Microbiology, Biochemistry, Genetics and Molecular Biology, Biotechnology, Agricultural and Biological Sciences
46
Scopus Publications
767
Scholar Citations
12
Scholar h-index
14
Scholar i10-index
Scopus Publications
Tuning the F695 fluorescent state in photosystem II using site-directed mutagenesis in Synechocystis sp. PCC 6803 Amala Phadkule, Amit Srivastava, Alexandria Alailima Martin, Lauren G. Dome, Steven D. McKenzie, Sujith Puthiyaveetil, Mike Reppert Photosynthesis Research, 2026 In photosynthetic proteins, pigments at a higher energy level funnel excitation energy to pigments at a lower energy level. Specifically, in Photosystem II (PSII), energy is transferred downhill to the reaction center (RC), where water splitting occurs. However, the lowest-energy state in PSII is not the RC, but the F695 state, which can be observed using low-temperature spectroscopy. This lowest-energy state is typically assigned to a monomeric pigment, Chl B16 (ligated by His114), but this assignment has been called into question based on theoretical fits to low-temperature spectra. In this study, we set out to test concretely whether the F695 state is localized on Chl B16 using site-directed mutagenesis and 77 K fluorescence spectroscopy. To reduce spectral congestion for whole-cell PSII studies, we developed a background strain (PSI-kd/ $$\Delta$$ PBS) that combines a Photosystem I (PSI) knockdown with a Phycobilisome (PBS) knockout. In this background strain, we made site-directed mutations at site Thr5 in the PsbH subunit, which forms a hydrogen bond with the $$13^{1}$$ -keto group of Chl B16. All mutants were capable of heterotrophic growth (without noticeable differences from wild-type), indicating the PSII function remains intact. As expected for Chl B16-localized fluorescence, the Thr5 $$\rightarrow$$ Arg mutation red-shifted the F695 state due to the strengthening of the hydrogen bond, while the Thr5 $$\rightarrow$$ Ala mutation exhibits a blue shift as the hydrogen bond is eliminated. Taken together, these findings provide strong confirmation that Chl B16 is responsible for the lowest-energy state.
Controlling Vibronic Coupling in Chlorophyll Proteins: The Effects of Excitonic Delocalization and Vibrational Localization Galina Grechishnikova, Jacob H. Wat, Nicolas de Cordoba, Ethan Miyake, Amala Phadkule, Amit Srivastava, Sergei Savikhin, Lyudmila Slipchenko, Libai Huang, Mike Reppert Journal of Physical Chemistry Letters, 2024 Vibrational-electronic (vibronic) coupling plays a critical role in excitation energy transfer in molecular aggregates and pigment-protein complexes (PPCs). But the interplay between excitonic delocalization and vibronic interactions is complex, often leaving even qualitative questions as to what conceptual framework (e.g., Redfield versus Förster theory) should be used to interpret experimental results. To shed light on this issue, we report here on the interplay between excitonic delocalization and vibronic coupling in site-directed mutants of the water-soluble chlorophyll protein (WSCP), as reflected in 77 K fluorescence spectra. Experimentally, we find that in PPCs where excitonic delocalization is disrupted (either by mutagenesis or heterodimer formation), the relative intensity of the vibrational sideband (VSB) in fluorescence spectra is suppressed by up to 37% compared to that of the native protein. Numerical simulations reveal that this effect results from the localization of high-frequency vibrations in the coupled system; while excitonic delocalization suppresses the purely electronic transition due to H-aggregate-like dipole-dipole interference, high-frequency vibrations are unaffected, leading to a relative enhancement of the VSB. By comparing VSB intensities of PPCs both in the presence and absence of excitonic delocalization, we extract a set of "local" Huang-Rhys (HR) factors for Chl a in WSCP. More generally, our results suggest a significant role for geometric effects in controlling energy-transfer rates (which depend sensitively on absorption/fluorescence line shapes) in molecular aggregates and PPCs.
