Department of Biological Science
National University of Singapore
14 Science Drive 4
Lab: Sanjay Lab
Deputy Director, NUS Environmental Research Institute (NERI) www.nus.edu.sg/neri
Director, Graduate Program | Singapore Centre for Environmental Life Sciences Engineering (SCELSE) | Nanyang Technological University | SBS-01n-15, 60 Nanyang Drive, Singapore 637551 | Tel: (65) 6316 2820 GMT+8h | Fax: (65) 6791 3856
PhD UF (USA), PhD, Msc IARI, BSc PAU India
Our research program involves understanding the biological role of small biomolecules. We work in two broad areas involving small molecules. First, to understand metabolic networks- including their modularity, connectivity, control mechanisms and to discover new products or pathways of applied value. Second, to understand the role of cyclic nucleotide 2nd messengers that control diverse pathways in model bacterial species Pseudomonas or in environmental bacterial communities.
In the metabolic networks program, we have adopted mostly a data-driven systems approach to understand cellular responses to perturbations caused by diverse intrinsic or extrinsic signals in the biological system(s). We combine both wet and dry laboratory work within our group. Our model organisms are diverse and include bacteria (Bacillus, Pseudomonas), Arabidopsis, rat and human skin cells. We have developed capabilities to comprehensively map out the changes in the metabolic complement or the 'metabolome' of cells in response to perturbations such as metabolic mutations, effector molecules, or environmental stresses. This approach has allowed us in various projects to:
In the signalling program, we have recently described the regulatory mechanism for a novel cyclic nucleotide 2nd messenger in microbes, cyclic diguanylate. The motility regulator MorA is especially conserved in Pseudomonas, modulates the intracellular messenger levels and controls pathways such as motility and biofilm formation. Current efforts in the laboratory are focused on the elucidation of the structure, function and regulatory circuit of the pathways.
In 2008, we have started applying our fundamental studies to addresses the role of plant-microbial interactions in urban freshwater ecology. This work is being carried out under the umbrella of Singapore-Delft Water Alliance (www.sdwa.nus.edu.sg) and funded by the National Research Foundation. We are taking a taking a multidisciplinary approach incorporating hydraulics, genomics, metabolomics, computational and graphical modelling, and high-resolution imaging to study mechanisms that govern biofilm formation and plant metabolic processes in urban freshwater conditions. Both, single-species (Pseudomonas sp.) model and bacterial communities in aquatic environments are being investigated. We focus on biofilm processes such as bacterial signaling that affect bacterial motility, adhesion, biofilm initiation and metabolic networks including roles of metabolites as nutrients and signals in microbial communities.
Since 2009, we have begun complementary studies at a fundamental level to understand the mechanical properties of motility and biofilm formation in bacteria in relation to their control mechanisms. We are especially interested in understanding the coordinated control of multiple appendages of bacteria such as flagella and pili, taking Pseudomonas as our biological model. This work is being carried out at the Research Centre of Excellence in Mechanobiology funded by the National Research Foundation.
Simone C. Birrer Katherine A. Dafforn Melanie Y. Sun Rohan B.H. Williams Jaimie Potts Peter Scanes Brendan P. Kelaher Stuart L. Simpson Staffan Kjelleberg Sanjay Swarup Peter Steinberg Emma L. Johnston (2018). Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation. Environmental Microbiology. DOI: https://doi.org/10.1111/1462-2920.14470
Balan P, Chong YS, Umashankar S, Swarup S, Loke WM, Lopez V, He HG and Seneviratne CJ. Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period (2018). Frontiers in Microbiology. 9:2360. doi: 10.3389/fmicb.2018.02360
Vello V, Umashankar S, Phang SM, Chu WL, Lim PE, Nazia AM, Liew K, Swarup S, Chew FT . Metabolomic profiles of tropical Chlorella and Parachlorella species in response to physiological changes during exponential and stationary growth phase (2018). Algal Research, 35, 61-75
Saxena G., Mitra S., Marzinelli E.M., Xie C., Wei T.J., Steinberg P. D., Williams R.B.H., Kjelleberg S., Lauro F. M., Swarup S. Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway. (2018). mSystems, 3, e00136-17 [Editor’s Pick, Highly accessed]
Keogh D., Lam L. N., Doyle L., Matysik A., Pavagadhi S., Umashankar S., Low P. M., Dale J. L., Song Y., Ng S. P., Boothroyd C. B., Dunny G. M., Swarup S., Williams R. B. H., Marsili E., Kline K. Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism. (2018). mBio, 9, e00626-17
Teh, B.T., Lim, K., Yong, C.H., Ng, C.C.Y., Rao, S.R., Rajasegaran, V., Lim, W.K., Ong, C.K., Chan, K., Cheng, V.K.Y., Soh P. S., Swarup S., Rozen S. G., Nagarajan N. and Tan P. (2017). The draft genome of tropical fruit durian (Durio zibethinus). Nature Genetics, doi:10.1038/ng.3972
Seneviratne, C.J., Suriyanarayanan, T., Swarup, S., Chia, K.H.B., Nagarajan, N., and Zhang, C. (2017). Transcriptomics Analysis Reveals Putative Genes Involved in Biofilm Formation and Biofilm-associated Drug Resistance of Enterococcus faecalis. Journal of Endodontics 6, 949-955.
