Dr. Ranjith N. Kumavath, Ph.D

School of Biological Sciences, Nanyang Technological University, Singapore.

Email:ranjith_kumavath@yahoo.com, ranjithkumavath@gmail.com .

Website:http://ranjithkumavath.googlepages.com

 Academic Records:

2003-2008:  Ph.D., (Biological Sciences), University of Hyderabad, Hyderabad, Andhra Pradesh, India.
2001-2003:  M.Sc., (Bio-Chemistry) Sri Venkateswara University, Tirupathi, Andhra Pradesh, India.
1996-1999:  B.Sc., (Biology and Chemistry) Sri Krishnadevaraya University, Anantapur, Andhra Pradesh, India.
  Research Experience:

2009-@Present: Post-Doctoral Research Fellow, in School of Biological Sciences, Nanyang Technological University, Singapore. Project entitle: “Towards understanding of eukaryotic translation termination: NMR structural studies of human peptide release factor eRF1 and its interactions with eRF3 and ribosomal pretermination complex by NMR in solution”.
2008-2009: UGC-Dr.D.S.Kothari-Post-Doctoral Research Fellow, in School of Life Sciences, University of Hyderabad. Project entitle: “Mining for novel enzymes in Rubrivivax benzoatilyticus OU5 using metaboloms studies”.
2003-2008:  Ph.D., in Microbial Biochemistry, University of Hyderabad, Hyderabad, Thesis title: “Biodegradation and Biotransformation of Aromatic Amino Acids: A Proteomics Approach for the Identification of Novel Metabolic Pathways in Photosynthetic Purple Non Sulfur Bacteria (PNSB) Rhodobacter sphaeroides OU5.
  Research Highlights: 


My current (Post-Doc) work is focus on towards understanding of eukaryotic translation termination: NMR structural studies of human peptide release factor eRF1 and its interactions with eRF3 and ribosomal pretermination complex by NMR in solution” and investigating the RNA-Protein (eRF1) interaction towards realizing the drug discovery. In eukaryotes, the N domain of polypeptide release factor eRF1 is involved in decoding all three stop codons, UAA, UAG or UGA. The N domain has two highly conserved motifs TASNIKS (amino acids 58-64) and YxCxxxF (amino acids 124-131), and they played an important role in the stop codon recognition. The UGA-only response has also been achieved by some substitutions of some amino acids located in this part. The four-site mutate QFM_F respond only to UGA.  

  We have cloned, expressed and purified the protein for NMR. For the backbone assignment, 2D 1H, 15N-TROSY and 3D HNCO, HNCA, and HNCACB spectra were used. Reverse labeling of phenylalanine and dual amino acid-selective 13C–15N labeling techniques are also used to get the backbone assignment. 15N-resolved and 13C-resolved NOESY experiments were used to assign 1H side-chain resonances and we have determined the solution structure of QFM_F mutation and performed chemical shift mapping experiments with UGA. Furthermore we found that the amino acids 91, 117 are involved in the specific recognition of UGA. Finally, we proposed a possible mechanism by which the four-site mutate QFM_F decode UGA specifically.

      In Post-Doc and Doctoral (PhD) research work, I have taken Metabolomics and proteomics approach to understand the aromatic amino acids catabolism in Anoxygenic Photosynthetic Purple Non Sulfur Bacteria (PNSB) Rhodobacter sphaeroides OU5. From that we have isolated few metabolites in L-phenylalanine and L-tryptophan metabolism and purified, characterized few enzymes in catabolic pathway, three of them proven to be novel enzymes those name so called as DOPARDA (3,4-dihydroxyphenyalaninereductivedeaminase)

(3, 4-dihydroxyphenylanaine oxidative deaminase, Tryptophan ammonia lyase by MALDI-TOF-finger printing and N-terminal Sequence of these enzymes to confirm a novel enzyme. DOPARDA and DOPAODA have assigned an enzyme code by nomenclature of IUBMB, under lyase and oxidase family of enzymes.

      The studies on the biodegradation and metabolism of hazardous homocyclic aromatic compounds under anaerobic conditions by purple non-sulfur bacteria were carried out mainly on the nitro, halo and hydroxyl derivatives. Biotransformation of nitrogen containing and heterocyclic aromatic compounds to value added products like antimicrobial, anti cancer and plant growth promoting substances. Metabolism and toxicity of heterocyclic aromatic compounds on purple bacteria studied with reference to indoles (Ranjith, et al., 2007), phenols (Ranjith, et al., 2007) and anilines Vijay and Ranjith, 2006) and we also discovered the capability of purple bacteria in synthesizing an array of conjugates when the precursors, L-tryptophan, L-phenylalanine and L-tyrosine were used resulting in the synthesis of terpenoid conjugated indoles or phenols (Vijay et al., 2006; Ranjith et al., 2007;Ranjith et al., 2009).They play an important role in the functioning of these organisms; particularly the carotenoids are the key components helping photosynthesis.Carotenoids also have an important function is in the process of detoxication of xenobiotics, through in the process of conjugation. We hypothesized that anoxygenic phototrophic bacterium can synthesis an array of carotenoid-conjugated molecules from various precursors due to the bioprocessing of conjugative detoxication.  Apart from this I have isolated Rhodethrin, Rubrivivaxin and few terpenoid conjugative phenols and indoles are novel. We investigated bioprospecting of these novel biomolecules as cytotoxicity against supT1 lymphoma, Colo-125, Jurkat, U937 cancer cell lines and COX-1&2 inhibitory activities, Phytoharmonal and antimicrobial and anti fungal activities. Among all biomolecules, Rhodethrin has been proven to be a good potential bioactive molecule against cancer cell lines SupT1 lymphoma and Colo-125, extensive effect at Pico mole concentrations.