Engineered bacteriophages: A panacea against pathogenic and drug resistant bacteria Anuja Kakkar, Garima Kandwal, Tanmayee Nayak, Lav Kumar Jaiswal, Amit Srivastava, Ankush Gupta Heliyon, 2024 Antimicrobial resistance (AMR) is a major global concern; antibiotics and other regular treatment methods have failed to overcome the increasing number of infectious diseases. Bacteriophages (phages) are viruses that specifically target/kill bacterial hosts without affecting other human microbiome. Phage therapy provides optimism in the current global healthcare scenario with a long history of its applications in humans that has now reached various clinical trials. Phages in clinical trials have specific requirements of being exclusively lytic, free from toxic genes with an enhanced host range that adds an advantage to this requisite. This review explains in detail the various phage engineering methods and their potential applications in therapy. To make phages more efficient, engineering has been attempted using techniques like conventional homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), clustered regularly interspaced short palindromic repeats (CRISPR)-Cas, CRISPY-BRED/Bacteriophage Recombineering with Infectious Particles (BRIP), chemically accelerated viral evolution (CAVE), and phage genome rebooting. Phages are administered in cocktail form in combination with antibiotics, vaccines, and purified proteins, such as endolysins. Thus, phage therapy is proving to be a better alternative for treating life-threatening infections, with more specificity and fewer detrimental consequences.
A thylakoid biogenesis BtpA protein is required for the initial step of tetrapyrrole biosynthesis in cyanobacteria Petra Skotnicová, Amit Srivastava, Divya Aggarwal, Jana Talbot, Iva Karlínová, Martin Moos, Jan Mareš, Lenka Bučinská, Peter Koník, Petr Šimek, Martin Tichý, Roman Sobotka New Phytologist, 2024 Summary Biogenesis of the photosynthetic apparatus requires complicated molecular machinery, individual components of which are either poorly characterized or unknown. The BtpA protein has been described as a factor required for the stability of photosystem I (PSI) in cyanobacteria; however, how the BtpA stabilized PSI remains unexplained. To clarify the role of BtpA, we constructed and characterized the btpA‐null mutant (ΔbtpA) in the cyanobacterium Synechocystis sp. PCC 6803. The mutant contained only c. 1% of chlorophyll and nearly no thylakoid membranes. However, this strain, growing only in the presence of glucose, was genetically unstable and readily generated suppressor mutations that restore the photoautotrophy. Two suppressor mutations were mapped into the hemA gene encoding glutamyl‐tRNA reductase (GluTR) – the first enzyme of tetrapyrrole biosynthesis. Indeed, the GluTR was not detectable in the ΔbtpA mutant and the suppressor mutations restored biosynthesis of tetrapyrroles and photoautotrophy by increased GluTR expression or by improved GluTR stability/processivity. We further demonstrated that GluTR associates with a large BtpA oligomer and that BtpA is required for the stability of GluTR. Our results show that the BtpA protein is involved in the biogenesis of photosystems at the level of regulation of tetrapyrrole biosynthesis.
Protein Engineering in Cyanobacterial Biotechnology: Tools and Recent Updates Swati Tyagi, Srabani Kar, Amit Srivastava, Pratyoosh Shukla Current Protein and Peptide Science, 2024 Cyanobacteria have emerged as a microbial cell factory to produce a variety of bioproducts, including peptides and proteins. Cyanobacteria stand out among other organisms due to their photoautotrophic metabolism and ability to produce a wide range of metabolites. As photoautotrophic hosts can produce industrial compounds and proteins by using minimal resources such as sunlight, atmospheric carbon dioxide, and fewer nutrients, cyanobacteria are cost-effective industrial hosts. Therefore, the use of protein engineering tools for rational protein design, and the desired modification of enzyme activity has become a desirable undertaking in cyanobacterial biology. Protein engineering can improve their biological functions as well as the stability of their intracellular proteins. This review aims to highlight the success of protein engineering in the direction of cyanobacterial biotechnology and outlines the emerging technologies, current challenges, and prospects of protein engineering in cyanobacterial biotechnology.
Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications Amit Srivastava, Shobit Thapa, Hillol Chakdar, Piyoosh Kumar Babele, Pratyoosh Shukla Critical Reviews in Biotechnology, 2024 Cyanobacteria safeguard their photosynthetic machinery from oxidative damage caused by adverse environmental factors such as high-intensity light. Together with many photoprotective compounds, they contain myxoxanthophylls, a rare group of glycosidic carotenoids containing a high number of conjugated double bonds. These carotenoids have been shown to: have strong photoprotective effects, contribute to the integrity of the thylakoid membrane, and upregulate in cyanobacteria under a variety of stress conditions. However, their metabolic potential has not been fully utilized in the stress biology of cyanobacteria and the pharmaceutical industry due to a lack of mechanistic understanding and their insufficient biosynthesis. This review summarizes current knowledge on: biological function, genetic regulation, biotechnological production, and pharmaceutical potential of myxoxanthophyll, with a focus on strain engineering and parameter optimization strategies for increasing their cellular content. The summarized knowledge can be utilized in cyanobacterial metabolic engineering to improve the stress tolerance of useful strains and enhance the commercial-scale synthesis of myxoxanthophyll for pharmaceutical uses.
