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Balagannavar G, Basavaraju K, Bajpai AK, Davuluri S, Kannan S, S Srini V, S Chandrashekar D, Chitturi N, K Acharya K. Transcriptomic analysis of the Non-Obstructive Azoospermia (NOA) to address gene expression regulation in human testis. Syst Biol Reprod Med 2023; 69:196-214. [PMID: 36883778 DOI: 10.1080/19396368.2023.2176268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
There is a need to understand the molecular basis of testes under Non-Obstructive Azoospermia (NOA), a state of failed spermatogenesis. There has been a lack of attention to the transcriptome at the level of alternatively spliced mRNAs (iso-mRNAs) and the mechanism of gene expression regulation. Hence, we aimed to establish a reliable iso-mRNA profile of NOA-testes, and explore molecular mechanisms - especially those related to gene expression regulation. We sequenced mRNAs from testicular samples of donors with complete spermatogenesis (control samples) and a failure of spermatogenesis (NOA samples). We identified differentially expressed genes and their iso-mRNAs via standard NGS data analyses. We then listed these iso-mRNAs hierarchically based on the extent of consistency of differential quantities across samples and groups, and validated the lists via RT-qPCRs (for 80 iso-mRNAs). In addition, we performed extensive bioinformatic analysis of the splicing features, domains, interactions, and functions of differentially expressed genes and iso-mRNAs. Many top-ranking down-regulated genes and iso-mRNAs, i.e., those down-regulated more consistently across the NOA samples, are associated with mitosis, replication, meiosis, cilium, RNA regulation, and post-translational modifications such as ubiquitination and phosphorylation. Most down-regulated iso-mRNAs correspond to full-length proteins that include all expected domains. The predominance of alternative promoters and termination sites in these iso-mRNAs indicate their gene expression regulation via promoters and UTRs. We compiled a new, comprehensive list of human transcription factors (TFs) and used it to identify TF-'TF gene' interactions with potential significance in down-regulating genes under the NOA condition. The results indicate that RAD51 suppression by HSF4 prevents SP1-activation, and SP1, in turn, could regulate multiple TF genes. This potential regulatory axis and other TF interactions identified in this study could explain the down-regulation of multiple genes in NOA-testes. Such molecular interactions may also have key regulatory roles during normal human spermatogenesis.
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Affiliation(s)
- Govindkumar Balagannavar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,Research Scholar, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Kavyashree Basavaraju
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Akhilesh Kumar Bajpai
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Sravanthi Davuluri
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Shruthi Kannan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Vasan S Srini
- Manipal Fertility, Manipal Hospital, Bengaluru, Karnataka, India
| | | | - Neelima Chitturi
- BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
| | - Kshitish K Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India.,BdataA: Biological data Analyzers' Association (virtual organization http://startbioinfo.com/BdataA/), India
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Circ-CREBBP inhibits sperm apoptosis via the PI3K-Akt signaling pathway by sponging miR-10384 and miR-143-3p. Commun Biol 2022; 5:1339. [PMID: 36476986 PMCID: PMC9729231 DOI: 10.1038/s42003-022-04263-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Male reproductive diseases are becoming increasingly prominent, and sperm quality is an important indicator to reflect these diseases. Seminal plasma extracellular vesicles (SPEVs) are involved in sperm motility. However, their effects on sperm remain unclear. Here, we identified 222 differentially expressed circRNAs in SPEVs between boars with high or low sperm motility. We found that circ-CREBBP promoted sperm motility and inhibited sperm apoptosis by sponging miR-10384 and miR-143-3p. In addition, miR-10384 and miR-143-3p can regulate the expression of MCL1, CREB1 and CREBBP. Furthermore, we demonstrated that MCL1 interacted directly with BAX and that CREBBP interacted with CREB1 in sperm. We showed that inhibition of circ-CREBBP can reduce the expression of MCL1, CREB1 and CREBBP and increase the expression of BAX and CASP3, thus promoting sperm apoptosis. Our results suggest that circ-CREBBP may be a promising biomarker and therapeutic target for male reproductive diseases.
