

Validation of hypothesis
Our predictions Experimental

reports
Short loop CGL2875 deletion mutant

- binds TDCM - low TDCM
concentration
Long loop CGL0343 deletion mutant

- does not bind TDCM - no effect on TDCM
concentration
- Varying number of isozymes in each genera, what

is the evolutionary relationship?
4 in M. tuberculosis and C. diphtheria each, 6 in C.
glutamicum, 5 in C. efficiens and 13 in N. farcinica.
- Genomic context analysis of Ag85 proteins from

related species of Mycobacteria, Corynebacteria
and Nocardia.
Genomic context analysis
Gene fusion Gene neighborhood Co-occurrence of genes

(operons) (Similar phyletic patterns)
Taken from Bork et al., 2004 Nat. Biotech. 22 : 911-917

The role of conserved noncoding sequences (CNSs) in DNA
The comparison of long genomic DNA sequences between two
species reveals CNSs. For example, a million base pair region of
human chromosomal region 5q31 consists 5 interlukins and 18 other
proteins. The alignment produced with orthologous mouse genome
revealed 90CNSs, the longest CNS-1 is between IL-4 and IL-13.
Transgenic mouse with CNS-1 deletion reduced the production of IL-
4, IL-13 and IL-5 (120 kb away) in type 2 helper cells (TH2).
RAD50, a gene between IL-13 and IL-5 was unaffected. I.e. the
effect of CNS-1 is over a long distance, in a highly selective manner
only regulating the expression of cytokines in specific cells.
Thank you

Comparative Genomics

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Perspectives and Current Trends in Bioinformatics Dr.

Lessons Learnt From Comparative Genomics

Perspectives and Current Trends in Bioinformatics

What is comparative genomics?

What are the goals of comparative

Why carry out comparative genomics?

• Analyse and compare genomic information from

What is the reference?

- all representative genome comparison (the

Of mice and men

Analysis of genes in microbial genomes

Comparison of M. tuberculosis complex

PE, PPE protein family

- The pair-wise sequence identity is greater than

-Conservation of 15 amino acid residues is

-α-helices and β-strands arranged in the order H1-

-Therefore this domain is likely to have a compact

-Cell surface proteins (CSPs) make up the surface layer

- These are multi-domain proteins.

- Responsible for various functions.

- They are responsible for the cell shape and contribute

DNRLRE 200 aa domain

SMART entry present

Offline Interpro and Pfam Yes

Protein structure modeling

comparative modeling: To predict the

Long loop length proteins:

From the binding pocket specificities and loop

1F0P Cgl1031 Cgl0343

Our predictions Experimental

Short loop CGL2875 deletion mutant

Long loop CGL0343 deletion mutant

- Varying number of isozymes in each genera, what

- Genomic context analysis of Ag85 proteins from

Genomic context analysis

Gene fusion Gene neighborhood Co-occurrence of genes

Taken from Bork et al., 2004 Nat. Biotech. 22 : 911-917

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