1
|
Ohara N, Kawakami N, Arai R, Adachi N, Ikeda A, Senda T, Miyamoto K. Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage. Chem Commun (Camb) 2024; 60:4605-4608. [PMID: 38586927 DOI: 10.1039/d4cc00115j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A split-protein system is a simple approach to introduce new termini which are useful as modification sites in protein engineering, but has been adapted mainly for monomeric proteins. Here we demonstrate the design of split subunits of the 60-mer artificial fusion-protein nanocage TIP60. The subunit fragments successfully reformed the cage structure in the same manner as prior to splitting. One of the newly introduced terminals at the interior surface can be modified using a tag peptide and green fluorescent protein. Therefore, the termini could serve as a versatile modification site for incorporating a wide variety of functional peptides and proteins.
Collapse
Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| |
Collapse
|
2
|
Hu W, Huo X, Bai H, Chen Z, Zhang J, Yang H, Feng S. Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress. World J Microbiol Biotechnol 2024; 40:105. [PMID: 38386219 DOI: 10.1007/s11274-024-03924-0] [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: 12/17/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Acidithiobacillus caldus is a typical extreme acidophile widely used in the biohydrometallurgical industry, which often experiences extreme environmental stress in its natural habitat. Hfq, an RNA-binding protein, typically functions as a global regulator involved in various cellular physiological processes. Yet, the biological functions of Hfq derived from such extreme acidophile have not been extensively investigated. In this study, the recombinant strain Δhfq/Achfq, constructed by CRISPR/Cas9-mediated chromosome integration, fully or partially restored the phenotypic defects caused by hfq deletion in Escherichia coli, including impaired growth performance, abnormal cell morphology, impaired swarming motility, decreased stress resistance, decreased intracellular ATP and free amino acid levels, and attenuated biofilm formation. Particularly noteworthy, the intracellular ATP level and biofilm production of the recombinant strain were increased by 12.2% and 7.0%, respectively, compared to the Δhfq mutant. Transcriptomic analysis revealed that even under heterologous expression, AcHfq exerted global regulatory effects on multiple cellular processes, including metabolism, environmental signal processing, and motility. Finally, we established a potential working model to illustrate the regulatory mechanism of AcHfq in bacterial resistance to environmental stress.
Collapse
Affiliation(s)
- Wenbo Hu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingyu Huo
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Haochen Bai
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Zongling Chen
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Jianxin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
| |
Collapse
|
3
|
Nasu E, Kawakami N, Ohara N, Hayashi K, Miyamoto K. Column-free purification of an artificial protein nanocage, TIP60. Protein Expr Purif 2023; 205:106232. [PMID: 36642237 DOI: 10.1016/j.pep.2023.106232] [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: 11/17/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
Protein nanocages, which have inner cavities and surface pores, are attractive materials for various applications, such as in catalysts and medicine. Recently, we produced an artificial protein nanocage, TIP60, and demonstrated its potential as a stimuli-responsive nanocarrier. In the present study, we report a simple purification method for TIP60 that can replace time-consuming and costly affinity chromatography purification. TIP60, which has an anionic surface charge, aggregated at mildly acidic pH and redissolved at neutral pH, maintaining its cage structure. This pH-responsive reversible precipitation allowed us to purify TIP60 from soluble fractions of the E. coli cell lysate by controlling the pH. Compared with conventional Ni-NTA column purification, the pH-responsive precipitation method provided purified TIP60 with similar purity (∼80%) and higher yield. This precipitation purification method should facilitate the large-scale investigation and practical use of TIP60 nanocages.
