1
|
Luckenbach T, Burkhardt-Medicke K. Differing temperature dependencies of functional homologs zebrafish Abcb4 and human ABCB1. Front Pharmacol 2024; 15:1426040. [PMID: 39166110 PMCID: PMC11333832 DOI: 10.3389/fphar.2024.1426040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/16/2024] [Indexed: 08/22/2024] Open
Abstract
The ATP binding cassette (ABC) transporters human ABCB1 and zebrafish (Danio rerio) Abcb4 are functionally homologous multixenobiotic/multidrug (MXR/MDR) efflux transporters that confer the efflux of a broad range of diverse chemical compounds from the cell. As ATPases, the transporters utilize the energy released by ATP cleavage for protein conformation changes and concomitant active transport of substrate compounds. The temperatures, at which human ABCB1 and zebrafish Abcb4 need to function, can substantially differ: Whereas the ambient temperature of human ABCB1, which is that of the human body, is constant, zebrafish Abcb4 has to be active in a wider temperature range as the body temperature of zebrafish can considerably vary, depending on the ambient water temperature (18°C-40°C). Here, we examined the effect of temperature on the ATPase activities of recombinant human ABCB1 and zebrafish Abcb4 generated with the baculovirus expression system. Incubation temperatures for enzyme reactions were set to 37°C and 27°C, corresponding to the human body temperature and the cultivation temperature of zebrafish in our lab, respectively. For stimulation and inhibition of zebrafish Abcb4 and human ABCB1 ATPase activities verapamil and cyclosporin A were added at different concentrations and 50% effect concentrations (EC50) were determined. The different temperatures had a stronger effect on the human ABCB1 than on the zebrafish Abcb4 ATPase: Differences between EC50 values for verapamil at 37°C and 27°C, respectively, were 1.8-fold for human ABCB1 but only 1.2-fold for zebrafish Abcb4. Activation energies (Ea) of basal and verapamil-stimulated ATPases, calculated based on the Arrhenius equation, were 2-fold (basal) and 1.5-fold (verapamil-stimulated) higher for human ABCB1 than for zebrafish Abcb4. The differences between zebrafish Abcb4 and human ABCB1 ATPases in temperature sensitivity and activation energy could be important for the comparison of the functional properties of the two transporter proteins in the context of pharmaco-/toxicokinetics. Related to this, our finding that at equal reaction conditions the zebrafish Abcb4 ATPase activity tended to be generally higher than that of human ABCB1 may also be important, as this may point to a higher substrate compound transport rate of Abcb4.
Collapse
Affiliation(s)
- Till Luckenbach
- Department Ecotoxicology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | | |
Collapse
|
2
|
Zhang L, Zhao ZW, Ma LX, Dong YW. Genome-wide sequencing reveals geographical variations in the thermal adaptation of an aquaculture species with frequent seedling introductions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172010. [PMID: 38575020 DOI: 10.1016/j.scitotenv.2024.172010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Climate change and human activity are essential factors affecting marine biodiversity and aquaculture, and understanding the impacts of human activities on the genetic structure to increasing high temperatures is crucial for sustainable aquaculture and marine biodiversity conservation. As a commercially important bivalve, the Manila clam Ruditapes philippinarum is widely distributed along the coast of China, and it has been frequently introduced from Fujian Province, China, to other regions for aquaculture. In this study, we collected four populations of Manila clams from different areas to evaluate their thermal tolerance by measuring cardiac performance and genetic variations using whole-genome resequencing. The upper thermal limits of the clams showed high variations within and among populations. Different populations displayed divergent genetic compositions, and the admixed population was partly derived from the Zhangzhou population in Fujian Province, implying a complex genomic landscape under the influence of local genetic sources and human introductions. Multiple single nucleotide polymorphisms (SNPs) were associated with the cardiac functional traits, and some of these SNPs can affect the codon usage and the structural stability of the resulting protein. This study shed light on the importance of establishing long-term ecological and genetic monitoring programs at the local level to enhance resilience to future climate change.
Collapse
Affiliation(s)
- Liang Zhang
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Zhan-Wei Zhao
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Lin-Xuan Ma
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Yun-Wei Dong
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao, 266001, China.
| |
Collapse
|
3
|
Aberuagba A, Joel EB, Bello AJ, Igunnu A, Malomo SO, Olorunniji FJ. Thermophilic PHP Protein Tyrosine Phosphatases (Cap8C and Wzb) from Mesophilic Bacteria. Int J Mol Sci 2024; 25:1262. [PMID: 38279261 PMCID: PMC10816263 DOI: 10.3390/ijms25021262] [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: 10/29/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) of the polymerase and histidinol phosphatase (PHP) superfamily with characteristic phosphatase activity dependent on divalent metal ions are found in many Gram-positive bacteria. Although members of this family are co-purified with metal ions, they still require the exogenous supply of metal ions for full activation. However, the specific roles these metal ions play during catalysis are yet to be well understood. Here, we report the metal ion requirement for phosphatase activities of S. aureus Cap8C and L. rhamnosus Wzb. AlphaFold-predicted structures of the two PTPs suggest that they are members of the PHP family. Like other PHP phosphatases, the two enzymes have a catalytic preference for Mn2+, Co2+ and Ni2+ ions. Cap8C and Wzb show an unusual thermophilic property with optimum activities over 75 °C. Consistent with this model, the activity-temperature profiles of the two enzymes are dependent on the divalent metal ion activating the enzyme.
Collapse
Affiliation(s)
- Adepeju Aberuagba
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| | - Enoch B. Joel
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos 930003, Nigeria
| | - Adebayo J. Bello
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| | - Adedoyin Igunnu
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin 234031, Nigeria; (A.I.); (S.O.M.)
| | - Sylvia O. Malomo
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin 234031, Nigeria; (A.I.); (S.O.M.)
| | - Femi J. Olorunniji
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK; (A.A.); (E.B.J.); (A.J.B.)
| |
Collapse
|
4
|
Clark MS, Hoffman JI, Peck LS, Bargelloni L, Gande D, Havermans C, Meyer B, Patarnello T, Phillips T, Stoof-Leichsenring KR, Vendrami DLJ, Beck A, Collins G, Friedrich MW, Halanych KM, Masello JF, Nagel R, Norén K, Printzen C, Ruiz MB, Wohlrab S, Becker B, Dumack K, Ghaderiardakani F, Glaser K, Heesch S, Held C, John U, Karsten U, Kempf S, Lucassen M, Paijmans A, Schimani K, Wallberg A, Wunder LC, Mock T. Multi-omics for studying and understanding polar life. Nat Commun 2023; 14:7451. [PMID: 37978186 PMCID: PMC10656552 DOI: 10.1038/s41467-023-43209-y] [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: 04/24/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
Collapse
Affiliation(s)
- M S Clark
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - J I Hoffman
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany.
| | - L S Peck
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - D Gande
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - C Havermans
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B Meyer
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - T Phillips
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - K R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, 14473, Potsdam, Germany
| | - D L J Vendrami
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - A Beck
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München (SNSB-BSM), Menzinger Str. 67, 80638, München, Germany
| | - G Collins
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - M W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - K M Halanych
- Center for Marine Science, University of North Carolina, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - J F Masello
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- Justus-Liebig-Universität Gießen, Giessen, Germany
| | - R Nagel
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - K Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - C Printzen
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - M B Ruiz
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Universität Duisburg-Essen, Universitätstrasse 5, 45151, Essen, Germany
| | - S Wohlrab
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - B Becker
- Universität zu Köln, Institut für Pflanzenwissenschaften, Zülpicher Str. 47b, 60674, Köln, Germany
| | - K Dumack
- Universität zu Köln, Terrestrische Ökologie, Zülpicher Str. 47b, 60674, Köln, Germany
| | - F Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - K Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Heesch
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - C Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U John
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Kempf
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - M Lucassen
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - A Paijmans
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - K Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - A Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - L C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - T Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| |
Collapse
|
5
|
Dong YW. Roles of multi-level temperature-adaptive responses and microhabitat variation in establishing distributions of intertidal species. J Exp Biol 2023; 226:jeb245745. [PMID: 37909420 DOI: 10.1242/jeb.245745] [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] [Indexed: 11/03/2023]
Abstract
How intertidal species survive their harsh environment and how best to evaluate and forecast range shifts in species distribution are two important and closely related questions for intertidal ecologists and global change biologists. Adaptive variation in responses of organisms to environmental change across all levels of biological organization - from behavior to molecular systems - is of key importance in setting distribution patterns, yet studies often neglect the interactions of diverse types of biological variation (e.g. differences in thermal optima owing to genetic and acclimation-induced effects) with environmental variation, notably at the scale of microhabitats. Intertidal species have to cope with extreme and frequently changing thermal stress, and have shown high variation in thermal sensitivities and adaptive responses at different levels of biological organization. Here, I review the physiological and biochemical adaptations of intertidal species to environmental temperature on multiple spatial and temporal scales. With fine-scale datasets for the thermal limits of individuals and for environmental temperature variation at the microhabitat scale, we can map the thermal sensitivity for each individual in different microhabitats, and then scale up the thermal sensitivity analysis to the population level and, finally, to the species level by incorporating physiological traits into species distribution models. These more refined mechanistic models that include consideration of physiological variations have higher predictive power than models that neglect these variations, and they will be crucial to answering the questions posed above concerning adaptive mechanisms and the roles they play in governing distribution patterns in a rapidly changing world.
