@article { ISI:000339880300021, title = {Proteomics of arsenic stress in the gram-positive organism Exiguobacterium sp PS NCIM 5463}, journal = {Applied Microbiology and Biotechnology}, volume = {98}, number = {15}, year = {2014}, month = {AUG}, pages = {6761-6773}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

The general responses of microorganisms to environmental onslaughts are modulated by altering the gene expression pattern to reduce damage in the cell and produce compensating stress responses. The present study attempts to unravel the response of the Gram-positive Exiguobacterium sp. PS NCIM 5463 in the presence of [As(III)] and arsenate [As(V)] using comparative proteomics via two-dimension gel electrophoresis (2-DE) coupled with identification of proteins using matrix-assisted laser desorption/ionisation (MALDI-TOF/MALDI-TOF/TOF). Out of 926 Coomassie-stained proteins, 45 were differentially expressed (p \< 0.05). Considering the resolution and abundance level, 24 spots (peptides) were subjected to MALDI analysis, identified and categorised into several functional categories, viz., nitrogen metabolism, energy and stress regulators, carbohydrate metabolism, protein synthesis components and others. A functional role of each protein is discussed in Exiguobacterium sp. PS 5463 under arsenic stress and validated at their transcript level using a quantitative real-time polymerase chain reaction. Unlike previous reports that unravel the responses toward arsenic stress in Gram-negative organisms, the present study identified new proteins under arsenic stress in a Gram-positive organism, Exiguobacterium sp. PS NCIM 5463, which could elucidate the physiology of organisms under arsenic stress.

}, keywords = {Arsenic, Exiguobacterium, proteomics, Stress, Transcriptomics}, issn = {0175-7598}, doi = {10.1007/s00253-014-5873-6}, author = {Sacheti, Poonam and Patil, Rajendra and Dube, Ankita and Bhonsle, Hemangi S. and Thombre, Dipalee and Marathe, Sayali and Vidhate, Ravindra and Wagh, Priyanka and Kulkarni, Mahesh J. and Rapole, Srikanth and Gade, Wasudeo N.} } @article { ISI:000357034800003, title = {Cell line development for biomanufacturing processes: recent advances and an outlook}, journal = {Biotechnology Letters}, volume = {37}, number = {8}, year = {2015}, month = {AUG}, pages = {1553-1564}, publisher = {SPRINGER}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {

At the core of a biomanufacturing process for recombinant proteins is the production cell line. It influences the productivity and product quality. Its characteristics also dictate process development, as the process is optimized to complement the producing cell to achieve the target productivity and quality. Advances in the past decade, from vector design to cell line screening, have greatly expanded our capability to attain producing cell lines with certain desired traits. Increasing availability of genomic and transcriptomic resources for industrially important cell lines coupled with advances in genome editing technology have opened new avenues for cell line development. These developments are poised to help biosimilar manufacturing, which requires targeting pre-defined product quality attributes, e.g., glycoform, to match the innovator{\textquoteright}s range. This review summarizes recent advances and discusses future possibilities in this area.

}, keywords = {Biomanufacturing, Biosimilars, Cell line development, CHO cells genomics, Genome editing, Transcriptomics}, issn = {0141-5492}, doi = {10.1007/s10529-015-1843-z}, author = {Le, Huong and Vishwanathan, Nandita and Jacob, Nitya M. and Gadgil, Mugdha and Hu, Wei-Shou} } @article {46724, title = {Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum}, journal = {Phytochemistry}, volume = {177}, year = {2020}, month = {SEP}, pages = {112451}, type = {Article}, abstract = {