Ling, H., Foo, J.L., Saxena, G., Swarup, S., and Chang, M.W. (2017). Drug Targeting of the Human Microbiome. Systems Biology 6.
Keogh, D., Lam, L.N., Doyle, L., Matysik, A., Pavagadhi, S., Umashankar, S., Dale, J.L., Boothroyd, C.B., Dunny, G.M., Swarup, S., Williams, R.B.H, Marsili, E., Kline, K. (2017). Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism. bioRxiv, 130146.
Chua, S.L., Ding, Y., Liu, Y., Cai, Z., Zhou, J., Swarup, S., Drautz-Moses, D.I., Schuster, S.C., Kjelleberg, S., and Givskov, M. (2016). Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels. Open Biology 6, 160162.
Suriyanarayanan T, Periasamy S, Lin M-H, Ishihama Y, and Swarup S (2016). Flagellin FliC Phosphorylation Affects Type 2 Protease Secretion and Biofilm Dispersal in Pseudomonas aeruginosa PAO1. PLoS ONE 11(10): e0164155. doi:10.1371/journal.pone.0164155
Rai A, Umashankar S, Lim BK, Rai M, Bing JAS, and Swarup S (2016). Coordinate Regulation of Metabolites Glycosylation and Stress Hormones Biosynthesis by TT8 in Arabidopsis. Plant Physiology, 171, 2499-2515.
Fazi S, Bandla A, Pizzetti I, and Swarup S (2016). Microbial biofilms as one of the key elements in modulating ecohydrological processes in both natural and urban water corridors. Ecohydrology & Hydrobiology 16, 33-38 .
Mynampati KC, Lee YJ, Wijdeveld A, Reuben S, Lakshminarayanan S, Kjelleberg S , and Swarup S (2015). RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere. Environmental Pollution 207, 205-210.
Patkar RN, Benke PI, Qu Z, Constance Chen YY, Yang, F, Swarup, S, and Naqvi NI (2015). A fungal monooxygenase-derived jasmonate attenuates host innate immunity. Nature Chemical Biology 11, 733-740.
Saxena G, Marzinelli EM, Naing NN, He Z, Liang Y, Tom L, Ping H, Josh, UM, Reuben S, Mynampati KC, Mishra S, Umashankar S, Mitra S, Zhou J, Andersen G, Kjelleberg S, and Swarup S (2015). Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environmental Science & Technology 49, 1462–1471.
Benke PI, Vinay Kumar MCS, Pan D, and Swarup S (2015). A mass spectrometry-based unique fragment approach for the identification of microcystins. The Analyst 140, 1198-1206.
Mishra S, Lee WA, Hooijer A, Reuben S, Sudiana IM, Idris A, and Swarup S (2014). Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands. Biogeosciences 11, 1727-1741.
Reuben S, Banas K, Banas A, and Swarup S (2014). Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms. Water Research 64, 123-133.
Reuben S, Rai A, Pillai, BV, Rodrigues A, and Swarup S (2013). A bacterial quercetin oxidoreductase QuoA-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in Arabidopsis. Journal of Experimental Botany 64, 5183-5194.
Nagarajan K, Loh K-C, Swarup S (2013) Bioinformatics and molecular biology for the quantification of closely related bacteria. Applied Microbiology Biotechnology 97, 6489-6502.
