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Lee J, Ryu B, Kim T, Kim KK. Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii. Int J Biol Macromol 2024; 258:128763. [PMID: 38103675 DOI: 10.1016/j.ijbiomac.2023.128763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from aggregation under stress conditions. This protein is the first sHSP characterized by X-ray crystallography, thereby contributing significantly to our understanding of sHSPs. However, despite numerous studies assessing its functions and structures, the precise arrangement of the N-terminal domains (NTDs) within this sHSP cage remains elusive. Here we present the cryo-electron microscopy (cryo-EM) structure of MjsHSP16.5 at 2.49-Å resolution. The subunits of MjsHSP16.5 in the cryo-EM structure exhibit lesser compaction compared to their counterparts in the crystal structure. This structural feature holds particular significance in relation to the biophysical properties of MjsHSP16.5, suggesting a close resemblance to this sHSP native state. Additionally, our cryo-EM structure unveils the density of residues 24-33 within the NTD of MjsHSP16.5, a feature that typically remains invisible in the majority of its crystal structures. Notably, these residues show a propensity to adopt a β-strand conformation and engage in antiparallel interactions with strand β1, both intra- and inter-subunit modes. These structural insights are corroborated by structural predictions, disulfide bond cross-linking studies of Cys-substitution mutants, and protein disaggregation assays. A comprehensive understanding of the structural features of MjsHSP16.5 expectedly holds the potential to inspire a wide range of interdisciplinary applications, owing to the renowned versatility of this sHSP as a nanoscale protein platform.
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Affiliation(s)
- Joohyun Lee
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bumhan Ryu
- Research Solution Center, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
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Shad M, Sajjad M, Gardner QA, Ahmad S, Akhtar MW. Structural engineering and truncation of α-amylase from the hyperthermophilic archaeon Methanocaldococcus jannaschii. Int J Biol Macromol 2024; 256:128387. [PMID: 38000593 DOI: 10.1016/j.ijbiomac.2023.128387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Alpha amylases catalyse the hydrolysis of α-1, 4-glycosidic bonds in starch, yielding glucose, maltose, dextrin, and short oligosaccharides, vital to various industrial processes. Structural and functional insights on α-amylase from Methanocaldococcus jannaschii were computationally explored to evaluate a catalytic domain and its fusion with a small ubiquitin-like modifier (SUMO). The recombinant proteins' production, characterization, ligand binding studies, and structural analysis of the cloned amylase native full gene (MjAFG), catalytic domain (MjAD) and fusion enzymes (S-MjAD) were thoroughly analysed in this comparative study. The MjAD and S-MjAD showed 2-fold and 2.5-fold higher specific activities (μmol min-1 mg -1) than MjAFG at 95 °C at pH 6.0. Molecular modelling and MD simulation results showed that the removal of the extra loop (178 residues) at the C-terminal of the catalytic domain exposed the binding and catalytic residues near its active site, which was buried in the MjAFG enzyme. The temperature ramping and secondary structure analysis of MjAFG, MjAD and S-MjAD through CD spectrometry showed no notable alterations in the secondary structures but verified the correct folding of MjA variants. The chimeric fusion of amylases with thermostable α-glucosidases makes it a potential candidate for the starch degrading processes.
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Affiliation(s)
- Mohsin Shad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
| | - Qurratulann Afza Gardner
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Saira Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhammad Waheed Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
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3
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Vitali J, Nix JC, Newman HE, Colaneri MJ. Crystal structure of Methanococcus jannaschii dihydroorotase. Proteins 2023; 91:91-98. [PMID: 35978488 PMCID: PMC9771888 DOI: 10.1002/prot.26412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022]
Abstract
In this paper, we report the structural analysis of dihydroorotase (DHOase) from the hyperthermophilic and barophilic archaeon Methanococcus jannaschii. DHOase catalyzes the reversible cyclization of N-carbamoyl-l-aspartate to l-dihydroorotate in the third step of de novo pyrimidine biosynthesis. DHOases form a very diverse family of enzymes and have been classified into types and subtypes with structural similarities and differences among them. This is the first archaeal DHOase studied by x-ray diffraction. Its structure and comparison with known representatives of the other subtypes help define the structural features of the archaeal subtype. The M. jannaschii DHOase is found here to have traits from all subtypes. Contrary to expectations, it has a carboxylated lysine bridging the two Zn ions in the active site, and a long catalytic loop. It is a monomeric protein with a large β sandwich domain adjacent to the TIM barrel. Loop 5 is similar to bacterial type III and the C-terminal extension is long.