Collapse
Affiliation(s)
- Erika Nasu
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
| | - Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Keiichi Hayashi
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
| |
Collapse
|
4
|
Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K. Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc 2023; 145:216-223. [PMID: 36541447 DOI: 10.1021/jacs.2c09537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein nanocages are of increasing interest for use as drug capsules, but the encapsulation and release of drug molecules at appropriate times require the reversible association and dissociation of the nanocages. One promising approach to addressing this challenge is the design of metal-dependent associating proteins. Such designed proteins typically have Cys or His residues at the protein surface for connecting the associating proteins through metal-ion coordination. However, Cys and His residues favor interactions with soft and borderline metal ions, such as Au+ and Zn2+, classified by the hard and soft acids and bases concept, restricting the types of metal ions available to drive association. Here, we show the alkaline earth (AE) metal-dependent association of the recently designed artificial protein nanocage TIP60, which is composed of 60-mer fusion proteins. The introduction of a Glu (hard base) mutation to the fusion protein (K67E mutant) prevented the formation of the 60-mer but formed the expected cage structure in the presence of Ca, Sr, or Ba ions (hard acids). Cryogenic electron microscopy (cryo-EM) analysis indicated a Ba ion at the interface of the subunits. Furthermore, we demonstrated the encapsulation and release of single-stranded DNA molecules using this system. Our results provide insights into the design of AE metal-dependent association and dissociation mechanisms for proteins.
Collapse
Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan.,Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| |
Collapse
|
5
|
Obata J, Kawakami N, Tsutsumi A, Nasu E, Miyamoto K, Kikkawa M, Arai R. Icosahedral 60-meric porous structure of designed supramolecular protein nanoparticle TIP60. Chem Commun (Camb) 2021; 57:10226-10229. [PMID: 34523636 DOI: 10.1039/d1cc03114g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Supramolecular protein nanoparticles and nanocages have potential in a broad range of applications. Recently, we developed a uniform supramolecular protein nanoparticle, TIP60, symmmetrically self-assembled from fusion proteins of a pentameric Sm-like protein and a dimeric MyoX-coil domain. Herein, we report the icosahedral 60-meric structure of TIP60 solved using single-particle cryo-electron microscopy. Interestingly, the structure revealed 20 regular-triangle-like pores on the surface. TIP60 and its mutants have many modifiable sites on their exterior and interior surfaces. The TIP60 architecture will be useful in the development of biomedical and biochemical nanoparticles/nanocages for future applications.
Collapse
Affiliation(s)
- Junya Obata
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Erika Nasu
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| |
Collapse
|
6
|
Alipov AA, Lekontseva NV, Mikhailina AO, Fando MS, Tishchenko SV, Nikulin AD. Structure of a Mutant Form of Translation Regulator Hfq with the Extended Loop L4. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Lekontseva NV, Stolboushkina EA, Nikulin AD. Diversity of LSM Family Proteins: Similarities and Differences. BIOCHEMISTRY (MOSCOW) 2021; 86:S38-S49. [PMID: 33827399 DOI: 10.1134/s0006297921140042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Members of the Lsm protein family are found in all three domains of life: bacteria, archaea, and eukarya. They are involved in numerous processes associated with RNA processing and gene expression regulation. A common structural feature of all Lsm family proteins is the presence of the Sm fold consisting of a five-stranded β-sheet and an α-helix at the N-terminus. Heteroheptameric eukaryotic Sm and Lsm proteins participate in the formation of spliceosomes and mRNA decapping. Homohexameric bacterial Lsm protein, Hfq, is involved in the regulation of transcription of different mRNAs by facilitating their interactions with small regulatory RNAs. Furthermore, recently obtained data indicate a new role of Hfq as a ribosome biogenesis factor, as it mediates formation of the productive structure of the 17S rRNA 3'- and 5'-sequences, facilitating their further processing by RNases. Lsm archaeal proteins (SmAPs) form homoheptamers and likely interact with single-stranded uridine-rich RNA elements, although the role of these proteins in archaea is still poorly understood. In this review, we discuss the structural features of the Lsm family proteins from different life domains and their structure-function relationships.
