1
|
Mejia S, Santos JLB, Noutsos C. Comprehensive Genome-Wide Natural Variation and Expression Analysis of Tubby-like Proteins Gene Family in Brachypodium distachyon. PLANTS (BASEL, SWITZERLAND) 2024; 13:987. [PMID: 38611516 PMCID: PMC11013449 DOI: 10.3390/plants13070987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3, 4, 7, and 14 are involved in light responses, and BdTLP1 is involved in ABA responses. Furthermore, BdTLP2, 7, 9, and 13 are expressed throughout vegetative and reproductive stages, whereas BdTLP1, 3, 5, and 14 are expressed at germinating grains and early vegetative development, and BdTLP4, 6, 8, and 10 are expressed at the early reproduction stage. The natural variation in the eleven most diverged B. distachyon lines revealed high conservation levels of BdTLP1-6 to high variation in BdTLP7-14 proteins. Based on diversifying selection, we identified amino acids in BdTLP1, 3, 8, and 13, potentially substantially affecting protein functions. This analysis provided valuable information for further functional studies to understand the regulation, pathways involved, and mechanism of BdTLPs.
Collapse
Affiliation(s)
- Sendi Mejia
- Biological Sciences Department, Suny Old Westbury, Old Westbury, NY 11568, USA
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN 47907, USA
| | | | - Christos Noutsos
- Biological Sciences Department, Suny Old Westbury, Old Westbury, NY 11568, USA
| |
Collapse
|
2
|
Zheng HC, Jiang HM. Shuttling of cellular proteins between the plasma membrane and nucleus (Review). Mol Med Rep 2021; 25:14. [PMID: 34779504 PMCID: PMC8600410 DOI: 10.3892/mmr.2021.12530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/09/2021] [Indexed: 11/23/2022] Open
Abstract
Recently accumulated evidence has indicated that the nucleomembrane shuttling of cellular proteins is common, which provides new insight into the subcellular translocation and biological functions of proteins synthesized in the cytoplasm. The present study aimed to clarify the trafficking of proteins between the plasma membrane and nucleus. These proteins primarily consist of transmembrane receptors, membrane adaptor proteins, adhesive proteins, signal proteins and nuclear proteins, which contribute to proliferation, apoptosis, chemoresistance, adhesion, migration and gene expression. The proteins frequently undergo cross-talk, such as the interaction of transmembrane proteins with signal proteins. The transmembrane proteins undergo endocytosis, infusion into organelles or proteolysis into soluble forms for import into the nucleus, while nuclear proteins interact with membrane proteins or act as receptors. The nucleocytosolic translocation involves export or import through nuclear membrane pores by importin or exportin. Nuclear proteins generally interact with other transcription factors, and then binding to the promoter for gene expression, while membrane proteins are responsible for signal initiation by binding to other membrane and/or adaptor proteins. Protein translocation occurs in a cell-specific manner and is closely linked to cellular biological events. The present review aimed to improve understanding of cytosolic protein shuttling between the plasma membrane and nucleus and the associated signaling pathways.
Collapse
Affiliation(s)
- Hua-Chuan Zheng
- Department of Oncology, The Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Hua-Mao Jiang
- Department of Urology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| |
Collapse
|
3
|
DiTirro D, Philbrook A, Rubino K, Sengupta P. The Caenorhabditis elegans Tubby homolog dynamically modulates olfactory cilia membrane morphogenesis and phospholipid composition. eLife 2019; 8:48789. [PMID: 31259686 PMCID: PMC6624019 DOI: 10.7554/elife.48789] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
Plasticity in sensory signaling is partly mediated via regulated trafficking of signaling molecules to and from primary cilia. Tubby-related proteins regulate ciliary protein transport; however, their roles in remodeling cilia properties are not fully understood. We find that the C. elegans TUB-1 Tubby homolog regulates membrane morphogenesis and signaling protein transport in specialized sensory cilia. In particular, TUB-1 is essential for sensory signaling-dependent reshaping of olfactory cilia morphology. We show that compromised sensory signaling alters cilia membrane phosphoinositide composition via TUB-1-dependent trafficking of a PIP5 kinase. TUB-1 regulates localization of this lipid kinase at the cilia base in part via localization of the AP-2 adaptor complex subunit DPY-23. Our results describe new functions for Tubby proteins in the dynamic regulation of cilia membrane lipid composition, morphology, and signaling protein content, and suggest that this conserved family of proteins plays a critical role in mediating cilia structural and functional plasticity.
