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Gupta T, Chahota R. Unique ankyrin repeat proteins in the genome of poxviruses-Boon or Wane, a critical review. Gene 2024; 927:148759. [PMID: 38992761 DOI: 10.1016/j.gene.2024.148759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/29/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Ankyrin repeat is a 33-amino acid motif commonly observed in eukaryotes and, to a lesser extent, in prokaryotes and archaea and rarely in viruses. This motif plays a crucial role in regulating various cellular processes like the cell cycle, transcription, cell signaling, and inflammatory responses through interactions between proteins. Poxviruses exhibit a distinctive feature of containing multiple ankyrin repeat proteins within their genomes. All the genera of poxviruses possess these proteins except molluscipox virus, crocodylidpox virus, and red squirrel poxvirus. An intriguing characteristic has generated notable interest in studying the functions of these proteins within poxvirus biology. Within poxviruses, ankyrin repeat proteins exhibit a distinct configuration, featuring ankyrin repeats in the N-terminal region and a cellular F-box homolog in the C-terminal region, which enables interactions with the cellular Skp, Cullin, F-box containing ubiquitin ligase complex. Through the examination of experimental evidences and discussions from current literature, this review elucidates the organization and role of ankyrin repeat proteins in poxviruses. Various research studies have highlighted the significant importance of these proteins in poxviral pathogenesis and, acting as factors that enhance virulence. Consequently, they represent viable targets for developing genetically altered viruses with decreased virulence, thus displaying potential as candidates for vaccines and antiviral therapeutic development contributing to safer and more effective strategies against poxviral infections.
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Affiliation(s)
- Tania Gupta
- Department of Veterinary Microbiology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, 141012 India; Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, 176062 India
| | - Rajesh Chahota
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, 176062 India.
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2
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Li L, Yang J, Zhang Q, Xue Q, Li M, Xue Q, Liu W, Niu Z, Ding X. Genome-wide identification of Ankyrin (ANK) repeat gene families in three Dendrobium species and the expression of ANK genes in D. officinale under gibberellin and abscisic acid treatments. BMC PLANT BIOLOGY 2024; 24:762. [PMID: 39123107 PMCID: PMC11316315 DOI: 10.1186/s12870-024-05461-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Dendrobium Sw. represents one of the most expansive genera within the Orchidaceae family, renowned for its species' high medicinal and ornamental value. In higher plants, the ankyrin (ANK) repeat protein family is characterized by a unique ANK repeat domain, integral to a plethora of biological functions and biochemical activities. The ANK gene family plays a pivotal role in various plant physiological processes, including stress responses, hormone signaling, and growth. Hence, investigating the ANK gene family and identifying disease-resistance genes in Dendrobium is of paramount importance. RESULTS This research identified 78 ANK genes in Dendrobium officinale Kimura et Migo, 77 in Dendrobium nobile Lindl., and 58 in Dendrobium chrysotoxum Lindl. Subsequently, we conducted comprehensive bioinformatics analyses on these ANK gene families, encompassing gene classification, chromosomal localization, phylogenetic relationships, gene structure and motif characterization, cis-acting regulatory element identification, collinearity assessment, protein-protein interaction network construction, and gene expression profiling. Concurrently, three DoANK genes (DoANK14, DoANK19, and DoANK47) in D. officinale were discerned to indirectly activate the NPR1 transcription factor in the ETI system via SA, thereby modulating the expression of the antibacterial PR gene. Hormonal treatments with GA3 and ABA revealed that 17 and 8 genes were significantly up-regulated, while 4 and 8 genes were significantly down-regulated, respectively. DoANK32 was found to localize to the ArfGAP gene in the endocytosis pathway, impacting vesicle transport and the polar movement of auxin. CONCLUSION Our findings provide a robust framework for the taxonomic classification, evolutionary analysis, and functional prediction of Dendrobium ANK genes. The three highlighted ANK genes (DoANK14, DoANK19, and DoANK47) from D. officinale may prove valuable in disease resistance and stress response research. DoANK32 is implicated in the morphogenesis and development of D. officinale through its role in vesicular transport and auxin polarity, with subcellular localization studies confirming its presence in the nucleus and cell membrane. ANK genes displaying significant expression changes in response to hormonal treatments could play a crucial role in the hormonal response of D. officinale, potentially inhibiting its growth and development through the modulation of plant hormones such as GA3 and ABA.
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Affiliation(s)
- Lingli Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Qian Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Qiqian Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Meiqian Li
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing, China.
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Costantini M, Esposito R, Ruocco N, Caramiello D, Cordella A, Ventola GM, Zupo V. De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816). Int J Mol Sci 2024; 25:1685. [PMID: 38338963 PMCID: PMC10855541 DOI: 10.3390/ijms25031685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans.
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Affiliation(s)
- Maria Costantini
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Via Ammiraglio Ferdinando Acton n. 55, 80133 Napoli, Italy;
| | - Roberta Esposito
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Via Ammiraglio Ferdinando Acton n. 55, 80133 Napoli, Italy;
| | - Nadia Ruocco
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Calabria Marine Centre, C.da Torre Spaccata, 87071 Amendolara, Italy;
| | - Davide Caramiello
- Stazione Zoologica Anton Dohrn, Department of Marine Animal Conservation and Public Engagement, Villa Comunale, 1, 80121 Naples, Italy;
| | - Angela Cordella
- Genomix4Life S.r.l., Baronissi, 84081 Salerno, Italy; (A.C.); (G.M.V.)
- Genome Research Center for Health-CRGS, Baronissi, 84081 Salerno, Italy
| | | | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, Department of Ecosustainable Marine Biotechnology, Ischia Marine Centre, 80121 Naples, Italy
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Davarinejad H, Arvanitis-Vigneault A, Nygard D, Lavallée-Adam M, Couture JF. Modus operandi: Chromatin recognition by α-helical histone readers. Structure 2024; 32:8-17. [PMID: 37922903 DOI: 10.1016/j.str.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Histone reader domains provide a mechanism for sensing states of coordinated nuclear processes marked by histone proteins' post-translational modifications (PTMs). Among a growing number of discovered histone readers, the 14-3-3s, ankyrin repeat domains (ARDs), tetratricopeptide repeats (TPRs), bromodomains (BRDs), and HEAT domains are a group of domains using various mechanisms to recognize unmodified or modified histones, yet they all are composed of an α-helical fold. In this review, we compare how these readers fold to create protein domains that are very diverse in their tertiary structures, giving rise to intriguing peptide binding mechanisms resulting in vastly different footprints of their targets.
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Affiliation(s)
- Hossein Davarinejad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Alexis Arvanitis-Vigneault
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Dallas Nygard
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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Mullenger JL, Zeidler MP, Fragiadaki M. Evaluating the Molecular Properties and Function of ANKHD1, and Its Role in Cancer. Int J Mol Sci 2023; 24:12834. [PMID: 37629022 PMCID: PMC10454556 DOI: 10.3390/ijms241612834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Ankyrin repeat and single KH domain-containing protein 1 (ANKHD1) is a large, scaffolding protein composed of two stretches of ankyrin repeat domains that mediate protein-protein interactions and a KH domain that mediates RNA or single-stranded DNA binding. ANKHD1 interacts with proteins in several crucial signalling pathways, including receptor tyrosine kinase, JAK/STAT, mechanosensitive Hippo (YAP/TAZ), and p21. Studies into the role of ANKHD1 in cancer cell lines demonstrate a crucial role in driving uncontrolled cellular proliferation and growth, enhanced tumorigenicity, cell cycle progression through the S phase, and increased epithelial-to-mesenchymal transition. Furthermore, at a clinical level, the increased expression of ANKHD1 has been associated with greater tumour infiltration, increased metastasis, and larger tumours. Elevated ANKHD1 resulted in poorer prognosis, more aggressive growth, and a decrease in patient survival in numerous cancer types. This review aims to gather the current knowledge about ANKHD1 and explore its molecular properties and functions, focusing on the protein's role in cancer at both a cellular and clinical level.
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Affiliation(s)
- Jordan L. Mullenger
- Department of Infection, Immunity, and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK;
- Department of Translational Medicine and Therapeutics, Queen Mary University London, London E1 4NS, UK
| | - Martin P. Zeidler
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK;
| | - Maria Fragiadaki
- Department of Translational Medicine and Therapeutics, Queen Mary University London, London E1 4NS, UK
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6
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Gabriele F, Palerma M, Ippoliti R, Angelucci F, Pitari G, Ardini M. Recent Advances on Affibody- and DARPin-Conjugated Nanomaterials in Cancer Therapy. Int J Mol Sci 2023; 24:ijms24108680. [PMID: 37240041 DOI: 10.3390/ijms24108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Affibodies and designed ankyrin repeat proteins (DARPins) are synthetic proteins originally derived from the Staphylococcus aureus virulence factor protein A and the human ankyrin repeat proteins, respectively. The use of these molecules in healthcare has been recently proposed as they are endowed with biochemical and biophysical features heavily demanded to target and fight diseases, as they have a strong binding affinity, solubility, small size, multiple functionalization sites, biocompatibility, and are easy to produce; furthermore, impressive chemical and thermal stability can be achieved. especially when using affibodies. In this sense, several examples reporting on affibodies and DARPins conjugated to nanomaterials have been published, demonstrating their suitability and feasibility in nanomedicine for cancer therapy. This minireview provides a survey of the most recent studies describing affibody- and DARPin-conjugated zero-dimensional nanomaterials, including inorganic, organic, and biological nanoparticles, nanorods, quantum dots, liposomes, and protein- and DNA-based assemblies for targeted cancer therapy in vitro and in vivo.