Collapse
Affiliation(s)
- Natalia V Lekontseva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Elena A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| |
Collapse
|
8
|
Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE. The Small β-Barrel Domain: A Survey-Based Structural Analysis. Structure 2018; 27:6-26. [PMID: 30393050 DOI: 10.1016/j.str.2018.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 11/27/2022]
Abstract
The small β-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an "urfold." To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure ↔ function versatility of the SBB.
Collapse
Affiliation(s)
- Philippe Youkharibache
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Stella Veretnik
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
| | - Qingliang Li
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Philip E Bourne
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
9
|
Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K. Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Norifumi Kawakami
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Hiroki Kondo
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Yuki Matsuzawa
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kaoru Hayasaka
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Erika Nasu
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kenji Sasahara
- Department of Applied Biology; Faculty of Textile Science and Technology; Shinshu University; Ueda Nagano 386-8567 Japan
| | - Ryoichi Arai
- Department of Applied Biology; Faculty of Textile Science and Technology; Shinshu University; Ueda Nagano 386-8567 Japan
- Department of Supramolecular Complexes; Research Center for Fungal and Microbial Dynamism; Shinshu University; Minamiminowa Nagano 399-4598 Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| |
Collapse
|
10
|
Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K. Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces. Angew Chem Int Ed Engl 2018; 57:12400-12404. [DOI: 10.1002/anie.201805565] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/03/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Norifumi Kawakami
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Hiroki Kondo
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Yuki Matsuzawa
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kaoru Hayasaka
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Erika Nasu
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| | - Kenji Sasahara
- Department of Applied Biology; Faculty of Textile Science and Technology; Shinshu University; Ueda Nagano 386-8567 Japan
| | - Ryoichi Arai
- Department of Applied Biology; Faculty of Textile Science and Technology; Shinshu University; Ueda Nagano 386-8567 Japan
- Department of Supramolecular Complexes; Research Center for Fungal and Microbial Dynamism; Shinshu University; Minamiminowa Nagano 399-4598 Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics; Faculty of Science and Technology; Keio University; 3-14-1 Hiyoshi, Kohoku-ku Yokohama Kanagawa 223-8522 Japan
| |
Collapse
|
11
|
Murina VN, Melnik BS, Filimonov VV, Ühlein M, Weiss MS, Müller U, Nikulin AD. Effect of conserved intersubunit amino acid substitutions on Hfq protein structure and stability. BIOCHEMISTRY (MOSCOW) 2014; 79:469-77. [DOI: 10.1134/s0006297914050113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Mura C, Randolph PS, Patterson J, Cozen AE. Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function. RNA Biol 2013; 10:636-51. [PMID: 23579284 PMCID: PMC3710371 DOI: 10.4161/rna.24538] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hfq and other Sm proteins are central in RNA metabolism, forming an evolutionarily conserved family that plays key roles in RNA processing in organisms ranging from archaea to bacteria to human. Sm-based cellular pathways vary in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in each of these pathways being mediated by an RNA-associated molecular assembly built upon Sm proteins. Though the first structures of Sm assemblies were from archaeal systems, the functions of Sm-like archaeal proteins (SmAPs) remain murky. Our ignorance about SmAP biology, particularly vis-à-vis the eukaryotic and bacterial Sm homologs, can be partly reduced by leveraging the homology between these lineages to make phylogenetic inferences about Sm functions in archaea. Nevertheless, whether SmAPs are more eukaryotic (RNP scaffold) or bacterial (RNA chaperone) in character remains unclear. Thus, the archaeal domain of life is a missing link, and an opportunity, in Sm-based RNA biology.
Collapse
Affiliation(s)
- Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | | |
Collapse
|
13
|
Abstract
Over the past years, small non-coding RNAs (sRNAs) emerged as important modulators of gene expression in bacteria. Guided by partial sequence complementarity, these sRNAs interact with target mRNAs and eventually affect transcript stability and translation. The physiological function of sRNAs depends on the protein Hfq, which binds sRNAs in the cell and promotes the interaction with their mRNA targets. This important physiological function of Hfq as a central hub of sRNA-mediated regulation made it one of the most intensely studied proteins in bacteria. Recently, a new model for sRNA binding by Hfq has been proposed that involves the direct recognition of the sRNA 3' end and interactions of the sRNA body with the lateral RNA-binding surface of Hfq. This review summarizes the current understanding of the RNA binding properties of Hfq and its (s)RNA complexes. Moreover, the implications of the new binding model for sRNA-mediated regulation are discussed.