Qian C, Wong CC, Swarup S, Chiam K-H (2013). Bacterial Tethering Analysis Reveals a "Run-Reverse-Turn" Mechanism for Pseudomonas Species Motility. Applied Environmental Microbiology 79,4734-4743.
Reuben S, Chua CL, Fam KD, Thian ZY, Kang MK, and Swarup S (2012). Bacterial diversity on different surfaces in urban freshwater. Water Science and Technology 65, 1869-1874.
Zhang WC, Shyh-Chang N, Yang H, Rai A, Umashankar S, Ma S, Soh BS, Sun LL, Tai BC, Nga ME, Bhakoo KK, Jayapal SR, Nichane M, Yu Q, Ahmed DA, Tan C, Sing WP, Tam J, Thirugananam A, Noghabi MS, Pang YH, Ang HS, Mitchell W, Robson P, Kaldis P, Soo RA, Swarup S, Lim EH, and Lim B (2012) Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis. Cell 148, 259-272.
Biswas A, Rao R, Umashankar S, Mynampati KC, Reuben S, Parab G, and Swarup S (2011). datPAV--an online processing, analysis and visualization tool for exploratory investigation of experimental data. Bioinformatics 27, 1585-1586.
Tao F, Swarup S, and Zhang LH (2010). Quorum sensing modulation of a putative glycosyltransferase gene cluster essential for Xanthomonas campestris biofilm formation. Environmental Microbiology 12, 3159-3170.
Tao F, He YW, Wu DH, Swarup S, and Zhang LH (2010). The cyclic nucleotide monophosphate domain of Xanthomonas campestris global regulator Clp defines a new class of cyclic di-GMP effectors. Journal of Bacteriology 192, 1020-1029.
Biswas A, Mynampati KC, Umashankar S, Reuben S, Parab G, Rao R, Kannan VS, and Swarup S (2010). MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation. Bioinformatics 26, 2639-2640.
Ravichandran A, Sugiyama N, Tomita M, Swarup S, and Ishihama Y (2009). Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species. Proteomics 9, 2764-2775.
Parab GS, Rao R, Lakshminarayanan S, Bing YV, Moochhala SM, and Swarup S (2009). Data-driven optimization of metabolomics methods using rat liver samples. Analytical Chemistry 81, 1315-1323.
Benaka Prasad SB, Vinaya K, Ananda Kumar CS, Swarup S, and Rangappa KS (2009). Synthesis of novel 6-fluoro-3-(4-piperidinyl)-1,2-benzisoxazole derivatives as antiproliferative agents: a structure-activity relationship study. Investigational New Drugs 27, 534-542.
Ananda Kumar CS, Prasad SB, Vinaya K, Chandrappa S, Thimmegowda NR, Ranganatha SR, Swarup S, and Rangappa KS (2009). Synthesis and antiproliferative activity of substituted diazaspiro hydantoins: a structure-activity relationship study. Investigational New Drugs 27, 131-139.
Ananda Kumar CS, Benaka Prasad SB, Vinaya K, Chandrappa S, Thimmegowda NR, Kumar YC, Swarup S, and Rangappa KS (2009). Synthesis and in vitro antiproliferative activity of novel 1-benzhydrylpiperazine derivatives against human cancer cell lines. European Journal of Medicinal Chemistry 44, 1223-1229.
Meier S, Gehring C, MacPherson C, Kaur M, Maqungo M, Reuben S, Muyanga S, Shih M-D, Wei F-J, Wanchana S, Mauleon R, Radovanovic A, Bruskiewich R, Tanaka T, Mohanty B, Itoh T, Wing R, Gojobori T, Sasaki T, Swarup S, Hsing Y-i, and Bajic V (2008). The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network. Rice 1, 177-187.
Domadia PN, Bhunia A, Sivaraman J, Swarup S, and Dasgupta D (2008) Berberine targets assembly of Escherichia coli cell division protein FtsZ. Biochemistry 47, 3225-3234.
Weng-Kenong C, Bajic VB, Mok-Eei H, Merlin V, and Swarup S (2008).Regulatory Networks of Genes Affected by MorA, A Global Regulator Containing GGDEF and EAL Domains in Pseudomonas Aeruginosa. In: Series on Advances in Bioinformatics and Computational Biology, World Scientific, Vol. 8: Regulatory Genomics. Proceedings of the RECOMB 2006 Conference on Gene Regulatory Networks, 123-129.