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Affiliation(s)
- Federica Gabriele
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Marta Palerma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Giuseppina Pitari
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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7
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Feng H, Chen W, Hussain S, Shakir S, Tzin V, Adegbayi F, Ugine T, Fei Z, Jander G. Horizontally transferred genes as RNA interference targets for aphid and whitefly control. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:754-768. [PMID: 36577653 PMCID: PMC10037149 DOI: 10.1111/pbi.13992] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
RNA interference (RNAi)-based technologies are starting to be commercialized as a new approach for agricultural pest control. Horizontally transferred genes (HTGs), which have been transferred into insect genomes from viruses, bacteria, fungi or plants, are attractive targets for RNAi-mediated pest control. HTGs are often unique to a specific insect family or even genus, making it unlikely that RNAi constructs targeting such genes will have negative effects on ladybugs, lacewings and other beneficial predatory insect species. In this study, we sequenced the genome of a red, tobacco-adapted isolate of Myzus persicae (green peach aphid) and bioinformatically identified 30 HTGs. We then used plant-mediated virus-induced gene silencing (VIGS) to show that several HTGs of bacterial and plant origin are important for aphid growth and/or survival. Silencing the expression of fungal-origin HTGs did not affect aphid survivorship but decreased aphid reproduction. Importantly, although there was uptake of plant-expressed RNA by Coccinella septempunctata (seven-spotted ladybugs) via the aphids that they consumed, we did not observe negative effects on ladybugs from aphid-targeted VIGS constructs. To demonstrate that this approach is more broadly applicable, we also targeted five Bemisia tabaci (whitefly) HTGs using VIGS and demonstrated that knockdown of some of these genes affected whitefly survival. As functional HTGs have been identified in the genomes of numerous pest species, we propose that these HTGs should be explored further as efficient and safe targets for control of insect pests using plant-mediated RNA interference.
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Affiliation(s)
| | - Wenbo Chen
- Boyce Thompson InstituteIthacaNYUSA
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative BiologyZhejiang UniversityHangzhouChina
| | - Sonia Hussain
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
National Institute for Biotechnology and Genetic Engineering CollegePakistan Institute of Engineering and Applied SciencesFaisalabadPakistan
| | - Sara Shakir
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Gembloux Agro‐Bio Tech InstituteThe University of LiegeGemblouxBelgium
| | - Vered Tzin
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Jacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSede BoqerIsrael
| | - Femi Adegbayi
- Boyce Thompson InstituteIthacaNYUSA
- Present address:
Drexel University College of MedicinePhiladelphiaPAUSA
| | - Todd Ugine
- Department of EntomologyCornell UniversityIthacaNYUSA
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8
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Walser M, Mayor J, Rothenberger S. Designed Ankyrin Repeat Proteins: A New Class of Viral Entry Inhibitors. Viruses 2022; 14:2242. [PMID: 36298797 PMCID: PMC9611651 DOI: 10.3390/v14102242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 08/08/2023] Open
Abstract
Designed ankyrin repeat proteins (DARPins) are engineered proteins comprising consensus designed ankyrin repeats as scaffold. Tightly packed repeats form a continuous hydrophobic core and a large groove-like solvent-accessible surface that creates a binding surface. DARPin domains recognizing a target of interest with high specificity and affinity can be generated using a synthetic combinatorial library and in vitro selection methods. They can be linked together in a single molecule to build multispecific and multifunctional proteins without affecting expression or function. The modular architecture of DARPins offers unprecedented possibilities of design and opens avenues for innovative antiviral strategies.
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Affiliation(s)
- Marcel Walser
- Molecular Partners AG, Wagistrasse 14, 8952 Zurich-Schlieren, Switzerland
| | - Jennifer Mayor
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
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9
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Wang Y, Zhang Y, Mi J, Jiang C, Wang Q, Li X, Zhao M, Geng Z, Song X, Li J, Zuo L, Ge S, Zhang Z, Wen H, Wang Z, Su F. ANKFN1 plays both protumorigenic and metastatic roles in hepatocellular carcinoma. Oncogene 2022; 41:3680-3693. [PMID: 35725908 PMCID: PMC9287179 DOI: 10.1038/s41388-022-02380-0] [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: 10/19/2021] [Revised: 05/19/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
Ankyrin repeat and fibronectin type III domain containing 1 (ANKFN1) is reported to be involved in human height and developmental abnormalities, but the expression profile and molecular function of ANKFN1 in hepatocellular carcinoma (HCC) remain unknown. This study aimed to evaluate the clinical significance and biological function of ANKFN1 in HCC and investigate whether ANKFN1 can be used for differential diagnosis in HCC. Here, we showed that ANKFN1 was upregulated in 126 tumor tissues compared with adjacent nontumorous tissues in HCC patients. The upregulation of ANKFN1 in HCC was associated with cirrhosis, alpha-fetoprotein (AFP) levels and poor prognosis. Moreover, silencing ANKFN1 expression suppressed HCC cell proliferation, migration, invasion, and metastasis in vitro and subcutaneous tumorigenesis in vivo. However, ANKFN1 overexpression promoted HCC proliferation and metastasis in an orthotopic liver transplantation model and attenuated the above biological effects in HCC cells. ANKFN1 significantly affected HCC cell proliferation by inducing G1/S transition and cell apoptosis. Mechanistically, we demonstrated that ANKFN1 promoted cell proliferation, migration, and invasion via activation of the cyclin D1/Cdk4/Cdk6 pathway by stimulating the MEK1/2-ERK1/2 pathway. Moreover, ANKFN1-induced cell proliferation, migration, and invasion were partially reversed by ERK1/2 inhibitors. Taken together, our results indicate that ANKFN1 promotes HCC cell proliferation and metastasis by activating the MEK1/2-ERK1/2 signaling pathway. Our work also suggests that ANKFN1 is a potential therapeutic target for HCC.
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Affiliation(s)
- Yanyan Wang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Yue Zhang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Jiaqi Mi
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Chenchen Jiang
- Cancer Neurobiology Group, School of Biomedical Sciences & Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.,School of Medicine & Public Health, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Qiang Wang
- Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Xinwei Li
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Menglin Zhao
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Zhijun Geng
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Xue Song
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Jing Li
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Lugen Zuo
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Sitang Ge
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Zining Zhang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Hexin Wen
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China
| | - Zishu Wang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China.
| | - Fang Su
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, PR China.
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10
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein–protein and protein–RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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Cui H, Fan C, Ding Z, Wang X, Tang L, Bi Y, Luan F, Gao P. CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in Melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1209-1222. [PMID: 34989827 DOI: 10.1007/s00122-021-04025-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Two genes for resistance to Podosphaera xanthii race 1 in melon were identified on chromosomes 10 and 12 of the Cucumis melo cultivar MR-1. Cucumis melo L. is an economically important crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P1; resistant to PM) and M4-7 (P2; susceptible to PM) accessions to assess the heritability of PM (race 1) resistance in these melon plants. PM resistance in MR-1 leaves was linked to a dominant gene (CmPMRl), whereas stem resistance was under the control of a recessive gene (CmPMrs), with the dominant gene having an epistatic effect on the recessive gene. The CmPMRl gene was mapped to a 50 Kb interval on chromosome 12, while CmPMrs was mapped to an 89 Kb interval on chromosome 10. The CmPMRl candidate gene MELO3C002441 and the CmPMrs candidate gene MELO3C012438 were identified through sequence alignment, functional annotation, and expression pattern analyzes of all genes within these respective intervals. MELO3C002441 and MELO3C012438 were both localized to the cellular membrane and were contained conserved NPR gene-like and MLO domains, respectively, which were linked to PM resistance. In summary, we identified patterns of PM resistance in the disease-resistant MR-1 melon cultivar and identified two putative genes linked to resistance. Our results offer new genetic resources and markers to guide future marker-assisted breeding for PM resistance in melon.
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Affiliation(s)
- Haonan Cui
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China
| | - Chao Fan
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150030, Heilongjiang, China
| | - Zhuo Ding
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China
| | - Lili Tang
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150030, Heilongjiang, China
| | - Yingdong Bi
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150030, Heilongjiang, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China.
| | - Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, No. 600 Changjiang Street, Harbin, 150030, Heilongjiang, China.
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, 150030, Heilongjiang, China.
