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Item Dual Role for Zn2+ in Maintaining Structural Integrity and Inducing DNA Sequence Specificity in a Promiscuous Endonuclease(Elsevier, 2007-11) Ghosh, SoumitraWe describe two uncommon roles for Zn2+ in enzyme KpnI restriction endonuclease (REase). Among all of the REases studied, KpnI REase is unique in its DNA binding and cleavage characteristics. The enzyme is a poor discriminator of DNA sequences, cleaving DNA in a promiscuous manner in the presence of Mg2+. Unlike most Type II REases, the active site of the enzyme comprises an HNH motif, which can accommodate Mg2+, Mn2+, or Ca2+. Among these metal ions, Mg2+ and Mn2+ induce promiscuous cleavage by the enzyme, whereas Ca2+-bound enzyme exhibits site-specific cleavage. Examination of the sequence of the protein revealed the presence of a zinc finger CCCH motif rarely found in proteins of prokaryotic origin. The zinc binding motif tightly coordinates zinc to provide a rigid structural framework for the enzyme needed for its function. In addition to this structural scaffold, another atom of zinc binds to the active site to induce high fidelity cleavage and suppress the Mg2+- and Mn2+-mediated promiscuous behavior of the enzyme. This is the first demonstration of distinct structural and catalytic roles for zinc in an enzyme, suggesting the distinct origin of KpnI REase.Item Moonlighting function of glutamate racemase from Mycobacterium tuberculosis: racemization and DNA gyrase inhibition are two independent activities of the enzyme(American Society for Microbiology, 2008-09) Ghosh, SoumitraGlutamate racemase (MurI) provides d-glutamate, a key building block in the peptidoglycan of the bacterial cell wall. Besides having a crucial role in cell wall biosynthesis, MurI proteins from some bacteria have been shown to act as an inhibitor of DNA gyrase. Mycobacterium tuberculosis and Mycobacterium smegmatis MurI exhibit these dual characteristics. Here, we show that the two activities of M. tuberculosis MurI are unlinked and independent of each other. The racemization function of MurI is not essential for its gyrase-inhibitory property. MurI–DNA gyrase interaction influences gyrase activity but has no effect on the racemization activity of MurI. Overexpression of MurI in vivo provides resistance to the action of ciprofloxacin, suggesting the importance of the interaction in gyrase modulation. We propose that the moonlighting activity of MurI has evolved more recently than its racemase function, to play a transient yet important role in gyrase modulation.Item Expression and functional analysis of rice genes involved in reproductive development and stress response(World Scientific, 2007) Sharma, RitaThe rice genome sequenced and annotated by the IRGSP has identified 37,544 protein-coding genes. In an effort to identify genes encoding transcription factors and signal transduction components, more than 7,000 genes belonging to 87 classes have been used to prepare a local database. Detailed analysis of genes for plant hormone response, CDPKs, C2H2 zinc-finger, and SET domain proteins unraveled interesting evolutionary aspects in relation to genes and the rice genome. A 51k microarray, SAGE analysis, and real-time polymerase chain reaction revealed differential expression of target genes during reproductive development and stress conditions. Several genes specific to reproductive floral organs and seed development have been identified. A large number of SAGE tags are observed from intergenic regions and antisense strands reflecting the unexplored transcription potential of the rice genome. Analysis of rice gene promoter activities has been undertaken in transgenic tobacco/Arabidopsis to demarcate regions conferring anther-/pollen-specific expression. OSISAP1, a gene coding for a stress-associated zinc-finger protein, and its promoter have been functionally validated in transgenic tobacco and rice. Genes for proteins interacting with OSISAP1 have also been found to be stress-inducible. Investigations on functional analysis of stress-responsive genes are in progress.Item Plasmodium falciparum: genetic diversity of C-terminal region of MSP-1 in isolates from Indian sub-continent(Elsiever, 2005-08) Saxena, Vishal; Das, AshisMalaria parasites exhibit sequence diversity for a number of stage specific antigens. Several studies have proved that merozoite surface protein-1 (MSP-1) is an effective target eliciting a protective immune response. The MSP-142 region comprising