1
|
Zheng Y, Yang M, Chen X, Zhang G, Wan S, Zhang B, Huo J, Liu H. Decreased tubulin-binding cofactor B was involved in the formation disorder of nascent astrocyte processes by regulating microtubule plus-end growth through binding with end-binding proteins 1 and 3 after chronic alcohol exposure. Front Cell Neurosci 2022; 16:989945. [PMID: 36385945 PMCID: PMC9641617 DOI: 10.3389/fncel.2022.989945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022] Open
Abstract
Fetal alcohol syndrome (FAS) is a neurological disease caused by excessive drinking during pregnancy and characterized by congenital abnormalities in the structure and function of the fetal brain. This study was proposed to provide new insights into the pathogenesis of FAS by revealing the possible mechanisms of alcohol-induced astrocyte injury. First, a chronic alcohol exposure model of astrocytes was established, and the formation disorder was found in astrocyte processes where tubulin-binding cofactor B (TBCB) was decreased or lost, accompanied by disorganized microtubules (MT). Second, to understand the relationship between TBCB reduction and the formation disorder of astrocyte processes, TBCB was silenced or overexpressed. It caused astrocyte processes to retract or lose after silencing, while the processes increased with expending basal part and obtuse tips after overexpressing. It confirmed that TBCB was one of the critical factors for the formation of astrocyte processes through regulating MT plus-end and provided a new view on the pathogenesis of FAS. Third, to explore the mechanism of TBCB regulating MT plus-ends, we first proved end-binding proteins 1 and 3 (EB1/3) were bound at MT plus-ends in astrocytes. Then, through interference experiments, we found that both EB1 and EB3, which formed in heterodimers, were necessary to mediate TBCB binding to MT plus-ends and thus regulated the formation of astrocyte processes. Finally, the regulatory mechanism was studied and the ERK1/2 signaling pathway was found as one of the main pathways regulating the expression of TBCB in astrocytes after alcohol injury.
Collapse
Affiliation(s)
- Yin Zheng
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China
- Department of Basic Medicine, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Mei Yang
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Xiaoqiao Chen
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Gaoli Zhang
- Institute for Viral Hepatitis, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shanshan Wan
- Department of Blood Transfusion, Sichuan Cancer Hospital and Institute, Chengdu, China
| | - Bingqiu Zhang
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Jiechao Huo
- Fujian Province University Engineering Research Center of Mindong She Medicine, Medical College, Ningde Normal University, Ningde, China
| | - Hui Liu
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China
- *Correspondence: Hui Liu
| |
Collapse
|
2
|
Kashani-Amin E, Tabatabaei-Malazy O, Sakhteman A, Larijani B, Ebrahim-Habibi A. A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools. Curr Drug Discov Technol 2020; 16:159-172. [PMID: 29493456 DOI: 10.2174/1570163815666180227162157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 02/15/2018] [Accepted: 02/22/2018] [Indexed: 01/22/2023]
Abstract
BACKGROUND Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. OBJECTIVE A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. METHODS Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. RESULTS Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. CONCLUSION This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.
Collapse
Affiliation(s)
- Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ozra Tabatabaei-Malazy
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Medicinal Chemistry and Natural Products Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
3
|
Su S, Hou Z, Liu D, Jia C, Wang L, Xu J, Tao J. Comparative transcriptome analysis of Eimeria necatrix third-generation merozoites and gametocytes reveals genes involved in sexual differentiation and gametocyte development. Vet Parasitol 2018; 252:35-46. [PMID: 29559148 DOI: 10.1016/j.vetpar.2018.01.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 11/17/2022]
Abstract
Eimeria necatrix is one of the most pathogenic parasites causing high mortality in chicken older than 8 weeks. Eimeria spp. possess a coccidian lifecycle including both sexual and asexual stages. Sexual differentiation and development occupies a central place in the life cycle of the Eimeria parasite. However, our knowledge of the sexual differentiation and gametocyte development of Eimeria is very limited. Here using RNA sequencing, we conducted a comparative transcriptome analysis between third-generation merozoites (MZ-3) and gametocytes (GAM) of E. necatrix to identify genes with functions related to sexual differentiation and gametocyte development. Approximately 4267 genes were differentially expressed between MZ-3 and GAM. Compared with MZ-3, 2789 genes were upregulated and 1478 genes were downregulated in GAM. Approximately 329 genes in MZ-3 and 1289 genes in GAM were further analyzed in the evaluation of stage-specific genes. Gene Ontology (GO) classification and KEGG analysis revealed that 953 upregulated gametocyte genes were annotated with 170 GO assignments, and 405 upregulated genes were associated with 231 signaling pathways. We also predicted a further 83 upregulated gametocyte genes, of which 53 were involved in the biosynthesis of the oocyst wall, and 30 were involved in microgametocyte development. This information offers insights into the mechanisms governing the sexual development of E. necatrix and may potentially allow the identification of targets for blocking parasite transmission.