In Ocimum kilimandscharicum, the relative volatile composition of camphor in leaves was as high as 55\%, while that of eugenol in roots was 57\%. These metabolites were differentially partitioned between the aerial and root tissues. Global metabolomics revealed tissue-specific biochemical specialization, evident by the differential distribution of 2588 putative metabolites across nine tissues. Next-generation sequencing analysis indicated differential expression of 51 phenylpropanoid and 55 terpenoid pathway genes in aerial and root tissues. By integrating metabolomics with transcriptomics, the camphor biosynthesis pathway in O. kilimandscharicum was elucidated. In planta bioassays revealed the role of geranyl diphosphate synthase (gpps) and borneol dehydrogenase (bdh) in camphor biosynthesis. Further, the partitioning of camphor was attributed to tissue-specific gene expression of both the pathway entry point (gpps) and terminal (bdh) enzyme. Unlike camphor, eugenol accumulated more in roots; however, absence of the eugenol synthase gene in roots indicated long distance transport from aerial tissues. In silico co-expression analysis indicated the potential involvement of ATP-binding cassette, multidrug and toxic compound extrusion, and sugar transporters in eugenol transport. Similar partitioning was evident across five other Ocimum species. Overall, our work indicates that metabolite partitioning maybe a finely regulated process, which may have implications on plant growth, development, and defense.

}, keywords = {Borneol dehydrogenase, Camphor, Eugenol, Geranyl diphosphate synthase, Lamiaceae, Metabolite partitioning, Metabolomics, Ocimum kilimandscharicum, Transcriptomics}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2020.112451}, author = {Singh, Priyanka and Kalunke, Raviraj M. and Shukla, Anurag and Tzfadia, Oren and Thulasiram, V. Hirekodathakallu and Giri, Ashok P.} } @article {48478, title = {Role of ions and their transporters in combating salt stress in Pandanus odorifer (Forssk.) Kuntze}, journal = {Acta Physiologiae Plantarum}, volume = {45}, year = {2023}, month = {MAY}, pages = {66}, type = {Article}, abstract = {

Soil salinity is a major environmental constraint causing huge losses in crop production. Pandanus odorifer (Forssk.) Kuntze is an aromatic monocot plant species belonging to the family Pandanaceae, which grows naturally on the saline soils along the coasts of Asia, Southeast Asia, and Polynesia. The plants are dioecious and highly fertile, and the consistent saline sprays, strong winds, and severe soil salinity hardly affect their growth and fertility. Hence, understanding the mechanism of high salinity tolerance in P. odorifer could provide major advances in overcoming salinity stress in crop plants. In the present study, we analyzed control (0 M NaCl) and treated (1 M NaCl treatment for 3 weeks) plants of P. odorifer to understand the role of ion distribution, ion transport, and related mechanisms under salt stress. Using a combination of ionomics and transcriptomics approaches, we identified the molecular mechanisms contributing to the high salinity stress in P. odorifer. Under NaCl stress, there was a significant increase in Na, Cl, and other ions in leaves, while the concentrations of Si, Fe, Ni, and Ti decreased. Similarly, in roots, the levels of Na, Mg, Cd, and Cr were significantly high, while the levels of other ions decreased. Most of the genes related to ion transport and homeostasis, such as NHX1, CLC-C, SOS1, HAK, and ABC transporters, were upregulated in 1 M NaCl stress conditions. This study revealed that vacuolar sequestration of Na+ and the distribution of ions in the roots and shoots play significant roles in the salt-stress tolerance mechanism of P. odorifer.

}, keywords = {Ion transport, Ionomics, Pandanus, Salinity tolerance, Transcriptomics, Vacuolar sequestration}, issn = {0137-5881}, doi = {10.1007/s11738-023-03541-8}, author = {Rashmi, Deo and Ansari, Waquar A. and Kadoo, Narendra Y. and Barvkar, Vitthal T. and Deshmukh, Rupesh and Nadaf, Altafhusain B.} } @article {49083, title = {Targeted metabolite profiling and de novo transcriptome sequencing reveal the key terpene synthase genes in medicinally important plant, Couroupita guianensis Aubl}, journal = {Plant Genetic Resources-Characterization and Utilization}, volume = {21}, year = {2023}, month = {DEC}, pages = {558-570}, type = {Article}, abstract = {

