DR. SAMAN HABIB
     
...

Senior Principal Scientist & In-Charge
Division of Molecular and Structural Biology
Central Drug Research Institute
Lucknow 226031

 
 
E-Mail

saman_habib@cdri.res.in

Educational Qualifications M Sc., Ph D
 
Research Group

Ankit Gupta, Research Fellow
Afreen Haider, Research Fellow
Manish Charan, Research Fellow
Suniti Vaishya, Research Fellow
Kanika Kanchan, Research Fellow
Kirti Gupta, Research Fellow


Current Research Programmes
   



The primary research interest of my laboratory is to understand aspects of malaria apicoplast biology using molecular approaches. The apicoplast is a relict plastid of Plasmodium and is of interest as a site for drug intervention against malaria. We work on the following aspects:


(a) Understanding the mechanism of DNA replication and organization of the Plasmodium falciparum apicoplast.


Studies by our group have helped generate insights into the mechanism of replication of the apicoplast genome. We demonstrated that the ori of P.falciparum plDNA are localized within the inverted repeat region (IR) and that there are at least two initiation sites within each inverted repeat segment of the circular plDNA of P.falciparum suggestive of a four D-loop/bidirectional ori mechanism of DNA replication. Moreover, plDNA replication was shown to initiate with differential efficiencies at multiple sites within the inverted repeat region.



Figure: Signals observed for plDNA fragments using 5’-end labeled nascent DNA from replicating apicoplast DNA as probe. Ori sequences were identified within the IR region.

The role of a P. falciparum nuclear-encoded bacterial histone-like protein (PfHU) in DNA compaction in the apicoplast has been revealed by studies in our laboratory. PfHU associates with apicoplast DNA and is expressed throughout the parasite’s intra-erythrocytic cycle. The protein displays a preference for supercoiled DNA and is capable of condensing E.coli nucleoids in vivo. The unique 42 aa C-terminal extension of PfHU influences its DNA condensation properties. In contrast to bacterial HUs that bend DNA, PfHU promotes concatenation of linear DNA and inhibits DNA circularization. Atomic Force Microscopy of PfHU-DNA complexes showed protein concentration-dependent DNA stiffening, intermolecular bundling and formation of DNA bridges followed by assembly of condensed DNA networks.

These results have provided the first functional characterization of an apicomplexan HU protein and give additional evidence for red algal ancestry of the apicoplast.


Figure: AFM images of PfHUp- DNA complexes with increasing dimer/bp ratio. (A) DNA in the absence of protein. (B) Dimer/bp ratio of 1:750. Stiffened DNA strands (panel i) as well as DNA bundles (panel ii) are shown. (C) Dimer/bp ratio of 1:500. Formation of complexes with a small number of foci and extruding DNA loops (panel i), a DNA bridge resulting in DNA looping (panel ii) and a nucleoprotein complex with a single focus (panel iii) are seen.

(b) Investigation of apicoplast ORFs, selected apicoplast-targeted proteins and their structure-function analysis.

Several proteins predicted to be involved in apicoplast-specific pathways are being studied. We attempt recombinant expression of these proteins and their functional analysis. The catalytic features of nuclear-encoded gyrase subunits have been analysed and the effect of novobiocin (a GyrB inhibitor) on apicoplast DNA replication and GyrB activity has indicated specific drug action on apicoplast GyrB.  Novobiocin also causes parasite death in culture.

(c)Translation in the Plasmodium apicoplast.
Translation within the apicoplast is an attractive process for the discovery of novel antimalarials. Studies in our laboratory that localized the apicoplast-encoded tufA gene product in the organelle and the effect of thiostrepton on EF-Tu levels provided evidence for active translation within the organelle
....................
Ribosome disassembly by apicoplast ribosome recycling factor (RRF) and EF-G .................


Under a collaborative project (project Mephitis) funded by European Commission’s Seventh Framework Programme, we carried out biochemical analysis of translation factors that function in the Plasmodium apicoplast. Continuing this work in an Indo-Spain project we now investigate mechanisms of peptide chain initiation, release, and ribosome recycling in Plasmodium organelles.

(d)An additional research area in the laboratory involves investigation of the role of human genetic variation and susceptibility to severe P. falciparum malaria in India. Drawing from SNP frequency data for a spectrum of Indian populations generated by the Indian Genome Variation Consortium, we analyse association of specific variants with disease susceptibility in a falciparum endemic and a non-endemic region of India. SNPs in genes encoding adhesion and immune regulatory molecules are being studied in a case-control format.

.

Figure: Frequency distribution of a TNF-α enhancer SNP in India and Pairwise FST analysis to study genetic differentiation among Indian populations (IGVC panel) using frequency data of SNPs previously associated with falciparum malaria.