Collapse
Affiliation(s)
- Shijie Su
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Zhaofeng Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Dandan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Chuanli Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Lele Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China.
| |
Collapse
|
4
|
Nithianantham S, Le S, Seto E, Jia W, Leary J, Corbett KD, Moore JK, Al-Bassam J. Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics. eLife 2015. [PMID: 26208336 PMCID: PMC4574351 DOI: 10.7554/elife.08811] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microtubule dynamics and polarity stem from the polymerization of
αβ-tubulin heterodimers. Five conserved tubulin cofactors/chaperones
and the Arl2 GTPase regulate α- and β-tubulin assembly into
heterodimers and maintain the soluble tubulin pool in the cytoplasm, but their
physical mechanisms are unknown. Here, we reconstitute a core tubulin chaperone
consisting of tubulin cofactors TBCD, TBCE, and Arl2, and reveal a cage-like
structure for regulating αβ-tubulin. Biochemical assays and electron
microscopy structures of multiple intermediates show the sequential binding of
αβ-tubulin dimer followed by tubulin cofactor TBCC onto this chaperone,
forming a ternary complex in which Arl2 GTP hydrolysis is activated to alter
αβ-tubulin conformation. A GTP-state locked Arl2 mutant inhibits
ternary complex dissociation in vitro and causes severe defects in microtubule
dynamics in vivo. Our studies suggest a revised paradigm for tubulin cofactors and
Arl2 functions as a catalytic chaperone that regulates soluble
αβ-tubulin assembly and maintenance to support microtubule
dynamics. DOI:http://dx.doi.org/10.7554/eLife.08811.001 Cells contain a network of protein filaments called microtubules. These filaments are
involved in many biological processes; for example, they help cells keep the right
shape, and they help to transport proteins and other materials inside cells. Two proteins called α-tubulin and β-tubulin are the building blocks of
microtubules. The filaments are very dynamic structures that can rapidly change
length as individual tubulin units are either added or removed to the filament ends.
Several proteins known as tubulin cofactors and an enzyme called Arl2 help to build a
vast pool of tubulin units that are able attach to the microtubules. These
units—called αβ-tubulin—are formed by α-tubulin
and β-tubulin binding to each other, but it not clear exactly what roles the
tubulin cofactors and Arl2 play in this process. Nithianantham et al. used a combination of microscopy and biochemical techniques to
study how the tubulin cofactors and Arl2 are organised, and their role in the
assembly of microtubules in yeast. The experiments show that Arl2 and two tubulin
cofactors associate with each other to form a stable ‘complex’ that has
a cage-like structure. A molecule of αβ-tubulin binds to the complex,
followed by another cofactor called TBCC. This activates the enzyme activity of Arl2,
which releases the energy needed to alter the shape of the αβ-tubulin.
Nithianantham et al. also found that yeast cells with a mutant form of Arl2 that
lacked enzyme activity had problems forming microtubules. Together, these findings show that the tubulin cofactors and Arl2 form a complex that
regulates the assembly and maintenance of αβ-tubulin. The next
challenge is to understand how this regulation influences the way that microtubules
grow and shrink inside cells. DOI:http://dx.doi.org/10.7554/eLife.08811.002
Collapse
Affiliation(s)
- Stanley Nithianantham
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Sinh Le
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Elbert Seto
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Weitao Jia
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Julie Leary
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Jawdat Al-Bassam
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| |
Collapse
|
5
|
Barrack KL, Fyfe PK, Finney AJ, Hunter WN. Crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major. Mol Biochem Parasitol 2015; 201:26-30. [PMID: 25982270 PMCID: PMC4539340 DOI: 10.1016/j.molbiopara.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 01/23/2023]
Abstract
Tubulin-binding cofactor C stimulates GTPase activity and contributes to the release of the heterodimeric α/β-tubulin from a super-complex of tubulin monomers and two ancillary cofactors. We have determined the 2.2 Å resolution crystal structure of the C-terminal domain of tubulin-binding cofactor C from Leishmania major based on single wavelength anomalous dispersion measurements targeting a selenomethionine derivative. Although previously predicted to consist of two domains the structure is best described as a single domain dominated by a right-handed β-helix of five turns that form a triangular prism. One face of the prism is covered by the C-terminal residues leaving another face solvent exposed. Comparisons with an orthologous human GTPase activating protein match key residues involved in binding nucleotide and identify the face of the β-helix fold likely involved in interacting with the β-tubulin:GTP complex.
Collapse
Affiliation(s)
- Keri L Barrack
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Paul K Fyfe
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alex J Finney
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - William N Hunter
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
| |
Collapse
|
6
|
Barrack KL, Fyfe PK, Hunter WN. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly. Acta Crystallogr F Struct Biol Commun 2015; 71:539-46. [PMID: 25945706 PMCID: PMC4427162 DOI: 10.1107/s2053230x15000990] [Citation(s) in RCA: 3] [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: 11/25/2014] [Accepted: 01/16/2015] [Indexed: 11/13/2022] Open
Abstract
Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.
Collapse
Affiliation(s)
- Keri L. Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Paul K. Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| |
Collapse
|