Collapse
Affiliation(s)
- Danielle DiTirro
- Department of Biology, Brandeis University, Waltham, United States
| | - Alison Philbrook
- Department of Biology, Brandeis University, Waltham, United States
| | - Kendrick Rubino
- Department of Biology, Brandeis University, Waltham, United States
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, United States
| |
Collapse
|
4
|
Wang M, Xu Z, Ahmed RI, Wang Y, Hu R, Zhou G, Kong Y. Tubby-like Protein 2 regulates homogalacturonan biosynthesis in Arabidopsis seed coat mucilage. PLANT MOLECULAR BIOLOGY 2019; 99:421-436. [PMID: 30707395 DOI: 10.1007/s11103-019-00827-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
A possible transcription factor TLP2 was identified to be involved in the regulation of HG biosynthesis in Arabidopsis seed mucilage. TLP2 can translocate into nucleus from plasma membrane by interacting with NF-YC3. The discovery of TLP2 gene function can further fulfill the regulatory network of pectin biosynthesis in Arabidopsis thaliana. Arabidopsis seed coat mucilage is an excellent model system to study the biosynthesis, function and regulation of pectin. Rhamnogalacturonan I (RG-I) and homogalacturonan (HG) are the major polysaccharides constituent of the Arabidopsis seed coat mucilage. Here, we identified a Tubby-like gene, Tubby-like protein 2 (TLP2), which was up-regulated in developing siliques when mucilage began to be produced. Ruthenium red (RR) staining of the seeds showed defective mucilage of tlp2-1 mutant after vigorous shaking compared to wild type (WT). Monosaccharide composition analysis revealed that the amount of total sugars and galacturonic acid (GalA) decreased significantly in the adherent mucilage (AM) of tlp2-1 mutant. Immunolabelling and dot immunoblotting analysis showed that unesterified HG decreased in the tlp2-1 mutant. Furthermore, TLP2 can translocate into nucleus by interacting with Nuclear Factor Y subunit C3 (NF-YC3) to function as a transcription factor. RNA-sequence and transactivation assays revealed that TLP2 could activate UDP-glucose 4-epimerase 1 (UGE1). In all, it is concluded that TLP2 could regulate the biosynthesis of HG possibly through the positive activation of UGE1.
Collapse
Affiliation(s)
- Meng Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Zongchang Xu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Rana Imtiaz Ahmed
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Yiping Wang
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Graduate School of University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruibo Hu
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Gongke Zhou
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yingzhen Kong
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| |
Collapse
|
5
|
Wang M, Xu Z, Kong Y. The tubby-like proteins kingdom in animals and plants. Gene 2018; 642:16-25. [PMID: 29109004 DOI: 10.1016/j.gene.2017.10.077] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 11/28/2022]
|
6
|
Choi YS, Song JE, Kong BS, Hong JW, Novelli S, Lee EJ. The Role of Foxo3 in Leydig Cells. Yonsei Med J 2015; 56:1590-6. [PMID: 26446641 PMCID: PMC4630047 DOI: 10.3349/ymj.2015.56.6.1590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/03/2014] [Accepted: 11/11/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Foxo3 in female reproduction has been reported to regulate proliferation of granulose cells that form follicles. There are no reports so far that discuss on the role of Foxo3 in males. This study was designed to outline the role of Foxo3 in the testes. MATERIALS AND METHODS Testes from mice at birth to postpartum week (PPW) 5 were isolated and examined for the expression of Foxo3 using immunostaining. To elucidate role of Foxo3 in Leydig cells, R2C cells were treated with luteinizing hormone (LH) and the phosphorylation of Foxo3. Testosterone and steroidogenic acute regulatory (StAR) protein levels were measured after constitutive active [triple mutant (TM)] human FOXO3 adenovirus was transduced and StAR promoter assay was performed. RESULTS Foxo3 expression in the testicles started from birth and lasted until PPW 3. After PPW 3, most Foxo3 expression occurred in the nuclei of Leydig cells; however, at PPW 5, Foxo3 was expressed in both the nucleus and cytoplasm. When R2C cells were treated with luteinizing hormone, Foxo3 phosphorylation levels by AKT increased. After blocking the PI3K pathway, LH-induced phosphorylated Foxo3 levels decreased, indicating that LH signaling regulates Foxo3 localization. When active FOXO3-TM adenovirus was introduced into a Leydig tumor cell line, the concentrations of testosterone and StAR protein decreased. When FOXO3 and a StAR promoter vector were co-transfected into HEK293 cells for a reporter assay, FOXO3 inhibited the StAR promoter. CONCLUSION FOXO3 affects testosterone synthesis by inhibiting the formation of StAR protein. LH hormone, meanwhile, influences Foxo3 localization, mediating its function.
Collapse
Affiliation(s)
- Young Suk Choi
- Endocrinology, Institute of Endocrine Research, Brain Korea 21 PLUS Project for Medical Science and Yonsei University College of Medicine, Seoul, Korea
| | - Joo Eun Song
- Endocrinology, Institute of Endocrine Research, Brain Korea 21 PLUS Project for Medical Science and Yonsei University College of Medicine, Seoul, Korea
| | - Byung Soo Kong
- Endocrinology, Institute of Endocrine Research, Brain Korea 21 PLUS Project for Medical Science and Yonsei University College of Medicine, Seoul, Korea
| | - Jae Won Hong
- Department of Internal Medicine, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Korea
| | - Silvia Novelli
- Endocrinology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eun Jig Lee
- Endocrinology, Institute of Endocrine Research, Brain Korea 21 PLUS Project for Medical Science and Yonsei University College of Medicine, Seoul, Korea.
| |
Collapse
|
7
|
Lee WY. Articles in 'endocrinology and metabolism' in 2014. Endocrinol Metab (Seoul) 2015; 30:47-52. [PMID: 25827457 PMCID: PMC4384668 DOI: 10.3803/enm.2015.30.1.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Won Young Lee
- Department of Endocrinology and Metabolism, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea.
| |
Collapse
|