Collapse
Affiliation(s)
- Yun-Wei Dong
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao 266001, China
| |
Collapse
|
6
|
Zhu YJ, Liao ML, Dong YW. Exploring the adaptability of the secondary structure of mRNA to temperature in intertidal snails based on SHAPE experiments. J Exp Biol 2023; 226:jeb246544. [PMID: 37767692 DOI: 10.1242/jeb.246544] [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: 08/16/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
RNA-based thermal regulation is an important strategy for organisms to cope with temperature changes. Inhabiting the intertidal rocky shore, a key interface of the ocean, atmosphere and terrestrial environments, intertidal species have developed variable thermal adaptation mechanisms; however, adaptions at the RNA level remain largely uninvestigated. To examine the relationship between mRNA structural stability and species distribution, in the present study, the secondary structure of cytosolic malate dehydrogenase (cMDH) mRNA of Echinolittorina malaccana, Echinolittorina radiata and Littorina brevicula was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), and the change in folding free energy of formation (ΔGfold) was calculated. The results showed that ΔGfold increased as the temperature increased. The difference in ΔGfold (ΔΔGfold) between two specific temperatures (25 versus 0°C, 37 versus 0°C and 57 versus 0°C) differed among the three species, and the ΔΔGfold value of E. malaccana was significantly lower than those of E. radiata and L. brevicula. The number of stems of cMDH mRNA of the snails decreased with increasing temperature, and the breakpoint temperature of E. malaccana was the highest among these. The number of loops was also reduced with increasing temperature, while the length of the loop structure increased accordingly. Consequently, these structural changes can potentially affect the translational efficiency of mRNA. These results imply that there were interspecific differences in the thermal stability of RNA secondary structures in intertidal snails, and these differences may be related to snail distribution.
Collapse
Affiliation(s)
- Ya-Jie Zhu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| |
Collapse
|
7
|
Krebs N, Bock C, Tebben J, Mark FC, Lucassen M, Lannig G, Pörtner HO. Evolutionary Adaptation of Protein Turnover in White Muscle of Stenothermal Antarctic Fish: Elevated Cold Compensation at Reduced Thermal Responsiveness. Biomolecules 2023; 13:1507. [PMID: 37892189 PMCID: PMC10605280 DOI: 10.3390/biom13101507] [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: 09/20/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Protein turnover is highly energy consuming and overall relates to an organism's growth performance varying largely between species, e.g., due to pre-adaptation to environmental characteristics such as temperature. Here, we determined protein synthesis rates and capacity of protein degradation in white muscle of the cold stenothermal Antarctic eelpout (Pachycara brachycephalum) and its closely related temperate counterpart, the eurythermal common eelpout (Zoarces viviparus). Both species were exposed to acute warming (P. brachycephalum, 0 °C + 2 °C day-1; Z. viviparus, 4 °C + 3 °C day-1). The in vivo protein synthesis rate (Ks) was monitored after injection of 13C-phenylalanine, and protein degradation capacity was quantified by measuring the activity of cathepsin D in vitro. Untargeted metabolic profiling by nuclear magnetic resonance (NMR) spectroscopy was used to identify the metabolic processes involved. Independent of temperature, the protein synthesis rate was higher in P. brachycephalum (Ks = 0.38-0.614 % day-1) than in Z. viviparus (Ks= 0.148-0.379% day-1). Whereas protein synthesis remained unaffected by temperature in the Antarctic species, protein synthesis in Z. viviparus increased to near the thermal optimum (16 °C) and tended to fall at higher temperatures. Most strikingly, capacities for protein degradation were about ten times higher in the Antarctic compared to the temperate species. These differences are mirrored in the metabolic profiles, with significantly higher levels of complex and essential amino acids in the free cytosolic pool of the Antarctic congener. Together, the results clearly indicate a highly cold-compensated protein turnover in the Antarctic eelpout compared to its temperate confamilial. Constant versus variable environments are mirrored in rigid versus plastic functional responses of the protein synthesis machinery.
Collapse
Affiliation(s)
- Nina Krebs
- Department of Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (C.B.); (F.C.M.); (M.L.); (G.L.)
| | - Christian Bock
- Department of Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (C.B.); (F.C.M.); (M.L.); (G.L.)
| | - Jan Tebben
- Department of Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany;
| | - Felix C. Mark
- Department of Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (C.B.); (F.C.M.); (M.L.); (G.L.)
| | - Magnus Lucassen
- Department of Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (C.B.); (F.C.M.); (M.L.); (G.L.)
| | - Gisela Lannig
- Department of Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (C.B.); (F.C.M.); (M.L.); (G.L.)
| | - Hans-Otto Pörtner
- Department of Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (C.B.); (F.C.M.); (M.L.); (G.L.)
| |
Collapse
|
8
|
Mendoza J, Purchal M, Yamada K, Koutmos M. Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo. Nat Commun 2023; 14:6365. [PMID: 37821448 PMCID: PMC10567725 DOI: 10.1038/s41467-023-42037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MS) is a key enzyme in methionine and folate one-carbon metabolism. MS is a large multi-domain protein capable of binding and activating three substrates: homocysteine, folate, and S-adenosylmethionine for methylation. Achieving three chemically distinct methylations necessitates significant domain rearrangements to facilitate substrate access to the cobalamin cofactor at the right time. The distinct conformations required for each reaction have eluded structural characterization as its inherently dynamic nature renders structural studies difficult. Here, we use a thermophilic MS homolog (tMS) as a functional MS model. Its exceptional stability enabled characterization of MS in the absence of cobalamin, marking the only studies of a cobalamin-binding protein in its apoenzyme state. More importantly, we report the high-resolution full-length MS structure, ending a multi-decade quest. We also capture cobalamin loading in crystallo, providing structural insights into holoenzyme formation. Our work paves the way for unraveling how MS orchestrates large-scale domain rearrangements crucial for achieving challenging chemistries.
Collapse
Affiliation(s)
- Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meredith Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- New England Biolabs, Inc., Ipswich, MA, 01938, England
| | - Kazuhiro Yamada
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
9
|
Araujo NDS, Perez R, Willot Q, Defrance M, Aron S. Facing lethal temperatures: Heat-shock response in desert and temperate ants. Ecol Evol 2023; 13:e10438. [PMID: 37720060 PMCID: PMC10500329 DOI: 10.1002/ece3.10438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023] Open
Abstract
Global climate changes may cause profound effects on species adaptation, particularly in ectotherms for whom even moderate warmer temperatures can lead to disproportionate heat failure. Still, several organisms evolved to endure high desert temperatures. Here, we describe the thermal tolerance survival and the transcriptomic heat stress response of three genera of desert (Cataglyphis, Melophorus, and Ocymyrmex) and two of temperate ants (Formica and Myrmica) and explore convergent and specific adaptations. We found heat stress led to either a reactive or a constitutive response in desert ants: Cataglyphis holgerseni and Melophorus bagoti differentially regulated very few transcripts in response to heat (0.12% and 0.14%, respectively), while Cataglyphis bombycina and Ocymyrmex robustior responded with greater expression alterations (respectively affecting 0.6% and 1.53% of their transcriptomes). These two responsive mechanisms-reactive and constitutive-were related to individual thermal tolerance survival and convergently evolved in distinct desert ant genera. Moreover, in comparison with desert species, the two temperate ants differentially expressed thousands of transcripts more in response to heat stress (affecting 8% and 12.71% of F. fusca and Myr. sabuleti transcriptomes). In summary, we show that heat adaptation in thermophilic ants involved changes in the expression response. Overall, desert ants show reduced transcriptional alterations even when under high thermal stress, and their expression response may be either constitutive or reactive to temperature increase.
Collapse
Affiliation(s)
| | - Rémy Perez
- Department of Evolutionary Biology & EcologyUniversité Libre de BruxellesBrusselsBelgium
| | - Quentin Willot
- Department of Evolutionary Biology & EcologyUniversité Libre de BruxellesBrusselsBelgium
- Zoophysiology, Department of BiologyAarhus UniversityAarhus‐CDenmark
| | - Matthieu Defrance
- Interuniversity Institute of Bioinformatics in BrusselsUniversité Libre de BruxellesBrusselsBelgium
| | - Serge Aron
- Department of Evolutionary Biology & EcologyUniversité Libre de BruxellesBrusselsBelgium
| |
Collapse
|
10
|
van den Elzen A, Helena-Bueno K, Brown CR, Chan LI, Melnikov S. Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA. Nucleic Acids Res 2023; 51:8048-8059. [PMID: 37395434 PMCID: PMC10450194 DOI: 10.1093/nar/gkad560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 05/29/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Ribosomal genes are widely used as 'molecular clocks' to infer evolutionary relationships between species. However, their utility as 'molecular thermometers' for estimating optimal growth temperature of microorganisms remains uncertain. Previously, some estimations were made using the nucleotide composition of ribosomal RNA (rRNA), but the universal application of this approach was hindered by numerous outliers. In this study, we aimed to address this problem by identifying additional indicators of thermal adaptation within the sequences of ribosomal proteins. By comparing sequences from 2021 bacteria with known optimal growth temperature, we identified novel indicators among the metal-binding residues of ribosomal proteins. We found that these residues serve as conserved adaptive features for bacteria thriving above 40°C, but not at lower temperatures. Furthermore, the presence of these metal-binding residues exhibited a stronger correlation with the optimal growth temperature of bacteria compared to the commonly used correlation with the 16S rRNA GC content. And an even more accurate correlation was observed between the optimal growth temperature and the YVIWREL amino acid content within ribosomal proteins. Overall, our work suggests that ribosomal proteins contain a more accurate record of bacterial thermal adaptation compared to rRNA. This finding may simplify the analysis of unculturable and extinct species.
Collapse
Affiliation(s)
| | - Karla Helena-Bueno
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lewis I Chan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
11
|
Yang J, Wang D, Liu H, Wang L, Jin L, Ahola V, Xu C, Wang R. Three amino acid substitutions contributing to thermostability of phosphoglucose isomerase in the Glanville fritillary butterfly. INSECT SCIENCE 2023; 30:758-770. [PMID: 36342954 DOI: 10.1111/1744-7917.13145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/15/2023]
Abstract
Temperature is one of the most important environmental factors that affect organisms, especially ectotherms, due to its effects on protein stability. Understanding the general rules that govern thermostability changes in proteins to adapt high-temperature environments is crucial. Here, we report the amino acid substitutions of phosphoglucose isomerase (PGI) related to thermostability in the Glanville fritillary butterfly (Melitaea cinxia, Lepidoptera: Nymphalidae). The PGI encoded by the most common allele in M. cinxia in the Chinese population (G3-PGI), which is more thermal tolerant, is more stable under heat stress than that in the Finnish population (D1-PGI). There are 5 amino acid substitutions between G3-PGI and D1-PGI. Site-directed mutagenesis revealed that the combination of amino acid substitutions of H35Q, M49T, and I64V may increase PGI thermostability. These substitutions alter the 3D structure to increase the interaction between 2 monomers of PGI. Through molecular dynamics simulations, it was found that the amino acid at site 421 is more stable in G3-PGI, confining the motion of the α-helix 420-441 and stabilizing the interaction between 2 PGI monomers. The strategy for high-temperature adaptation through these 3 amino acid substitutions is also adopted by other butterfly species (Boloria eunomia, Aglais urticae, Colias erate, and Polycaena lua) concurrent with M. cinxia in the Tianshan Mountains of China, i.e., convergent evolution in butterflies.
