Upload
zoe
View
28
Download
1
Tags:
Embed Size (px)
DESCRIPTION
Microbial Research Commons Including Viruses. Prof. A.S. Kolaskar Bioinformatics Center University of Pune Pune, India. Introduction. Increasing research in life sciences and biotechnology in Indian Universities and national research institutions - PowerPoint PPT Presentation
Citation preview
Microbial Research Commons Including Viruses
Prof. A.S. KolaskarBioinformatics Center
University of PunePune, India
Introduction
• Increasing research in life sciences and biotechnology in Indian Universities and national research institutions
• Increased need for microbial and genetic resources
• Establishment of microbial and other biological culture collections in universities and research institutions
Culture Collections In India
• Microbial Type Culture Collection and Gene Bank (MTCC), Chandigarh – World Intellectual Property Organization (WIPO, recognized as International Depository Authority)
• National Collection of Industrial Microorganisms (NCIM), Pune – Cultures are deposited for patenting
• Virus cultures at National Institute of Virology (NIV)• National Facility for Animal Tissue and Cell Cuture, Pune
Culture Collections In India
• Anaerobic Bacterial Resource Center (ABRC), Hyderabad
• National Collection of Dairy Cultures, Karnal
• National Fungal Culture Collection of India, Pune
• University of Mumbai Food and Fermentation Technology Division
21 Culture Collections from India registered with WDCM
Thailand Network of Culture Collections
• Biotech Culture Collection (BCC) – 3430
• Department of Medical Sciences Thailand (DMST) – 442
• Department of Agriculture (DOA) – 1163
• Thailand Institute of Scientific and Technological Research – 515
Issues• Limited characterization• Very few cultures characterized at DNA finger printing level• Data not fully computerized and information not available on the
web• Duplication of cultures in the repository• Material Transfer Agreement similar to that in ATCC is followed by
most repositories• No systems in place to detect or prevent misuse of MTA• Redistribution of cultures at informal level• Very few scientists conversant with taxonomic classification even at
the national culture collections• Issues related to Biosafety and National security are not given due
importance
PUMP-E: Salient Features
• Dynamic Representation of pathways• Dynamically building the organism-specific pathways
from genomic data• Development of Software for
– Automated data updating (Perl scripts) – Reformatting and organization of relevant
information from different databases– Drawing pathways diagrams – Comparison of pathways– Visualization of ligands, enzymes– Prediction of enzyme-substrate interactions
• URL- http://202.41.70.51/mpe/
Approaches
Data acquisition & Integration Dynamic Visualization of Metabolic
Pathways Query Interface Molecular Visualization Structure Prediction of Proteins Simulation of 3D Structures of Enzymes
and Metabolites
PUMP-E
Database
Enzyme
Reaction
Compound
Pathway
Organism Gene
User-friendly Query interface
Search by keywords
Dynamic generation of queried pathway
Molecular viewer
Homology models
Source Databases for Data Acquisition
• Sequence databases: TIGR, NCBI, EBI• Metabolite databases: KEGG• Metabolic pathway database: KEGG• 3D Structure database: PDB • Enzyme Database: KEGG, EXPASY,
IUBMB, BRENDA• Kinetics Data: NIST• Organism List : GOLD
Motifs, patterns & signatures : PROSITE
• Web-based query interface • Supports complex advanced queries • Developed using ASP, HTML and java • Tested by various testing tools such as
Winrunner, Test Director etc.
PUMP-E Front End and Query System
PUMP-E : Front End and Query System
PUMP-E
Organism name Phylum Genome Size (Mbp)
Total number of pathways
Agrobacterium tumefaciens
Bacillus anthracis
Bacillus subtilis
Caulobacter crescentus
Chlamydia trachomatis
Escherichia coli
Francisella tularensis
Haemophilus influenzae
Helicobacter pylori
Mycoplasma pneumoniae
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv
Shigella flexneri
Treponema pallidum
Vibrio cholerae
Proteobacteria
Firmicutes
Firmicutes Proteobacteria
Chlamydiae
Proteobacteria
Proteobacteria
Proteobacteria
Proteobacteria
Firmicutes
Actinobacteria
Actinobacteria
Proteobacteria
Spirochaetes
Proteobacteria
5.673462
5.22729
4.21463
4.01695
1.04252
4.63968
1.89282
1.83014
1.66787
0.816394
4.40384
4.41153
4.6072
1.13801
4.03346
207
254
145
176
61
198
184
127
123
48
186
184
179
56
207
Total number of pathways in bacteria under study as per BioCyc 9.1
Hamming Distance Calculations
• Identical Pathways (0): – Start and end products are identical;
intermediate steps are same.