Tuning the F695 fluorescent state in photosystem II using site-directed mutagenesis in Synechocystis sp. PCC 6803 A Phadkule, A Srivastava, AA Martin, LG Dome, SD McKenzie, ... Photosynthesis Research 164 (3), 29 , 2026 2026
Advances in organic acid production using cyanobacteria: strategies and applications R Pathania, A Srivastava Blue Biotechnology 2 (1), 22 , 2025 2025 Citations: 2
Stress genomics of the toxigenic cyanobacteria: environmental and biotechnological perspectives A Srivastava, E Chot, V Gupta, N Singhvi, P Shukla World Journal of Microbiology and Biotechnology 41 (8), 295 , 2025 2025 Citations: 2
Controlling vibronic coupling in chlorophyll proteins: The effects of excitonic delocalization and vibrational localization G Grechishnikova, JH Wat, N de Cordoba, E Miyake, A Phadkule, ... The Journal of Physical Chemistry Letters 15 (37), 9456-9465 , 2024 2024 Citations: 10
Engineered bacteriophages: A panacea against pathogenic and drug resistant bacteria A Kakkar, G Kandwal, T Nayak, LK Jaiswal, A Srivastava, A Gupta Heliyon , 2024 2024 Citations: 26
Protein Engineering in Cyanobacterial Biotechnology: Tools and Recent Updates S Tyagi, S Kar, A Srivastava, P Shukla Current Protein and Peptide Science 25 (2), 95-106 , 2024 2024
Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications A Srivastava, S Thapa, H Chakdar, PK Babele, P Shukla Critical Reviews in Biotechnology 44 (1), 63-77 , 2024 2024 Citations: 9
A thylakoid biogenesis BtpA protein is required for the initial step of tetrapyrrole biosynthesis in cyanobacteria P Skotnicová, A Srivastava, D Aggarwal, J Talbot, I Karlínová, M Moos, ... New Phytologist , 2023 2023 Citations: 9
Metabolic flux phenotyping of secondary metabolism in cyanobacteria PK Babele, A Srivastava, JD Young Trends in Microbiology 31 (11), 1118-1130 , 2023 2023 Citations: 18
Millet-inspired systems metabolic engineering of NUE in crops PK Babele, A Srivastava, KA Selim, A Kumar Trends in Biotechnology 41 (5), 701-713 , 2023 2023 Citations: 8
Algal genomics tools: technological updates and progress N Kumar, S Kar, A Srivastava, C Banerjee, P Shukla Microbial Bioprocesses: Applications and Perspectives, 67-77 , 2023 2023 Citations: 2
Inheritable nanotubes boost bioimaging and photovoltaics in cyanobacteria A Srivastava, KA Selim Nature Nanotechnology 17 (10), 1046-1047 , 2022 2022 Citations: 6
Point mutation changes vibrational coupling in Lepidium virginicum water soluble chlorophyll binding protein G Grechisnikova, L Huang, M Reppert, S Ahad, A Srivastava International Symposium on Molecular Spectroscopy, 2022 , 2022 2022
Biosynthesis and biotechnological interventions for commercial production of microalgal pigments: A review A Srivastava, M Kalwani, H Chakdar, S Pabbi, P Shukla Bioresource Technology 352, 127071 , 2022 2022 Citations: 83
Cyanobacterial peptides: metabolic potential and environmental fate A Srivastava, P Shukla Protein and Peptide Letters 29 , 2022 2022 Citations: 1
Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria H Chakdar, S Thapa, A Srivastava, P Shukla Journal of Hazardous Materials 424, 127609 , 2022 2022 Citations: 128
Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions R Pathania, A Srivastava, S Srivastava, P Shukla Bioresource Technology 343, 126007 , 2022 2022 Citations: 51
Effects of nanofertilizers on soil and plant-associated microbial communities: Emerging trends and perspectives M Kalwani, H Chakdar, A Srivastava, S Pabbi, P Shukla Chemosphere 287, 132107 , 2022 2022 Citations: 209
Accurate prediction of mutation-induced frequency shifts in chlorophyll proteins with a simple electrostatic model A Srivastava, S Ahad, JH Wat, M Reppert The Journal of Chemical Physics 155 (15), 151102 , 2021 2021 Citations: 20
Emerging tools and strategies in cyanobacterial omics A Srivastava, P Shukla Trends in Biotechnology 40 (1), 4-7 , 2021 2021 Citations: 14
MOST CITED SCHOLAR PUBLICATIONS