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Whole-Genome Profile of Greek Patients with Teratozοοspermia: Identification of Candidate Variants and Genes. Genes (Basel) 2022; 13:genes13091606. [PMID: 36140773 PMCID: PMC9498395 DOI: 10.3390/genes13091606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 01/09/2023] Open
Abstract
Male infertility is a global health problem that affects a large number of couples worldwide. It can be categorized into specific subtypes, including teratozoospermia. The present study aimed to identify new variants associated with teratozoospermia in the Greek population and to explore the role of genes on which these were identified. For this reason, whole-genome sequencing (WGS) was performed on normozoospermic and teratozoospermic individuals, and after selecting only variants found in teratozoospermic men, these were further prioritized using a wide range of tools, functional and predictive algorithms, etc. An average of 600,000 variants were identified, and of them, 61 were characterized as high impact and 153 as moderate impact. Many of these are mapped in genes previously associated with male infertility, yet others are related for the first time to teratozoospermia. Furthermore, pathway enrichment analysis and Gene ontology (GO) analyses revealed the important role of the extracellular matrix in teratozoospermia. Therefore, the present study confirms the contribution of genes studied in the past to male infertility and sheds light on new molecular mechanisms by providing a list of variants and candidate genes associated with teratozoospermia in the Greek population.
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Ma J, Han R, Sun B, Lin J, Deng P, Wang S, Sun S. Differentially expressed microRNA in testicular tissues of hyperuricaemia rats. Andrologia 2021; 53:e14184. [PMID: 34255383 DOI: 10.1111/and.14184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
This study is to identify the differentially expressed miRNAs in testicular tissues of rats with hyperuricaemia-induced male infertility. We found that the hyperuricaemia model group had significantly increased serum uric acid, while significantly decreased sperm concentration and motile sperm percentage than normal group (p < .05). A total of 39 differentially expressed miRNAs were identified in the testicular tissues of hyperuricaemia rats compared with the control rats, ten of which were validated by real-time PCR. The target mRNAs of 7 differentially expressed miRNAs (miR-10b-5p, miR-26a-5p, miR-136-5p, miR-151-3p, miR-183-5p, miR-362-3p and miR-509-5p) from 3'-untranslated region binding perspective were enriched in signalling pathways of Wnt, Jak-STAT, mTOR and MAPK. The target mRNAs of 6 differentially expressed miRNAs (miR-136-5p, miR-144-3p, miR-99a-5p, miR-509-5p, miR-451-5p and miR-362-3p) from coding sequence binding perspective were enriched in signalling pathways of Calcium, Notch and MAPK. The functions of miRNAs in testicular tissues of rats with hyperuricaemia were revealed by the differentially expressed miRNAs (miR-183-5p, miR-99a-5p, miR-10b-5p, miR-151-3p, miR-26a-5p, miR-451-5p, miR-362-3p, miR-136-5p, miR-144-3p and miR-509-5p)-mRNAs interaction network. The differentially expressed miRNAs in the testicular tissues of hyperuricaemia rats might shed light on the mechanism of hyperuricaemia-induced male infertility.
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Affiliation(s)
- Jing Ma
- NHC Key Laboratory of Family Planning and Healthy, Hebei Key Laboratory of Reproductive Medicine, Hebei Research Institute for Family Planning Science and Technology, Shijiazhuang, China
| | - Ruiyu Han
- NHC Key Laboratory of Family Planning and Healthy, Hebei Key Laboratory of Reproductive Medicine, Hebei Research Institute for Family Planning Science and Technology, Shijiazhuang, China
| | - Bo Sun
- NHC Key Laboratory of Family Planning and Healthy, Hebei Key Laboratory of Reproductive Medicine, Hebei Research Institute for Family Planning Science and Technology, Shijiazhuang, China.,Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang, China
| | - Jiajie Lin
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang, China
| | - Peipei Deng
- NHC Key Laboratory of Family Planning and Healthy, Hebei Key Laboratory of Reproductive Medicine, Hebei Research Institute for Family Planning Science and Technology, Shijiazhuang, China
| | - Shusong Wang
- NHC Key Laboratory of Family Planning and Healthy, Hebei Key Laboratory of Reproductive Medicine, Hebei Research Institute for Family Planning Science and Technology, Shijiazhuang, China.,Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang, China
| | - Shaoguang Sun
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang, China
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Altered Gene Expression in the Testis of Infertile Patients with Nonobstructive Azoospermia. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5533483. [PMID: 34221106 PMCID: PMC8211532 DOI: 10.1155/2021/5533483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/14/2021] [Accepted: 05/28/2021] [Indexed: 11/18/2022]
Abstract
Background The molecular mechanism of nonobstructive azoospermia (NOA) remains unclear. The aim of this study was to identify gene expression changes in NOA patients and to explore potential biomarkers and therapeutic targets. Methods The gene expression profiles of GSE45885 and GSE145467 were collected from the Gene Expression Omnibus (GEO) database, and the differences between NOA and normal spermatogenesis were analyzed. Enrichment analysis was performed to explore biological functions for common differentially expressed genes (DEGs) in GSE45885 and GSE145467. Coexpression analysis of DEGs in GSE45885 was performed, and two modules with the highest correlation with NOA were screened. Key genes were then screened from the intersection genes of the two modules and common DEGs and PPI network. The expression of key genes was validated by quantitative real-time polymerase chain reaction (qRT-PCR) experiments. Finally, through miRTarBase, miRDB, and RAID, the miRNAs were predicted to regulate key genes, respectively. Results A total of 345 common DEGs were identified and they were mainly related to spermatogenesis, insulin signaling pathway. Coexpression analysis of DEGs in GSE45885 yielded eight modules; MEblack and MEturquoise had the highest correlation with NOA. Six genes in MEturquoise and RNF141 in MEblack were identified as key genes. qRT-PCR experiments validated the differential expression of key genes between NOA and control. Furthermore, RNF141 was regulated by the largest number of miRNAs. Conclusion Our findings suggest that the significant change expression of key genes may be potential markers and therapeutic targets of NOA and may have some impact on the development of NOA.