Collapse
Affiliation(s)
- Jianing Yang
- School of Life Sciences, Peking University, Beijing, China
| | - Di Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Hui Liu
- School of Life Sciences, Peking University, Beijing, China
| | - Lin Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Ling Jin
- School of Life Sciences, Peking University, Beijing, China
| | - Virpi Ahola
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Chongren Xu
- School of Life Sciences, Peking University, Beijing, China
| | - Rongjiang Wang
- School of Life Sciences, Peking University, Beijing, China
| |
Collapse
|
12
|
Rummel AD, Swartz SM, Marsh RL. Thermal Stability of Contractile Proteins in Bat Wing Muscles Explains Differences in Temperature Dependence of Whole-Muscle Shortening Velocity. Physiol Biochem Zool 2023; 96:100-105. [PMID: 36921272 DOI: 10.1086/722449] [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] [Indexed: 11/04/2022]
Abstract
AbstractMuscle contractile properties are dependent on temperature: cooler temperatures generally slow contractile rates. Contraction and relaxation are driven by underlying biochemical systems, which are inherently sensitive to temperature. Carollia perspicillata, a small Neotropical bat, experiences large temperature differentials among body regions, resulting in a steep gradient in temperature along the wing. Although the bats maintain high core body temperatures during flight, the wing muscles may operate at more than 10°C below body temperature. Partially compensating for these colder operating temperatures, distal wing muscles have lower temperature sensitivities in their contractile properties, including shortening velocity, relative to the proximal pectoralis. Shortening velocity is correlated with the activity of myosin ATPase, an enzyme that drives the cross-bridge cycle. We hypothesized that the thermal properties of myofibrillar ATPase from the pectoralis and forearm muscles of the bat wing would correlate with the temperature sensitivity of those muscles. Using myofibrillar ATPases from the proximal and distal muscles, we measured enzyme activity across a range of temperatures and enzyme thermal stability after heat incubation across a range of time points. We found that forearm muscle myofibrillar ATPase was significantly less thermally stable than pectoralis myofibrillar ATPase but that there was no significant difference in the acute temperature dependence of enzyme activity between the two muscles.
Collapse
|
13
|
Rivera M, Mjaavatten A, Smith SB, Baez M, Wilson CAM. Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers. Biophys J 2023; 122:513-521. [PMID: 36587240 PMCID: PMC9941719 DOI: 10.1016/j.bpj.2022.12.034] [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: 02/07/2022] [Revised: 06/15/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Temperature is a useful system variable to gather kinetic and thermodynamic information from proteins. Usually, free energy and the associated entropic and enthalpic contributions are obtained by quantifying the conformational equilibrium based on melting experiments performed in bulk conditions. Such experiments are suitable only for those small single-domain proteins whose side reactions of irreversible aggregation are unlikely to occur. Here, we avoid aggregation by pulling single-protein molecules in a thermo-regulated optical tweezers. Thus, we are able to explore the temperature dependence of the thermodynamic and kinetic parameters of MJ0366 from Methanocaldococcus jannaschii at the single-molecule level. By performing force-ramp experiments between 2°C and 40°C, we found that MJ0366 has a nonlinear dependence of free energy with temperature and a specific heat change of 2.3 ± 1.2 kcal/mol∗K. These thermodynamic parameters are compatible with a two-state unfolding/refolding mechanism for MJ0366. However, the kinetics measured as a function of the temperature show a complex behavior, suggesting a three-state folding mechanism comprising a high-energy intermediate state. The combination of two perturbations, temperature and force, reveals a high-energy species in the folding mechanism of MJ0366 not detected in force-ramp experiments at constant temperature.
Collapse
Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | | | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| |
Collapse
|
14
|
Choudhary P, Waseem M, Kumar S, Subbarao N, Srivastava S, Chakdar H. Y12F mutation in Pseudomonas plecoglossicida S7 lipase enhances its thermal and pH stability for industrial applications: a combination of in silico and in vitro study. World J Microbiol Biotechnol 2023; 39:75. [PMID: 36637534 DOI: 10.1007/s11274-023-03518-2] [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: 10/06/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023]
Abstract
Appropriate amino acid substitutions are critical for protein engineering to redesign catalytic properties of industrially important enzymes like lipases. The present study aimed for improving the environmental stability of lipase from Pseudomonas plecoglossicida S7 through site-directed mutagenesis driven by computational studies. lipA gene was amplified and sequenced. Both wild type (WT) and mutant type (MT) lipase genes were expressed into the pET SUMO system. The expressed proteins were purified and characterized for pH and thermostability. The lipase gene belonged to subfamily I.1 lipase. Molecular dynamics revealed that Y12F-palmitic acid complex had a greater binding affinity (-6.3 Kcal/mol) than WT (-6.0 Kcal/mol) complex. Interestingly, MDS showed that the binding affinity of WT-complex (-130.314 ± 15.11 KJ/mol) was more than mutant complex (-108.405 ± 69.376 KJ/mol) with a marked increase in the electrostatic energy of mutant (-26.969 ± 12.646 KJ/mol) as compared to WT (-15.082 ± 13.802 KJ/mol). Y12F mutant yielded 1.27 folds increase in lipase activity at 55 °C as compared to the purified WT protein. Also, Y12F mutant showed increased activity (~ 1.2 folds each) at both pH 6 and 10. P. plecoglossicida S7. Y12F mutation altered the kinetic parameters of MT (Km- 1.38 mM, Vmax- 22.32 µM/min) as compared to WT (Km- 1.52 mM, Vmax- 29.76 µM/min) thus increasing the binding affinity of mutant lipase. Y12F mutant lipase with better pH and thermal stability can be used in biocatalysis.
Collapse
Affiliation(s)
- Prassan Choudhary
- Microbial Technology Unit-II, ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Maunath Bhanjan, India
- Amity Institute of Biotechnology, Amity University, 226010, Lucknow, India
| | - Mohd Waseem
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, 110012, New Delhi, India
| | - Sunil Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Library Avenue, 110012, Pusa, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, 110012, New Delhi, India
| | - Shilpi Srivastava
- Amity Institute of Biotechnology, Amity University, 226010, Lucknow, India
| | - Hillol Chakdar
- Microbial Technology Unit-II, ICAR-National Bureau of Agriculturally Important Microorganisms, 275103, Maunath Bhanjan, India.
| |
Collapse
|
15
|
Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, Chen G, Ng WL, Islam MN, Punnarak P, Zheng H, Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea. FRONTIERS IN PLANT SCIENCE 2023; 13:1075353. [PMID: 36684775 PMCID: PMC9845719 DOI: 10.3389/fpls.2022.1075353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
Collapse
Affiliation(s)
- Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuchen Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qianying Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Luzhen Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Md Nazrul Islam
- Forestry and Wood Technology Discipline, Khulna University, Khulna, Bangladesh
| | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| |
Collapse
|
16
|
Fusco G, Biancaniello C, Vrettas MD, De Simone A. Thermal tuning of protein hydration in a hyperthermophilic enzyme. Front Mol Biosci 2022; 9:1037445. [PMID: 36518847 PMCID: PMC9742426 DOI: 10.3389/fmolb.2022.1037445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/14/2022] [Indexed: 10/24/2023] Open
Abstract
Water at the protein surface is an active biological molecule that plays a critical role in many functional processes. Using NMR-restrained MD simulations, we here addressed how protein hydration is tuned at high biological temperatures by analysing homologous acylphosphatase enzymes (AcP) possessing similar structure and dynamics under very different thermal conditions. We found that the hyperthermophilic Sso AcP at 80°C interacts with a lower number of structured waters in the first hydration shell than its human homologous mt AcP at 37°C. Overall, the structural and dynamical properties of waters at the surface of the two enzymes resulted similar in the first hydration shell, including solvent molecules residing in the active site. By contrast the dynamical content of water molecules in the second hydration shell was found to diverge, with higher mobility observed in Sso AcP at 80°C. Taken together the results delineate the subtle differences in the hydration properties of mt AcP and Sso AcP, and indicate that the concept of corresponding states with equivalent dynamics in homologous mesophilic and hyperthermophylic proteins should be extended to the first hydration shell.
Collapse
Affiliation(s)
- Giuliana Fusco
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Michail D. Vrettas
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Alfonso De Simone
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| |
Collapse
|
17
|
Molecular and thermodynamic mechanisms for protein adaptation. EUROPEAN BIOPHYSICS JOURNAL 2022; 51:519-534. [DOI: 10.1007/s00249-022-01618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
|
18
|
Palumbo RJ, McKean N, Leatherman E, Namitz KEW, Connell L, Wolfe A, Moody K, Gostinčar C, Gunde-Cimerman N, Bah A, Hanes SD. Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance. SCIENCE ADVANCES 2022; 8:eabq3235. [PMID: 36070379 PMCID: PMC9451162 DOI: 10.1126/sciadv.abq3235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 06/14/2023]
Abstract
Most of the world's biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS)26 and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.