   
 


 

Selected Publications

Gupta  A, Mir SS, Jackson KE, Lim EE, Shah P, Sinha A, Siddiqi MI, Ralph SA and Habib S* (2013) Recycling factors for ribosome disassembly in the apicoplast and mitochondrion of Plasmodium falciparum. Molecular Microbiology 88: 891-905

Jha P, Sinha S, Kanchan K, Qidwai T, Narang A, Singh PK, Pati SS, Mohanty S, Mishra SK, Sharma SK, Awasthi S, Venkatesh V, Jain S, Basu A, Xu S, Indian Genome Variation Consortium, Mukerji M*, Habib S* (2012). Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria. Infection, Genetics & Evolution 12:142-148.

Jackson KE^, Habib S^, Frugier M, Hoen R, Khan S, Pham J, de Pouplana LR, Royo M, Santos MAS, Sharma A, Ralph SA (2011) Protein translation in Plasmodium parasites. Trends in Parasitology 27: 467-476.   ^equal contribution

Kumar B, Chaubey S, Shah P, Tanveer A, Charan M, Siddiqi MI and Habib S* (2011) Interaction between SufB and SufC: evidence for an iron-sulfur cluster biogenesis pathway in the apicoplast of Plasmodium falciparum. International Journal for Parasitology 41: 991-999.

Biswas S, Lim EE, Gupta A, Saqib U, Mir SS, Siddiqi MI, Ralph SA and Habib S* (2011) Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodium falciparum plastid. International Journal for Parasitology41: 417-427.

Penman B, Habib S, Kanchan K, Gupta S (2011) Negative epistasis between α+ thalassaemia and sickle cell trait can explain inter population variation in South Asia. Evolution 65-12: 3625-3632.

Ambrish Kumar, Aiman Tanveer, Subir Biswas, EVS Raghu Ram, Ankit Gupta, Bijay Kumar and Habib S* (2010) Nuclear-encoded DnaJ homolog of Plasmodium falciparum interacts with replication ori of the apicoplast genome. Molecular Microbiology 75(4): 942-956.    
Sinha S, Qidwai T, Kanchan K, Jha GN, Anand P, Pati SS, Mohanty S, Mishra SK, Tyagi PK, Sharma SK, Awasthi S, Venkatesh V and Habib S* (2010) Distinct cytokine profiles define clinical immune response to falciparum malaria in regions of high or low disease transmission. European Cytokine Network. 21 (4): 232-240.         
Sinha S, Jha GN, Anand P, Qidwai T, Pati SS, Mohanty S, Mishra SK, Tyagi PK, Sharma SK, Venkatesh V, Habib S* (2009). CR1 levels and gene polymorphisms exhibit differential association with falciparum malaria in regions of varying disease endemicity. Human Immunology 70: 244-250.
Raghu Ram EVS, Naik R, Ganguli M and Habib S* (2008) DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum. Nucleic Acids Research 36 (15): 5061-5073.
Sinha S, Qidwai T, Kanchan K, Anand P, Jha GN, Pati SS, Mohanty S, Mishra SK, Tyagi PK, Sharma SK, Indian Genome Variation Consortium, Venkatesh V, and Habib S* (2008) Variations in host genes encoding adhesion molecules and susceptibility to falciparum malaria in India. Malaria Journal 7:250.
Sinha S, Mishra SK, Sharma S, Patibandla PK, Mallick PK, Sharma SK, Mohanty S, Pati SS, Mishra SK, Ramteke BK, Bhatt RM, Joshi H, Dash AP, Ahuja RC, Awasthi S, Indian Genome Variation Consortium, Venkatesh V and Habib S* (2008) Polymorphisms of TNF-enhancer and gene for FcyRIIa correlate with the severity of falciparum malaria in the ethnically diverse Indian population. Malaria Journal 7:13.
Brahmachari SK, Majumder PP, Mukerji M, Habib S, Dash D, Ray K, Bahl S et al. (The Indian Genome Variation Consortium) (2008) Genetic landscape of the people of India: a canvas for disease gene exploration. Journal of Genetics 87:3-20.
Raghu Ram EVS, Kumar A, Biswas S, Kumar A, Chaubey S, Siddiqi MI and Habib S* (2007) Nuclear gyrB encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication. Molecular & Biochemical Parasitology 154:30-39.
Singh D, Kumar A, Raghu Ram EVS and Habib S (2005) Multiple replication origins within the inverted repeat region of the Plasmodium falciparum apicoplast genome are differentially activated. Molecular & Biochemical Parasitology 139(1):99-106.
Chaubey S, Kumar A, Singh D and Habib S (2005) The apicoplast of Plasmodium falciparum is translationally active. Molecular Microbiology 56(1): 81-89.
Singh D, Chaubey S and Habib S (2003) Replication of the Plasmodium falciparum apicoplast DNA initiates within the inverted repeat region. Molecular & Biochemical Parasitology 126 (1): 9-14.