Dr. Amanjot Singh

Dr. Amanjot Singh

IBAB Faculty Fellow
Joined IBAB in 2023.

Research Focus Key Words

Chaperones, Ubiquitin Proteasome System, Stress Granules, Protein Misfolding, Aging, Neurodegeneration

Background

Aman received his Ph.D from the University of Delhi South Campus working with Prof. Anil Grover. He worked on the transcriptional and translational regulation of Hsp100/ClpB-cyt gene in rice. For work done during his Ph.D, he was awarded the prestigious Young Scientist Medal by the Indian National Science Academy (INSA). He joined Dr. Vincent Mauro’s lab at The Scripps Research Institute, La Jolla where his research focused on the identification of cellular factors involved in the recognition of non-AUG start codons and translation re-initiation. Later he moved to the University of California San Diego (UCSD), where he worked with Prof. Randolph Hampton and showed how Ubr1, a venerated ubiquitin E3 ligase involved in the N-end rule pathway, also played an important role in cytoplasmic protein quality control where it interacted with both chaperones and the ubiquitin proteasome system to degrade misfolded cytoplasmic proteins. This work proposed a “Folding Escape Model” in which chaperones aid in the folding of proteins while an E3 ligase ubiquitinates these proteins and there is a “kinetic-race” between the two pathways; if a protein needs less time for folding, it escapes degradation and if a protein needs more time for folding, as in the case of terminally misfolded proteins, it gets degraded. Subsequently, as an INSA Young Scientist, he joined National Centre for Biological Sciences (NCBS), Bengaluru to work in collaboration with Prof. Mani Ramaswami (Trinity College, Dublin) and Prof. K VijayRaghavan (NCBS, Bengaluru). At NCBS, Aman used TRIBE (Targets of RNA binding proteins Identified By Editing) technology and showed that Ataxin2, a ubiquitous eukaryotic RNA binding protein, binds at AU-rich regions in 3’UTRs of the mRNAs. His work also showed that Ataxin2 interacted with mRNAs in granules and different domains of Ataxin2 were involved in regulating granule dynamics and hence, its interaction with mRNAs. Using comparative transcriptomics, his work also showed that specific mRNAs involved in protein quality control are differentially regulated during oxidative stress and subsequent recovery.

Education:

UG: B.Sc. (Agriculture), College of Agriculture, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, India
PG: M.Sc. (Biotechnology), Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
Ph.D.: University of Delhi, New Delhi, India

Professional experience:

  • Faculty Fellow, Institute of Bioinformatics and Applied Biotechnology
  • INSA Young Scientist, National Centre for Biological Sciences, Bengaluru, India
  • Post-doctoral employee at University of California San Diego, La Jolla, USA
  • Research Associate at The Scripps Research Institute, La Jolla, USA

Research Interest

Protein quality control (PQC) system, which include chaperones and components of proteasome, ubiquitin, autophagy and lysosomal systems play important roles in almost all aspects of biology.  Recent research has revealed new roles for PQC in dynamics of biological condensates which are rapidly reversible assemblies formed via quinary interactions (which are both transient and multivalent) among the component RNAs and proteins. Such condensates sequester proteins involved in specific biological pathways or serve as an environment for the management of misfolded proteins. High concentration of misfolded and disordered proteins in condensates makes them prone to support formation of pathogenic protein aggregates of an irreversible nature.

Our recent analyses of oxidative-stress transcriptome and Ataxin2-associated proteome have helped identify a class of PQC components associated with stress granules. Stress granules are transient and dynamic membrane-less cytoplasmic entities which are assembled in response to several types of stresses (including viral infections) and unexpectedly are related to pathological aggregates formed in several neurodegenerative diseases. Our studies further identify unexpected classes of proteins including metabolic enzymes associated with SGs. These findings are significant for three reasons:  first, because why and how stress controls metabolism is poorly understood; second, neurodegenerative diseases, which have been causally connected to defects in condensate biology, are associated with altered metabolic defects; third, potential important molecular effects of metabolic alterations remain unexplored. Future work in the lab will involve elucidating how the PQC might be required for the dynamics of SGs. We would also like to test the molecular basis of such sequestration of metabolic enzymes in SGs or pathological aggregates and how this rewires cellular homeostasis during stress, aging and neurodegeneration.

We are looking for people with an aptitude for research and those who wish to work in the field of dynamics of stress granules, their role in aging and neurodegenerative diseases.

Publications (last 5 years)

  • Singh A*, Kandi AR#, Jayaprakashappa D#, Thuery G, Purohit DJ, Huelsmeier J, Singh R, Pothapragada SS, Ramaswami M* and Bakthavachalu B* (2022) The transcriptional response to oxidative stress is independent of stress granule formation. Molecular Biology of the Cell33:ar25, 1-16.  (*Co-corresponding authors, # equal contribution)
  • Singh A*, Huelsmeier J*, Kandi AR, Pothapragada SS, Hillebrand J, Petrauskas A, Agarwal K, Krishnan RT, Thiagarajan D, Jayaprakashappa D, VijayRaghavan K, Ramaswami M and Bakthavachalu B (2021) Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation. eLife 10:e60326 (*Equal contribution)
  • Singh A*, Vashistha N, Heck J, Tang X, Wipf P, Brodsky J, Hampton RY* (2020) Direct involvement of HSP70 ATP hydrolysis in Ubr1-dependent quality control. Molecular Biology of the Cell 31 (24) 2669-2686 (* Corresponding authors) “A Highlights from MBoC Selection”
  • Bakthavachalu B, Huelsmeier J, Sudhakaran I, Hillebrand J, Singh A, Petrauskas A, Thiagarajan D, Sankaranarayanan M, MizoeL, Anderson E, Pandey UB, Ross E, VijayRaghavan K, Parker R and Ramaswami M (2018)RNP-granule assembly via Ataxin-2 disordered domains is required for long-term memory and neurodegeneration. Neuron98: 754-766.
  • Vashistha N, Neal S, Singh A, Caroll S and Hampton RY (2016) Direct and essential function for Hrd3 in ER-associated degradation. Proceedings of the National Academy of Sciences USA 113: 5934-5939.

For the full list of publications, visit https://scholar.google.com/citations?hl=en&user=u9UXulYAAAAJ

Collaborators

  • Prof. Mani Ramaswami, Trinity College Dublin, Ireland
  • Prof. Roy Parker, HHMI-University of Colorado Boulder
  • Dr. Chandan Sahi, IISER Bhopal
  • Dr. Shyam Masakapalli, IIT Mandi
  • Dr. Baskar Bakthavachalu, IIT Mandi
  • Dr. Dimple Notani, NCBS Bengaluru

Address

Institute of Bioinformatics and Applied Biotechnology
Biotech Park, Electronic City Phase I,
Bengaluru 560100,
India

Phone

080 285 289 00/01/02, extension 124

Email

amanjsingh@ibab.ac.in