The Lecythidaceae family tree, Couroupita guianensis Aubl, popularly known as Nagpushpa, is a widely cultivated ornamental tree with several uses in traditional medicine. The tree is revered as highly sacred in Indian traditional culture due to its uniquely shaped, fragrant flowers. Considering the significance, we were prompted to carry out the metabolite and transcriptome analysis of Nagapushpa. The flower, petals, stamen, stem and leaf of C. guianensis were metabolically profiled, and it was discovered that the flower tissue contained the highest terpenoid reservoir. A number of terpenoid pathway transcripts were also found in the flower tissue after transcriptome profiling. KEGG pathway mapping was carried out to correlate transcript sequences with the biosynthesis of different types of terpenes. We were able to clone three full-length terpene synthase gene candidates, i.e. monoterpene ocimene synthase, diterpene ent-kaurene synthase and sesquiterpene farnesene synthase. The transcript expression of selected terpene synthase genes was also verified in flower tissue. These cloned sequences were used for in silico structural investigations and protein function prediction at the level of 3D structure. The data presented in this study provide a comprehensive resource for the metabolic and transcriptomic profiles of C. guianensis. The study paves the way towards the elucidation of terpene biosynthetic pathway in C. guianensis and heterologous production of useful terpenoids in the future.

}, keywords = {Couroupita guianensis Aubl, flower, Metabolite profiling, terpene synthases, Transcriptomics}, issn = {1479-2621}, doi = {10.1017/S1479262123000953}, author = {Thulasiram, Hirekodathakallu V. and Karegaonkar, Shrikant Jagannathrao and Sharma, Poojadevi and Kumar, Ashish and Ramkumar, Sudha and Pandreka, Avinash} } @article {49242, title = {Trehalase inhibition in Helicoverpa armigera activates machinery for alternate energy acquisition}, journal = {JOURNAL OF BIOSCIENCES}, volume = {49}, year = {2024}, month = {JUL }, pages = {74}, type = {Journal Article}, keywords = {Energy metabolism, glucose, Metabolomics, Transcriptomics, trehalase, validamycin A}, issn = {0250-5991}, doi = {10.1007/s12038-024-00453-8}, author = {Tellis, Meenakshi and Mohite, Sharada and Joshi, Rakesh} } @article {49702, title = {Transcriptome analyses reveal TaWRKY41 as a potential candidate governing spot blotch resistance in wheat}, journal = {Physiology and Molecular Biology of Plants}, volume = {31}, year = {2025}, month = {APR}, pages = {591-608}, type = {Article}, abstract = {

Spot blotch disease caused by Bipolaris sorokiniana poses a significant threat to wheat production. Cultivation of disease-resistant wheat genotypes appears to be the most practical approach to mitigate the impact of this devastating disease. However, the molecular responses of wheat plants during spot blotch disease progression remain poorly understood. This study employed RNA-sequencing to unravel the spatiotemporal molecular events underlying the resistance mechanism in the spot blotch susceptible and resistant wheat genotypes. This study further provides a comprehensive overview of differentially expressed transcripts through functional analysis and transcription factor identification, elucidating the biological mechanisms governing wheat-B. sorokiniana interaction. In the resistant genotype, the expression of one of the key transcription factors, TaWRKY41, was significantly induced upon pathogen inoculation. Computational studies, electrophoretic-mobility shift assay, and yeast one-hybrid assay confirmed the interaction of the recombinant TaWRKY41 protein with W-box elements present in the promoters of plant defense-related genes. Furthermore, co-expression network analyses identified downstream genes positively correlated with TaWRKY41, providing insights into their probable involvement in the defense response. Overall, our investigation suggests that TaWRKY41 contributes to spot blotch resistance in wheat. This knowledge can help develop new disease-resistant wheat varieties.

}, keywords = {Plant defense, plant-pathogen interaction, TaWRKY41, Transcription factors, Transcriptomics}, issn = {0971-5894}, doi = {10.1007/s12298-025-01583-5}, author = {Dayama, Bhakti R. and Mahadik, Varsha A. and Somani, Deepika and Shinde, Balkrishna A. and Kondhare, Kirtikumar R. and Karthikeyan, Muthukumarasamy and Kadoo, Narendra Y.} }