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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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Toorani T, Mackie PM, Mastromonaco GF. Investigating Markers of Reprogramming Potential in Somatic Cell Lines Derived from Matched Donors. Cell Reprogram 2021; 23:73-88. [PMID: 33861640 DOI: 10.1089/cell.2020.0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Somatic cell biobanking and related technologies, somatic cell nuclear transfer (SCNT), and induction of pluripotent stem cells offer significant promise for wildlife conservation, but have yet to achieve optimal success. Inefficiency and variability in outcome have been linked to incomplete nuclear reprogramming, highlighting the importance of donor cell contribution. Studies show significant differences in SCNT outcome in donor cell lines within and between individuals, highlighting the necessity for a standardized characterization method to evaluate cell line reprogramming potential. Stringently standardized bovine fibroblast cell lines were generated and assessed for inter- and intraindividual variability on cellular (morphology, chromosome number, apoptotic incidence; Experiment 1) and molecular (pluripotency and epigenetic-related gene expression; Experiment 2) levels encompassing putative biomarkers of reprogramming potential. Cellular parameters were similar across cell lines. While some statistically significant differences were observed in DNMT1, DNMT3B, and HAT1, but not HDAC1, their biological relevance could not be determined with the information at hand. This study lays the foundation for understanding cellular characteristics in cultured cell lines; however, further studies are required to determine any correlation with reprogramming potential.
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Affiliation(s)
- Tahmineh Toorani
- Reproductive Sciences, Toronto Zoo, Scarborough, Canada.,Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | | | - Gabriela F Mastromonaco
- Reproductive Sciences, Toronto Zoo, Scarborough, Canada.,Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Canada
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Parreira JR, Hernández-Castellano LE, Argüello A, Capote J, Castro N, de Sousa Araújo S, de Almeida AM. Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach. BMC Genomics 2020; 21:629. [PMID: 32928114 PMCID: PMC7489022 DOI: 10.1186/s12864-020-06968-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
Background Seasonal weight loss (SWL) is a very important limitation to the production of ruminants in the Mediterranean and Tropical regions. In these areas, long dry seasons lead to poor pastures with low nutritional value. During the dry season, ruminants, particularly those raised in extensive production systems, lose around 30% of their body weight. Seasonal weight loss has important consequences on animal productive performance and health. In this study, RNA sequencing was used to characterize feed restriction effects in dairy goat of 2 breeds with different SWL tolerance: Majorera (tolerant) and Palmera (susceptible). Nine Majorera and ten Palmera goats were randomly distributed in a control and a restricted group: Majorera Control (adequately fed; MC; n = 4), Palmera Control (adequately fed; PC; n = 6), Majorera Restricted (feed restricted; ME; n = 5) and Palmera Restricted (feed restricted; PE; n = 4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis. Results From these samples, 24,260 unique transcripts were identified. From those, 82 transcripts were differentially expressed between MC and ME, 99 between PC and PE, twelve between both control groups and twenty-nine between both restricted groups. Conclusions Feed restriction affected several biochemical pathways in both breeds such as: carbohydrate and lipid transport; intracellular trafficking, RNA processing and signal transduction. This research also highlights the importance or involvement of the genes in tolerance (ENPP1, S-LZ, MT2A and GPNB) and susceptibility (GPD1, CTPS1, ELOVL6 and NR4A1) to SWL with respectively higher expression in the Majorera restriced group and the Palmera restricted group in comparison to the control groups. In addition, results from the study may be extrapolated to other dairy ruminant species.
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Affiliation(s)
- José Ricardo Parreira
- IBET - Instituto de Biologia Experimental e Tecnológica, Av. da República, 2780-157, Oeiras, Portugal.,ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Anastasio Argüello
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413, Arucas, Spain
| | - Juan Capote
- Unit of Animal Production, Pasture, and Forage in Arid and Subtropical Areas, Canary Islands Institute for Agricultural Research, 38270, La Laguna, Spain
| | - Noemí Castro
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413, Arucas, Spain
| | - Susana de Sousa Araújo
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - André Martinho de Almeida
- LEAF - Linking Landscape, Environment, Agriculture And Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 13409-017, Lisbon, Portugal.
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Li Y, Li YH, Zhou X, Wu B, Chen JP, Wang ZK, Wang X, Shi HJ, Li RS. DNA hydroxymethylation rate in the AChE and HoxC4 promoter associated with human sperm quality. Andrologia 2018; 50:e12963. [PMID: 29430663 DOI: 10.1111/and.12963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 12/23/2022] Open
Abstract
The relationship of altered DNA 5'-hydroxymethylation in human spermatozoa with seminal parameters remains unclear. The aim of the study was to investigate the association between the 5'-hydroxymethylcytosine (5hmC) rate in the promoters of acetylcholinesterase (AChE) and homeobox C4 (HoxC4) genes and human sperm concentration/motility. The study population consisted of three groups: asthenozoospermia (AZ), oligoasthenozoospermia (OAZ) and normozoospermia (NZ). The 5hmC rate in the promoter was measured by CCGG loci-dependent MspI/HpaII restriction mapping of glycosylation-modified sperm DNA combined with a hydroxymethylation-specific real-time polymerase chain reaction assay. The 5hmC rate in the AChE promoter in group AZ and OAZ was higher than that in group NZ (p < .05). A weak inverse correlation between 5hmC rate of AChE and sperm motility was observed in all subjects (r = -.172, p < .05). The 5hmC rate in the HoxC4 promoter in group OAZ was lower than that in group NZ (p < .05). These results indicated that altered 5hmC rates of AChE and HoxC4 promoters are associated with low sperm motility and sperm concentration respectively.
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Affiliation(s)
- Y Li
- School of Pharmacy, Fudan University, Shanghai, China
| | - Y H Li
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - X Zhou
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - B Wu
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - J P Chen
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - Z K Wang
- The hospital affiliated to Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - X Wang
- The hospital affiliated to Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - H J Shi
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - R S Li
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
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