@article {8739, title = {Proteomic and metabolomic insights into seed germination of Ferula assa-foetida [Mass Spectrometry - Proteomics Facility]}, journal = {J Proteomics}, volume = {300}, year = {2024}, month = {2024 May 30}, pages = {105176}, abstract = {

Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4\ {\textdegree}C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in F. assa-foetida germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in F. assa-foetida germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of Ferula assa-foetida. SIGNIFICANCE: Seed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. Ferula assa-foetida L., commonly known as "asafoetida," is a medicinal and food crop with huge therapeutic potential. To date, our understanding of F. assa-foetida seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in F. assa-foetida is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.

}, keywords = {Ferula, Gene Expression Regulation, Plant, Germination, Metabolomics, Plant Proteins, Protein Interaction Maps, Proteome, Proteomics, Seeds}, issn = {1876-7737}, doi = {10.1016/j.jprot.2024.105176}, author = {Punia, Ashwani and Kumari, Manglesh and Chouhan, Monika and Saini, Vishal and Joshi, Robin and Kumar, Ashok and Kumar, Rajiv} } @article {1008, title = {Shotgun proteomics provides an insight into pathogenesis related proteins using anamorphic stage of the biotroph, Erysiphe pisi pathogen of garden pea [Mass Spectrometry Facility - Proteomics]}, journal = {Microbiological Research}, year = {2019}, abstract = {

E. pisi is an ascomycete member causing powdery mildew disease of garden pea. It is a biotrophic pathogen requiring a living host for its survival. Our understanding of molecular mechanisms underlying its pathogenesis is limited. The identification of proteins expressed in the pathogen is required to gain an insight into the functional mechanisms of an obligate biotrophic fungal pathogen. In this study, the proteome of the anamorphic stage of E. pisi pathogen has been elucidated through the nano LC-MS/MS approach. A total of 328 distinct proteins were detected from Erysiphe isolates infecting the susceptible pea cultivar, Arkel. The proteome is available via ProteomeXchange with identifier PXD010238. The functional classification of protein accessions based on Gene Ontology revealed proteins related to signal transduction, secondary metabolite formation and stress which might be involved in virulence and pathogenesis. The functional validation carried through differential expression of genes encoding G-protein beta subunit, a Cyclophilin (Peptidyl prolyl cis-transisomerase) and ABC transporter in a time course study confirmed their putative role in pathogenesis between resistant and susceptible genotypes, JI2480 and Arkel. The garden pea-powdery mildew pathosystem is largely unexplored, therefore, the identified proteome provides a first-hand information and will form a basis to analyse mechanisms involving pathogen survival, pathogenesis and virulence.

}, keywords = {garden pea, nano-LC-MS/MS, powdery mildew, Proteome, shotgun proteomics}, issn = {0944-5013}, doi = {https://doi.org/10.1016/j.micres.2019.02.006}, url = {http://www.sciencedirect.com/science/article/pii/S0944501318308826}, author = {Malathi Bheri and Sheetal M. Bhosle and Ragiba Makandar} } @article {8898, title = {Shotgun proteomics provides an insight into pathogenesis-related proteins using anamorphic stage of the biotroph, Erysiphe pisi pathogen of garden pea [Mass Spectrometry - Proteomics Facility]}, journal = {Microbiol Res}, volume = {222}, year = {2019}, month = {2019 May}, pages = {25-34}, abstract = {

E. pisi is an ascomycete member causing powdery mildew disease of garden pea. It is a biotrophic pathogen, requiring a living host for its survival. Our understanding of molecular mechanisms underlying its pathogenesis is limited. The identification of proteins expressed in the pathogen is required to gain an insight into the functional mechanisms of an obligate biotrophic fungal pathogen. In this study, the proteome of the anamorphic stage of E. pisi pathogen has been elucidated through the nano LC-MS/MS approach. A total of 328 distinct proteins were detected from Erysiphe isolates infecting the susceptible pea cultivar, Arkel. The proteome is available via ProteomeXchange with identifier PXD010238. The functional classification of protein accessions based on Gene Ontology revealed proteins related to signal transduction, secondary metabolite formation and stress which might be involved in virulence and pathogenesis. The functional validation carried through differential expression of genes encoding G-protein beta subunit, a Cyclophilin (Peptidyl prolyl cis-transisomerase) and ABC transporter in a time course study confirmed their putative role in pathogenesis between resistant and susceptible genotypes, JI2480 and Arkel. The garden pea-powdery mildew pathosystem is largely unexplored, therefore, the identified proteome provides a first-hand information and will form a basis to analyze mechanisms involving pathogen survival, pathogenesis and virulence.