• Similar Pathways (1):– Start and end products are identical;
intermediate steps are different
• Pathways are absent (2):– Start or end products are not same
Metabolic pathway path profile
Columns represents ‘n’ number of pathways and rows represent 15 bacteria under study. Each column corresponds to a particular type of pathway. 2 denote pathway follows same path, 1 denotes pathway follows different path while 0 denotes absence of pathway. This represents a part of the organism specific metabolic pathway path profile.
Metabolic pathway path profile based tree
Comparison of Pathways from Genus Bacillus with E.Coli
Bacillus anthracis Bacillus cereus 10987
Bacillus subtilis Bacillus cereus Zk
Bacillus anthracis Sterne Bacillus halodurans C-125
Bacillus anthracis strain A2012 Bacillus licheniformis ATCC 14580
Bacillus cereus ATCC14579 Bacillus anthracis Ames Ancestor
198 Pathways of E.Coli are compared with pathways data from Biocyc for each of these organisms
Pathways absent in Genus Bacillus; Present in E.Coli
• Electron transport (aerobic and anaerobic)• Phenyl ethyl amine degradation• L-lyxose degradation• Pyridoxal 5’-phosphate salvage pathway• Super pathway of pyridoxal 5’-phosphate
biosynthesis and salvage• D-allose degradation• Fructose lysine degradation • Taurine degradation
Effect of pathways absent in genus Bacillus
• Because of absence of L-lyxose degradation pathways in genus bacillus, it cannot utilize L-lyxose sugar as source of energy
• D-Allose cannot be utilized as a sole carbon source by bacteria of genus bacillus as D-allose degradation pathway is absent
• Under sulfate starvation conditions, bacteria from genus bacillus cannot utilizes taurine as a sulfur source owing to absence of Taurine degradation pathway.
• Bacillus cannot grow on fructoselysine or psicoselysine as the sole carbon source because of absence of Fructose lysine degradation.
Pathways present in Genus Bacillus; Absent in E.Coli
• 2 Nitro propane degradation• Denitrification pathway• Folate transformations• Formaldehyde assimilation• Methanogenesis from acetate• Octane oxidation• Spermine biosynthesis• Xylulose monophosphate cycle
Effect of pathways absent in E.coli
• Xylulose monophosphate cycle and Methanogenesis from acetate are characteristic pathways of methanogenic bacteria and E.coli is not a methanogenic bacteria. Hence these pathways are absent in E.coli
• E.coli cannot reduce nitrate to dinitrogen because of absence of Denitrification pathway
• Formaldehyde produced from the oxidation of methane and methanol by methanotrophic bacteria is assimilated by Formaldehyde assimilation pathway. This pathway is absent in E.coli as it is not methanogenic
Issues
• Taxonomic classification as per NCBI and thus errors can creep in
• No standard system to represent metabolic pathways
• Errors in annotation at gene level translate into errors in metabolic pathways
• Usefulness of metabolic pathways for characterization of microbes is not exploited
Animal Virus Information System
Signature peptide sequences for animal virus families Family Genus Protein Peptide
Togaviridae
Alphavirus Structural polyprotein AYEHXXV/TXPN
Filoviridae Filovirus Nucleocapsid protein PQLSAIALGVATAHGSTLAGVNVGEQYQQLREAA
Iridoviridae LymphocystivirusIridovirus
Capsid protein TSXFIDXATIEKXXYGGSRXGDYXL
Papovaviridae Papillomavirus L1 protein CKYPDF/YGHPLF/YNKV/L
Polyomavirus Coat protein VP1 PDPXXNENGVGPLCKQVEEVR
Coat protein VP2 WXLPLXLGLYG
Arenaviridae Arenavirus Surface glycoprotein MLXKEYXXRQXXTPPTHXHIXGXXCPXPHRLXLXGRSC
Flaviviridae Flavivirus Non structural protein 1 CWYXMEIRP
Envelope glycoprotein DRGWGNXCGXFGKG
Adenoviridae Hexon protein FKPYSGTAGVLAGQPNYCFPL ,NPFNHHRN
Species specific peptides Family – Flaviviridae Protein –
Envelope glycoproteins
Virus Peptide
Unique upto -number of mismatches
St. Louis encephalitis virus VNPFISTGGAN 3EGRPAT 0
Murray valley encephalitis virus VTANPYVASSTA 3
Japanese encephalitis virus LDVRMINIEA[S/V]Q 3West Nile virus TTKATGWIIQK 3Kunjin virus STKATGRTILKE 3Langat virus DGAEAWNEAGR 3
FTCEDKK 0VGFSGTRP 0
Yellow fever virus MRVTKDTN[D/G][N/S]NL 3
Powassan virus KDNQDWNSVE 3Dengue type 1 virus GTVLVQV 0Dengue type 2 virus GTIVIRV 0Dengue type 3 virus TEATQL 0
GTILIKV 0Dengue type 4 virus TTAKEVA 0
GTTVVKV 0Tick borne encephalitis virus GFLTSVGKA 0Louping ill virus NPHWNNVER 0
VirGenComparative genomics & data
mining of viral genomes