Reza MA, Swarup S, and Kini RM (2007). Structure of two genes encoding parallel prothrombin activators in Tropidechis carinatus snake: gene duplication and recruitment of factor X gene to the venom gland. Journal of Thrombosis and Haemostasis 5, 117-126.
Domadia P, Swarup S, Bhunia A, Sivaraman J, and Dasgupta D (2007). Inhibition of bacterial cell division protein FtsZ by cinnamaldehyde. Biochemical Pharmacology 74, 831-840.
Reza MA, Minh Le TN, Swarup S, and Manjunatha Kini R (2006). Molecular evolution caught in action: gene duplication and evolution of molecular isoforms of prothrombin activators in Pseudonaja textilis (brown snake). Journal of Thrombosis and Haemostasis 4, 1346-1353.
Bhalla R, Narasimhan K, and Swarup S (2006). Metabolomics and its role in understanding cellular responses in plants. Plant Cell Rep 24,562-71.
Reza MA, Swarup S, and Kini RM (2005). Gene structures of trocarin D and coagulation factor X, two functionally diverse prothrombin activators from Australian rough scaled snake. Pathophysiology of Haemostasis and Thrombosis 34, 205-208.
Reza A, Swarup S, and Manjunatha Kini R (2005). Two parallel prothrombin activator systems in Australian rough-scaled snake, Tropidechis carinatus. Structural comparison of venom prothrombin activator with blood coagulation factor X. Thrombosis and Haemostasis 93, 40-47.
Mohanty B, Krishnan SP, Swarup S, and Bajic VB (2005). Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species. Annals of Botany 96, 669-681.
Minh Le TN, Reza MA, Swarup S, and Kini RM (2005). Gene duplication of coagulation factor V and origin of venom prothrombin activator in Pseudonaja textilis snake. Thrombosis and Haemostasis 93, 420-429.
Bhalla R, Narasimhan K, and Swarup S (2005). Metabolomics and its role in understanding cellular responses in plants. Plant Cell Reports 24, 562-571.
Bajic VB, Veronika M, Veladandi PS, Meka A, Heng MW, Rajaraman K, Pan H, and Swarup S (2005). Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists. Plant Physiology 138, 1914-1925.
Adaikkalam V and Swarup S (2005). Characterization of copABCD operon from a copper-sensitive Pseudomonas putida strain. Canadian Journal of Microbiology 51, 209-216.
Tamilselvi D, Anand G, and Swarup S (2004). A geminivirus AYVV-derived shuttle vector for tobacco BY2 cells. Plant Cell Reports 23, 81-90.
Syn CK, Magnuson JK, Kingsley MT, and Swarup S (2004). Characterization of Pseudomonas putida genes responsive to nutrient limitation. Microbiology 150, 1661-1669.
Rao VS, Swarup S, and Manjunatha Kini R (2004). The catalytic subunit of pseutarin C, a group C prothrombin activator from the venom of Pseudonaja textilis, is structurally similar to mammalian blood coagulation factor Xa. Thrombosis and Haemostasis 92, 509-521.
Choy WK, Zhou L, Syn CK, Zhang LH, and Swarup S (2004). MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species. Journal of Bacteriology 186, 7221-7228.
Rao VS, Swarup S, and Kini RM (2003). The nonenzymatic subunit of pseutarin C, a prothrombin activator from eastern brown snake (Pseudonaja textilis) venom, shows structural similarity to mammalian coagulation factor V. Blood 102, 1347-1354.
Narasimhan K, Basheer C, Bajic VB, and Swarup S (2003). Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiology 132, 146-153.
Pillai BV and Swarup S (2002). Elucidation of the flavonoid catabolism pathway in Pseudomonas putida PML2 by comparative metabolic profiling. Applied and Environmental Microbiology 68, 143-151.
Adaikkalam V and Swarup S (2002). Molecular characterization of an operon, cueAR, encoding a putative P1-type ATPase and a MerR-type regulatory protein involved in copper homeostasis in Pseudomonas putida. Microbiology 148, 2857-2867.