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12
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Notch signaling pathway: architecture, disease, and therapeutics. Signal Transduct Target Ther 2022; 7:95. [PMID: 35332121 PMCID: PMC8948217 DOI: 10.1038/s41392-022-00934-y] [Citation(s) in RCA: 291] [Impact Index Per Article: 145.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
The NOTCH gene was identified approximately 110 years ago. Classical studies have revealed that NOTCH signaling is an evolutionarily conserved pathway. NOTCH receptors undergo three cleavages and translocate into the nucleus to regulate the transcription of target genes. NOTCH signaling deeply participates in the development and homeostasis of multiple tissues and organs, the aberration of which results in cancerous and noncancerous diseases. However, recent studies indicate that the outcomes of NOTCH signaling are changeable and highly dependent on context. In terms of cancers, NOTCH signaling can both promote and inhibit tumor development in various types of cancer. The overall performance of NOTCH-targeted therapies in clinical trials has failed to meet expectations. Additionally, NOTCH mutation has been proposed as a predictive biomarker for immune checkpoint blockade therapy in many cancers. Collectively, the NOTCH pathway needs to be integrally assessed with new perspectives to inspire discoveries and applications. In this review, we focus on both classical and the latest findings related to NOTCH signaling to illustrate the history, architecture, regulatory mechanisms, contributions to physiological development, related diseases, and therapeutic applications of the NOTCH pathway. The contributions of NOTCH signaling to the tumor immune microenvironment and cancer immunotherapy are also highlighted. We hope this review will help not only beginners but also experts to systematically and thoroughly understand the NOTCH signaling pathway.
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13
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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14
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Massey JH, Newton ILG. Diversity and function of arthropod endosymbiont toxins. Trends Microbiol 2022; 30:185-198. [PMID: 34253453 PMCID: PMC8742837 DOI: 10.1016/j.tim.2021.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023]
Abstract
Bacterial endosymbionts induce dramatic phenotypes in their arthropod hosts, including cytoplasmic incompatibility, feminization, parthenogenesis, male killing, parasitoid defense, and pathogen blocking. The molecular mechanisms underlying these effects remain largely unknown but recent evidence suggests that protein toxins secreted by the endosymbionts play a role. Here, we describe the diversity and function of endosymbiont proteins with homology to known bacterial toxins. We focus on maternally transmitted endosymbionts belonging to the Wolbachia, Rickettsia, Arsenophonus, Hamiltonella, Spiroplasma, and Cardinium genera because of their ability to induce the above phenotypes. We identify at least 16 distinct toxin families with diverse enzymatic activities, including AMPylases, nucleases, proteases, and glycosyltransferases. Notably, several annotated toxins contain domains with homology to eukaryotic proteins, suggesting that arthropod endosymbionts mimic host biochemistry to manipulate host physiology, similar to bacterial pathogens.
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Affiliation(s)
| | - Irene L. G. Newton
- Department of Biology, Indiana University, Bloomington, Indiana, USA,Corresponding author,
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15
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Fang YD, Zhao J, Zhuang XJ, Xu JB, Cai TT, Yang XR, Mu KD, Zhang JA. Association of ANKRD55 Gene Polymorphism with HT: A Protective Factor for Disease Susceptibility. Int J Endocrinol 2022; 2022:7300796. [PMID: 35983018 PMCID: PMC9381225 DOI: 10.1155/2022/7300796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
PURPOSE Recent studies have shown that Ankyrin Repeat Domain 55 (ANKRD55) gene polymorphism is a risk factor for multiple autoimmune diseases, but its association with autoimmune thyroid diseases (AITDs) has not been reported. The purpose of this study was to investigate the potential relationship between polymorphism of the ANKRD55 gene and AITDs. METHODS For this study, we enrolled 2050 subjects, consisting of 1220 patients with AITD and 830 healthy subjects. Five loci (rs321776, rs191205, rs7731626, rs415407, and rs159572) of the ANKRD55 gene were genotyped using Multiplex PCR combined with high-throughput sequencing. RESULTS The results showed that the allele frequencies of rs7731626 and rs159572 loci in HT patients were lower than those in normal controls (P=0.048 and P=0.03, respectively). In different genetic model analyses, rs7731626 and rs159572 were also significantly correlated with HT in allele, dominant and additive models before and after age and sex adjustment. There were no differences in rs321776, rs191205, or rs415407 of the ANKRD55 gene in allele frequency or genotype frequency between AITDs patients and controls. CONCLUSIONS This study for the first time found that rs7731626 and rs159572 of ANKRD55 were significantly correlated with HT, and individuals carrying the A allele at these two loci had a lower probability of developing HT.
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Affiliation(s)
- Yu-die Fang
- Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jing Zhao
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Xin-juan Zhuang
- Department of Endocrinology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai 201318, China
| | - Jian-bin Xu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Tian-tian Cai
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Xiao-rong Yang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Kai-da Mu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Jin-an Zhang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
- Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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16
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Stephan OOH. Interactions, structural aspects, and evolutionary perspectives of the yeast 'START'-regulatory network. FEMS Yeast Res 2021; 22:6461095. [PMID: 34905017 DOI: 10.1093/femsyr/foab064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/11/2021] [Indexed: 11/12/2022] Open
Abstract
Molecular signal transduction networks which conduct transcription at the G1 to S phase transition of the eukaryotic cell division cycle have been identified in diverse taxa from mammals to baker´s yeast with analogous functional organization. However, regarding some network components, such as the transcriptional regulators STB1 and WHI5, only few orthologs exist which are confined to individual Saccharomycotina species. While Whi5 has been characterized as yeast analog of human Rb protein, in the particular case of Stb1 (Sin three binding protein 1) identification of functional analogs emerges as difficult because to date its exact functionality still remains obscured. By aiming to resolve Stb1´s enigmatic role this Perspectives article especially surveys works covering relations between Cyclin/CDKs, the heteromeric transcription factor complexes SBF (Swi4/Swi6) and MBF (Mbp1/Swi6), as well as additional coregulators (Whi5, Sin3, Rpd3, Nrm1) which are collectively associated with the orderly transcription at 'Start' of the Saccharomyces cerevisiae cell cycle. In this context, interaction capacities of the Sin3-scaffold protein are widely surveyed because its four PAH domains (Paired Amphiphatic Helix) represent a 'recruitment-code' for gene-specific targeting of repressive histone deacetylase activity (Rpd3) via different transcription factors. Here Stb1 plays a role in Sin3´s action on transcription at the G1/S-boundary. Through bioinformatic analyses a potential Sin3-interaction domain (SID) was detected in Stb1, and beyond that, connections within the G1/S-regulatory network are discussed in structural and evolutionary context thereby providing conceptual perspectives.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Bavaria, Germany
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17
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Genome-wide survey and characterization of ACD6-like genes in leguminous plants. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00829-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Folding and Stability of Ankyrin Repeats Control Biological Protein Function. Biomolecules 2021; 11:biom11060840. [PMID: 34198779 PMCID: PMC8229355 DOI: 10.3390/biom11060840] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ankyrin repeat proteins are found in all three kingdoms of life. Fundamentally, these proteins are involved in protein-protein interaction in order to activate or suppress biological processes. The basic architecture of these proteins comprises repeating modules forming elongated structures. Due to the lack of long-range interactions, a graded stability among the repeats is the generic properties of this protein family determining both protein folding and biological function. Protein folding intermediates were frequently found to be key for the biological functions of repeat proteins. In this review, we discuss most recent findings addressing this close relation for ankyrin repeat proteins including DARPins, Notch receptor ankyrin repeat domain, IκBα inhibitor of NFκB, and CDK inhibitor p19INK4d. The role of local folding and unfolding and gradual stability of individual repeats will be discussed during protein folding, protein-protein interactions, and post-translational modifications. The conformational changes of these repeats function as molecular switches for biological regulation, a versatile property for modern drug discovery.
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19
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Structural Insights into Ankyrin Repeat-Containing Proteins and Their Influence in Ubiquitylation. Int J Mol Sci 2021; 22:ijms22020609. [PMID: 33435370 PMCID: PMC7826745 DOI: 10.3390/ijms22020609] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Ankyrin repeat (AR) domains are considered the most abundant repeat motif found in eukaryotic proteins. AR domains are predominantly known to mediate specific protein-protein interactions (PPIs) without necessarily recognizing specific primary sequences, nor requiring strict conformity within its own primary sequence. This promiscuity allows for one AR domain to recognize and bind to a variety of intracellular substrates, suggesting that AR-containing proteins may be involved in a wide array of functions. Many AR-containing proteins serve a critical role in biological processes including the ubiquitylation signaling pathway (USP). There is also strong evidence that AR-containing protein malfunction are associated with several neurological diseases and disorders. In this review, the structure and mechanism of key AR-containing proteins are discussed to suggest and/or identify how each protein utilizes their AR domains to support ubiquitylation and the cascading pathways that follow upon substrate modification.