Browse VirGen at
http://bioinfo.ernet.in/virgen/virgen.html
Salient Features of VirGen• Organizes genomic data in a structured fashion navigating from the
family to an isolate • Full genomes of viruses • Compilation of representative genome entries for every viral species
(Virus Taxonomy, 7th report of ICTV) • Complete annotation of every genomic entry • Graphical representation of genome organization • Generation of alternative names of proteins • On-the-fly genome comparisons using BLAST2 • Multiple Sequence Alignment (MSA) of genomes, proteomes and
individual proteins • Whole genome phylogeny • Prediction of B-cell epitopes
VirGen Home
Menu to browse viral
families
Genome analysis &Comparative
genomics resourcesGuided tour
& Help
Navigation bar
Search using Keywords &
Motifs
Tabular display of genome annotation
Retrieve sequence
in FASTA format
Genome Sample Record in VirGen
‘Alternate names’ of proteins
Browsing the Module of Whole Genome Phylogenetic Trees
Most parsimonious tree of genus Flavivirus
Input data: Whole genome
Method: DNA parsimony
Bootstrapping: 1000
Most parsimonious tree of genus Flavivirus
Input data: Whole genome
Method: DNA parsimony
Bootstrapping: 1000
Case Study: Insertions in Pestivirus 1
891-1787 bp region remains unannotated using representative strain
BLAST with VirGen confirmed the non-viral origin of the insert
What is the origin of the
insert ???
BLAST with GenBank produced significant
match with Bos taurus J-domain protein
Issues
• ICTV classification and information available in published literature do not always match
• No standard method to describe viral isolates/strains • Electron micrograph and other image data are not
readily available making identification difficult and inaccurate
• Recombination occurs much faster in viruses than in bacteria/other microbes
• Host/vector information needs to be described in standard language
• Minimal availability of Immunological properties and therapeutic options in the databases
Suggestions• Devise measures to build confidence amongst underdeveloped and
developing nations that their resources will not be exploited• Networking and consortia among scientists, curators of culture
collections, policy makers from developed and developing countries• Material transfer agreements should be standardized by taking into
consideration national security and biosafety• Create awareness about open access and open educational
resources • Lobbying to policy makers to make publicly available the outcomes
of government funded research• Encouraging scientists to publish in open access journals • Organize training programs by international experts to improve
quality of culture collections and databases• Improve access to specialized culture collections
National Knowledge Commission
• The National Knowledge Commission (NKC) was constituted in 2005 as a high-level advisory body to the Prime Minister of India. The Commission has been given a mandate to guide policy and direct reforms, focusing on certain key areas such as education, science and technology, agriculture, industry, e-governance etc. Easy access to knowledge, creation and preservation of knowledge systems, dissemination of knowledge and better knowledge services are core concerns of the commission.
National Knowledge Commission
Access
Concepts
ApplicationsServices
Creation
NKC Working Model
• Identify focus areas/target groups• Consultations – formal and informal• Background research and analysis• Constitution of Working Groups• Internal deliberations of NKC• Finalization of recommendations• Submission to PM• Widespread dissemination• Implementation
Suggestions• Devise measures to build confidence amongst underdeveloped and
developing nations that their resources will not be exploited• Networking and consortia among scientists, curators of culture
collections, policy makers from developed and developing countries• Material transfer agreements should be standardized by taking into
consideration national security and biosafety• Create awareness about open access and open educational
resources • Lobbying to policy makers to make publicly available the outcomes
of government funded research• Encouraging scientists to publish in open access journals • Organize training programs by international experts to improve
quality of culture collections and databases• Improve access to specialized culture collections