The Wangikar Lab

The Wangikar laboratory provides an effective research interface between the fields of engineering and biology. Our dedicated group of researchers are focused on the development of quantitative and model driven biotechnology. Our areas of research expertise include but are not limited to (i) Investigations into cellular metabolic pathways through 13C Metabolic Flux Analysis (ii) Bioprocess development for therapeutic proteins and enzymes (iii) Enzyme engineering for chiral synthesis and (iv) Metabolic engineering of cyanobacteria. The laboratory is equipped with state-of-the-art facilities like LC-MS/MS, Photo-bioreactors, Incubator shakers (with light and CO2 control), Computer controlled fermentators, Multimode readers and many more. The lab is currently funded by DBT (Government of India), Praj Industries Ltd., the Wadhwani Foundation, Reliance India Ltd., and the Indo-US Science and Technology Forum (IUSSTF). With its thriving group of PhD students, postdocs and project staff, the Wangikar lab provides a productive research environment with opportunities for significant collaborations with both academia and industry.

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LAB HIGHLIGHTS

New research from the Wangikar lab

Jaiswal, D., Prasannan, C. B., Hendry, J. I., & Wangikar, P. P. (2018). SWATH Tandem Mass Spectrometry Workflow for Quantification of Mass Isotopologue Distribution of Intracellular Metabolites and Fragments Labeled with Isotopic 13C Carbon. Analytical chemistry, 90(11), 6486-6493

Accurate quantification of mass isotopologue distribution (MID) of metabolites is a prerequisite for 13C-metabolic flux analysis. Currently used mass spectrometric (MS) techniques based on multiple reaction monitoring (MRM) place limitations on the number of MIDs that can be analyzed in a single run. Moreover, the deconvolution step results in amplification of error. Here, we demonstrate that SWATH MS/MS, a data independent acquisition (DIA) technique allows quantification of a large number of precursor and product MIDs in a single run. SWATH sequentially fragments all precursor ions in stacked mass isolation windows. Co-fragmentation of all precursor isotopologues in a single SWATH window yields higher sensitivity enabling quantification of MIDs of fragments with low abundance and lower systematic and random errors. We quantify the MIDs of 53 precursor and product ions corresponding to 19 intracellular metabolites from a dynamic 13C-labeling of a model cyanobacterium, Synechococcus sp. PCC 7002. The use of product MIDs resulted in an improved precision of many measured fluxes compared to when only precursor MIDs were used for flux analysis. The approach is truly untargeted and allows additional metabolites to be quantified from the same data.

Shah, S., Agera, R., Sharma, P., Sunder, A. V., Bajwa, H., James, H. M., ... & Wangikar, P. P. (2018). Development of biotransformation process for asymmetric reduction with novel anti-Prelog NADH-dependent alcohol dehydrogenases. Process Biochemistry.

Alcohol dehydrogenases or carbonyl reductases have been extensively developed for the asymmetric reduction of ketones to chiral alcohols, which are important pharmaceutical precursors. Ideal biotransformation using alcohol dehydrogenases requires (i) the identification of novel enzymes with broad substrate range, high substrate tolerance, enantioselectivity and preference for cheaper cofactor (NADH) and (ii) the development of an optimized biocatalytic process with a mechanism for efficient cofactor recycling. This report details the mining and identification of a subfamily of novel NADH-dependent alcohol dehydrogenases with anti-Prelog stereo selectivity, that exhibit high specific activity on β-ketoesters. Further, an efficient biocatalytic process has been developed using ADH from Acetobacter aceti mined in this study for the enantioselective reduction of up to 10 M ethyl 4-chloro-3-oxobutanoate to (S)-Ethyl-4-chloro-3-hydroxybutanoate (CHBE). The process employed lyophilized cell-free extract and reduction was achieved with > 99% yield and high enantiomeric excess (> 99% ee) in 24 h using a biphasic reaction system. A space-time yield of approximately 650 g/L. d and cofactor TTN of 106 has been achieved using the process, with potential application in industrial biocatalysis.

Sengupta, A., Pakrasi, H. B., & Wangikar, P. P. (2018). Recent advances in synthetic biology of cyanobacteria. Applied microbiology and biotechnology, 1-15.

Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO2. Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO2, diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this “green” chassis.

Recent Conference Attended:
Researchers from the Wangikar lab recently presented their work at the International conference ( https://www.aiche.org/sbe/conferences/metabolic-engineering-conference/2018) held in Munich, Germany from June 24-28, 2018

Recent graduation:
Prachi Varshney graduated with a PhD recently for her thesis on ‘CO2 CAPTURE WITH EXTREMOPHILIC MICROALGAE-ISOLATION AND CHARACTERIZATION OF NOVEL STRAINS’

more than 90
JOURNAL ARTICLES
4 Current Grants
1.5 MILLION USD
More than 15
RESEARCH MEMBERS