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20
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Ash1 and Tup1 dependent repression of the Saccharomyces cerevisiae HO promoter requires activator-dependent nucleosome eviction. PLoS Genet 2020; 16:e1009133. [PMID: 33382702 PMCID: PMC7806131 DOI: 10.1371/journal.pgen.1009133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/13/2021] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Transcriptional regulation of the Saccharomyces cerevisiae HO gene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in the HO promoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar to HO. We demonstrate that Ash1 binding to the HO promoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle. Nucleosomes inhibit both gene expression and DNA-binding by regulatory factors. Here we examine the role of nucleosomes in regulating the binding of repressive transcription factors to the complex promoter for the yeast HO gene. Ash1 is a sequence-specific DNA-binding protein, and we show that it recruits the Tup1 global repressive factor to the HO promoter. Using a method to determine where Ash1 and Tup1 are bound to DNA throughout the genome, we discovered that Tup1 is also present at most places where Ash1 binds. The majority of these sites are in “Nucleosome Depleted Regions,” or NDRs, where the absence of chromatin makes factor binding easier. We discovered that the HO promoter is an exception, in that the two places where Ash1 binds overlap nucleosomes. Activation of the HO promoter is a complex, multi-step process, and we demonstrated that chromatin factors transiently evict these nucleosomes from the HO promoter during the cell cycle, allowing Ash1 to bind and recruit Tup1. Thus, activators must evict nucleosomes from the promoter to allow the repressive machinery to bind.
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21
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22
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Steenwyk JL. A portrait of budding yeasts: A symbol of the arts, sciences and a whole greater than the sum of its parts. Yeast 2020; 38:54-56. [PMID: 32869892 DOI: 10.1002/yea.3518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Early Career Leadership Program Communication and Outreach Subcommittee, Genetics Society of America, Rockville, MD, USA
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23
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Lopez-Ortiz C, Peña-Garcia Y, Natarajan P, Bhandari M, Abburi V, Dutta SK, Yadav L, Stommel J, Nimmakayala P, Reddy UK. The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile. Sci Rep 2020; 10:4044. [PMID: 32132613 PMCID: PMC7055287 DOI: 10.1038/s41598-020-61057-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
The ankyrin (ANK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. It is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding ANK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. Next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. Phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. Our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper.
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Affiliation(s)
- Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Yadira Peña-Garcia
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.,Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India
| | - Menuka Bhandari
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Sudip Kumar Dutta
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.,ICAR RC NEH Region, Mizoram Centre, Kolasib, Mizoram, India
| | - Lav Yadav
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (USDA, ARS), Beltsville, MD, 20705, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.
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24
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Medina EM, Walsh E, Buchler NE. Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain. Curr Opin Genet Dev 2019; 58-59:103-110. [PMID: 31600629 DOI: 10.1016/j.gde.2019.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/27/2019] [Accepted: 08/31/2019] [Indexed: 10/25/2022]
Abstract
Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.
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Affiliation(s)
- Edgar M Medina
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Evan Walsh
- Bioinformatics Program, North Carolina State University, Raleigh, NC 27607, USA
| | - Nicolas E Buchler
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27606, USA.
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25
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Wolf D, Hofbrucker-MacKenzie SA, Izadi M, Seemann E, Steiniger F, Schwintzer L, Koch D, Kessels MM, Qualmann B. Ankyrin repeat-containing N-Ank proteins shape cellular membranes. Nat Cell Biol 2019; 21:1191-1205. [PMID: 31548610 DOI: 10.1038/s41556-019-0381-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 07/25/2019] [Indexed: 01/02/2023]
Abstract
Cells of multicellular organisms need to adopt specific morphologies. However, the molecular mechanisms bringing about membrane topology changes are far from understood-mainly because knowledge of membrane-shaping proteins that can promote local membrane curvatures is still limited. Our analyses unveiled that several members of a large, previously unrecognised protein family, which we termed N-Ank proteins, use a combination of their ankyrin repeat array and an amino (N)-terminal amphipathic helix to bind and shape membranes. Consistently, functional analyses revealed that the N-Ank protein ankycorbin (NORPEG/RAI14), which was exemplarily characterised further, plays an important, ankyrin repeat-based and N-terminal amphipathic helix-dependent role in early morphogenesis of neurons. This function furthermore required coiled coil-mediated self-assembly and manifested as ankycorbin nanodomains marked by protrusive membrane topologies. In summary, here, we unveil a class of powerful membrane shapers and thereby assign mechanistic and cell biological functions to the N-Ank protein superfamily.
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Affiliation(s)
- David Wolf
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | | | - Maryam Izadi
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Eric Seemann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Frank Steiniger
- Electron Microscopy Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Lukas Schwintzer
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Dennis Koch
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Michael Manfred Kessels
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany.
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany.
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26
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Yang Q, Liu H, Li Z, Wang Y, Liu W. Purification and mutagenesis studies of TANC1 ankyrin repeats domain provide clues to understand mis-sense variants from diseases. Biochem Biophys Res Commun 2019; 514:358-364. [PMID: 31040020 DOI: 10.1016/j.bbrc.2019.04.151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Abstract
TANC1 and its close relative TANC2 are two important synaptic scaffold proteins which play critical roles in regulating densities of synaptic spines and excitatory synapse strength. Recent studies indicated TANC1 and TANC2 are candidate genes of several neurodevelopmental disorders (NDD). So far, the biochemical properties of TANC1/2 proteins remain largely unknown. In this study, Ankyrin-repeats (AR) domain of TANC1 was expressed and purified using Escherichia coli. (E. coli.) cells, which showed low solubility and stability after removing the maltose binding protein (MBP) tag. Sequence analysis revealed that the TANC1 AR domain is lack of canonical N, C-capping units. By introducing two point mutations in the C-capping unit and replacing the N-capping unit, monomeric and well-folded TANC1 AR domain was purified and characterized by size exclusion chromatography coupled with multi-angle static light scattering (SEC-MALS) and circular dichroism spectroscopy (CD). In addition, mutations from intellectual disability (ID) patients and cancer patients were imported into the TANC1 AR domain. The ID mutant exhibited marginal effects in terms of conformation and protein folding stability changes. By contrast, the cancer mutants dramatically decreased protein solubility. Combined with structural prediction, we speculated that mis-sense variants tested in this study may either affect protein folding or disrupt the interaction between TANC1/2 AR domains and their binding partners.
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Affiliation(s)
- Qingqing Yang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China
| | - Haiyang Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China; Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhiwei Li
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China
| | - Yue Wang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, Guangdong province, China.
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Kang Y, Xie H, Zhao C. Ankrd45 Is a Novel Ankyrin Repeat Protein Required for Cell Proliferation. Genes (Basel) 2019; 10:genes10060462. [PMID: 31208154 PMCID: PMC6628321 DOI: 10.3390/genes10060462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 11/16/2022] Open
Abstract
Ankyrin repeats, the most common protein-protein interaction motifs in nature, are widely present in proteins of both eukaryotic and prokaryotic cells. Ankyrin repeat-containing proteins play diverse biological functions. Here, we identified the gene ankrd45, which encodes a novel, two ankyrin repeat-containing protein. Zebrafish ankrd45 displayed a tissue specific expression pattern during early development, with high expression in ciliated tissues, including otic vesicles, Kupffer's vesicles, pronephric ducts, and floor plates. Surprisingly, zebrafish ankrd45 mutants were viable and developed grossly normal cilia. In contrast, mutant larvae developed enlarged livers when induced with liver specific expression of KrasG12V, one of the common mutations of KRAS that leads to cancer in humans. Further, histological analysis suggested that multiple cysts developed in the mutant liver due to cell apoptosis. Similarly, knockdown of ANKRD45 expression with either siRNA or CRISPR/Cas9 methods induced apoptosis in cultured cells, similar to those in zebrafish ankrd45 mutant livers after induction. Using different cell lines, we show that the distribution of ANKRD45 protein was highly dynamic during mitosis. ANKRD45 is preferably localized to the midbody ring during cytokinesis. Together, our results suggest that Ankrd45 is a novel ankyrin repeat protein with a conserved role during cell proliferation in both zebrafish embryos and mammalian cells.
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Affiliation(s)
- Yunsi Kang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Haibo Xie
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Chengtian Zhao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Kunalan S, Othman I, Syed Hassan S, Hodgson WC. Proteomic Characterization of Two Medically Important Malaysian Snake Venoms, Calloselasma rhodostoma (Malayan Pit Viper) and Ophiophagus hannah (King Cobra). Toxins (Basel) 2018; 10:toxins10110434. [PMID: 30373186 PMCID: PMC6266455 DOI: 10.3390/toxins10110434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023] Open
Abstract
Calloselasma rhodostoma (CR) and Ophiophagus hannah (OH) are two medically important snakes found in Malaysia. While some studies have described the biological properties of these venoms, feeding and environmental conditions also influence the concentration and distribution of snake venom toxins, resulting in variations in venom composition. Therefore, a combined proteomic approach using shotgun and gel filtration chromatography, analyzed by tandem mass spectrometry, was used to examine the composition of venoms from these Malaysian snakes. The analysis revealed 114 proteins (15 toxin families) and 176 proteins (20 toxin families) in Malaysian Calloselasma rhodostoma and Ophiophagus hannah species, respectively. Flavin monoamine oxidase, phospholipase A2, phosphodiesterase, snake venom metalloproteinase, and serine protease toxin families were identified in both venoms. Aminopeptidase, glutaminyl-peptide cyclotransferase along with ankyrin repeats were identified for the first time in CR venom, and insulin, c-type lectins/snaclecs, hepatocyte growth factor, and macrophage colony-stimulating factor together with tumor necrosis factor were identified in OH venom for the first time. Our combined proteomic approach has identified a comprehensive arsenal of toxins in CR and OH venoms. These data may be utilized for improved antivenom production, understanding pathological effects of envenoming, and the discovery of biologically active peptides with medical and/or biotechnological value.