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Affiliation(s)
- Jacqueline Vitali
- Department of PhysicsCleveland State UniversityClevelandOhioUSA
- Department of Biological, Geological and Environmental SciencesCleveland State UniversityClevelandOhioUSA
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light SourceLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Haley E. Newman
- Department of Biological, Geological and Environmental SciencesCleveland State UniversityClevelandOhioUSA
| | - Michael J. Colaneri
- Department of Chemistry and PhysicsThe State University of New York CollegeOld WestburyNew YorkUSA
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Knyazev DG, Kuttner R, Zimmermann M, Sobakinskaya E, Pohl P. Driving Forces of Translocation Through Bacterial Translocon SecYEG. J Membr Biol 2018; 251:329-343. [PMID: 29330604 PMCID: PMC6028853 DOI: 10.1007/s00232-017-0012-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022]
Abstract
This review focusses on the energetics of protein translocation via the Sec translocation machinery. First we complement structural data about SecYEG's conformational rearrangements by insight obtained from functional assays. These include measurements of SecYEG permeability that allow assessment of channel gating by ligand binding and membrane voltage. Second we will discuss the power stroke and Brownian ratcheting models of substrate translocation and the role that the two models assign to the putative driving forces: (i) ATP (SecA) and GTP (ribosome) hydrolysis, (ii) interaction with accessory proteins, (iii) membrane partitioning and folding, (iv) proton motive force (PMF), and (v) entropic contributions. Our analysis underlines how important energized membranes are for unravelling the translocation mechanism in future experiments.
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Affiliation(s)
- Denis G Knyazev
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria.
| | - Roland Kuttner
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | - Mirjam Zimmermann
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
| | | | - Peter Pohl
- Johannes Kepler University Linz, Institute of Biophysics, Linz, Austria
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Concha-Marambio L, Maldonado P, Lagos R, Monasterio O, Montecinos-Franjola F. Thermal adaptation of mesophilic and thermophilic FtsZ assembly by modulation of the critical concentration. PLoS One 2017; 12:e0185707. [PMID: 28982174 PMCID: PMC5628889 DOI: 10.1371/journal.pone.0185707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/18/2017] [Indexed: 01/16/2023] Open
Abstract
Cytokinesis is the last stage in the cell cycle. In prokaryotes, the protein FtsZ guides cell constriction by assembling into a contractile ring-shaped structure termed the Z-ring. Constriction of the Z-ring is driven by the GTPase activity of FtsZ that overcomes the energetic barrier between two protein conformations having different propensities to assemble into polymers. FtsZ is found in psychrophilic, mesophilic and thermophilic organisms thereby functioning at temperatures ranging from subzero to >100°C. To gain insight into the functional adaptations enabling assembly of FtsZ in distinct environmental conditions, we analyzed the energetics of FtsZ function from mesophilic Escherichia coli in comparison with FtsZ from thermophilic Methanocaldococcus jannaschii. Presumably, the assembly may be similarly modulated by temperature for both FtsZ orthologs. The temperature dependence of the first-order rates of nucleotide hydrolysis and of polymer disassembly, indicated an entropy-driven destabilization of the FtsZ-GTP intermediate. This destabilization was true for both mesophilic and thermophilic FtsZ, reflecting a conserved mechanism of disassembly. From the temperature dependence of the critical concentrations for polymerization, we detected a change of opposite sign in the heat capacity, that was partially explained by the specific changes in the solvent-accessible surface area between the free and polymerized states of FtsZ. At the physiological temperature, the assembly of both FtsZ orthologs was found to be driven by a small positive entropy. In contrast, the assembly occurred with a negative enthalpy for mesophilic FtsZ and with a positive enthalpy for thermophilic FtsZ. Notably, the assembly of both FtsZ orthologs is characterized by a critical concentration of similar value (1–2 μM) at the environmental temperatures of their host organisms. These findings suggest a simple but robust mechanism of adaptation of FtsZ, previously shown for eukaryotic tubulin, by adjustment of the critical concentration for polymerization.