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Kumar S, Suyal DC, Yadav A, Shouche Y, Goel R. Psychrophilic Pseudomonas helmanticensis proteome under simulated cold stress. Cell Stress Chaperones 2020; 25:1025-1032. [PMID: 32683538 PMCID: PMC7591641 DOI: 10.1007/s12192-020-01139-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Himalayan mountains are distinctly characterized for their unique climatic and topographic variations; therefore, unraveling the cold-adaptive mechanisms and processes of native life forms is always being a matter of concern for scientific community. In this perspective, the proteomic response of psychrophilic diazotroph Pseudomonas helmanticensis was studied towards low-temperature conditions. LC-MS-based analysis revealed that most of the differentially expressed proteins providing cold stress resistance were molecular chaperons and cold shock proteins. Enzymes involved in proline, polyamines, unsaturated fatty acid biosynthesis, ROS-neutralizing pathways, and arginine degradation were upregulated. However, proteins involved in the oxidative pathways of energy generation were severalfold downregulated. Besides these, the upregulation of uncharacterized proteins at low temperature suggests the expression of novel proteins by P. helmanticensis for cold adaptation. Protein interaction network of P. helmanticensis under cold revealed that Tif, Tig, DnaK, and Adk were crucial proteins involved in cold adaptation. Conclusively, this study documents the proteome and protein-protein interaction network of the Himalayan psychrophilic P. helmanticensis under cold stress.
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Affiliation(s)
- Saurabh Kumar
- Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmaur, Himachal Pradesh, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, First floor, Central tower, Sai Trinity building, Pashan, Pune, Maharashtra, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, First floor, Central tower, Sai Trinity building, Pashan, Pune, Maharashtra, India
| | - Reeta Goel
- Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
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Roca J, Perez-Patiño C, Barranco I, Padilla LC, Martínez EA, Rodriguez-Martinez H, Parrilla I. Proteomics in fresh and preserved pig semen: Recent achievements and future challenges. Theriogenology 2020; 150:41-47. [PMID: 32088031 DOI: 10.1016/j.theriogenology.2020.01.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/11/2022]
Abstract
Proteins in semen, either in spermatozoa (SPZ) or seminal plasma (SP), are directly involved in molecular processes and biological pathways regulating sperm function, including fertilizing ability. Therefore, semen proteins are candidates of choice for biomarkers discovery for fertility and for sperm (dys)function. Mass spectrometry (MS)-based proteomics has opened up a new era for characterizing and quantifying the protein profile of SP and SPZ, as well as for unveiling the complex protein interactions involved in the activation of sperm functionality. This article overviews existing literature on MS-based proteomics regarding porcine semen, with a specific focus on the potential practical application of the results achieved so far. The weaknesses of current studies and the perspectives for future research in MS-based pig semen proteomics are also addressed.
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Affiliation(s)
- Jordi Roca
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Murcia, 30100, Spain.
| | - Cristina Perez-Patiño
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Murcia, 30100, Spain
| | - Isabel Barranco
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Murcia, 30100, Spain; Biotechnology of Animal and Human Reproduction (TechnoSperm), Department of Biology, Faculty of Sciences, Institute of Food and Agricultural Technology, University of Girona, Girona, 17003, Spain
| | - Lorena C Padilla
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Murcia, 30100, Spain
| | - Emilio A Martínez
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Murcia, 30100, Spain
| | | | - Inmaculada Parrilla
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, Murcia, 30100, Spain
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Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency. Sci Rep 2019; 9:20378. [PMID: 31889061 PMCID: PMC6937269 DOI: 10.1038/s41598-019-56592-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Protein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.