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Affiliation(s)
- Sugita Kunalan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Wayne C Hodgson
- Monash Venom Group, Department of Pharmacology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria 3800, Australia.
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Vaira AM, Lim HS, Bauchan G, Gulbronson CJ, Miozzi L, Vinals N, Natilla A, Hammond J. The interaction of Lolium latent virus major coat protein with ankyrin repeat protein NbANKr redirects it to chloroplasts and modulates virus infection. J Gen Virol 2018; 99:730-742. [PMID: 29557771 DOI: 10.1099/jgv.0.001043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lolium latent virus (LoLV) major coat protein sequence contains a typical chloroplast transit peptide (cTP) domain. In infected Nicotiana benthamiana leaf tissue, LoLV coat proteins can be detected at the chloroplast. In transient expression, several N-terminal deletions of the CP sequence, increasing in length, result in disruption of the domain functionality, markedly affecting intracellular localization. A yeast two-hybrid-based study using LoLV CP as bait identified several potentially interacting Arabidopsis host proteins, most of them with chloroplast-linked pathways. One of them, an ankyrin repeat protein, was studied in detail. The N. benthamiana homologue (NbANKr) targets chloroplasts, is able to co-localize with LoLV CP at chloroplast membranes in transient expression and shows a robust interaction with LoLV CP in vivo by BiFC, which has been confirmed by yeast two-hybrid data. Silencing NbANKr genes in N. benthamiana plants, prior to challenging with LoLV by mechanical inoculation, affects LoLV infection, significantly reducing the level of viral RNA in young leaves, compared to levels in control plants, and suggesting an inhibition of virus movement. Silencing of NbANKr has no obvious effect on plant phenotype, but is able to interfere with LoLV infection, opening the way for a new strategy for virus infection control.
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Affiliation(s)
- A M Vaira
- Institute for Sustainable Plant Protection, IPSP-CNR, Strada delle Cacce 73, 10135, Torino, Italy
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
| | - H S Lim
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
- Department of Applied Biology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - G Bauchan
- USDA-ARS, BARC, Electron and Confocal Microscopy Unit, 10300 Baltimore Ave, Beltsville, MD, USA
| | - C J Gulbronson
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
- Oak Ridge Institute for Science and Education (ORISE) Postdoctoral Fellow, USA
| | - L Miozzi
- Institute for Sustainable Plant Protection, IPSP-CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - N Vinals
- Institute for Sustainable Plant Protection, IPSP-CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - A Natilla
- USDA-ARS, BARC, Molecular Plant Pathology Laboratory, 10300 Baltimore Ave, Beltsville, MD, USA
- Present address: Arc Horizon, LLC, Innovation Park, 1736 West Paul Dirac Dr., Tallahassee, FL, USA
| | - J Hammond
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
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Majumder S, Zhu G, Xu X, Senchanthisai S, Jiang D, Liu H, Xue C, Wang X, Coia H, Cui Z, Smolock EM, Libby RT, Berk BC, Pang J. G-Protein-Coupled Receptor-2-Interacting Protein-1 Controls Stalk Cell Fate by Inhibiting Delta-like 4-Notch1 Signaling. Cell Rep 2017; 17:2532-2541. [PMID: 27926858 DOI: 10.1016/j.celrep.2016.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 04/12/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022] Open
Abstract
The spatiotemporal localization and expression of Dll4 are critical for sprouting angiogenesis. However, the related mechanisms are poorly understood. Here, we show that G-protein-coupled receptor-kinase interacting protein-1 (GIT1) is a robust endogenous inhibitor of Dll4-Notch1 signaling that specifically controls stalk cell fate. GIT1 is highly expressed in stalk cells but not in tip cells. GIT1 deficiency remarkably enhances Dll4 expression and Notch1 signaling, resulting in impaired retinal sprouting angiogenesis, which can be rescued by treatment with the Notch inhibitor or Dll4 neutralizing antibody. Notch1 regulates Dll4 expression by binding to recombining binding protein suppressor of hairless (RBP-J, a transcriptional regulator of Notch) via a highly conserved ankyrin (ANK) repeat domain. We show that GIT1, which also contains an ANK domain, inhibits the Notch1-Dll4 signaling pathway by competing with Notch1 ANK domain for binding to RBP-J in stalk cells.
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Affiliation(s)
- Syamantak Majumder
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - GuoFu Zhu
- Department of Cardiology, Pan-Vascular Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiangbin Xu
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sharon Senchanthisai
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Dongyang Jiang
- Department of Cardiology, Pan-Vascular Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hao Liu
- Department of Cardiology, Pan-Vascular Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Chao Xue
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Xiaoqun Wang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Heidi Coia
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Zhaoqiang Cui
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Elaine M Smolock
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Richard T Libby
- Flaum Eye Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Bradford C Berk
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Jinjiang Pang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Cardiology, Pan-Vascular Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
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31
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Islam Z, Nagampalli RSK, Fatima MT, Ashraf GM. New paradigm in ankyrin repeats: Beyond protein-protein interaction module. Int J Biol Macromol 2017; 109:1164-1173. [PMID: 29157912 DOI: 10.1016/j.ijbiomac.2017.11.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023]
Abstract
Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins. Three-dimensional structures of these repeats determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. Recent work on the ANK has proposed novel structural information, especially protein-lipid, protein-sugar and protein-protein interaction. Self-assembly of these repeats was also shown to prevent the associated protein in forming filaments. In this review, we summarize the latest findings and how the new structural information has increased our understanding of the structural determinants of ANK proteins. We discussed latest findings on how these proteins participate in various interactions to diversify the ANK roles in numerous biological processes, and explored the emerging and evolving field of designer ankyrins and its framework for protein engineering emphasizing on biotechnological applications.
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Affiliation(s)
- Zeyaul Islam
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, 13083-100, Brazil.
| | | | - Munazza Tamkeen Fatima
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia.
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Tyrkalska SD, Candel S, Pérez-Oliva AB, Valera A, Alcaraz-Pérez F, García-Moreno D, Cayuela ML, Mulero V. Identification of an Evolutionarily Conserved Ankyrin Domain-Containing Protein, Caiap, Which Regulates Inflammasome-Dependent Resistance to Bacterial Infection. Front Immunol 2017; 8:1375. [PMID: 29123523 PMCID: PMC5662874 DOI: 10.3389/fimmu.2017.01375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/05/2017] [Indexed: 11/13/2022] Open
Abstract
Many proteins contain tandemly repeated modules of several amino acids, which act as the building blocks that form the underlying architecture of a specific protein-binding interface. Among these motifs and one of the most frequently observed is ankyrin repeats (ANK), which consist of 33 amino acid residues that are highly conserved. ANK domains span a wide range of functions, including protein–protein interactions, such as the recruitment of substrate to the catalytic domain of an enzyme, or the assembly of stable multiprotein complexes. Here, we report the identification of an evolutionarily conserved protein, that we term Caiap (from CARD- and ANK-containing Inflammasome Adaptor Protein), which has an N-terminal CARD domain and 16 C-terminal ANK domains and is required for the inflammasome-dependent resistance to Salmonella Typhimurium in zebrafish. Intriguingly, Caiap is highly conserved from cartilaginous fish to marsupials but is absent in placental mammals. Mechanistically, Caiap acts downstream flagellin and interacts with catalytic active Caspa, the functional homolog of mammalian caspase-1, through its ANK domain, while its CARD domain promotes its self-oligomerization. Our results therefore point to ANK domain-containing proteins as key inflammasome adaptors required for the stabilization of active caspase-1 in functionally stable, high molecular weight complexes.