Collapse
Affiliation(s)
- Evelyn Sauer
- Biozentrum, University of Basel, Basel, Switzerland.
| |
Collapse
|
14
|
Abstract
Hfq is an RNA-binding protein that is common to diverse bacterial lineages and has key roles in the control of gene expression. By facilitating the pairing of small RNAs with their target mRNAs, Hfq affects the translation and turnover rates of specific transcripts and contributes to complex post-transcriptional networks. These functions of Hfq can be attributed to its ring-like oligomeric architecture, which presents two non-equivalent binding surfaces that are capable of multiple interactions with RNA molecules. Distant homologues of Hfq occur in archaea and eukaryotes, reflecting an ancient origin for the protein family and hinting at shared functions. In this Review, we describe the salient structural and functional features of Hfq and discuss possible mechanisms by which this protein can promote RNA interactions to catalyse specific and rapid regulatory responses in vivo.
Collapse
Affiliation(s)
- Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Joseph-Schneider-Strasse 2, D-97080 Würzburg, Germany.
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| |
Collapse
|
15
|
Godzik A. Metagenomics and the protein universe. Curr Opin Struct Biol 2011; 21:398-403. [PMID: 21497084 DOI: 10.1016/j.sbi.2011.03.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/07/2011] [Accepted: 03/24/2011] [Indexed: 02/07/2023]
Abstract
Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones.
Collapse
Affiliation(s)
- Adam Godzik
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
16
|
Prlić A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL. Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics 2010; 11:220. [PMID: 20429930 PMCID: PMC2880030 DOI: 10.1186/1471-2105-11-220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 04/29/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB). RESULTS BioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. Among other functions, it identifies PDB IDs that are mentioned in the open access literature, by parsing the full text for all research articles in PubMed Central (PMC) and exposing the results as simple XML Web Services. Here, we integrate BioLit results with the RCSB PDB website by using these services to find PDB IDs that are mentioned in research articles and subsequently retrieving abstract, figures, and text excerpts for those articles. A new RCSB PDB literature view permits browsing through the figures and abstracts of the articles that mention a given structure. The BioLit Web Services that are providing the underlying data are publicly accessible. A client library is provided that supports querying these services (Java). CONCLUSIONS The integration between literature and websites, as demonstrated here with the RCSB PDB, provides a broader view for how a given structure has been analyzed and used. This approach detects the mention of a PDB structure even if it is not formally cited in the paper. Other structures related through the same literature references can also be identified, possibly providing new scientific insight. To our knowledge this is the first time that database and literature have been integrated in this way and it speaks to the opportunities afforded by open and free access to both database and literature content.
Collapse
Affiliation(s)
- Andreas Prlić
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA
| | - Marco A Martinez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA, 92093-0743 USA
| | - Dimitris Dimitropoulos
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA
| | - Bojan Beran
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA
| | - Benjamin T Yukich
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA
| | - Peter W Rose
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA
| | - Philip E Bourne
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA, 92093-0743 USA
| | - J Lynn Fink
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA, 92093-0743 USA
| |
Collapse
|
17
|
Tuffin M, Anderson D, Heath C, Cowan DA. Metagenomic gene discovery: how far have we moved into novel sequence space? Biotechnol J 2010; 4:1671-83. [PMID: 19946882 DOI: 10.1002/biot.200900235] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.
Collapse
Affiliation(s)
- Marla Tuffin
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of Western Cape, Cape town, South Africa
| | | | | | | |
Collapse
|