Collapse
Affiliation(s)
- Ryan J. Palumbo
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Nathan McKean
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Erinn Leatherman
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Laurie Connell
- School of Marine Sciences and Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - Aaron Wolfe
- Ichor Life Sciences Inc., 2651 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Kelsey Moody
- Ichor Life Sciences Inc., 2651 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| | - Steven D. Hanes
- Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY 13210, USA
| |
Collapse
|
19
|
Fusco G, Bemporad F, Chiti F, Dobson CM, De Simone A. The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes. Front Mol Biosci 2022; 9:981312. [PMID: 36158582 PMCID: PMC9490001 DOI: 10.3389/fmolb.2022.981312] [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: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins from hyperthermophilic organisms are evolutionary optimised to adopt functional structures and dynamics under conditions in which their mesophilic homologues are generally inactive or unfolded. Understanding the nature of such adaptation is of crucial interest to clarify the underlying mechanisms of biological activity in proteins. Here we measured NMR residual dipolar couplings of a hyperthermophilic acylphosphatase enzyme at 80°C and used these data to generate an accurate structural ensemble representative of its native state. The resulting energy landscape was compared to that obtained for a human homologue at 37°C, and additional NMR experiments were carried out to probe fast (15N relaxation) and slow (H/D exchange) backbone dynamics, collectively sampling fluctuations of the two proteins ranging from the nanosecond to the millisecond timescale. The results identified key differences in the strategies for protein-protein and protein-ligand interactions of the two enzymes at the respective physiological temperatures. These include the dynamical behaviour of a β-strand involved in the protection against aberrant protein aggregation and concerted motions of loops involved in substrate binding and catalysis. Taken together these results elucidate the structure-dynamics-function relationship associated with the strategies of thermal adaptation of protein molecules.
Collapse
Affiliation(s)
- Giuliana Fusco
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco Bemporad
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | | | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
- *Correspondence: Alfonso De Simone,
| |
Collapse
|
20
|
Somero GN. Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:389-413. [PMID: 37073170 PMCID: PMC10077225 DOI: 10.1007/s42995-022-00140-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/15/2022] [Indexed: 05/03/2023]
Abstract
The seas confront organisms with a suite of abiotic stressors that pose challenges for physiological activity. Variations in temperature, hydrostatic pressure, and salinity have potential to disrupt structures, and functions of all molecular systems on which life depends. During evolution, sequences of nucleic acids and proteins are adaptively modified to "fit" these macromolecules for function under the particular abiotic conditions of the habitat. Complementing these macromolecular adaptations are alterations in compositions of solutions that bathe macromolecules and affect stabilities of their higher order structures. A primary result of these "micromolecular" adaptations is preservation of optimal balances between conformational rigidity and flexibility of macromolecules. Micromolecular adaptations involve several families of organic osmolytes, with varying effects on macromolecular stability. A given type of osmolyte generally has similar effects on DNA, RNA, proteins and membranes; thus, adaptive regulation of cellular osmolyte pools has a global effect on macromolecules. These effects are mediated largely through influences of osmolytes and macromolecules on water structure and activity. Acclimatory micromolecular responses are often critical in enabling organisms to cope with environmental changes during their lifetimes, for example, during vertical migration in the water column. A species' breadth of environmental tolerance may depend on how effectively it can vary the osmolyte composition of its cellular fluids in the face of stress. Micromolecular adaptations remain an under-appreciated aspect of evolution and acclimatization. Further study can lead to a better understanding of determinants of environmental tolerance ranges and to biotechnological advances in designing improved stabilizers for biological materials.
Collapse
Affiliation(s)
- George N. Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950 USA
| |
Collapse
|
21
|
Blessing EM, Parekh A, Betensky RA, Babb J, Saba N, Debure L, Varga AW, Ayappa I, Rapoport DM, Butler TA, de Leon MJ, Wisniewski T, Lopresti BJ, Osorio RS. Association between lower body temperature and increased tau pathology in cognitively normal older adults. Neurobiol Dis 2022; 171:105748. [PMID: 35550158 DOI: 10.1016/j.nbd.2022.105748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND Preclinical studies suggest body temperature (Tb) and consequently brain temperature has the potential to bidirectionally interact with tau pathology in Alzheimer's Disease (AD). Tau phosphorylation is substantially increased by a small (<1 °C) decrease in temperature within the human physiological range, and thermoregulatory nuclei are affected by tau pathology early in the AD continuum. In this study we evaluated whether Tb (as a proxy for brain temperature) is cross-sectionally associated with clinically utilized markers of tau pathology in cognitively normal older adults. METHODS Tb was continuously measured with ingestible telemetry sensors for 48 h. This period included two nights of nocturnal polysomnography to delineate whether Tb during waking vs sleep is differentially associated with tau pathology. Tau phosphorylation was assessed with plasma and cerebrospinal fluid (CSF) tau phosphorylated at threonine 181 (P-tau), sampled the day following Tb measurement. In addition, neurofibrillary tangle (NFT) burden in early Braak stage regions was imaged with PET-MR using the [18F]MK-6240 radiotracer on average one month later. RESULTS Lower Tb was associated with increased NFT burden, as well as increased plasma and CSF P-tau levels (p < 0.05). NFT burden was associated with lower Tb during waking (p < 0.05) but not during sleep intervals. Plasma and CSF P-tau levels were highly correlated with each other (p < 0.05), and both variables were correlated with tau tangle radiotracer uptake (p < 0.05). CONCLUSIONS These results, the first available for human, suggest that lower Tb in older adults may be associated with increased tau pathology. Our findings add to the substantial preclinical literature associating lower body and brain temperature with tau hyperphosphorylation. CLINICAL TRIAL NUMBER NCT03053908.
Collapse
Affiliation(s)
- Esther M Blessing
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY 10016, United States of America.
| | - Ankit Parekh
- Mount Sinai Integrative Sleep Center, Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, United States of America.
| | - Rebecca A Betensky
- Department of NYU School of Global Public Health, New York, NY 10016, United States of America.
| | - James Babb
- Alzheimer's Disease Research Center, Department of Neurology, NYU Grossman School of Medicine, New York, NY 10016, United States of America.
| | - Natalie Saba
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY 10016, United States of America.
| | - Ludovic Debure
- Alzheimer's Disease Research Center, Department of Neurology, NYU Grossman School of Medicine, New York, NY 10016, United States of America.
| | - Andrew W Varga
- Mount Sinai Integrative Sleep Center, Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, United States of America.
| | - Indu Ayappa
- Mount Sinai Integrative Sleep Center, Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, United States of America.
| | - David M Rapoport
- Mount Sinai Integrative Sleep Center, Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, United States of America.
| | - Tracy A Butler
- Department of Neurology, Weill Cornell Medicine, New York, NY 10065, United States of America.
| | - Mony J de Leon
- Department of Neurology, Weill Cornell Medicine, New York, NY 10065, United States of America.
| | - Thomas Wisniewski
- Alzheimer's Disease Research Center, Department of Neurology, NYU Grossman School of Medicine, New York, NY 10016, United States of America.
| | - Brian J Lopresti
- Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
| | - Ricardo S Osorio
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY 10016, United States of America; Alzheimer's Disease Research Center, Department of Neurology, NYU Grossman School of Medicine, New York, NY 10016, United States of America.
| |
Collapse
|
22
|
Radhakrishnan R, Manna B, Ghosh A. Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127123. [PMID: 34530268 DOI: 10.1016/j.jhazmat.2021.127123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The growing demands of solvent-based industries like paint, pharmaceutical, petrochemical, paper and pulp, etc., have directly increased the release of effluents that are rich in hazardous aromatic compounds in the environment. A sustainable biotechnological approach utilizing laccases as biocatalyst enable in biodegradation of these aromatic toxin-rich effluents. However, this enzymatic process is ineffective as laccases lose their stability and catalytic activity at high organic solvent concentrations. In this study, molecular dynamic simulations of a novel solvent tolerant laccase, DLac from Cerrena sp. RSD1 was performed to explore the molecular-level understanding of DLac in 30%(v/v) acetone and acetonitrile. Solvent-induced conformational changes were analyzed via protein structure network, which was illustrated with respect to cliques and communities. In the presence of acetonitrile, the cliques around the active site and substrate-binding site were disjoined, thus the communities lost their network integrity. Whereas with acetone, the community near the substrate-binding site gained new residues and formed a rigidified network that corresponded to enhanced DLac's activity. Moreover, prominent solvent binding sites were speculated, which can be probable mutation targets to further improve solvent tolerance and catalytic activity. The molecular basis behind solvent induced catalytic activity will further aid in engineering laccase for its industrial application.
Collapse
Affiliation(s)
- Rokesh Radhakrishnan
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Bharat Manna
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India; School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
| |
Collapse
|
23
|
Stark C, Bautista-Leung T, Siegfried J, Herschlag D. Systematic investigation of the link between enzyme catalysis and cold adaptation. eLife 2022; 11:72884. [PMID: 35019838 PMCID: PMC8754429 DOI: 10.7554/elife.72884] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a dominant adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To systematically test rate enhancement as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism's optimal growth temperature (TGrowth) and analyzed trends of rate constants as a function of TGrowth. These data do not support a general increase in rate enhancement in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there is prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Nevertheless, we found that little of the rate constant variation for 20 KSI variants was accounted for by TGrowth. In contrast, and consistent with prior expectations, we observed a correlation between stability and TGrowth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate constants than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate constant variation.
Collapse
Affiliation(s)
- Catherine Stark
- ChEM-H, Stanford University, Stanford, United States.,Department of Biochemistry, Stanford University, Stanford, United States
| | | | - Joanna Siegfried
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Daniel Herschlag
- ChEM-H, Stanford University, Stanford, United States.,Department of Biochemistry, Stanford University, Stanford, United States.,Department of Chemical Engineering, Stanford University, Stanford, United States
| |
Collapse
|
24
|
Somero GN. The Goldilocks Principle: A Unifying Perspective on Biochemical Adaptation to Abiotic Stressors in the Sea. ANNUAL REVIEW OF MARINE SCIENCE 2022; 14:1-23. [PMID: 34102065 DOI: 10.1146/annurev-marine-022521-102228] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The ability of marine organisms to thrive over wide ranges of environmental stressors that perturb structures of proteins, nucleic acids, and lipids illustrates the effectiveness of adaptation at the biochemical level. A critical role of these adaptations is to achieve a proper balance between structural rigidity, which is necessary for maintaining three-dimensional conformation, and flexibility, which is required to allow changes in conformation during function. The Goldilocks principle refers to this balancing act, wherein structural stability and functional properties are poised at values that are just right for the environment the organism faces. Achieving this balance involves changes in macromolecular sequence and adaptive change in the composition of the aqueous or lipid milieu in which macromolecules function. This article traces the development of the field of biochemical adaptation throughout my career and shows how comparative studies of marine animals from diverse habitats have shed light on fundamental properties of life common to all organisms.