}, keywords = {Ascomycota, Chromatography, Liquid, Disease Resistance, Fungal Proteins, Gardens, Gene Ontology, Genes, Plant, Genotype, Host-Pathogen Interactions, Pisum sativum, Plant Diseases, Plant Leaves, Proteome, Proteomics, Tandem Mass Spectrometry}, issn = {1618-0623}, doi = {10.1016/j.micres.2019.02.006}, author = {Bheri, Malathi and M Bhosle, Sheetal and Makandar, Ragiba} } @article {8903, title = {Comparative sperm protein profiling in bulls differing in fertility and identification of phosphatidylethanolamine-binding protein 4, a potential fertility marker [Mass Spectrometry - Proteomics]}, journal = {Andrology}, volume = {5}, year = {2017}, month = {2017 Sep}, pages = {1032-1051}, abstract = {

This study aimed to identify sperm proteomic signatures regulating sperm functions and fertility by: (i) comparing the sperm electrophoretic protein profiles and identifying the differentially abundant proteins among breeding bulls differing in fertility status and (ii) elucidating the possible role of one of the identified novel proteins, PEBP4 on sperm function and fertility. The grouping of bulls as fertile (n\ =\ 6) and low fertile (n\ =\ 6) was performed based on bull fertility index and infertile (n\ =\ 6) based on semen rejection rate (\>33\%). The sperm motility, fructolysis index, acrosomal reaction, intracellular calcium levels, and seminal plasma fructose and calcium levels were studied among fertility groups. The differentially expressed sperm proteins observed in single- and two-dimensional gel electrophoresis (2DE) were identified using Nano-LC-MS/MS. In the fertile bulls, the expression levels of calmodulin (CALM1), spermadhesinZ13 (SPADH2), and phosphatidylethanolamine-binding protein 4 (PEBP4) were significantly (p\ \<\ 0.05) higher than in other fertility groups. In bovine, expression of PEBP4 a novel seminal protein was not observed in spermatozoa of infertile bulls. When the bulls were grouped based on the presence (n\ =\ 8) or absence (n\ =\ 10) of PEBP4 protein in spermatozoa, a positive significant (p\ \<\ 0.05) association of this protein with the percentage of motile, type-A spermatozoa, and sperm fructose uptake was observed. Further, PEBP4 was localized in elongated spermatids, Leydig cells, excurrent duct system, and principal piece of spermatozoa. These findings suggest a crucial role for the PEBP4 protein in spermiogenesis, epididymal sperm maturation, and sperm motility. This first study in bovine indicates the positive association of PEBP4 in regulating sperm maturation, functions, and fertility and could be a potential marker for predicting semen quality and fertility.

}, keywords = {Acrosome Reaction, Animals, Biomarkers, Calcium Signaling, Cattle, Cattle Diseases, Epididymis, Fertility, Fructose, Infertility, Male, Male, Phosphatidylethanolamine Binding Protein, Proteome, Semen, Sperm Maturation, Sperm Motility, Spermatozoa}, issn = {2047-2927}, doi = {10.1111/andr.12404}, author = {Somashekar, L and Selvaraju, S and Parthipan, S and Patil, S K and Binsila, B K and Venkataswamy, M M and Karthik Bhat, S and Ravindra, J P} } @article {780, title = {Exploring Packaged Microvesicle Proteome Composition of Chinese Hamster Ovary Secretome [Mass Spectrometry - Proteomics]}, journal = {Journal of Bioprocessing \& Biotechniques}, volume = {6}, year = {2016}, pages = {1-11}, keywords = {

CHO, Microvesicles, Proteome, Recombinant protein production

, Secretome}, issn = {2155-9821}, doi = {10.4172/2155-9821.1000274}, url = {https://www.omicsonline.org/open-access/exploring-packaged-microvesicle-proteome-composition-of-chinesehamster-ovary-secretome-2155-9821-1000274.php?aid=71599}, author = {Niraj Kumar and Dixat Gopal Gupta and Srikant Kumar and et. al.} }