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Affiliation(s)
- Luis Concha-Marambio
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Paula Maldonado
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail: (OM); (FMF)
| | - Felipe Montecinos-Franjola
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail: (OM); (FMF)
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Willkomm S, Zander A, Grohmann D, Restle T. Mechanistic Insights into Archaeal and Human Argonaute Substrate Binding and Cleavage Properties. PLoS One 2016; 11:e0164695. [PMID: 27741323 PMCID: PMC5065165 DOI: 10.1371/journal.pone.0164695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022] Open
Abstract
Argonaute (Ago) proteins from all three domains of life are key players in processes that specifically regulate cellular nucleic acid levels. Some of these Ago proteins, among them human Argonaute2 (hAgo2) and Ago from the archaeal organism Methanocaldococcus jannaschii (MjAgo), are able to cleave nucleic acid target strands that are recognised via an Ago-associated complementary guide strand. Here we present an in-depth kinetic side-by-side analysis of hAgo2 and MjAgo guide and target substrate binding as well as target strand cleavage, which enabled us to disclose similarities and differences in the mechanistic pathways as a function of the chemical nature of the substrate. Testing all possible guide-target combinations (i.e. RNA/RNA, RNA/DNA, DNA/RNA and DNA/DNA) with both Ago variants we demonstrate that the molecular mechanism of substrate association is highly conserved among archaeal-eukaryotic Argonautes. Furthermore, we show that hAgo2 binds RNA and DNA guide strands in the same fashion. On the other hand, despite striking homology between the two Ago variants, MjAgo cannot orientate guide RNA substrates in a way that allows interaction with the target DNA in a cleavage-compatible orientation.
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Affiliation(s)
- Sarah Willkomm
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
| | - Adrian Zander
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Tobias Restle
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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Paulino C, Wöhlert D, Kapotova E, Yildiz Ö, Kühlbrandt W. Structure and transport mechanism of the sodium/proton antiporter MjNhaP1. eLife 2014; 3:e03583. [PMID: 25426803 PMCID: PMC4381896 DOI: 10.7554/elife.03583] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 11/14/2014] [Indexed: 11/13/2022] Open
Abstract
Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. (22)Na(+) uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na(+) ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm.
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Affiliation(s)
- Cristina Paulino
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - David Wöhlert
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - Ekaterina Kapotova
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - Özkan Yildiz
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural
Biology, Max Planck Institute of
Biophysics, Frankfurt
am Main, Germany
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Igarashi K, Kuwabara T. Fe(III) oxides protect fermenter-methanogen syntrophy against interruption by elemental sulfur via stiffening of Fe(II) sulfides produced by sulfur respiration. Extremophiles 2014; 18:351-61. [PMID: 24420607 DOI: 10.1007/s00792-013-0620-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 12/29/2013] [Indexed: 11/27/2022]
Abstract
Thermosipho globiformans (rod-shaped thermophilic fermenter) and Methanocaldococcus jannaschii (coccal hyperthermophilic hydrogenotrophic methanogen) established H2-mediated syntrophy at 68 °C, forming exopolysaccharide-based aggregates. Electron microscopy showed that the syntrophic partners connected to each other directly or via intercellular bridges made from flagella, which facilitated transfer of H2. Elemental sulfur (S(0)) interrupted syntrophy; polysulfides abiotically formed from S(0) intercepted electrons that were otherwise transferred to H(+) to produce H2, resulting in the generation of sulfide (sulfur respiration). However, Fe(III) oxides significantly reduced the interruption by S(0), accompanied by stiffening of Fe(II) sulfides produced by the reduction of Fe(III) oxides with the sulfur respiration-generated sulfide. Sea sand replacing Fe(III) oxides failed to generate stiffening or protect the syntrophy. Several experimental results indicated that the stiffening of Fe(II) sulfides shielded the liquid from S(0), resulting in methane production in the liquid. Field-emission scanning electron microscopy showed that the stiffened Fe(II) sulfides formed a network of spiny structures in which the microorganisms were buried. The individual fermenter rods likely produced Fe(II) sulfides on their surface and became local centers of a core of spiny structures, and the connection of these cores formed the network, which was macroscopically recognized as stiffening.