Collapse
Affiliation(s)
- George N Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA;
| |
Collapse
|
25
|
Khrapunov S, Waterman A, Persaud R, Chang EP. Structure, Function, and Thermodynamics of Lactate Dehydrogenases from Humans and the Malaria Parasite P. falciparum. Biochemistry 2021; 60:3582-3595. [PMID: 34747601 DOI: 10.1021/acs.biochem.1c00470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Temperature adaptation is ubiquitous among all living organisms, yet the molecular basis for this process remains poorly understood. It can be assumed that for parasite-host systems, the same enzymes found in both organisms respond to the same selection factor (human body temperature) with similar structural changes. Herein, we report the existence of a reversible temperature-dependent structural transition for the glycolytic enzyme lactate dehydrogenase (LDH) from the malaria parasite Plasmodium falciparum (pfLDH) and human heart (hhLDH) occurring in the temperature range of human fever. This transition is observed for LDHs from psychrophiles, mesophiles, and moderate thermophiles in their operating temperature range. Thermodynamic analysis reveals unique thermodynamic signatures of the LDH-substrate complexes defining a specific temperature range to which human LDH is adapted and parasite LDH is not, despite their common mesophilic nature. The results of spectroscopic analysis combined with the available crystallographic data reveal the existence of an active center within pfLDH that imparts psychrophilic structural properties to the enzyme. This center consists of two pockets, one formed by the five amino acids (5AA insert) within the substrate specificity loop and the other by the active site, that mutually regulate one another in response to temperature and induce structural and functional changes in the Michaelis complex. Our findings pave the way toward a new strategy for malaria treatments and drug design using therapeutic agents that inactivate malarial LDH selectively at a specific temperature range of the cyclic malaria paroxysm.
Collapse
Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Akiba Waterman
- Department of Chemistry and Physical Sciences, Pace University, 1 Pace Plaza, New York, New York 10038, United States
| | - Rudra Persaud
- Department of Chemistry and Physical Sciences, Pace University, 1 Pace Plaza, New York, New York 10038, United States
| | - Eric P Chang
- Department of Chemistry and Physical Sciences, Pace University, 1 Pace Plaza, New York, New York 10038, United States
| |
Collapse
|
26
|
Dong YW, Liao ML, Han GD, Somero GN. An integrated, multi-level analysis of thermal effects on intertidal molluscs for understanding species distribution patterns. Biol Rev Camb Philos Soc 2021; 97:554-581. [PMID: 34713568 DOI: 10.1111/brv.12811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022]
Abstract
Elucidating the physiological mechanisms that underlie thermal stress and discovering how species differ in capacities for phenotypic acclimatization and evolutionary adaptation to this stress is critical for understanding current latitudinal and vertical distribution patterns of species and for predicting their future state in a warming world. Such mechanistic analyses require careful choice of study systems (species and temperature-sensitive traits) and design of laboratory experiments that reflect the complexities of in situ conditions. Here, we critically review a wide range of studies of intertidal molluscs that provide mechanistic accounts of thermal effects across all levels of biological organization - behavioural, organismal, organ level, cellular, molecular, and genomic - and show how temperature-sensitive traits govern distribution patterns and capacities for coping with thermal stress. Comparisons of congeners from different thermal habitats are especially effective means for identifying adaptive variation. We employ these mechanistic analyses to illustrate how species differ in the severity of threats posed by rising temperature. Counterintuitively, we show that some of the most heat-tolerant species may be most threatened by increases in temperatures because of their small thermal safety margins and minimal abilities to acclimatize to higher temperatures. We discuss recent molecular biological and genomic studies that provide critical foundations for understanding the types of evolutionary changes in protein structure, RNA secondary structure, genome content, and gene expression capacities that underlie adaptation to temperature. Duplication of stress-related genes, as found in heat-tolerant molluscs, may provide enhanced capacity for coping with higher temperatures. We propose that the anatomical, behavioural, physiological, and genomic diversity found among intertidal molluscs, which commonly are of critical importance and high abundance in these ecosystems, makes this group of animals a highly appropriate study system for addressing questions about the mechanistic determinants of current and future distribution patterns of intertidal organisms.
Collapse
Affiliation(s)
- Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, 266003, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, 266003, China
| | - Guo-Dong Han
- College of Life Science, Yantai University, Yantai, 264005, China
| | - George N Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California, 93950, U.S.A
| |
Collapse
|
27
|
Feng J, Xu S, Feng R, Kovalevsky A, Zhang X, Liu D, Wan Q. Identification and structural analysis of a thermophilic β-1,3-glucanase from compost. BIORESOUR BIOPROCESS 2021; 8:102. [PMID: 38650272 PMCID: PMC10992293 DOI: 10.1186/s40643-021-00449-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/24/2021] [Indexed: 11/10/2022] Open
Abstract
β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.
Collapse
Affiliation(s)
- Jianwei Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shenyuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ruirui Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, Shandong, 266000, People's Republic of China
| | - Dongyang Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
28
|
Arifin M, Budiman C, Fujiyama K, Arief II. Kinetic and Thermodynamic Study of Plantaricin IIA-1A5, a Bacteriocin Produced by Indonesian Probiotic Lactobacillus plantarum IIA-1A5. Protein Pept Lett 2021; 28:680-686. [PMID: 33231143 DOI: 10.2174/0929866527999201123213841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 08/01/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Plantaricin IIA-1A5 is a bacteriocin produced by Lactobacillus plantarum IIA-1A5, a locally isolated probiotic from Indonesia. Plantaricin IIA-1A5 exhibits antibacterial activity against wide spectrum of pathogenic bacteria, thus promising to be applied in various food products. Nevertheless, thermal stability of this bacteriocin remains to be fully investigated. OBJECTIVE This study aims to determine thermal stability of plantaricin IIA-1A5 through kinetic and thermodynamic parameters. METHOD To address, plantaricin IIA-1A5 was purified from Lactobacillus plantarum IIA-1A5, which was growth under whey media, using ammonium sulfate precipitation followed by ionexchange chromatography. Purified plantaricin IIA-IA5 was then subjected to analysis of its bacteriocin activity. The thermal inactivation of bacteriocin from L. plantarum IIA-1A5 was calculated by incubating the bacteriocin at different temperatures ranging from 60-80 °C for 30 to 90 min, which was then used to calculate its kinetic and thermodynamic parameters. RESULTS The result showed the inactivation rates (k-value) were ranging from 0.008 to 0.013 min-1. Heat resistance of plantaricin IIA-1A5 (D-value) at constant heating temperature of 60, 65, 70, 75, and 80 °C were 311.6, 305.9, 294.5, 198.9, and 180.2 min, which indicated a faster inactivation at higher temperatures. D-value sensitivity for temperature changes (z-value) was calculated to be 75.76 °C. Further, thermodynamic analysis suggested that plantaricin IIA-1A5 is thermostable, with activation energy (Ea) of 29.02 kJ mol-1. CONCLUSION This result showed that plantaricin IIA-1A5 is considerably more heat-stable than plantaricin members and promises to be applied in food industries where heat treatments are applied. Furthermore, a possible mechanism by which plantaricin IIA-1A5 maintains its stability was also discussed by referring to its thermodynamic parameters.
Collapse
Affiliation(s)
- Muhamad Arifin
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor, Indonesia
| | - Cahyo Budiman
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor, Indonesia
| | - Kazuhito Fujiyama
- The International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Irma Isnafia Arief
- Department of Animal Production and Technology, Faculty of Animal Science, Bogor Agricultural University, Bogor, Indonesia
| |
Collapse
|
29
|
Czubinski J. Insight into thermally induced structural changes of lupin seed γ-conglutin. Food Chem 2021; 354:129480. [PMID: 33765465 DOI: 10.1016/j.foodchem.2021.129480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 11/17/2022]
Abstract
A multidimensional analysis aimed to determine the thermal impact on γ-conglutin at the two oligomeric states was carried out. A wide range of biophysical and bioinformatic methods allowed to get insight into a thermal unfolding mechanism. The determined midpoint transition temperature (Tm) values were remarkably different, being 56.5 °C and 71.1 °C for γ-conglutin monomer and hexamer, respectively. The unfolding pattern for hexamer molecules included aggregation/precipitation, while monomers tended to form soluble aggregates after heat exposure. Interestingly, differences in the aromatic amino acid residues movements indicate that during thermal treatment of γ-conglutin hexamer red-shift occurred contrary to the monomer in the case of which blue-shift was noted. The obtained results provide an essential contribution to expand our knowledge about the molecular characterization of this intriguing lupin seed protein.
Collapse
Affiliation(s)
- Jaroslaw Czubinski
- Department of Food Biochemistry and Analysis, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznan, Poland.
| |
Collapse
|
30
|
Effect of Selection for Pyrethroid Resistance on Abiotic Stress Tolerance in Aedes aegypti from Merida, Yucatan, Mexico. INSECTS 2021; 12:insects12020124. [PMID: 33572520 PMCID: PMC7910840 DOI: 10.3390/insects12020124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/19/2022]
Abstract
Simple Summary Aedes aegypti is the principal vector of major human pathogens, including dengue, Zika, chikungunya, and yellow fever viruses. Vector control relies mostly on the use of pyrethroid insecticides that kill mosquitoes by disabling the nervous system through binding to the voltage-gated sodium channel (vgsc). Resistance mechanisms have evolved most commonly as mutations in the vgsc gene or in genes associated with detoxification. These mutations are thought to associate with fitness costs, such that the frequency of resistant genotypes should decrease in the absence of insecticide use, and this assumption is critical to managing resistance through insecticide rotation strategies. While most studies to date have investigated life history parameters such as fecundity, we sought to investigate whether environmental stress resistance traits might also vary with insecticide resistance. We found, contrary to our expectations, that a strain selected for enhanced insecticide resistance had higher thermotolerance than its sister insecticide susceptible counterpart. Overall, our results indicate that abiotic resistance traits can correlate with insecticide resistance in surprising and variable ways, potentially complicating the management of insecticide resistance in the field. Abstract The study of fitness costs of insecticide resistance mutations in Aedes aegypti has generally been focused on life history parameters such as fecundity, mortality, and energy reserves. In this study we sought to investigate whether trade-offs might also exist between insecticide resistance and other abiotic stress resistance parameters. We evaluated the effects of the selection for permethrin resistance specifically on larval salinity and thermal tolerance. A population of A. aegypti originally from Southern Mexico was split into two strains, one selected for permethrin resistance and the other not. Larvae were reared at different salinities, and the fourth instar larvae were subjected to acute thermal stress; then, survival to both stresses was compared between strains. Contrary to our predictions, we found that insecticide resistance correlated with significantly enhanced larval thermotolerance. We found no clear difference in salinity tolerance between strains. This result suggests that insecticide resistance does not necessarily carry trade-offs in all traits affecting fitness and that successful insecticide resistance management strategies must account for genetic associations between insecticide resistance and abiotic stress resistance, as well as traditional life history parameters.
