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Rodriguez MC, Mehta D, Tan M, Uhrig RG. Quantitative Proteome and PTMome Analysis of Arabidopsis thaliana Root Responses to Persistent Osmotic and Salinity Stress. PLANT & CELL PHYSIOLOGY 2021; 62:1012-1029. [PMID: 34059891 DOI: 10.1093/pcp/pcab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h to d) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while post-translational modifications (PTMs) do not. Further, we find significant changes in PTMs, and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulfur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
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Affiliation(s)
- Maria C Rodriguez
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Richard G Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
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2
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Caccavale F, Annona G, Subirana L, Escriva H, Bertrand S, D'Aniello S. Crosstalk between nitric oxide and retinoic acid pathways is essential for amphioxus pharynx development. eLife 2021; 10:e58295. [PMID: 34431784 PMCID: PMC8387019 DOI: 10.7554/elife.58295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
During animal ontogenesis, body axis patterning is finely regulated by complex interactions among several signaling pathways. Nitric oxide (NO) and retinoic acid (RA) are potent morphogens that play a pivotal role in vertebrate development. Their involvement in axial patterning of the head and pharynx shows conserved features in the chordate phylum. Indeed, in the cephalochordate amphioxus, NO and RA are crucial for the correct development of pharyngeal structures. Here, we demonstrate the functional cooperation between NO and RA that occurs during amphioxus embryogenesis. During neurulation, NO modulates RA production through the transcriptional regulation of Aldh1a.2 that irreversibly converts retinaldehyde into RA. On the other hand, RA directly or indirectly regulates the transcription of Nos genes. This reciprocal regulation of NO and RA pathways is essential for the normal pharyngeal development in amphioxus and it could be conserved in vertebrates.
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Affiliation(s)
- Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn NapoliNapoliItaly
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn NapoliNapoliItaly
| | - Lucie Subirana
- Sorbonne Université CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Hector Escriva
- Sorbonne Université CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Stephanie Bertrand
- Sorbonne Université CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn NapoliNapoliItaly
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Li J, Guo Y, Deng Y, Hu L, Li B, Deng S, Zhong J, Xie L, Shi S, Hong X, Zheng X, Cai M, Li M. Subcellular Localization of Epstein-Barr Virus BLLF2 and Its Underlying Mechanisms. Front Microbiol 2021; 12:672192. [PMID: 34367081 PMCID: PMC8339435 DOI: 10.3389/fmicb.2021.672192] [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: 02/25/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Epstein-Barr virus (EBV), the pathogen of several human malignancies, encodes many proteins required to be transported into the nucleus for viral DNA reproduction and nucleocapsids assembly in the lytic replication cycle. Here, fluorescence microscope, mutation analysis, interspecies heterokaryon assays, co-immunoprecipitation assay, RNA interference, and Western blot were performed to explore the nuclear import mechanism of EBV encoded BLLF2 protein. BLLF2 was shown to be a nucleocytoplasmic shuttling protein neither by a chromosomal region maintenance 1 (CRM1)- nor by a transporter associated with antigen processing (TAP)-dependent pathway. Yet, BLLF2's two functional nuclear localization signals (NLSs), NLS1 (16KRQALETVPHPQNRGR31) and NLS2 (44RRPRPPVAKRRRFPR58), were identified, whereas the predicted NES was nonfunctional. Finally, BLLF2 was proven to transport into the nucleus via a Ran-dependent and importin β1-dependent pathway. This mechanism may contribute to a more extensive insight into the assembly and synthesis of EBV virions in the nucleus, thus affording a new direction for the treatment of viruses.
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Affiliation(s)
- Jingjing Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yingjie Guo
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yangxi Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Hu
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Bolin Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Shenyu Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jiayi Zhong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Xie
- Centralab, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Shaoxuan Shi
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xuejun Hong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xuelong Zheng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Mingsheng Cai
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Meili Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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Peng X, Wang T, Gao H, Yue X, Bian W, Mei J, Zhang Y. The interplay between IQGAP1 and small GTPases in cancer metastasis. Biomed Pharmacother 2021; 135:111243. [PMID: 33434854 DOI: 10.1016/j.biopha.2021.111243] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/31/2020] [Indexed: 01/07/2023] Open
Abstract
The metastatic spread of tumor cells to distant anatomical locations is a critical cause for disease progression and leads to more than 90 % of cancer-related deaths. IQ motif-containing GTPase-activating protein 1 (IQGAP1), a prominent regulator in the cancer metastasis process, is a scaffold protein that interacts with components of the cytoskeleton. As a critical node within the small GTPase network, IQGAP1 acts as a binding partner of several small GTPases, which in turn function as molecular switches to control most cellular processes, including cell migration and invasion. Given the significant interaction between IQGAP1 and small GTPases in cancer metastasis, we briefly elucidate the role of IQGAP1 in regulating cancer metastasis and the varied interactions existing between IQGAP1 and small GTPases. In addition, the potential regulators for IQGAP1 activity and its interaction with small GTPases are also incorporated in this review. Overall, we comprehensively summarize the role of IQGAP1 in cancer tumorigenicity and metastasis, which may be a potential anti-tumor target to restrain cancer progression.
