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Ahlqvist J, Linares-Pastén JA, Håkansson M, Jasilionis A, Kwiatkowska-Semrau K, Friðjónsson ÓH, Kaczorowska AK, Dabrowski S, Ævarsson A, Hreggviðsson GÓ, Al-Karadaghi S, Kaczorowski T, Nordberg Karlsson E. Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6. Acta Crystallogr D Struct Biol 2022; 78:212-227. [PMID: 35102887 PMCID: PMC8805305 DOI: 10.1107/s2059798321012298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA–Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E–SD–EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
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Kato Y. An Unnatural Amino Acid-Regulated Growth Controller Based on Informational Disturbance. Life (Basel) 2021; 11:life11090920. [PMID: 34575069 PMCID: PMC8467816 DOI: 10.3390/life11090920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 01/10/2023] Open
Abstract
We designed a novel growth controller regulated by feeding of an unnatural amino acid, Nε-benzyloxycarbonyl-l-lysine (ZK), using a specific incorporation system at a sense codon. This system is constructed by a pair of modified pyrrolisyl-tRNA synthetase (PylRS) and its cognate tRNA (tRNApyl). Although ZK is non-toxic for normal organisms, the growth of Escherichia coli carrying the ZK incorporation system was inhibited in a ZK concentration-dependent manner without causing rapid bacterial death, presumably due to generation of non-functional or toxic proteins. The extent of growth inhibition strongly depended on the anticodon sequence of the tRNApyl gene. Taking advantage of the low selectivity of PylRS for tRNApyl anticodons, we experimentally determined the most effective anticodon sequence among all 64 nucleotide sequences in the anticodon region of tRNApyl gene. The results suggest that the ZK-regulated growth controller is a simple, target-specific, environmental noise-resistant and titratable system. This technique may be applicable to a wide variety of organisms because the growth inhibitory effects are caused by "informational disturbance", in which the highly conserved system for transmission of information from DNA to proteins is perturbed.
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Affiliation(s)
- Yusuke Kato
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba 305-8634, Ibaraki, Japan
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Freitag-Pohl S, Jasilionis A, Håkansson M, Svensson LA, Kovačič R, Welin M, Watzlawick H, Wang L, Altenbuchner J, Płotka M, Kaczorowska AK, Kaczorowski T, Nordberg Karlsson E, Al-Karadaghi S, Walse B, Aevarsson A, Pohl E. Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS. Acta Crystallogr D Struct Biol 2019; 75:1028-1039. [PMID: 31692476 PMCID: PMC6834076 DOI: 10.1107/s2059798319013330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022] Open
Abstract
As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.
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Affiliation(s)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Rebeka Kovačič
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Hildegard Watzlawick
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lei Wang
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Magdalena Płotka
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Anna Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | | | | | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, England
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Milias-Argeitis A, Rullan M, Aoki SK, Buchmann P, Khammash M. Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. Nat Commun 2016; 7:12546. [PMID: 27562138 PMCID: PMC5007438 DOI: 10.1038/ncomms12546] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/08/2016] [Indexed: 12/18/2022] Open
Abstract
Dynamic control of gene expression can have far-reaching implications for biotechnological applications and biological discovery. Thanks to the advantages of light, optogenetics has emerged as an ideal technology for this task. Current state-of-the-art methods for optical expression control fail to combine precision with repeatability and cannot withstand changing operating culture conditions. Here, we present a novel fully automatic experimental platform for the robust and precise long-term optogenetic regulation of protein production in liquid Escherichia coli cultures. Using a computer-controlled light-responsive two-component system, we accurately track prescribed dynamic green fluorescent protein expression profiles through the application of feedback control, and show that the system adapts to global perturbations such as nutrient and temperature changes. We demonstrate the efficacy and potential utility of our approach by placing a key metabolic enzyme under optogenetic control, thus enabling dynamic regulation of the culture growth rate with potential applications in bacterial physiology studies and biotechnology.
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Affiliation(s)
| | - Marc Rullan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Stephanie K. Aoki
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Peter Buchmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
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de Maré L, Cimander C, Elfwing A, Hagander P. Feeding strategies for E. coli fermentations demanding an enriched environment. Bioprocess Biosyst Eng 2006; 30:13-25. [PMID: 17082912 DOI: 10.1007/s00449-006-0090-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Accepted: 10/01/2006] [Indexed: 11/26/2022]
Abstract
The addition of a carbon nutrient feed to a fed-batch cultivation is often not enough to obtain satisfactory growth and/or production. In some cases, an additional feed with for example supplementary amino acids or complex media is required. This work presents the development of feeding strategies where more than one feed is required and the knowledge of the growth requirements is low. Simulations and cultivations with E. coli are shown using the proposed feed controllers which are based on a probing control concept. The strategies work well and they can be used to shorten the process development phase considerably.
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Affiliation(s)
- L de Maré
- Department of Automatic Control, LTH, Lund University, Box 118, 221 00 Lund, Sweden.
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