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Stafuzza NB, Costa E Silva EVD, Silva RMDO, Costa Filho LCCD, Barbosa FB, Macedo GG, Lobo RB, Baldi F. Genome-wide association study for age at puberty in young Nelore bulls. J Anim Breed Genet 2019; 137:234-244. [PMID: 31515857 DOI: 10.1111/jbg.12438] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022]
Abstract
Selection for bulls that would reach puberty early reduces the generation interval and increases fertility and herd productivity. Despite its economic importance, there are few QTL associated with age at puberty described in the literature. In this study, a weighted single-step genome-wide association study was performed to detect genomic regions and putative candidate genes related to age at puberty in young Nelore bulls. Several protein-coding genes related to spermatogenesis functions were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for age at puberty in Nelore bulls, such as ADAM11, BRCA1, CSNK2A, CREBBP, MEIOC, NDRG2, NECTIN3, PARP2, PARP9, PRSS21, RAD51C, RNASE4, SLX4, SPA17, TEX14, TIMP2 and TRIP13 gene. Enrichment analysis by DAVID also revealed several GO terms related to spermatogenesis such as DNA replication (GO:0006260), male meiosis I (GO:0007141), double-strand break repair (GO:0006302), base excision repair (GO:0006284), apoptotic process (GO:0006915), cell-cell adhesion (GO: 0098609) and focal adhesion (GO:0005925). The heritability for age at puberty shows that this trait can be improved based on traditional EBV selection. Adding genomic information to the system helps to elucidate genes and molecular mechanisms controlling the sexual precocity and could help to predict sexual precocity in Nelore bulls with greater accuracy at younger age, which would speed up the breeding programme for this breed.
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Affiliation(s)
| | - Eliane Vianna da Costa E Silva
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil
| | | | - Luiz Carlos Cesar da Costa Filho
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil.,PROCRIAR Assistência Veterinária, Campo Grande, Brazil
| | - Fernanda Battistotti Barbosa
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil.,PROCRIAR Assistência Veterinária, Campo Grande, Brazil
| | - Gustavo Guerino Macedo
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil
| | - Raysildo B Lobo
- Associação Nacional dos Criadores e Pesquisadores (ANCP), Ribeirão Preto, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Brazil
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Suyal DC, Kumar S, Joshi D, Soni R, Goel R. Quantitative proteomics of psychotrophic diazotroph in response to nitrogen deficiency and cold stress. J Proteomics 2018; 187:235-242. [PMID: 30092381 DOI: 10.1016/j.jprot.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/20/2018] [Accepted: 08/04/2018] [Indexed: 12/11/2022]
Abstract
Effective protocols and novel biomarkers are the need of this hour to screen potential cold adapted diazotrophs for sustainable mountain agricultural plans. LC-MS/MS based gel less quantitative proteomics was employed to investigate the metabolic response of Himalayan cold adapted diazotroph Pseudomonas palleroniana N26 (JN055435) for nitrogen deficiency and cold stress. More than 5000 proteins were identified, and 125 of them showed significant difference with a 2-fold or greater change (p < .05) between normal and stress conditions, including 29 up-regulated proteins and 35 down-regulated proteins. Expression of nifA, nifL, nifH, nifB, nifD, and nifK during N2 fixing conditions reveals that nitrogenase system was successfully activated. Further, 8% of the upregulated proteins showed similarity with uncharacterized proteins of several nitrogen fixing genera which suggests their in-depth investigation. Additionally, as per earlier studies, cowN was differentially expressed under nitrogen fixing conditions; thereby, confirming its potential to be a potent biomarker for monitoring the nitrogen fixation in cold niches. BIOLOGICAL SIGNIFICANCE Understanding of nitrogenase expression and regulation is essential to employ potential diazotrophs under diverse ecological niches to achieve agricultural as well as environmental sustainability. The molecular mechanisms of cold adapted diazotrophy are still unaddressed. In this scenario, present study, besides characterizing diazotrophic proteins, is helpful in identifying the protein(s) or a biomarker viz. CowN to facilitate the monitoring of nitrogen fixation in cold niches. To the best of our knowledge, this is the first gel-less quantitative free-living diazotrophic proteome study using label free mass spectrometry having high mass accuracy in both MS and MS/MS scans. It enriches the diazotrophic proteome database and will complement the other "omics" technologies for improved crop protection and sustainability strategies.
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Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Saurabh Kumar
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Divya Joshi
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Viswavidyalaya, Raipur, C.G., India
| | - Reeta Goel
- Department of Microbiology, College of Basic Sciences and Humanities, G.B.Pant University of Agriculture and Technology, Pantnagar 263145, Uttarakhand, India.
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11
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Cri-du-Chat Syndrome interactome network: Correlating genotypic variations to associated phenotypes. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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