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Affiliation(s)
- Sylwia D Tyrkalska
- Facultad de Biología, Departamento de Biología Celular e Histología, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Sergio Candel
- Facultad de Biología, Departamento de Biología Celular e Histología, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Ana B Pérez-Oliva
- Facultad de Biología, Departamento de Biología Celular e Histología, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Ana Valera
- Facultad de Biología, Departamento de Biología Celular e Histología, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
| | - Francisca Alcaraz-Pérez
- Grupo de Telomerasa, Envejecimiento y Cáncer, CIBERehd, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain
| | - Diana García-Moreno
- Facultad de Biología, Departamento de Biología Celular e Histología, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain.,Grupo de Telomerasa, Envejecimiento y Cáncer, CIBERehd, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain
| | - María L Cayuela
- Grupo de Telomerasa, Envejecimiento y Cáncer, CIBERehd, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain
| | - Victoriano Mulero
- Facultad de Biología, Departamento de Biología Celular e Histología, Universidad de Murcia, IMIB-Arrixaca, Murcia, Spain
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Up-regulation of ANKDR49, a poor prognostic factor, regulates cell proliferation of gliomas. Biosci Rep 2017; 37:BSR20170800. [PMID: 28694302 PMCID: PMC6435464 DOI: 10.1042/bsr20170800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 11/30/2022] Open
Abstract
The Ankyrin repeat domain 49 (ANKRD49) is an evolutionarily conserved protein, which is related to mediate protein–protein interaction. However, the function of ANKRD49 in human glioma remains elusive. Mining through The Cancer Genome Atlas (TCGA) database, we found that the expression of ANKRD49 was increased in glioma tissues and that high expression of ANKRD49 was strongly associated with high disease grade and poor overall survival. To investigate the role of ANKRD49 in malignant glioma, lentivirus expressing shRNA targetting ANKRD49 was constructed in U251 and U87 malignant glioma cells. We demonstrated that ANKRD49 knockdown reduced the proliferation rate of U251 and U87 cells. Further mechanism analysis indicated that depletion of ANKRD49 led to the cell-cycle arrest and induced apoptosis in U251 and U87 cells. ANKRD49 knockdown also changed the expression of key effectors that are involved in stress response, cell cycle, and apoptosis, including p-HSP27 (heat shock protein 27), p-Smad2 (SMAD family member 2), p-p53, p-p38, p-MAPK (mitogen-activated protein kinase), p-SAPK/JNK (stress-activated protein kinase/c-jun n-terminal kinase), cleveagated Caspase-7, p-Chk1 (checkpoint kinase 1), and p-eIF2a (eukaryotic translation initiation factor 2a). Taken together, our findings implicate that ANKRD49 promotes the proliferation of human malignant glioma cells. ANKRD49 maybe an attractive target for malignant glioma therapy.
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Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes. PLoS One 2017; 12:e0169677. [PMID: 28158262 PMCID: PMC5291466 DOI: 10.1371/journal.pone.0169677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
Severe xerostomia (dry mouth) compromises the quality of life in patients with Sjögren's syndrome or radiation therapy for head and neck cancer. A clinical management of xerostomia is often unsatisfactory as most interventions are palliative with limited efficacy. Following up our previous study demonstrating that mouse BM-MSCs are capable of differentiating into salivary epithelial cells in a co-culture system, we further explored the molecular basis that governs the MSC reprogramming by utilizing high-throughput iTRAQ-2D-LC-MS/MS-based proteomics. Our data revealed the novel induction of pancreas-specific transcription factor 1a (PTF1α), muscle, intestine and stomach expression-1 (MIST-1), and achaete-scute complex homolog 3 (ASCL3) in 7 day co-cultured MSCs but not in control MSCs. More importantly, a common notion of pancreatic-specific expression of PTF1 α was challenged for the first time by our verification of PTF1 α expression in the mouse salivary glands. Furthermore, a molecular network simulation of our selected putative MSC reprogramming factors demonstrated evidence for their perspective roles in salivary gland development. In conclusion, quantitative proteomics with extensive data analyses narrowed down a set of MSC reprograming factors potentially contributing to salivary gland regeneration. Identification of their differential/synergistic impact on MSC conversion warrants further investigation.
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Zhang D, Wan Q, He X, Ning L, Huang Y, Xu Z, Liu J, Shao H. Genome-wide characterization of the ankyrin repeats gene family under salt stress in soybean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 568:899-909. [PMID: 27335162 DOI: 10.1016/j.scitotenv.2016.06.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/11/2016] [Accepted: 06/12/2016] [Indexed: 05/24/2023]
Abstract
Ankyrin repeats (ANK) gene family are common in diverse organisms and play important roles in cell growth, development and response to environmental stresses. Recently, genome-wide identification and evolutionary analyses of the ANK gene family have been carried out in Arabidopsis, rice and maize. However, little is known about the ANK genes in the whole soybean genome. In this study, we described the identification and structural characterization of 162ANK genes in soybean (GmANK). Then, comprehensive bioinformatics analyses of GmANK genes family were performed including gene locus, phylogenetic, domain composition analysis, chromosomal localization and expression profiling. Domain composition analyses showed that GmANK proteins formed eleven subfamilies in soybean. In sicilo expression analysis of these GmANK genes demonstrated that GmANK genes show a diverse/various expression pattern, suggesting that functional diversification of GmANK genes family. Based on digital gene expression profile (DGEP) data between cultivated soybean and wild type under salt treatment, some GmANKs related to salt/drought response were investigated. Moreover, the expression pattern and subcellular localization of GmANK6 were performed. The results will provide important clues to explore ANK genes expression and function in future studies in soybean.
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Affiliation(s)
- Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Qun Wan
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaolan He
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lihua Ning
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yihong Huang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhaolong Xu
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jia Liu
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongbo Shao
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai 264003, China.
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36
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Zlopasa L, Brachner A, Foisner R. Nucleo-cytoplasmic shuttling of the endonuclease ankyrin repeats and LEM domain-containing protein 1 (Ankle1) is mediated by canonical nuclear export- and nuclear import signals. BMC Cell Biol 2016; 17:23. [PMID: 27245214 PMCID: PMC4888674 DOI: 10.1186/s12860-016-0102-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ankyrin repeats and LEM domain containing protein 1 (Ankle1) belongs to the LEM protein family, whose members share a chromatin-interacting LEM motif. Unlike most other LEM proteins, Ankle1 is not an integral protein of the inner nuclear membrane but shuttles between the nucleus and the cytoplasm. It contains a GIY-YIG-type nuclease domain, but its function is unknown. The mammalian genome encodes only one other GIY-YIG domain protein, termed Slx1. Slx1 has been described as a resolvase that processes Holliday junctions during homologous recombination-mediated DNA double strand break repair. Resolvase activity is regulated in a spatial and temporal manner during the cell cycle. We hypothesized that Ankle1 may have a similar function and its nucleo-cytoplasmic shuttling may contribute to the regulation of Ankle1 activity. Hence, we aimed at identifying the domains mediating Ankle1 shuttling and investigating whether cellular localization is affected during DNA damage response. RESULTS Sequence analysis predicts the presence of two canonical nuclear import and export signals in Ankle1. Immunofluorescence microscopy of cells expressing wild-type and various mutated Ankle1-fusion proteins revealed a C-terminally located classical monopartite nuclear localization signal and a centrally located CRM1-dependent nuclear export signal that mediate nucleo-cytoplasmic shuttling of Ankle1. These sequences are also functional in heterologous proteins. The predominant localization of Ankle1 in the cytoplasm, however, does not change upon induction of several DNA damage response pathways throughout the cell cycle. CONCLUSIONS We identified the domains mediating nuclear import and export of Ankle1. Ankle1's cellular localization was not affected following DNA damage.
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Affiliation(s)
- Livija Zlopasa
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Andreas Brachner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Roland Foisner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
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Wang HL, Fan SS, Pang M, Liu YH, Guo M, Liang JB, Zhang JL, Yu BF, Guo R, Xie J, Zheng GP. The Ankyrin Repeat Domain 49 (ANKRD49) Augments Autophagy of Serum-Starved GC-1 Cells through the NF-κB Pathway. PLoS One 2015; 10:e0128551. [PMID: 26043108 PMCID: PMC4455995 DOI: 10.1371/journal.pone.0128551] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/28/2015] [Indexed: 11/18/2022] Open
Abstract
The ankyrin repeat domain 49 (ANKRD49) is an evolutionarily conserved protein highly expressed in testes. However, the function of ANKRD49 in spermatogenesis is unknown. In this study, we found that ANKRD49 resides primarily in nucleus of spermatogonia, spermatocytes and round spermatids. ANKRD49 overexpression augments starvation-induced autophagy in male germ GC-1 cells whereas shRNA knockdown of ANKRD49 attenuates the autophagy. Inhibition of NF-κB pathway by its inhibitors or p65 siRNA prevents the ANKRD49-dependent autophagy augmentation, demonstrating that ANKRD49 enhances autophagy via NF-κB pathway. Our findings suggest that ANKRD49 plays an important role in spermatogenesis via promotion of autophagy-dependent survival.
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Affiliation(s)
- Hai-long Wang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Sha-sha Fan
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Min Pang
- Department of Respiratory, the First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Yi-heng Liu
- Class 041002, Department of Anestesioloy, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Min Guo
- Center of Laboratory Animal, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Jun-bo Liang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Jian-lin Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Bao-feng Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
| | - Rui Guo
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
- * E-mail: (RG); (JX); (GPZ)
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
- * E-mail: (RG); (JX); (GPZ)
| | - Guo-ping Zheng
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, PR China
- * E-mail: (RG); (JX); (GPZ)
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38
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Herbert MH, Squire CJ, Mercer AA. Poxviral ankyrin proteins. Viruses 2015; 7:709-38. [PMID: 25690795 PMCID: PMC4353913 DOI: 10.3390/v7020709] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 02/08/2023] Open
Abstract
Multiple repeats of the ankyrin motif (ANK) are ubiquitous throughout the kingdoms of life but are absent from most viruses. The main exception to this is the poxvirus family, and specifically the chordopoxviruses, with ANK repeat proteins present in all but three species from separate genera. The poxviral ANK repeat proteins belong to distinct orthologue groups spread over different species, and align well with the phylogeny of their genera. This distribution throughout the chordopoxviruses indicates these proteins were present in an ancestral vertebrate poxvirus, and have since undergone numerous duplication events. Most poxviral ANK repeat proteins contain an unusual topology of multiple ANK motifs starting at the N-terminus with a C-terminal poxviral homologue of the cellular F-box enabling interaction with the cellular SCF ubiquitin ligase complex. The subtle variations between ANK repeat proteins of individual poxviruses suggest an array of different substrates may be bound by these protein-protein interaction domains and, via the F-box, potentially directed to cellular ubiquitination pathways and possible degradation. Known interaction partners of several of these proteins indicate that the NF-κB coordinated anti-viral response is a key target, whilst some poxviral ANK repeat domains also have an F-box independent affect on viral host-range.
