| 101 |
IPD3790 |
SWATH-LC MS-based quantitative secretomics reveals trigger factor as a novel drug |
Manish Kumar |
In the present study, we have analysed the secretory proteins of multidrug resistant
(MDR) and -sensitive strains of E. coli isolated from a prominent urban river (Yamuna)
which traverses through the National Capital Region of India. Both the strains
investigated in this study were phylogroup D strains and of the same genomic clade...
In the present study, we have analysed the secretory proteins of multidrug resistant
(MDR) and -sensitive strains of E. coli isolated from a prominent urban river (Yamuna)
which traverses through the National Capital Region of India. Both the strains
investigated in this study were phylogroup D strains and of the same genomic clade as
revealed by REP-, ERIC- and BOX-PCR based genotypic fingerprinting.
Comparative secretomic analysis of multidrug-resistant and -sensitive strains was performed
and the biological functions and metabolic pathways of the differentially expressed
secreted proteins were elucidated. Subsequently, Protein-protein interaction (PPI) networks of the differentially expressed secretory proteins were determined followed by identification of hub proteins. The similarity of the hub proteins with the human proteins was determined and those exhibiting non-homology with human proteins were explored as potential drug targets against MDR E. coli.
Our results revealed 675 differentially expressed proteins of which 54 proteins were overexpressed and 235 proteins were underexpressed . The differentially expressed secreted proteins were primarily involved in metabolic pathways, biosynthesis of amino acids/proteins and secondary metabolites and stress response. The PPI networks of the overexpressed proteins revealed a hub protein — trigger factor (tig) which was non-homologous to the human proteins. Tig is a cold stress molecular chaperones protein which regulates several biological pathways directly/indirectly related to antibiotic stress.
To combat antimicrobial resistance, new drugs which bind to novel biological
pathways/components of the pathogens are urgently needed. Microbial secreted proteins
(secretome) are important for pathogenesis and adaptation/survival in various environmental
stresses, including antibiotics. Thus, they can be explored as novel drug targets. Thus, the protein identified in our study can be explored as a novel drug target against E. coli, inhibitors of which might not cross-react with human proteins.To the best of our knowledge, this is the first study comparing the secretomes of MDR and -sensitive strains of E. coli isolated from a waterbody.
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University of Delhi, New Delhi, Delhi, India |
Bottom-up |
2025-04-23 |
|
| 102 |
IPD1450 |
Total proteome analysis of engineered/adapted E.coli strains with glucose/xylose co-utilization ability |
Dr Syed Shams Yazdani |
This project was about developing a bacterial strain that could consume a mixture of glucose and xylose simultaneously with higher ethanol productivity. In this study, an ethanologenic strain (SSK42) was made deficient in Carbon Catabolite Repression (CCR) by deleting the ptsG gene encoding EIIBCGlc component of PTS transport system. This...
This project was about developing a bacterial strain that could consume a mixture of glucose and xylose simultaneously with higher ethanol productivity. In this study, an ethanologenic strain (SSK42) was made deficient in Carbon Catabolite Repression (CCR) by deleting the ptsG gene encoding EIIBCGlc component of PTS transport system. This strain (SCD00) was then evolved for several generations on xylose containing minimal media. A strain (SCD78) was finally obtained that, unlike its parent strain could consume glucose and xylose simultaneously. Then we performed proteomics analysis of evolved and un-evolved strain. The strain SSK42 was also considered for proteome analysis as a reference for analysis. The starting strain – SSK42, is the derivative of E.coli B.
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Group Leader, Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi, India |
Shotgun proteomics |
2025-05-11 |
35933385
|
| 103 |
IPD1913 |
Proteomics and metabolic burden analysis to understand the impact of recombinant protein production on host cells |
Dr Syed Shams Yazdani |
Recombinant protein production (RPP) using Escherichia coli as an expression host is highly efficient, however, it also in¬ leads to strong host cell metabolic burden. Energy and biomass precursors are withdrawn from the host’s metabolism as they are required for plasmid replication, heterologous gene expression and protein production. In this...
Recombinant protein production (RPP) using Escherichia coli as an expression host is highly efficient, however, it also in¬ leads to strong host cell metabolic burden. Energy and biomass precursors are withdrawn from the host’s metabolism as they are required for plasmid replication, heterologous gene expression and protein production. In this study, we aim to investigate the effect of early and growth phase induction point on RPP. We have analysed and compared the proteomics data for growth-and protein production-phase to understand the cellular dynamics and recombinant protein-dependent product formation in process with respect to the two different hosts (M15 and DH5âº) and medium (minimal and complex) cultures. Differential gene analysis shows that significant changes in carbohydrate metabolism, transport metabolism, nucleotide metabolism, amino acid metabolism and energy metabolism. Comprehension of the obtain results suggest that growth inhibition does not showing effect on recombinant protein and product yield but there is an changes in intracellular nucleobases, translation, transcription and cellular metabolism which leads to the degradation and instability during product formation. Overall, deeper knowledge of the cellular behaviour during recombinant protein production can be used to better exploit omics data with the goal of rational strain development.