  Research expertise:

(i) Molecular biology: DNA, RNA, Plasmid isolation, Genetic transformation, Southern, Northern and Western blotting analysis, Primer designing, Site-Directed Mutagenesis, PCR, Gene cloning, and Recombinant Proteins Expression and Purification.

(ii).Protein Expression, Purification and Characterization: UV-vis spectroscopy, SDS-PAGE, 2D-Electrophresis, Gel filtration, Affinity, Ion-exchange chromatography, FPLC, iTRAQ, Protein digestion, and MALDI-TOF-TOF analysis.

(iii).Metabolites Purification and Structural elucidation: TLC, HPLC, LC-MS, IR, 1H & 13C NMR & TROSY- NMR Spectroscopy

(iii).Protein structure determination: Circular Dichroism Spectroscopy (CD), Isothermal Titration Calorimeter (ITC). 

      I have working knowledge of the following software packages: MS modeling, Swiss-Port (PDB viewer), Rasmol, BLAST, Microcal-Origin, ChemDraw, ISIS, Microsoft Office, SAXS-Data analysis, Auto-Dock-4.2, Pymol, Molmol, CARA (Computer Aided Resonance Analysis).

  Awards and Professional affiliations:

Awarded Junior Research Fellowship (JRF/SRF), by University grants commission (UGC-RNF), Govt. of India (2003-2007)
Awarded UGC-Dr.D.S.Kothari Post-Doctoral Fellow, by University Grant Commission (UGC), New Delhi, India (August, 2008).
Post-Doctoral Research Fellow (PDF), in School of Biological Sciences, NanYang Technological University, 60-Nanyan Drives, Singapore. (March 2009).
Bio-Asia 2008 Innovation for young scientist award, presented paper (Feb, 2008).
Dr.K.V.Rao Memorial young scientist award-2008 nominated for paper presented (April, 2008).
Invited Lectures:
Title: Biodegradation and Biotransformation of Aromatic amino acids: A Proteomics and metabolomics approaches for the Identification of Novel Metabolic Pathways in Photosynthetic Purple Non Sulfur Bacteria (PNSB). Inviters: Dr. Micheal M. Meijler and Dr. Amir Aharoni, Dept. of Biotechnology and Chemistry, Ben-Gurion University of the Negev, Israel.
Title: Structure and Functions of eukaryotic and prokaryotic RNAs. School of Life Sciences Management Development Institute of Singapore.
Reviewer:
Natural Product Research (Taylor & Francis), Two articles reviewed.
Journal of Microbiology and antimicrobials, one article reviewed.
Current Microbiology, one article reviewed
Supervision: Eventual supervision of 3 Doctoral (PhD) and few Master students

  List of Publications:

Li Yan 1, Ranjith N.K1, Leo Wong E 1, Shubadra P1 Konstantin Pervushin 1*.NMR Structural determination of QFM-F mutation of N-domain of Human eukaryotic release factor (eRF1) and its recognition and mechanism of stop-codon UGA.  MS- to be communicated (2010).
Ranjith, N.K, Sasikala, Ch. and Ramana, Ch.V. Tryptophan ammonia lyase an enzyme catalyzes the formation of indole 3-acrylic acid from L-tryptophan isolated from Rhodobacter sphaeroides OU5. Journal of Bacterial (2010) (MS-revision).
Ranjith, N.K, Sasikala, Ch. and Ramana, Ch.V. L-tryptophan catabolism by Rubrivivax benzoatilyticus JA2 occurs through indole 3-pyruvic acid pathway. Biodegradation (DOI: 10.1007/s10532-010-9347-y) (Inpress-2010)
Ranjith, N.K, Sasikala, Ch. and Ramana, Ch.V. Rubrivivaxin: a novel phenol terpenoid ester produced by Rhodobacter sphaeroides OU5 has cytotoxic activity. J. Natural Prod. Comm. (2010) (MS-accepted)
Ranjith, N.K, Sasikala, Ch. and Ramana, Ch.V. Production of Phenols and Gallate-esters by Rhodobacter sphaeroides OU5. Curr. Microbiol.60 (2): 107-111 (2010).
Ranjith,N.K, Ramana Ch.V and Sasikala Ch. Purification and characterization of 3, 4-dihydroxyphenylalanine oxidative deaminase from Rhodobacter sphaeroides OU5. Can J Microbiol. 54(10): 829-34 (2008).
Ranjith, N.K, Sasikala Ch and Ramana Ch.V. Rhodethrin: Novel indole terpenoid ether produced by Rhodobacter sphaeroides has Cytotoxic and Phytohormonal activities. Biotechnol. Lett.29 (9): 1399-402. (2007).
Ranjith, N.K, Sasikala Ch and Ramana Ch.V. Catabolism of L-phenylalanine and L-tyrosine by Rhodobacter sphaeroides OU5 occurs through 3, 4-dihydroxyphenylalanine. Res. Microbiol. 158(6): 506-11 (2007).
Shanker, V, Rayabandla, S.M, Kumavath, R.N, Chintalapati S and Chintalapati R. Light-dependent transformation of aniline to indole esters by the purple bacterium Rhodobacter sphaeroides OU5. Curr Microbiol. 52(6): 413-7 (2006).
  Additional Publication:

Ranjith, N.K., Sasikala, Ch., and Ramana, Ch.V. A novel Tryptophan ammonia lyase enzyme to be deposited in database as EC by Nomenclature Committee of the international Union of Biochemistry and Molecular Biology [EC 4.3.1.xx]
Ranjith, N.K., Sasikala, Ch., and Ramana, Ch.V. A novel 3,4-dihydroxyphenylalanine oxidative deaminase (DOPAODA) enzyme deposited in database as EC by Nomenclature Committee of the international Union of Biochemistry and Molecular Biology [EC 1.13.12.15 created 2008]
Ranjith, N.K., Sasikala, Ch., and Ramana, Ch.V. A novel 3,4-dihydroxyphenylalanine reductive deaminase (DOPARDA) enzyme deposited in database as EC by Nomenclature Committee of the international Union of Biochemistry and Molecular Biology  [EC 4.3.1.22 created 2007]
Ranjith, N.K., Sasikala, Ch., and Ramana, Ch.V. 3,4-dihydroxyphenylalanine 2-oxoglutarate aminotransferase (DOPAATS) enzyme updated in database as EC by Nomenclature Committee of the international Union of Biochemistry and Molecular Biology [EC 2.6.1.49 created 2007] (Ref: Funnum and Larsen, 1965).
  Participation in Conferences & Workshops:

Ranjith, N.K., Sasikala, Ch and Ch.V.Ramana (2005). Photometabolism of L-phenylalanine by Rhodobacter sphaeroides OU5. Poster presented in “Micro-Biotech 2005” Association of Microbiologists of India, 46th Annual Conference, at Dept. of Microbiology, Osmania University, Hyderabad on Dec.2005.
Ranjith, N.K., Sasikala, Ch and Ch.V.Ramana (2006).Isolation, purification and characterization of 3, 4-dihydroxy, 2-oxoglutarate aminotransferase (DOPAATS) by Rhodobacter sphaeroides OU5. Poster presented and published full-length paper in National Seminar on “Recent advances in Biotechnology and Bioinformatics” held in MGNIRSA, Centre for    Biotechnology at Hyderabad.
Ranjith, N.K., Sasikala, Ch and Ch.V.Ramana (2008). Rhodethrin: Novel indole terpenoid ether has Phytohormonal, COX inhibitory and Cytotoxicity activities. Paper presented at “BIO-ASIA 2008” innovation award for young scientist at Hyderabad on Feb-9th 2008.
Satellite Symposium on “Molecular Aspects of Cellular Signaling” held in University of Hyderabad, Dec. 2003.
Participated in “93rd Indian science congress-2006” at Acharya N.G.Ranga Agricultural University, Hyderabad on Feb 2006.
Active participation at the Inaugural” Singapore Proteomics Forum 2009”. Organizers of Singapore Proteomics Forum 2009, on 15th May, 2009,
Actively participated in Solution X-ray scattering; Application to Structural Biology Practical course in SAXS-data analysis” held on Nanyang Technological University’s School of Biological Science has partnered the European Molecular Biology Laboratory (EMBL) in Hamburg to conduct a remotely controlled Solution X-Ray Scattering (SAXS) experiment. On the date of 25th, 26th May 2009.
Participated in Proteomics: New strategies for targeted therapies in cancer” organized by Institute of Molecular and cell biology, Singapore, on 2nd June 2009.
Participated in "ProteOn' XPR36 Protein Interaction Assay System: Regulatory Tools for Protein Interaction and Drug Development". Organized by Bio-Rad Laboratories at School of Biological Sciences, NanYang Technological University, Singapore, on 17th August 2009.
Participated in " Intellectual Property: Capitalizing, Managing and Protecting" a part of the NTU E&I festival 2009 on 26th Aug 2009.

Biographical information:
Country of Birth:  India                                                  State: Andhra Pradesh                          
Country of citizenship: India                                          Passport No: F9923539                      
Date of Birth:       08th  April, 1979
Nationality:          Indian
Sex:                       Male
Marital status:     Single
 Posted on March 22, 2010---------------------------------------------------------------------------------