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Affiliation(s)
- Michael H Herbert
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
| | - Christopher J Squire
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
| | - Andrew A Mercer
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.
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39
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Woodford CR, Thoden JB, Holden HM. New role for the ankyrin repeat revealed by a study of the N-formyltransferase from Providencia alcalifaciens. Biochemistry 2015; 54:631-8. [PMID: 25574689 DOI: 10.1021/bi501539a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
N-Formylated sugars such as 3,6-dideoxy-3-formamido-d-glucose (Qui3NFo) have been observed on the lipopolysaccharides of various pathogenic bacteria, including Providencia alcalifaciens, a known cause of gastroenteritis. These unusual carbohydrates are synthesized in vivo as dTDP-linked sugars. The biosynthetic pathway for the production of dTDP-Qui3NFo requires five enzymes with the last step catalyzed by an N-formyltransferase that utilizes N(10)-tetrahydrofolate as a cofactor. Here we describe a structural and functional investigation of the P. alcalifaciens N-formyltransferase, hereafter referred to as QdtF. For this analysis, the structure of the dimeric enzyme was determined in the presence of N(5)-formyltetrahydrofolate, a stable cofactor, and dTDP-3,6-dideoxy-3-amino-d-glucose (dTDP-Qui3N) to 1.5 Å resolution. The overall fold of the subunit consists of three regions with the N-terminal and middle motifs followed by an ankyrin repeat domain. Whereas the ankyrin repeat is a common eukaryotic motif involved in protein-protein interactions, reports of its presence in prokaryotic enzymes have been limited. Unexpectedly, this ankyrin repeat houses a second binding pocket for dTDP-Qui3N, which is characterized by extensive interactions between the protein and the ligand. To address the effects of this second binding site on catalysis, a site-directed mutant protein, W305A, was constructed. Kinetic analyses demonstrated that the catalytic activity of the W305A variant was reduced by approximately 7-fold. The structure of the W305A mutant protein in complex with N(5)-formyltetrahydrofolate and dTDP-Qui3N was subsequently determined to 1.5 Å resolution. The electron density map clearly showed that ligand binding had been completely abolished in the auxiliary pocket. The wild-type enzyme was also tested for activity against dTDP-3,6-dideoxy-3-amino-d-galactose (dTDP-Fuc3N) as a substrate. Strikingly, sigmoidal kinetics indicating homotropic allosteric behavior were observed. Although the identity of the ligand that regulates QdtF activity in vivo is at present unknown, our results still provide the first example of an ankyrin repeat functioning in small molecule binding.
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Affiliation(s)
- Colin R Woodford
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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40
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Jernigan KK, Bordenstein SR. Tandem-repeat protein domains across the tree of life. PeerJ 2015; 3:e732. [PMID: 25653910 PMCID: PMC4304861 DOI: 10.7717/peerj.732] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 12/29/2014] [Indexed: 12/19/2022] Open
Abstract
Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.
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Affiliation(s)
- Kristin K Jernigan
- Department of Cell and Developmental Biology, Vanderbilt University , Nashville, TN , USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University , Nashville, TN , USA ; Department of Pathology, Microbiology, and Immunology, Vanderbilt University , Nashville, TN , USA
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41
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Spatiotemporal cascade of transcription factor binding required for promoter activation. Mol Cell Biol 2014; 35:688-98. [PMID: 25512608 DOI: 10.1128/mcb.01285-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Promoters often contain multiple binding sites for a single factor. The yeast HO gene contains nine highly conserved binding sites for the SCB (Swi4/6-dependent cell cycle box) binding factor (SBF) complex (composed of Swi4 and Swi6) in the 700-bp upstream regulatory sequence 2 (URS2) promoter region. Here, we show that the distal and proximal SBF sites in URS2 function differently. Chromatin immunoprecipitation (ChIP) experiments show that SBF binds preferentially to the left side of URS2 (URS2-L), despite equivalent binding to the left-half and right-half SBF sites in vitro. SBF binding at URS2-L sites depends on prior chromatin remodeling events at the upstream URS1 region. These signals from URS1 influence chromatin changes at URS2 but only at sites within a defined distance. SBF bound at URS2-L, however, is unable to activate transcription but instead facilitates SBF binding to sites in the right half (URS2-R), which are required for transcriptional activation. Factor binding at HO, therefore, follows a temporal cascade, with SBF bound at URS2-L serving to relay a signal from URS1 to the SBF sites in URS2-R that ultimately activate gene expression. Taken together, we describe a novel property of a transcription factor that can have two distinct roles in gene activation, depending on its location within a promoter.
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42
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Park YJ, Koh J, Gauna AE, Chen S, Cha S. Identification of regulatory factors for mesenchymal stem cell-derived salivary epithelial cells in a co-culture system. PLoS One 2014; 9:e112158. [PMID: 25402494 PMCID: PMC4234408 DOI: 10.1371/journal.pone.0112158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/13/2014] [Indexed: 01/12/2023] Open
Abstract
Patients with Sjögren’s syndrome or head and neck cancer patients who have undergone radiation therapy suffer from severe dry mouth (xerostomia) due to salivary exocrine cell death. Regeneration of the salivary glands requires a better understanding of regulatory mechanisms by which stem cells differentiate into exocrine cells. In our study, bone marrow-derived mesenchymal stem cells were co-cultured with primary salivary epithelial cells from C57BL/6 mice. Co-cultured bone marrow-derived mesenchymal stem cells clearly resembled salivary epithelial cells, as confirmed by strong expression of salivary gland epithelial cell-specific markers, such as alpha-amylase, muscarinic type 3 receptor, aquaporin-5, and cytokeratin 19. To identify regulatory factors involved in this differentiation, transdifferentiated mesenchymal stem cells were analyzed temporarily by two-dimensional-gel-electrophoresis, which detected 58 protein spots (>1.5 fold change, p<0.05) that were further categorized into 12 temporal expression patterns. Of those proteins only induced in differentiated mesenchymal stem cells, ankryin-repeat-domain-containing-protein 56, high-mobility-group-protein 20B, and transcription factor E2a were selected as putative regulatory factors for mesenchymal stem cell transdifferentiation based on putative roles in salivary gland development. Induction of these molecules was confirmed by RT-PCR and western blotting on separate sets of co-cultured mesenchymal stem cells. In conclusion, our study is the first to identify differentially expressed proteins that are implicated in mesenchymal stem cell differentiation into salivary gland epithelial cells. Further investigation to elucidate regulatory roles of these three transcription factors in mesenchymal stem cell reprogramming will provide a critical foundation for a novel cell-based regenerative therapy for patients with xerostomia.
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Affiliation(s)
- Yun-Jong Park
- Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Adrienne E. Gauna
- Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Sixue Chen
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
- Department of Biology, UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Seunghee Cha
- Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, Florida, United States of America
- * E-mail:
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43
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Kodchakorn K, Dokmaisrijan S, Chong WL, Payaka A, Wisitponchai T, Nimmanpipug P, Zain SM, Rahman NA, Tayapiwatana C, Lee VS. GPU Accelerated Molecular Dynamics Simulations for Protein-Protein Interaction of Ankyrin Complex. INTEGRATED FERROELECTRICS 2014; 156:137-146. [DOI: 10.1080/10584587.2014.906894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- Kanchanok Kodchakorn
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supaporn Dokmaisrijan
- Theoretical and Computational Modeling (TCM) Research Group, School of Science, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | - Wei Lim Chong
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Apirak Payaka
- Theoretical and Computational Modeling (TCM) Research Group, School of Science, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | - Tanchanok Wisitponchai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Piyarat Nimmanpipug
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sharifuddin M. Zain
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Noorsaadah Abd. Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Biomedical Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Vannajan Sanghiran Lee
- Computational Simulation and Modeling Laboratory (CSML), Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
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44
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Jernigan KK, Bordenstein SR. Ankyrin domains across the Tree of Life. PeerJ 2014; 2:e264. [PMID: 24688847 PMCID: PMC3932732 DOI: 10.7717/peerj.264] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 01/15/2014] [Indexed: 11/20/2022] Open
Abstract
Ankyrin (ANK) repeats are one of the most common amino acid sequence motifs that mediate interactions between proteins of myriad sizes, shapes and functions. We assess their widespread abundance in Bacteria and Archaea for the first time and demonstrate in Bacteria that lifestyle, rather than phylogenetic history, is a predictor of ANK repeat abundance. Unrelated organisms that forge facultative and obligate symbioses with eukaryotes show enrichment for ANK repeats in comparison to free-living bacteria. The reduced genomes of obligate intracellular bacteria remarkably contain a higher fraction of ANK repeat proteins than other lifestyles, and the number of ANK repeats in each protein is augmented in comparison to other bacteria. Taken together, these results reevaluate the concept that ANK repeats are signature features of eukaryotic proteins and support the hypothesis that intracellular bacteria broadly employ ANK repeats for structure-function relationships with the eukaryotic host cell.