Collapse
|
31
|
Comparative characterization of the hemocyanin-derived phenol oxidase activity from spiders inhabiting different thermal habitats. Comp Biochem Physiol B Biochem Mol Biol 2021; 253:110548. [PMID: 33388391 DOI: 10.1016/j.cbpb.2020.110548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 11/23/2022]
Abstract
Enzymes adapted to cold temperatures are commonly characterized for having higher Michaelis-Menten constants (KM) values and lower optimum and denaturation temperature, when compared to other meso or thermophilic enzymes. Phenoloxidase (PO) enzymes are ubiquitous in nature, however, they have not been reported in spiders. It is the oxygen carrier protein hemocyanin (Hc), found at high concentrations in their hemolymph, which displays an inducible PO activity. Hence, we hypothesize that Hc-derived PO activity could show features of cold adaptation in alpine species. We analyzed the Hc from two species of Theraphosidae from different thermal environments: Euathlus condorito (2400 m a.s.l.) and Grammostola rosea (500 m a.s.l.). Hc was purified from the hemolymph of both spiders and was characterized by identifying subunit composition and measuring the sodium dodecyl sulfate (SDS)-induced PO activity. The high-altitude spider Hc showed higher PO activity under all conditions and higher apparent Michaelis-Menten constant. Moreover, the optimum temperature for PO activity was lower for E. condorito Hc. These findings suggest a potential adaptation at the level of Hc-derived PO activity in Euathlus condorito, giving insights on possible mechanisms used by this mygalomorph spider to occupy extremes and variable thermal environments.
Collapse
|
32
|
Accelerated evolution and positive selection of rhodopsin in Tibetan loaches living in high altitude. Int J Biol Macromol 2020; 165:2598-2606. [PMID: 33470199 DOI: 10.1016/j.ijbiomac.2020.10.151] [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: 07/31/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 11/22/2022]
Abstract
Rhodopsin (RH1), the temperature-sensitive visual pigment, attained cold adaptation by functional trade-offs between protein stability and activity. Recent studies suggested convergent selection pressures drove cold adaptation of rhodopsin in high altitude catfishes through nonparallel molecular mechanisms. Here, we tested whether the similar shift occurred in RH1 of Tibetan loaches on the Qinghai-Tibet Plateau (QTP) by investigating the molecular evolution and potential effect on function of RH1. We sequenced RH1 from 27 Triplophysa species, and four lowland loaches and combined these data with published sequences. Tests using a series of models of molecular evolution resulted in strong evidence for accelerated evolution and positive selection in Triplophysa RH1. Three positively selected sites were near key functional domains modulating nonspectral properties of rhodopsin, substitutions of which were likely to compensate for cold-induced decrease in rhodopsin kinetics in cold environments. Moreover, although accelerated evolutionary rates in Tibetan loaches was convergent with those in high altitude catfishes, the sites under positive selection were nonoverlapping. Our findings provide evidence for convergent shift in selection pressures of RH1 in high altitude fish during the ecological transition to cold environment of the QTP.
Collapse
|
33
|
Doukov T, Herschlag D, Yabukarski F. Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures. J Appl Crystallogr 2020; 53:1493-1501. [PMID: 33312102 PMCID: PMC7710493 DOI: 10.1107/s1600576720013503] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/08/2020] [Indexed: 11/10/2022] Open
Abstract
Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293-363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.
Collapse
Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
34
|
Weber AAT, Hugall AF, O’Hara TD. Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα. Genome Biol Evol 2020; 12:1929-1942. [PMID: 32780796 PMCID: PMC7643608 DOI: 10.1093/gbe/evaa167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a "cold-shock" protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.
Collapse
Affiliation(s)
- Alexandra A -T Weber
- Sciences, Museums Victoria, Melbourne, Victoria, Australia
- Centre de Bretagne, REM/EEP, Ifremer, Laboratoire Environnement Profond, Plouzané, France
- Zoological Institute, University of Basel, Switzerland
| | | | | |
Collapse
|
35
|
Bellone R, Failloux AB. The Role of Temperature in Shaping Mosquito-Borne Viruses Transmission. Front Microbiol 2020; 11:584846. [PMID: 33101259 PMCID: PMC7545027 DOI: 10.3389/fmicb.2020.584846] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/07/2020] [Indexed: 12/28/2022] Open
Abstract
Mosquito-borne diseases having the greatest impact on human health are typically prevalent in the tropical belt of the world. However, these diseases are conquering temperate regions, raising the question of the role of temperature on their dynamics and expansion. Temperature is one of the most significant abiotic factors affecting, in many ways, insect vectors and the pathogens they transmit. Here, we debate the veracity of this claim by synthesizing current knowledge on the effects of temperature on arboviruses and their vectors, as well as the outcome of their interactions.
Collapse
Affiliation(s)
- Rachel Bellone
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Anna-Bella Failloux
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France
| |
Collapse
|
36
|
Meemongkolkiat T, Allison J, Seebacher F, Lim J, Chanchao C, Oldroyd BP. Thermal adaptation in the honeybee ( Apis mellifera) via changes to the structure of malate dehydrogenase. ACTA ACUST UNITED AC 2020; 223:jeb.228239. [PMID: 32680901 DOI: 10.1242/jeb.228239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022]
Abstract
In honeybees there are three alleles of cytosolic malate dehydrogenase gene: F, M and S. Allele frequencies are correlated with environmental temperature, suggesting that the alleles have temperature-dependent fitness benefits. We determined the enzyme activity of each allele across a range of temperatures in vitro The F and S alleles have higher activity and are less sensitive to high temperatures than the M allele, which loses activity after incubation at temperatures found in the thorax of foraging bees in hot climates. Next, we predicted the protein structure of each allele and used molecular dynamics simulations to investigate their molecular flexibility. The M allozyme is more flexible than the S and F allozymes at 50°C, suggesting a plausible explanation for its loss of activity at high temperatures, and has the greatest structural flexibility at 15°C, suggesting that it can retain some enzyme activity at cooler temperatures. MM bees recovered from 2 h of cold narcosis significantly better than all other genotypes. Combined, these results explain clinal variation in malate dehydrogenase allele frequencies in the honeybee at the molecular level.
Collapse
Affiliation(s)
- Thitipan Meemongkolkiat
- Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.,Macleay Building A12, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jane Allison
- Digital Life Institute and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag, 92019 Auckland, New Zealand
| | - Frank Seebacher
- Heyden Laurence Building, The University of Sydney, Sydney, NSW 2006, Australia
| | - Julianne Lim
- Macleay Building A12, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chanpen Chanchao
- Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Benjamin P Oldroyd
- Macleay Building A12, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
37
|
Miller WT. Temperature sensitivities of metazoan and pre-metazoan Src kinases. Biochem Biophys Rep 2020; 23:100775. [PMID: 32566764 PMCID: PMC7298416 DOI: 10.1016/j.bbrep.2020.100775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/24/2022] Open
Abstract
Homologous enzymes from different species display functional characteristics that correlate with the physiological and environmental temperatures encountered by the organisms. In this study, we have investigated the temperature sensitivity of the nonreceptor tyrosine kinase Src. We compared the temperature dependencies of c-Src and two Src kinases from single-celled eukaryotes, the choanoflagellate Monosiga brevicollis and the filasterean Capsaspora owczarzaki. Metazoan c-Src exhibits temperature sensitivity, with high activity at 30 °C and 37 °C. This sensitivity is driven by changes in substrate binding as well as maximal velocity, and it is dependent on the amino acid sequence surrounding tyrosine in the substrate. When tested with a peptide that displays temperature-dependent phosphorylation by c-Src, the enzymatic rates for the unicellular Src kinases show much less variation over the temperatures tested. The data demonstrate that unicellular Src kinases are temperature compensated relative to metazoan c-Src, consistent with an evolutionary adaptation to their environments.
Collapse
Affiliation(s)
- W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY, 11768, USA
| |
Collapse
|
38
|
Prahlad V. The discovery and consequences of the central role of the nervous system in the control of protein homeostasis. J Neurogenet 2020; 34:489-499. [PMID: 32527175 PMCID: PMC7736053 DOI: 10.1080/01677063.2020.1771333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/14/2020] [Indexed: 12/30/2022]
Abstract
Organisms function despite wide fluctuations in their environment through the maintenance of homeostasis. At the cellular level, the maintenance of proteins as functional entities at target expression levels is called protein homeostasis (or proteostasis). Cells implement proteostasis through universal and conserved quality control mechanisms that surveil and monitor protein conformation. Recent studies that exploit the powerful ability to genetically manipulate specific neurons in C. elegans have shown that cells within this metazoan lose their autonomy over this fundamental survival mechanism. These studies have uncovered novel roles for the nervous system in controlling how and when cells activate their protein quality control mechanisms. Here we discuss the conceptual underpinnings, experimental evidence and the possible consequences of such a control mechanism. PRELUDE: Whether the detailed examination of parts of the nervous system and their selective perturbation is sufficient to reconstruct how the brain generates behavior, mental disease, music and religion remains an open question. Yet, Sydney Brenner's development of C. elegans as an experimental organism and his faith in the bold reductionist approach that 'the understanding of wild-type behavior comes best after the discovery and analysis of mutations that alter it', has led to discoveries of unexpected roles for neurons in the biology of organisms.