Teo WL, Kumar P, Goh CJ, and Swarup S (2001). The expression of Brostm, a KNOTTED1-like gene, marks the cell type and timing of in vitro shoot induction in Brassica oleracea. Plant Molecular Biology 46, 567-580.
Cheng P-K, Lakshmanan P, Swarup S (2001). High-frequency direct shoot regeneration and continuous production of rapid-cycling Brassica oleracea in vitro. Vitro Cell Developmental Biology, Plant 37, 592-598.
Low R, Prakash A, Swarup S, Goh C-J, Kumar P (2001). A differentially expressed bZIP gene is associated with adventitious shoot regeneration in leaf cultures of Paulownia kawakamii. Plant Cell Reports, 20,696-700.
Low RK, Prakash AP, Swarup S, Goh CJ, and Kumar PP (2001). Lambda exonuclease-based subtractive hybridization approach to isolate differentially expressed genes from leaf cultures of Paulownia kawakamii. Analytical Biochemistry 295, 240-247.
Syn CK and Swarup S (2000). A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Analytical Biochemistry 278, 86-90.
Syn CK, Teo WL, and Swarup S (1999). Three-detergent method for the extraction of RNA from several bacteria. BioTechniques 27, 1140-1141.
Rai A, Umashankar S, and Swarup S (2013). Plant Metabolomics: From Experimental Design to Knowledge Extraction. Legume Genomics, Methods in Molecular Biology, ed Rose RJ (Humana Press), 279-312.
Lee YJ, Narasimhan K, and Swarup S (2013). Enhancement of Plant–Microbe Interactions using Rhizosphere Metabolomics-Driven Approach and its Application in the Removal of Polychlorinated Biphenyls. Molecular Microbial Ecology of the Rhizosphere, (John Wiley and Sons, Inc.), 1191-1198.
Yung P Y, and Swarup S (2012). Combining modern life sciences toolbox to tackle current bottlenecks for algal biofuels. Under "Features" section in Asia-Pacific Biotech News, 16-24.
Mynampati KC, Reuben S, and Swarup S (2011). Rhizosphere Metabolomics. Sustainable Agriculture and New Biotechnologies, Advances in Agroecology, (CRC Press), 173-186.
Reuben S, Bhinu VS, and Swarup S (2008) Rhizosphere Metabolomics: Methods and Applications. Secondary Metabolites in Soil Ecology, Soil Biology, ed Karlovsky P (Springer Berlin Heidelberg), 37-68.
Bhinu VS, Kothandarman N and Swarup S (2006). Plant Natural Products in the Rhizosphere. Natural Products from Plants, Second Edition, (CRC Press), 143-164.
Reuben S, Bhinu VS, Leland JC, Masilamani J, Kothandarman N, and Swarup S (2006). Molecular Biology of Plant Natural Products. Natural Products from Plants, Second Edition, (CRC Press), 165-202.
Swarup, S and B L Ong (2004). Enhanced Food Production and Security of Asian Leafy Vegetables. In Food Security and Vegetables- A Global Perspective, ed. P Nath, P G Gaddagimath and O P Datta Publishers. Bangalore: PNASF, 2004.
Pan H, Zuo L, Kanagasabai R, Zhang Z, Choudhary V, Mohanty B, Tan SL, Krishnan SPT, Veladandi PS, Meka A, Choy WK, Swarup S , and Bajic VB (2004). Extracting information for meaningful function inference through text-mining. In: Discovering Biomolecular Mechanisms with Computational Biology. Ed. Frank Eisenhaber. Landes Bioscience Publishers. Texas, U.S.A.
MetDAT: We have developed an interactive user-friendly online software called Metabolite Data Analysis Tool (MetDAT) for mass spectrometry data. It offers a pipeline of tools for file handling, data pre-processing, univariate and multivariate statistical analyses, database searching and pathway mapping. MetDAT allows users to combine data management and experiment-centric workflows for optimization of metabolomics methods and metabolite analysis. http://smbl.nus.edu.sg/METDAT2/
datPAV: Data processing, analysis and visualization (datPAV) is an exploratory tool that allows experimentalists to quickly assess the general characteristics of the data. This platform-independent software is designed as a generic tool to process and visualize data matrices. This tool explores organization of the data, detect errors and supports basic statistical analyses. http://smbl.nus.edu.sg/DATPAV/