Effects of nanofertilizers on soil and plant-associated microbial communities: Emerging trends and perspectives M Kalwani, H Chakdar, A Srivastava, S Pabbi, P Shukla Chemosphere 287, 132107 , 2022 2022 Citations: 209
Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria H Chakdar, S Thapa, A Srivastava, P Shukla Journal of Hazardous Materials 424, 127609 , 2022 2022 Citations: 128
Biosynthesis and biotechnological interventions for commercial production of microalgal pigments: A review A Srivastava, M Kalwani, H Chakdar, S Pabbi, P Shukla Bioresource Technology 352, 127071 , 2022 2022 Citations: 83
Cyanobacterial sigma factors: Current and future applications for biotechnological advances A Srivastava, ML Summers, R Sobotka Biotechnology Advances 40, 107517 , 2020 2020 Citations: 55
Metabolic systems biology and multi-omics of cyanobacteria: Perspectives and future directions R Pathania, A Srivastava, S Srivastava, P Shukla Bioresource Technology 343, 126007 , 2022 2022 Citations: 51
Down-regulation of the alternative sigma factor SigJ confers a photoprotective phenotype to Anabaena PCC 7120 A Srivastava, K Brilisauer, AK Rai, A Ballal, K Forchhammer, AK Tripathi Plant and Cell Physiology 58 (2), 287-297 , 2017 2017 Citations: 34
Engineered bacteriophages: A panacea against pathogenic and drug resistant bacteria A Kakkar, G Kandwal, T Nayak, LK Jaiswal, A Srivastava, A Gupta Heliyon , 2024 2024 Citations: 26
Sigma factor modulation for cyanobacterial metabolic engineering A Srivastava, RK Varshney, P Shukla Trends in Microbiology 29 (3), 266-277 , 2020 2020 Citations: 25
Accurate prediction of mutation-induced frequency shifts in chlorophyll proteins with a simple electrostatic model A Srivastava, S Ahad, JH Wat, M Reppert The Journal of Chemical Physics 155 (15), 151102 , 2021 2021 Citations: 20
Metabolic flux phenotyping of secondary metabolism in cyanobacteria PK Babele, A Srivastava, JD Young Trends in Microbiology 31 (11), 1118-1130 , 2023 2023 Citations: 18
Catalase expression in Azospirillum brasilense Sp7 is regulated by a network consisting of OxyR and two RpoH paralogs and including an RpoE1→RpoH5 regulatory cascade AK Rai, S Singh, SK Dwivedi, A Srivastava, P Pandey, S Kumar, BN Singh, ... Applied and Environmental Microbiology 84 (23), e01787-18 , 2018 2018 Citations: 16
Emerging tools and strategies in cyanobacterial omics A Srivastava, P Shukla Trends in Biotechnology 40 (1), 4-7 , 2021 2021 Citations: 14
Piriformospora indica: A friend in need is a friend in deed DK Trivedi, A Srivastava, PK Verma, N Tuteja, SS Gill Research & Reviews: Journal of Botanical Sciences 5 (1), 16-19 , 2016 2016 Citations: 11
Controlling vibronic coupling in chlorophyll proteins: The effects of excitonic delocalization and vibrational localization G Grechishnikova, JH Wat, N de Cordoba, E Miyake, A Phadkule, ... The Journal of Physical Chemistry Letters 15 (37), 9456-9465 , 2024 2024 Citations: 10
Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications A Srivastava, S Thapa, H Chakdar, PK Babele, P Shukla Critical Reviews in Biotechnology 44 (1), 63-77 , 2024 2024 Citations: 9
A thylakoid biogenesis BtpA protein is required for the initial step of tetrapyrrole biosynthesis in cyanobacteria P Skotnicová, A Srivastava, D Aggarwal, J Talbot, I Karlínová, M Moos, ... New Phytologist , 2023 2023 Citations: 9
Tightening the screws on PsbA in cyanobacteria A Srivastava, P Shukla Trends in Genetics 37 (3), 211-215 , 2020 2020 Citations: 9
Millet-inspired systems metabolic engineering of NUE in crops PK Babele, A Srivastava, KA Selim, A Kumar Trends in Biotechnology 41 (5), 701-713 , 2023 2023 Citations: 8
Engineering photosynthetic microbes for sustainable bioenergy production A Srivastava, MB Villalobos, RK Singh Contemporary Environmental Issues and Challenges in Era of Climate Change … , 2020 2020 Citations: 7
Role of nematode-trapping fungi for crop improvement under adverse conditions RK Singh, DK Trivedi, A Srivastava Crop Improvement Under Adverse Conditions, 271-283 , 2013 2013 Citations: 7