Collapse
Affiliation(s)
- Veena Prahlad
- Department of Biology, Aging Mind and Brain Initiative, University of Iowa, Iowa City, IA, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
39
|
Vornanen M. Feeling the heat: source–sink mismatch as a mechanism underlying the failure of thermal tolerance. J Exp Biol 2020; 223:223/16/jeb225680. [DOI: 10.1242/jeb.225680] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ABSTRACT
A mechanistic explanation for the tolerance limits of animals at high temperatures is still missing, but one potential target for thermal failure is the electrical signaling off cells and tissues. With this in mind, here I review the effects of high temperature on the electrical excitability of heart, muscle and nerves, and refine a hypothesis regarding high temperature-induced failure of electrical excitation and signal transfer [the temperature-dependent deterioration of electrical excitability (TDEE) hypothesis]. A central tenet of the hypothesis is temperature-dependent mismatch between the depolarizing ion current (i.e. source) of the signaling cell and the repolarizing ion current (i.e. sink) of the receiving cell, which prevents the generation of action potentials (APs) in the latter. A source–sink mismatch can develop in heart, muscles and nerves at high temperatures owing to opposite effects of temperature on source and sink currents. AP propagation is more likely to fail at the sites of structural discontinuities, including electrically coupled cells, synapses and branching points of nerves and muscle, which impose an increased demand of inward current. At these sites, temperature-induced source–sink mismatch can reduce AP frequency, resulting in low-pass filtering or a complete block of signal transmission. In principle, this hypothesis can explain a number of heat-induced effects, including reduced heart rate, reduced synaptic transmission between neurons and reduced impulse transfer from neurons to muscles. The hypothesis is equally valid for ectothermic and endothermic animals, and for both aquatic and terrestrial species. Importantly, the hypothesis is strictly mechanistic and lends itself to experimental falsification.
Collapse
Affiliation(s)
- Matti Vornanen
- Department of Environmental and Biological Sciences , University of Eastern Finland, 80101 Joensuu, Finland
| |
Collapse
|
40
|
Lecheta MC, Awde DN, O’Leary TS, Unfried LN, Jacobs NA, Whitlock MH, McCabe E, Powers B, Bora K, Waters JS, Axen HJ, Frietze S, Lockwood BL, Teets NM, Cahan SH. Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in Drosophila melanogaster. Front Genet 2020; 11:658. [PMID: 32655626 PMCID: PMC7324644 DOI: 10.3389/fgene.2020.00658] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022] Open
Abstract
Thermal tolerance of an organism depends on both the ability to dynamically adjust to a thermal stress and preparatory developmental processes that enhance thermal resistance. However, the extent to which standing genetic variation in thermal tolerance alleles influence dynamic stress responses vs. preparatory processes is unknown. Here, using the model species Drosophila melanogaster, we used a combination of Genome Wide Association mapping (GWAS) and transcriptomic profiling to characterize whether genes associated with thermal tolerance are primarily involved in dynamic stress responses or preparatory processes that influence physiological condition at the time of thermal stress. To test our hypotheses, we measured the critical thermal minimum (CTmin) and critical thermal maximum (CTmax) of 100 lines of the Drosophila Genetic Reference Panel (DGRP) and used GWAS to identify loci that explain variation in thermal limits. We observed greater variation in lower thermal limits, with CTmin ranging from 1.81 to 8.60°C, while CTmax ranged from 38.74 to 40.64°C. We identified 151 and 99 distinct genes associated with CTmin and CTmax, respectively, and there was strong support that these genes are involved in both dynamic responses to thermal stress and preparatory processes that increase thermal resistance. Many of the genes identified by GWAS were involved in the direct transcriptional response to thermal stress (72/151 for cold; 59/99 for heat), and overall GWAS candidates were more likely to be differentially expressed than other genes. Further, several GWAS candidates were regulatory genes that may participate in the regulation of stress responses, and gene ontologies related to development and morphogenesis were enriched, suggesting many of these genes influence thermal tolerance through effects on development and physiological status. Overall, our results suggest that thermal tolerance alleles can influence both dynamic plastic responses to thermal stress and preparatory processes that improve thermal resistance. These results also have utility for directly comparing GWAS and transcriptomic approaches for identifying candidate genes associated with thermal tolerance.
Collapse
Affiliation(s)
- Melise C. Lecheta
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - David N. Awde
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Thomas S. O’Leary
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Laura N. Unfried
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Nicholas A. Jacobs
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Miles H. Whitlock
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Eleanor McCabe
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Beck Powers
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Katie Bora
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - James S. Waters
- Department of Biology, Providence College, Providence, RI, United States
| | - Heather J. Axen
- Department of Biology and Biomedical Sciences, Salve Regina College, Providence, RI, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Brent L. Lockwood
- Department of Biology, University of Vermont, Burlington, VT, United States
| | - Nicholas M. Teets
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Sara H. Cahan
- Department of Biology, University of Vermont, Burlington, VT, United States
| |
Collapse
|
41
|
Dahlke F, Lucassen M, Bickmeyer U, Wohlrab S, Puvanendran V, Mortensen A, Chierici M, Pörtner HO, Storch D. Fish embryo vulnerability to combined acidification and warming coincides with a low capacity for homeostatic regulation. J Exp Biol 2020; 223:jeb212589. [PMID: 32366687 DOI: 10.1242/jeb.212589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/22/2020] [Indexed: 08/26/2023]
Abstract
The vulnerability of fish embryos and larvae to environmental factors is often attributed to a lack of adult-like organ systems (gills) and thus insufficient homeostatic capacity. However, experimental data supporting this hypothesis are scarce. Here, by using Atlantic cod (Gadus morhua) as a model, the relationship between embryo vulnerability (to projected ocean acidification and warming) and homeostatic capacity was explored through parallel analyses of stage-specific mortality and in vitro activity and expression of major ion pumps (ATP-synthase, Na+/K+-ATPase, H+-ATPase) and co-transporters (NBC1, NKCC1). Immunolocalization of these transporters was used to study ionocyte morphology in newly hatched larvae. Treatment-related embryo mortality until hatching (+20% due to acidification and warming) occurred primarily during an early period (gastrulation) characterized by extremely low ion transport capacity. Thereafter, embryo mortality decreased in parallel with an exponential increase in activity and expression of all investigated ion transporters. Significant changes in transporter activity and expression in response to acidification (+15% activity) and warming (-30% expression) indicate some potential for short-term acclimatization, although this is probably associated with energetic trade-offs. Interestingly, whole-larvae enzyme activity (supported by abundant epidermal ionocytes) reached levels similar to those previously measured in gill tissue of adult cod, suggesting that early-life stages without functional gills are better equipped in terms of ion homeostasis than previously thought. This study implies that the gastrulation period represents a critical transition from inherited (maternal) defenses to active homeostatic regulation, which facilitates enhanced resilience of later stages to environmental factors.
Collapse
Affiliation(s)
- Flemming Dahlke
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- University of Bremen, NW 2 Leobener Str., 28359 Bremen, Germany
| | - Magnus Lucassen
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Ulf Bickmeyer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Sylke Wohlrab
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Ammerländer Heersstraße 231, 26129 Oldenburg, Germany
| | | | | | | | - Hans-Otto Pörtner
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- University of Bremen, NW 2 Leobener Str., 28359 Bremen, Germany
| | - Daniela Storch
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| |
Collapse
|
42
|
Mangiagalli M, Lapi M, Maione S, Orlando M, Brocca S, Pesce A, Barbiroli A, Camilloni C, Pucciarelli S, Lotti M, Nardini M. The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase relies on its hexameric quaternary arrangement. FEBS J 2020; 288:546-565. [PMID: 32363751 DOI: 10.1111/febs.15354] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
To survive in cold environments, psychrophilic organisms produce enzymes endowed with high specific activity at low temperature. The structure of these enzymes is usually flexible and mostly thermolabile. In this work, we investigate the structural basis of cold adaptation of a GH42 β-galactosidase from the psychrophilic Marinomonas ef1. This enzyme couples cold activity with astonishing robustness for a psychrophilic protein, for it retains 23% of its highest activity at 5 °C and it is stable for several days at 37 °C and even 50 °C. Phylogenetic analyses indicate a close relationship with thermophilic β-galactosidases, suggesting that the present-day enzyme evolved from a thermostable scaffold modeled by environmental selective pressure. The crystallographic structure reveals the overall similarity with GH42 enzymes, along with a hexameric arrangement (dimer of trimers) not found in psychrophilic, mesophilic, and thermophilic homologues. In the quaternary structure, protomers form a large central cavity, whose accessibility to the substrate is promoted by the dynamic behavior of surface loops, even at low temperature. A peculiar cooperative behavior of the enzyme is likely related to the increase of the internal cavity permeability triggered by heating. Overall, our results highlight a novel strategy of enzyme cold adaptation, based on the oligomerization state of the enzyme, which effectively challenges the paradigm of cold activity coupled with intrinsic thermolability. DATABASE: Structural data are available in the Protein Data Bank database under the accession number 6Y2K.