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Affiliation(s)
- Xiafeng Peng
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China; First Clinical Medicine College, Nanjing Medical University, Nanjing, 211166, China.
| | - Tiejun Wang
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China.
| | - Han Gao
- School of Medicine, Jiangnan University, Wuxi, 214122, China.
| | - Xin Yue
- First Clinical Medicine College, Nanjing Medical University, Nanjing, 211166, China.
| | - Weiqi Bian
- First Clinical Medicine College, Nanjing Medical University, Nanjing, 211166, China.
| | - Jie Mei
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China; Wuxi Clinical Medical College, Nanjing Medical University, Wuxi, 214023, China.
| | - Yan Zhang
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital, the Affiliated Hospital to Nanjing Medical University, Wuxi, 214023, China.
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Coppola U, Olivo P, D’Aniello E, Johnson CJ, Stolfi A, Ristoratore F. Rimbp, a New Marker for the Nervous System of the Tunicate Ciona robusta. Genes (Basel) 2020; 11:genes11091006. [PMID: 32867148 PMCID: PMC7565545 DOI: 10.3390/genes11091006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/16/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Establishment of presynaptic mechanisms by proteins that regulate neurotransmitter release in the presynaptic active zone is considered a fundamental step in animal evolution. Rab3 interacting molecule-binding proteins (Rimbps) are crucial components of the presynaptic active zone and key players in calcium homeostasis. Although Rimbp involvement in these dynamics has been described in distantly related models such as fly and human, the role of this family in most invertebrates remains obscure. To fill this gap, we defined the evolutionary history of Rimbp family in animals, from sponges to mammals. We report, for the first time, the expression of the two isoforms of the unique Rimbp family member in Ciona robusta in distinct domains of the larval nervous system. We identify intronic enhancers that are able to drive expression in different nervous system territories partially corresponding to Rimbp endogenous expression. The analysis of gene expression patterns and the identification of regulatory elements of Rimbp will positively impact our understanding of this family of genes in the context of Ciona embryogenesis.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Paola Olivo
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
| | - Enrico D’Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Correspondence: (A.S.); (F.R.)
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
- Correspondence: (A.S.); (F.R.)
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Coppola U, Ristoratore F, Albalat R, D'Aniello S. The evolutionary landscape of the Rab family in chordates. Cell Mol Life Sci 2019; 76:4117-4130. [PMID: 31028425 PMCID: PMC11105323 DOI: 10.1007/s00018-019-03103-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/30/2022]
Abstract
Intracellular traffic amongst organelles represents a key feature for eukaryotes and is orchestrated principally by members of Rab family, the largest within Ras superfamily. Given that variations in Rab repertoire have been fundamental in animal diversification, we provided the most exhaustive survey regarding the Rab toolkit of chordates. Our findings reveal the existence of 42 metazoan conserved subfamilies exhibiting a univocal intron/exon structure preserved from cnidarians to vertebrates. Since the current view does not capture the Rab complexity, we propose a new Rab family classification in three distinct monophyletic clades. The Rab complement of chordates shows a dramatic diversification due to genome duplications and independent gene duplications and losses with sharp differences amongst cephalochordates, tunicates and gnathostome vertebrates. Strikingly, the analysis of the domain architecture of this family highlighted the existence of chimeric calcium-binding Rabs, which are animal novelties characterized by a complex evolutionary history in gnathostomes and whose role in cellular metabolism is obscure. This work provides novel insights in the knowledge of Rab family: our hypothesis is that chordates represent a hotspot of Rab variability, with many events of gene gains and losses impacting intracellular traffic capabilities. Our results help to elucidate the role of Rab members in the transport amongst endomembranes and shed light on intracellular traffic routes in vertebrates. Then, since the predominant role of Rabs in the molecular communication between different cellular districts, this study paves to way to comprehend inherited or acquired human disorders provoked by dysfunctions in Rab genes.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale 1, 80121, Naples, Italy
- Molecular Cardiovascular Biology Division, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale 1, 80121, Naples, Italy
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain.
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale 1, 80121, Naples, Italy.
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