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Group Leader, Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi, India |
Top-down |
2025-05-11 |
|
| 104 |
IPD2854 |
Intelligent versus Blind response”- Unveiling a Hypercellulolytic Fungus Strategy for Efficient Polymeric Carbon Deconstruction via Multiplexed Quantitative Proteomics |
Dr Syed Shams Yazdani |
Fungi are ubiquitous and are often confronted with the need to secure utilisable carbon from their external growth milieu through the use of extracellular proteins to scavenge for carbon from a vast array of complex polymeric carbon sources. This attribute is conserved across evolution in fungi. To understand how filamentous...
Fungi are ubiquitous and are often confronted with the need to secure utilisable carbon from their external growth milieu through the use of extracellular proteins to scavenge for carbon from a vast array of complex polymeric carbon sources. This attribute is conserved across evolution in fungi. To understand how filamentous fungi extracellular proteins are modulated in response to the presence polymeric carbons in the environment, we have typed the array of the main extracellular proteins involved and their dynamics using a known hypercellulolytic fungus – Penicillium funiculosum (NCIM 1228), through multiplexed quantitative proteomics
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Group Leader, Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi, India |
Shotgun proteomics |
2025-05-11 |
29597011
|
| 105 |
IPD3843 |
Comparative proteomic analysis of secretomes from engineered Penicillium funiculosum modulated with sugarcane bagasse |
Dr Syed Shams Yazdani |
Sugarcane bagasse (SCB), one of the most abundant plant feedstocks is at the leading front of the biofuel industry based on the potential to promote economic, social and environmental development worldwide through sustainable set-ups related to energy production. This complex biomass requires a vast array of carbohydrate active enzymes (CAZymes)...
Sugarcane bagasse (SCB), one of the most abundant plant feedstocks is at the leading front of the biofuel industry based on the potential to promote economic, social and environmental development worldwide through sustainable set-ups related to energy production. This complex biomass requires a vast array of carbohydrate active enzymes (CAZymes) mostly from filamentous fungi for its deconstruction to monomeric sugars for the production of value-added fuels and chemicals. In this study, we attempted to evaluate the comprehensive repertoire of proteins in the secretome of an engineered Penicillium funiculosum, (PfMig188) in response to SCB. For this, a systematic approach was utilized for the cultivation of the fungus towards production of tailored enzymes specific for saccharification of SCB. This was done through the modulation of the production media with different concentrations of pretreated SCB (0 – 45 g/L) and the array of secreted proteins were identified by enzyme activity assay and liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 280 proteins were detected in the secretome of PfMig188 with 46% of them being CAZymes. Modulation of the cultivation media with SCB up till 15 g/L enhanced the secretion of some importanthemicellulasesand cell wall modifying enzymes such as β-xylosidase (GH5, GH43), β-1,3-galactosidase (GH43), endo-1,3(4)-beta-glucanase (GH16), cutinase (CE5) and hydrophobic surface binding protein (HsbA)that works in synergy with the cellulases in the secretome to improve SCB saccharification by 20%. Our findings provide more insight on the enzyme system of PfMig188 for degradation of complex biomass such as SCB and highlights the important role of adjusting the culture medium composition with SCB for secretion of enzymes specific for its saccharification.
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Group Leader, Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi, India |
Top-down |
2025-05-11 |
34446097
|
| 106 |
IPD2008 |
Contryphan sequence diversity:Conus inscriptus |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 107 |
IPD2840 |
Analysis of venom peptide from Conus betulinus |
Prof. P. Balaram |
Characterization of venom peptides from Conus betulinus using mass spectrometry
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Shotgun proteomics |
2025-05-25 |
38009400
|
| 108 |
IPD3563 |
Contryphan sequence diversity:Conus virgo |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 109 |
IPD3969 |
Contryphan sequence diversity:Conus lividus |
Prof. P. Balaram |
Mass Spectrometric Characterisation of contryphans.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Top-down |
2025-05-25 |
36587728
|
| 110 |
IPD4773 |
Analysis of C.monile venom peptides. |
Prof. P. Balaram |
Mass Spectrometric Characterisation of conophysin/ conopressin.
|
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India |
Gel-based experiment |
2025-05-25 |
32058072
|