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Affiliation(s)
- Kensuke Igarashi
- Graduate School, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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Ver Eecke HC, Akerman NH, Huber JA, Butterfield DA, Holden JF. Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions. Environ Microbiol Rep 2013; 5:665-671. [PMID: 24115616 DOI: 10.1111/1758-2229.12065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/18/2013] [Indexed: 06/02/2023]
Abstract
A hyperthermophilic deep-sea methanogen, Methanocaldococcus strain JH146, was isolated from 26°C hydrothermal fluid at Axial Volcano to model high temperature methanogenesis in the subseafloor. Emphasis was placed on defining growth kinetics, cell yields and growth energy demand (GE) across a range of conditions. The organism uses H2 and CO2 as its sole carbon and energy sources. At various temperatures, pHs, and chlorinities, its growth rates and cell yields co-varied while GE remained uniform at 1.69 × 10(-11) J cell(-1)s(-1) ± 0.68 × 10(-11) J cell(-1)s(-1) (s.d., n = 23). An exception was at superoptimal growth temperatures where GE increased to 7.25 × 10(-11) J cell(-1)s(-1) presumably due to heat shock. GE also increased from 5.1 × 10(-12) J cell(-1)s(-1) to 7.61 × 10(-11) J cell(-1)s(-1) as NH4 (+) concentrations decreased from 9.4 mM to 0.14 mM. JH146 did not fix N2 or assimilate NO3 (-), lacked the N2-fixing (cluster II) nifH gene, and became nitrogen limited below 0.14 mM NH4Cl. Nitrogen availability may impact growth in situ since ammonia concentrations at Axial Volcano are < 18 μM. Our approach contributes to refining bioenergetic and carbon flux models for methanogens and other organisms in hydrothermal vents and other environments.
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Affiliation(s)
- Helene C Ver Eecke
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
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Bhuiya MW, Suryadi J, Zhou Z, Brown BA. Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:979-88. [PMID: 23989144 PMCID: PMC3758144 DOI: 10.1107/s1744309113021799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/05/2013] [Indexed: 11/11/2022]
Abstract
Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that directs post-transcriptional modification of archaeal RNAs. The L7Ae protein from Aeropyrum pernix (Ap L7Ae), a member of the Crenarchaea, was found to have an extremely high melting temperature (>383 K). The crystal structure of Ap L7Ae has been determined to a resolution of 1.56 Å. The structure of Ap L7Ae was compared with the structures of two homologs: hyperthermophilic Methanocaldococcus jannaschii L7Ae and the mesophilic counterpart mammalian 15.5 kD protein. The primary stabilizing feature in the Ap L7Ae protein appears to be the large number of ion pairs and extensive ion-pair network that connects secondary-structural elements. To our knowledge, Ap L7Ae is among the most thermostable single-domain monomeric proteins presently observed.
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Affiliation(s)
| | - Jimmy Suryadi
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Zholi Zhou
- Bristol-Myers Squibb, Syracuse, NY 13221, USA
| | - Bernard Andrew Brown
- Womble Carlyle Sandridge and Rice LLP, One West Fourth Street, Winston-Salem, NC 27101, USA
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Xiang L, Moncivais K, Jiang F, Willams B, Alfonta L, Zhang ZJ. Crucial optimization of translational components towards efficient incorporation of unnatural amino acids into proteins in mammalian cells. PLoS One 2013; 8:e67333. [PMID: 23874413 PMCID: PMC3709914 DOI: 10.1371/journal.pone.0067333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
The ability to site-specifically incorporate unnatural amino acids (UAAs) into proteins is a powerful tool in protein engineering. While dozens of UAAs have been successfully introduced into proteins expressed by Escherichia coli cells, it has been much more challenging to create tRNA and tRNA-Synthetase pairs that enable UAAs incorporation, for use in mammalian systems. By altering the orthogonality properties of existing unnatural pairs, previously evolved pairs for use in E. coli could be used in mammalian cells. This would bypass the cumbersome step of having to evolve mutant synthetases and would allow for the rapid development of new mammalian pairs. A major limitation to the amount of UAA-containing proteins that can be expressed in the cell is the availability of UAA-charged orthogonal suppressor tRNA. By using a natural mammalian tRNA promoter, the amount of functional suppressor tRNA can be greatly increased. Furthermore, increasing recognition of the suppressor tRNA by the mutant synthetase will ultimately lead to the appearance of more UAA-charged tRNA.
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Affiliation(s)
- Liang Xiang
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, California, United States of America
- Biomedical Engineering Department, University of Texas at Austin, Austin, Texas, United States of America
| | - Kathryn Moncivais
- Biomedical Engineering Department, University of Texas at Austin, Austin, Texas, United States of America
| | - Faqin Jiang
- School of Pharmacy, Shanghai Jiaotong University, Shanghai, China
| | - Blake Willams
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, California, United States of America
| | - Lital Alfonta
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (LF); (ZJZ)
| | - Zhiwen J. Zhang
- Department of Bioengineering, School of Engineering, Santa Clara University, Santa Clara, California, United States of America
- * E-mail: (LF); (ZJZ)
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