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Affiliation(s)
- Kristin K Jernigan
- Department of Biological Sciences, Vanderbilt University , Nashville , Tennessee , United States of America
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University , Nashville , Tennessee , United States of America ; Department of Pathology, Microbiology, and Immunology, Vanderbilt University , Nashville , Tennessee , United States of America
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45
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Hou Q, He J, Yu J, Ye Y, Zhou D, Sun Y, Zhang D, Ma L, Shen B, Zhu C. A case of horizontal gene transfer from Wolbachia to Aedes albopictus C6/36 cell line. Mob Genet Elements 2014; 4:e28914. [PMID: 24812591 PMCID: PMC4013104 DOI: 10.4161/mge.28914] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/01/2014] [Accepted: 04/15/2014] [Indexed: 11/28/2022] Open
Abstract
Horizontal gene transfer plays an essential role in evolution and ecological adaptation, yet this phenomenon has remained controversial, particularly where it occurs between prokaryotes and eukaryotes. There are a handful of reported examples of horizontal gene transfer occurring between prokaryotes and eukaryotes in the literature, with most of these documented cases pertaining to invertebrates and endosymbionts. However, the vast majority of these horizontally transferred genes were either eventually excluded or rapidly became nonfunctional in the recipient genome. In this study, we report the discovery of a horizontal gene transfer from the endosymbiont Wolbachia in the C6/36 cell line derived from the mosquito Aedes albopictus. Moreover, we report that this horizontally transferred gene displayed high transcription level. This finding and the results of further experimentation strongly suggest this gene is functional and has been expressed and translated into a protein in the mosquito host cells.
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Affiliation(s)
- Qing Hou
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Ji He
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China ; State Key Laboratory of Surveillance and Detection for Medical Vectors; Xiamen Entry-Exit Inspection and Quarantine Bureau; Xiamen, Fujian People's Republic of China
| | - Jing Yu
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Yuting Ye
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Dan Zhou
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Yan Sun
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Donghui Zhang
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Lei Ma
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Bo Shen
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
| | - Changliang Zhu
- Department of Pathogen Biology; Nanjing Medical University; Nanjing, Jiangsu People's Republic of China
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46
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Jiang H, Wu Q, Jin J, Sheng L, Yan H, Cheng B, Zhu S. Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize. Dev Genes Evol 2013; 223:303-18. [PMID: 23839078 DOI: 10.1007/s00427-013-0447-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/08/2013] [Indexed: 01/10/2023]
Abstract
Members of the ankyrin repeats (ANK) gene family encode ANK domain that are common in diverse organisms and play important roles in cell growth and development, such as cell-cell signal transduction and cell cycle regulation. Recently, genome-wide identification and evolutionary analyses of the ANK gene family have been carried out in Arabidopsis and rice. However, little is known regarding the ANK genes in the entire maize genome. In this study, we described the identification and structural characterization of 71 ANK genes in maize (ZmANK). Then, comprehensive bioinformatics analyses of ZmANK genes family were performed including phylogenetic, domain and motif analysis, chromosomal localization, intron/exon structural patterns, gene duplications and expression profiling. Domain composition analyses showed that ZmANK genes formed ten subfamilies. Five tandem duplications and 14 segmental duplications were identified in ZmANK genes. Furthermore, we took comparative analysis of the total ANK gene family in Arabidopsis, rice and maize, ZmANKs were more closely paired with OsANKs than with AtANKs. At last, expression profile analyses were performed. Forty-one members of ZmANK genes held EST sequences records. Semi-quantitative expression and microarray data analysis of these 41 ZmANK genes demonstrated that ZmANK genes exhibit a various expression pattern, suggesting that functional diversification of ZmANK genes family. The results will present significant insights to explore ANK genes expression and function in future studies in maize.
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Affiliation(s)
- Haiyang Jiang
- Key Laboratory of Crop Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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47
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Yuan X, Zhang S, Qing X, Sun M, Liu S, Su H, Shu H, Li X. Superfamily of ankyrin repeat proteins in tomato. Gene 2013; 523:126-36. [PMID: 23587915 DOI: 10.1016/j.gene.2013.03.122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/11/2013] [Accepted: 03/27/2013] [Indexed: 01/18/2023]
Abstract
The ankyrin repeat (ANK) protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for tomato (Solanum lycopersicum) due to the limited information on whole genome sequences. In this study, we identified a total of 130 ANK genes in tomato genome (SlANK), and these genes were distributed across all 12 chromosomes at various densities. And chromosomal localizations of SlANK genes indicated 25 SlANK genes were involved in tandem duplications. Based on their domain composition, all of the SlANK proteins were grouped into 13 subgroups. A combined phylogenetic tree was constructed with the aligned SlANK protein sequences. This tree revealed that the SlANK proteins comprise five major groups. An analysis of the expression profiles of SlANK genes in tomato in different tissues and in response to stresses showed that the SlANK proteins play roles in plant growth, development and stress responses. To our knowledge, this is the first report of a genome-wide analysis of the tomato ANK gene family. This study provides valuable information regarding the classification and putative functions of SlANK genes in tomato.
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Affiliation(s)
- Xiaowei Yuan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong 271018, China
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48
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Yuan X, Zhang S, Liu S, Yu M, Su H, Shu H, Li X. Global analysis of ankyrin repeat domain C3HC4-type RING finger gene family in plants. PLoS One 2013; 8:e58003. [PMID: 23516424 PMCID: PMC3596331 DOI: 10.1371/journal.pone.0058003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/29/2013] [Indexed: 12/22/2022] Open
Abstract
Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.
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Affiliation(s)
- Xiaowei Yuan
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China
| | - Shizhong Zhang
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, Shandong, China
| | - Shiyang Liu
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China
| | - Mingli Yu
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China
| | - Hongyan Su
- Ludong University, Yantai, Shandong, China
| | - Huairui Shu
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China
- National Research Center for Apple Engineering and Technology, Shandong Agricultural University, Tai-An, Shandong, China
| | - Xinzheng Li
- National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai-An, Shandong, China
- * E-mail:
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49
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Neves J, Abelló G, Petrovic J, Giraldez F. Patterning and cell fate in the inner ear: a case for Notch in the chicken embryo. Dev Growth Differ 2012; 55:96-112. [PMID: 23252974 DOI: 10.1111/dgd.12016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 10/09/2012] [Accepted: 10/09/2012] [Indexed: 01/08/2023]
Abstract
The development of the inner ear provides a beautiful example of one basic problem in development, that is, to understand how different cell types are generated at specific times and domains throughout embryonic life. The functional unit of the inner ear consists of hair cells, supporting cells and neurons, all deriving from progenitor cells located in the neurosensory competent domain of the otic placode. Throughout development, the otic placode resolves into the complex inner ear labyrinth, which holds the auditory and vestibular sensory organs that are innervated in a highly specific manner. How does the early competent domain of the otic placode give rise to the diverse specialized cell types of the different sensory organs of the inner ear? We review here our current understanding on the role of Notch signaling in coupling patterning and cell fate determination during inner ear development, with a particular emphasis on contributions from the chicken embryo as a model organism. We discuss further the question of how these two processes rely on two modes of operation of the Notch signaling pathway named lateral induction and lateral inhibition.
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Affiliation(s)
- Joana Neves
- CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
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50
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Mahmood N, Moosa MM, Tamanna N, Sarker SK, Najnin RA, Alam SS. In silico analysis reveals the presence of a large number of Ankyrin repeat containing proteins in Ectocarpus siliculosus. Interdiscip Sci 2012; 4:291-5. [PMID: 23354818 DOI: 10.1007/s12539-012-0134-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 06/29/2012] [Accepted: 08/14/2012] [Indexed: 11/26/2022]
Abstract
Proteins with Ankyrin repeat motifs (ANK) are found to be associated with diverse biological processes and molecular functions in most of the studied organisms. Several studies have been done on the ANK-motif containing proteins of various model species, but similar studies on their counterparts in brown algae are not available. In this study, we have identified a total of 1,372 ankyrin repeats in 339 proteins of the model brown algae Ectocarpus siliculosus and the consensus sequence of the ANK repeats was determined. The proteins were classified into eight different subfamilies depending on their structural diversity. The data provided in this study may provide useful basis for future reverse genetics analysis of the members of this family.
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Affiliation(s)
- Niaz Mahmood
- Molecular Biology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Ramna, Dhaka, Bangladesh.
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