two EGF-like domains is involved in generating protective immune response in humans and other experimental animals. Searching for point mutations in this region is essential in view of vaccine development. We have investigated the sequence variations in Plasmodium falciparum MSP-1 carboxy terminal region in field isolates from different regions in India. Our study reveals the presence of eight variant types of MSP-119 in the Indian sub-continent, which comprise of E-TSR-L, Q-TSR-L, E-TSG-L, Q-KNG-L, Q-KNG-F, E-KNG-L, E-KNG-F, and E-KYG-F. The last named allele is a novel variant being reported for the first time.Item A Handbook of Genetic Engineering(Kalyani Publishers, 2007) Saxena, VishalItem Inhibition of mitochondrial electron transport is the prime cause behind proline accumulation during mineral deficiency in Oryza sativa(Springer, 1993) Bhagavatula, VaniThe concentration of proline in shoots of rice (Oryza sativa) seedlings raised in distilled water was about 3.3 times higher than in the seedlings raised in modified B5 medium. The shoots of seedlings raised in B5 medium which was depleted of calcium, iron, magnesium or potassium had a higher concentration of proline than those grown in standard B5 medium. The shoots of seedlings raised in distilled water with iron had a lower level of proline than those in distilled water. These results suggest that iron deficiency leads to high proline accumulation.Item Effect of short-term heat treatment of rice seedlings on sensitivity of thylakoid membranes to photoinhibition(Springer, 1996) Bhagavatula, VaniThe after-effects of 24 h high temperature (35 or 45 ~ treatment on the photochemical activities and photooxidative lipid peroxidation, subsequent to their irradiation were studied in 7-d-old etiolated rice (Oryza sativa) seedlings. Photosystem (PS) 1 and PS 2 mediated photoreactions of thylakoids isolated from the seedlings exposed to high temperature did not differ significantly from the thylakoids isolated from control seedlings (25 ~ Hence, all kinds of tested thylakoids were equally efficient in capturing and utilizing radiant energy. The high irradiance induced loss in PS 2 activity and lipid peroxidation measured in terms of malondialdehyde production was more rapid in thylakoids isolated from stressed seedlings as compared to that of control seedlings. Thus the thylakoids isolated from the stressed seedlings were more prone to photodamage than those from the control seedlings.Item Alteration in NAD+/NADH ratio regulates salt stress induced proline accumulation in Vigna radiata.(NAS, 1996) Bhagavatula, VaniFive-day-old vigna radiata seedlings exposed to NaCI stress induced a significant enhancement in proline levels accompanied by reduction in growthItem Structure-function correlation during the etioplast-chloroplast transition in cucumber cotyledonary leaves(IJPR, 1998) Bhagavatula, VaniWe studied the development of chloroplasts from etioplasts in the cotyledonary leaves of 4-d-old dark-grown cucumber (Cucumis sativus) seedlings after irradiation (20 μmol m-2 s-1). Upon irradiation, the triggering of chlorophyll (Chl) synthesis and accumulation showed a relatively short lag phase. The irradiation of etiolated seedlings initiated the synthesis of apoproteins of pigment-protein complexes. While Chl-protein 2 (CP2) was detected at 6 h after irradiation, CP1 only after 29 h. The appearance and accumulation of some of the apoproteins were monitored by Western-blotting. LHC2 apoprotein was detected after a 6 h-irradiation. The amounts of D1 protein of photosystem (PS) 2 and PsaA/B protein of PS1 were quantitated by ELISA. Further, the thylakoid membrane function during this time period in terms of PS1- and PS2-mediated electron transfer activity and intersystem electron pool size were analyzed. While PS1 activity was detected after 4 h, PS2-mediated O2 evolution was detected only after a 17 h-irradiation. Fv/Fm value of Chl a fluorescence measurements indicated that the photochemical efficiency of these leaves reached its maximum after 29 h of irradiation. The intersystem pool size of cotyledonary leaves was equivalent to that of the control cotyledonary leaves grown for 25 h under continuous irradiation. Thus etioplasts develop into fully functional chloroplasts after approximately 25 h when 4 d-dark grown cucumber seedlings are continuously moderately irradiated. The development of photosynthetic electron transport chain seems to be limited in time at the level of PS2, possibly at the donor side.