Collapse
Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Michela Lapi
- Department of Biosciences, University of Milano, Italy
| | - Serena Maione
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | | | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Italy
| | | | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
| |
Collapse
|
43
|
Bhatt HB, Singh SP. Cloning, Expression, and Structural Elucidation of a Biotechnologically Potential Alkaline Serine Protease From a Newly Isolated Haloalkaliphilic Bacillus lehensis JO-26. Front Microbiol 2020; 11:941. [PMID: 32582046 PMCID: PMC7283590 DOI: 10.3389/fmicb.2020.00941] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
An alkaline protease gene of Bacillus lehensis JO-26 from saline desert, Little Rann of Kutch, was cloned and expressed in Escherichia coli BL21 (DE3). A 1,014-bp ORF encoded 337 amino acids. The recombinant protease (APrBL) with Asp 97, His 127, and Ser 280 forming catalytic triad belongs to the subtilase S8 protease family. The gene was optimally expressed in soluble fraction with 0.2 mM isopropyl β-D-thiogalactopyranoside (IPTG), 2% (w/v) NaCl at 28°C. APrBL, a monomer with a molecular mass of 34.6 kDa was active over pH 8–11 and 30°C−70°C, optimally at pH 10 and 50°C. The enzyme was highly thermostable and retained 73% of the residual activity at 80°C up to 3 h. It was significantly stimulated by sodium dodecyl sulfate (SDS), Ca2+, chloroform, toluene, n-butanol, and benzene while completely inhibited by phenylmethylsulfonyl fluoride (PMSF) and Hg2+. The serine nature of the protease was confirmed by its strong inhibition by PMSF. The APrBL gene was phylogenetically close to alkaline elastase YaB (P20724) and was distinct from the well-known commercial proteases subtilisin Carlsberg (CAB56500) and subtilisin BPN′ (P00782). The structural elucidation revealed 31.75% α-helices, 22.55% β-strands, and 45.70% coils. Although high glycine and fewer proline residues are a characteristic feature of the cold-adapted enzymes, the similar observation in thermally active APrBL suggests that this feature cannot be solely responsible for thermo/cold adaptation. The APrBL protease was highly effective as a detergent additive and in whey protein hydrolysis.
Collapse
Affiliation(s)
- Hitarth B Bhatt
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, India
| |
Collapse
|
44
|
Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
Collapse
Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| |
Collapse
|
45
|
Giordano D, Boubeta FM, di Prisco G, Estrin DA, Smulevich G, Viappiani C, Verde C. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins. Antioxid Redox Signal 2020; 32:396-411. [PMID: 31578873 DOI: 10.1089/ars.2019.7887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Temperature is one of the most important drivers in shaping protein adaptations. Many biochemical and physiological processes are influenced by temperature. Proteins and enzymes from organisms living at low temperature are less stable in comparison to high-temperature adapted proteins. The lower stability is generally due to greater conformational flexibility. Recent Advances: Adaptive changes in the structure of cold-adapted proteins may occur at subunit interfaces, distant from the active site, thus producing energy changes associated with conformational transitions transmitted to the active site by allosteric modulation, valid also for monomeric proteins in which tertiary structural changes may play an essential role. Critical Issues: Despite efforts, the current experimental and computational methods still fail to produce general principles on protein evolution, since many changes are protein and species dependent. Environmental constraints or other biological cellular signals may override the ancestral information included in the structure of the protein, thus introducing inaccuracy in estimates and predictions on the evolutionary adaptations of proteins in response to cold adaptation. Future Directions: In this review, we describe the studies and approaches used to investigate stability and flexibility in the cold-adapted globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. In fact, future research directions will be prescient on more detailed investigation of cold-adapted proteins and the role of fluctuations between different conformational states.
Collapse
Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Fernando Martín Boubeta
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| |
Collapse
|
46
|
Chao YC, Merritt M, Schaefferkoetter D, Evans TG. High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. BMC Evol Biol 2020; 20:28. [PMID: 32054457 PMCID: PMC7020559 DOI: 10.1186/s12862-020-1593-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background Temperature exerts a strong influence on protein evolution: species living in thermally distinct environments often exhibit adaptive differences in protein structure and function. However, previous research on protein temperature adaptation has focused on small numbers of proteins and on proteins adapted to extreme temperatures. Consequently, less is known about the types and quantity of evolutionary change that occurs to proteins when organisms adapt to small shifts in environmental temperature. In this study, these uncertainties were addressed by developing software that enabled comparison of structural changes associated with temperature adaptation (hydrogen bonding, salt bridge formation, and amino acid use) among large numbers of proteins from warm- and cold-adapted species of marine mussels, Mytilus galloprovincialis and Mytilus trossulus, respectively. Results Small differences in habitat temperature that characterize the evolutionary history of Mytilus mussels were sufficient to cause protein structural changes consistent with temperature adaptation. Hydrogen bonds and salt bridges that increase stability and protect against heat-induced denaturation were more abundant in proteins from warm-adapted M. galloprovincialis compared with proteins from cold-adapted M. trossulus. These structural changes were related to deviations in the use of polar and charged amino acids that facilitate formation of hydrogen bonds and salt bridges within proteins, respectively. Enzymes, in particular those within antioxidant and cell death pathways, were over-represented among proteins with the most hydrogen bonds and salt bridges in warm-adapted M. galloprovincialis. Unlike extremophile proteins, temperature adaptation in Mytilus proteins did not involve substantial changes in the number of hydrophobic or large volume amino acids, nor in the content of glycine or proline. Conclusions Small shifts in organism temperature tolerance, such as that needed to cope with climate warming, may result from structural and functional changes to a small percentage of the proteome. Proteins in which function is dependent on large conformational change, notably enzymes, may be particularly sensitive to temperature perturbation and represent foci for natural selection. Protein temperature adaptation can occur through different types and frequencies of structural change, and adaptive mechanisms used to cope with small shifts in habitat temperature appear different from mechanisms used to retain protein function at temperature extremes.
Collapse
Affiliation(s)
- Ying-Chen Chao
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Melanie Merritt
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Devin Schaefferkoetter
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA.
| |
Collapse
|
47
|
Irvine SQ. Embryonic canalization and its limits-A view from temperature. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:128-144. [PMID: 32011096 DOI: 10.1002/jez.b.22930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 02/06/2023]
Abstract
Many animals are able to produce similar offspring over a range of environmental conditions. This property of the developmental process has been termed canalization-the channeling of developmental pathways to generate a stable outcome despite varying conditions. Temperature is one environmental parameter that has fundamental effects on cell physiology and biochemistry, yet developmental programs generally result in a stable phenotype under a range of temperatures. On the other hand, there are typically upper and lower temperature limits beyond which the developmental program is unable to produce normal offspring. This review summarizes data on how development is affected by temperature, particularly high temperature, in various animal species. It also brings together information on potential cell biological and developmental genetic factors that may be responsible for developmental stability in varying temperatures, and likely critical mechanisms that break down at high temperature. Also reviewed are possible means for studying temperature effects on embryogenesis and how to determine which factors are most critical at the high-temperature limits for normal development. Increased knowledge of these critical factors will point to the targets of selection under climate change, and more generally, how developmental robustness in varying environments is maintained.
Collapse
Affiliation(s)
- Steven Q Irvine
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island
| |
Collapse
|
48
|
Elucidating the preference of dimeric over monomeric form for thermal stability of Thermus thermophilus isopropylmalate dehydrogenase: A molecular dynamics perspective. J Mol Graph Model 2020; 96:107530. [PMID: 31986322 DOI: 10.1016/j.jmgm.2020.107530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/23/2022]
Abstract
An oligomer usually refers to a macromolecular complex formed by non-covalent interactions of monomers. Several thermophilic proteins are oligomers. The significance of oligomerization of individual proteins for stability at higher temperature is of prime importance for understanding evolution and increasing industrial productivity. The functional form of Thermus thermophilius isopropylmalate dehydrogenase (IPMDH), a widely studied protein to understand the factors affecting the thermal stability of a protein is a dimer, a simplest oligomer. To decipher the relationship between the effects of oligomerization on thermal stability of a protein, we have applied all-atom molecular mechanics approach by analyzing how temperature effects dynamics of a subunit in the presence and absence of another subunit in dimeric (SS) and monomeric forms (SA), respectively, before its denaturation begins. Comparing the difference in overall dynamic structural aspects at two different temperatures, 300 K and 337 K. Analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and Cα-Cα distance with an increase in temperature from 300 K to 337 K for a total of 0.2 μs reveals higher thermal stability of the dimer as compared to monomer. In contrast to dimeric form, the monomer is relatively stable at 300 K but cannot withstand the structural stability at 337 K leading to loosening of intramolecular interactions with maximum fluctuation at B23-B24 within a subunit. Energetic and structural properties indicate that B24-B24' is the major contributor to maintaining subunit-subunit interaction at 337 K. Correlation between the favorable interaction energy (IE) with the minimal perturbance in Cα atoms of domain 2 in a subunit in the presence of another subunit enhances the rigidity of the domain with subunit-subunit interaction. Overall, the study indicates that the dimeric over monomeric form enhances the protein's thermal stability and not all major subunit interacting regions contribute equally in maintaining the former.
Collapse
|
49
|
Popovic I, Riginos C. Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels. Mol Ecol 2020; 29:519-535. [DOI: 10.1111/mec.15339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Iva Popovic
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Cynthia Riginos
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| |
Collapse
|
50
|
Effects of the substituted amino acid residues on the thermal properties of monomeric isocitrate dehydrogenases from a psychrophilic bacterium, Psychromonas marina, and a mesophilic bacterium, Azotobacter vinelandii. Extremophiles 2019; 23:809-820. [PMID: 31595369 DOI: 10.1007/s00792-019-01137-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/23/2019] [Indexed: 10/25/2022]
Abstract
A cold-adapted monomeric isocitrate dehydrogenase from a psychrophilic bacterium, Psychromonas marina (PmIDH), showed a high degree of amino acid sequential identity (64%) to a mesophilic one from a mesophilic bacterium, Azotobacter vinelandii (AvIDH). In this study, eight corresponding amino acid residues were substituted between them by site-directed mutagenesis, and several thermal properties of the mutated IDHs were examined. In the PmIDH mutants, PmL735F, substituted Leu735 of PmIDH by the corresponding Phe of AvIDH, showed higher specific activity and thermostability of activity than wild-type PmIDH, while the H600Y and N741P mutations of PmIDH resulted in decreased specific activity and thermostability of activity. On the other hand, among the AvIDH mutants, AvP718T showed lower optimum temperature and thermostability of activity than wild-type AvIDH. In PmIDH variously combined the H600Y, L735F and N741P mutations, PmH600YL735F, including the H600Y and L735F mutations, showed higher specific activity than PmH600Y and similar optimum temperature and thermostability of activity to PmH600Y. Furthermore, PmL735FN741P exhibited higher specific activity and thermostability of activity than PmN741P. These results indicated that the effects of the three mutations of PmIDH are additive on the specific activity of both PmH600YL735F and PmL735FN741P and on thermostability of PmL735FN741P.
Collapse
|