areas of research expertise

Metabolic Engineering of Cyanobacteria
Cyanobacteria are an emerging platform for biotechnological applications due to their efficient photoautotrophic growth and amenability to genetic engineering.
Cyanobacteria are an emerging platform for biotechnological applications due to their efficient photoautotrophic growth and amenability to genetic engineering. In a future biorefinery, engineered cyanobacteria could be deployed for the production of biofuels and platform chemicals by harnessing solar energy and using CO 2 as feedstock. Engineering metabolic pathways in cyanobacteria will facilitate their use as potential ‘cell factories’ for the mass-production of a host of high value chemicals with a minimal investment of resources. By making modifications to existing pathways and introducing novel ones, the metabolic engineers and synthetic biologists in the Wangikar laboratory are striving towards higher titers of desired products through allocation of larger amounts of the fixed carbon towards the target pathways.
Enzyme Engineering
Altering the properties of existing enzymes to create their new and improved versions, is an exciting dimension of enzyme technology today.
Altering the properties of existing enzymes to create their new and improved versions, is an exciting dimension of enzyme technology today. Using various protein engineering approaches, factors like the yield and kinetics of the enzyme, the ease of downstream processing and various safety aspects can be vastly improved upon. Useful enzymes from undesirable or slow growing organisms could be cloned and produced in large quantities in other high-efficiency expression systems. This would prove to be a highly profitable resource for industrial applications such as the manufacturing of bulk chemicals and pharmaceuticals. In the Wangikar laboratory, scientists are mining enzyme sequences and through rational design trying to modify existing ones to produce ‘custom-made’ enzymes tailored for use in important industrial processes.
Bioprocess development
Bioprocessing is an essential part of many food, chemical, and pharmaceutical industries. Bioprocesses have been traditionally developed for a varied range of commercial products.
Bioprocessing is an essential part of many food, chemical, and pharmaceutical industries. Bioprocesses have been traditionally developed for a varied range of commercial products, from relatively cheap materials such as industrial alcohol and organic solvents, to expensive specialty chemicals such as antibiotics, therapeutic proteins, and vaccines. In the Wangikar laboratory, bioprocessing focuses on the use of enzymes in bacterial cell lysates to carry out commercially important bioconversions. Every aspect of this technology from process development, strain improvement to lab-scale production is fine-tuned towards maximizing yield of the target. Once tested on a smaller scale, the eventual goal of the successful development of a process is further scale-up and commercialization.
13C Metabolic Flux Analysis
In order to manipulate organisms to carry out fermentative and other processes towards production of important chemicals you need to understand metabolic fluxes of these organisms.
In order to manipulate organisms to carry out fermentative and other processes towards production of important chemicals you need to understand metabolic fluxes of these organisms so as to redirect or enhance fluxes towards products of interest. Currently the productivity of target chemicals is fairly low in cyanobacteria for instance, and the understanding of metabolic fluxes in these photosynthetic organisms especially those that have been metabolically engineered, will greatly help in improving the chances of using them as ‘cell factories’. With this and other interests in mind, researchers in the Wangikar laboratory are developing detailed protocols to study metabolomics through the lens of 13 C Metabolic Flux Analysis ( 13 C MFA). A defined 13 C-labeled substrate is incorporated into the carbon backbone of a wide range of metabolites of the metabolome, either through exchange or by synthesis. The distribution of labeled carbon traversing along metabolic pathways generates a characteristic imprint of labeling patterns whose mass signature is then observed by mass spectrometry (MS). The Wangikar lab has developed a sophisticated workflow for isotopic non-stationary 13 C-MFA of cyanobacteria and is striving to provide reliable flux maps for a number of strains of interest. This will provide the scientific community with an in-depth insight into the metabolomics of many cyanobacterial and algal strains.

ABOUT PRAMOD WANGIKAR

Pramod P Wangikar

Prof. Pramod P. Wangikar is a faculty of the Department of Chemical Engineering in the Institute of Technology- Bombay (IIT-B). Prof. Wangikar obtained his Bachelor of Chemical Engineering from the Institute of Chemical Technology (ICT), Mumbai and then earned his Ph.D. from the University of Iowa,

  1. 1991

    Bachelor of Chemical Engineering

    Institute of Chemical Technology (ICT), Mumbai
  2. 1995

    Ph. D on Tailoring Enzyme Function in Organic Media

    University of Iowa
  3. 1996

    Assistant Professor

    Indian Institute of Technology (IIT)-Kanpur
  4. 1997

    Assistant Professor

    Indian Institute of Technology (IIT)-Bombay
  5. 2003

    Associate Professor

    IIT Bombay
  6. 2009

    Professor

    IIT Bombay
  7. 2014

    Professor-in-Charge

    Wadhwani Research Center for Bioengineering (WRCB)
  8. 2014

    Centre Coordinator

    DBT-Pan IIT Center for Bioenergy

ABOUT THE LABORATORY

State of the art facilities
The Wangikar lab is equipped with modern and sophisticated machinery to support most of its current research endeavors. Students and project staff are well-trained to use, collect and interpret data with frequent refresher courses, thereby facilitating the execution of their research goals. In-house availability of necessary equipment has saved Wangikar lab members valuable time and effort in collecting data, leading to quicker and high quality publications. Many of these facilities are accessible to others for a fee (see FACILITIES)
Dedicated group of researchers
With a large group of PhD Scholars, Postdoctoral Researchers, and Research Staff supporting ongoing projects, the Wangikar research team is strong in numbers and scientific talent. Most PhD scholars graduating from this lab have gone on to secure promising postdoctoral research positions in both academia and industry. Members of the lab have created a very conducive environment to achieve the best in all scientific endeavors through cooperation, collaboration and active scientific discourse.
Well funded laboratory
Financially viable with grants form both national and international agencies. The Wangikar lab is currently supported by large grants from the Department of Biotechnology (DBT), Government of India and the Indo US Science and Technology Forum (IUSSTF) to carry out innovative research in the field of bioenergy. The Wangikar lab also collaborates with leading Indian Industries such as Reliance India Limited (RIL) and Praj Industries to name a few, and has multiple active industry collaborations going on at any given time.
At the cutting edge of science and technology
The Wangikar research team always endeavors to tackle the most important and pertinent problems facing the scientific community in their fields of interest. They are constantly taking on and overcoming challenges associated with such ambitious research aims. As evident from the publication record, research scholars from the lab have steadily and successfully produced high impact scientific and technological advances through the years and continue to do so under the able leadership of their mentor, Prof. Wangikar.