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O'Connor PBF. The Evolutionary Transition of the RNA World to Obcells to Cellular-Based Life. J Mol Evol 2024; 92:278-285. [PMID: 38683368 DOI: 10.1007/s00239-024-10171-2] [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: 09/04/2023] [Accepted: 04/08/2024] [Indexed: 05/01/2024]
Abstract
The obcell hypothesis is a proposed route for the RNA world to develop into a primitive cellular one. It posits that this transition began with the emergence of the proto-ribosome which enabled RNA to colonise the external surface of lipids by the synthesis of amphipathic peptidyl-RNAs. The obcell hypothesis also posits that the emergence of a predation-based ecosystem provided a selection mechanism for continued sophistication amongst early life forms. Here, I argue for this hypothesis owing to its significant explanatory power; it offers a rationale why a ribosome which initially was capable only of producing short non-coded peptides was advantageous and it forgoes issues related to maintaining a replicating RNA inside a lipid enclosure. I develop this model by proposing that the evolutionary selection for improved membrane anchors resulted in the emergence of primitive membrane pores which enabled obcells to gradually evolve into a cellular morphology. Moreover, I introduce a model of obcell production which advances that tRNAs developed from primers of the RNA world.
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2
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Mitra K, Krishnan Y. Lightly counting membrane proteins in native nanodiscs. NATURE NANOTECHNOLOGY 2024; 19:5-6. [PMID: 38012272 DOI: 10.1038/s41565-023-01538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Affiliation(s)
- Koushambi Mitra
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Neuroscience Institute, The University of Chicago, Chicago, IL, USA.
- Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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3
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García-Morales A, Balleza D. Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors. J Mol Evol 2023; 91:819-836. [PMID: 37955698 DOI: 10.1007/s00239-023-10140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
The voltage-sensing domain (VSD) is a module capable of responding to changes in the membrane potential through conformational changes and facilitating electromechanical coupling to open a pore gate, activate proton permeation pathways, or promote enzymatic activity in some membrane-anchored phosphatases. To carry out these functions, this module acts cooperatively through conformational changes. The VSD is formed by four transmembrane segments (S1-S4) but the S4 segment is critical since it carries positively charged residues, mainly Arg or Lys, which require an aqueous environment for its proper function. The discovery of this module in voltage-gated ion channels (VGICs), proton channels (Hv1), and voltage sensor-containing phosphatases (VSPs) has expanded our understanding of the principle of modularity in the voltage-sensing mechanism of these proteins. Here, by sequence comparison and the evaluation of the relationship between sequence composition, intrinsic flexibility, and structural analysis in 14 selected representatives of these three major protein groups, we report five interesting differences in the folding patterns of the VSD both in prokaryotes and eukaryotes. Our main findings indicate that this module is highly conserved throughout the evolutionary scale, however: (1) segments S1 to S3 in eukaryotes are significantly more hydrophobic than those present in prokaryotes; (2) the S4 segment has retained its hydrophilic character; (3) in eukaryotes the extramembranous linkers are significantly larger and more flexible in comparison with those present in prokaryotes; (4) the sensors present in the kHv1 proton channel and the ciVSP phosphatase, both of eukaryotic origin, exhibit relationships of flexibility and folding patterns very close to the typical ones found in prokaryotic voltage sensors; and (5) archaeal channels KvAP and MVP have flexibility profiles which are clearly contrasting in the S3-S4 region, which could explain their divergent activation mechanisms. Finally, to elucidate the obscure origins of this module, we show further evidence for a possible connection between voltage sensors and TolQ proteins.
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Affiliation(s)
- Abigail García-Morales
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico
| | - Daniel Balleza
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico.
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4
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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5
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De Rosa A, McGaughey S, Magrath I, Byrt C. Molecular membrane separation: plants inspire new technologies. THE NEW PHYTOLOGIST 2023; 238:33-54. [PMID: 36683439 DOI: 10.1111/nph.18762] [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: 08/07/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants draw up their surrounding soil solution to gain water and nutrients required for growth, development and reproduction. Obtaining adequate water and nutrients involves taking up both desired and undesired elements from the soil solution and separating resources from waste. Desirable and undesirable elements in the soil solution can share similar chemical properties, such as size and charge. Plants use membrane separation mechanisms to distinguish between different molecules that have similar chemical properties. Membrane separation enables distribution or retention of resources and efflux or compartmentation of waste. Plants use specialised membrane separation mechanisms to adapt to challenging soil solution compositions and distinguish between resources and waste. Coordination and regulation of these mechanisms between different tissues, cell types and subcellular membranes supports plant nutrition, environmental stress tolerance and energy management. This review considers membrane separation mechanisms in plants that contribute to specialised separation processes and highlights mechanisms of interest for engineering plants with enhanced performance in challenging conditions and for inspiring the development of novel industrial membrane separation technologies. Knowledge gained from studying plant membrane separation mechanisms can be applied to developing precision separation technologies. Separation technologies are needed for harvesting resources from industrial wastes and transitioning to a circular green economy.
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Affiliation(s)
- Annamaria De Rosa
- Division of Plant Science, Research School of Biology, Australian National University, 2601, ACT, Acton, Australia
| | - Samantha McGaughey
- Division of Plant Science, Research School of Biology, Australian National University, 2601, ACT, Acton, Australia
| | - Isobel Magrath
- Division of Plant Science, Research School of Biology, Australian National University, 2601, ACT, Acton, Australia
| | - Caitlin Byrt
- Division of Plant Science, Research School of Biology, Australian National University, 2601, ACT, Acton, Australia
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6
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Implanted synthetic cells trigger tissue angiogenesis through de novo production of recombinant growth factors. Proc Natl Acad Sci U S A 2022; 119:e2207525119. [PMID: 36095208 PMCID: PMC9499519 DOI: 10.1073/pnas.2207525119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Progress in bottom-up synthetic biology has stimulated the development of synthetic cells (SCs), autonomous protein-manufacturing particles, as dynamic biomimetics for replacing diseased natural cells and addressing medical needs. Here, we report that SCs genetically encoded to produce proangiogenic factors triggered the physiological process of neovascularization in mice. The SCs were constructed of giant lipid vesicles and were optimized to facilitate enhanced protein production. When introduced with the appropriate genetic code, the SCs synthesized a recombinant human basic fibroblast growth factor (bFGF), reaching expression levels of up to 9⋅106 protein copies per SC. In culture, the SCs induced endothelial cell proliferation, migration, tube formation, and angiogenesis-related intracellular signaling, confirming their proangiogenic activity. Integrating the SCs with bioengineered constructs bearing endothelial cells promoted the remodeling of mature vascular networks, supported by a collagen-IV basement membrane-like matrix. In vivo, prolonged local administration of the SCs in mice triggered the infiltration of blood vessels into implanted Matrigel plugs without recorded systemic immunogenicity. These findings emphasize the potential of SCs as therapeutic platforms for activating physiological processes by autonomously producing biological drugs inside the body.
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7
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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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8
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Sephus CD, Fer E, Garcia AK, Adam ZR, Schwieterman EW, Kaçar B. Earliest photic zone niches probed by ancestral microbial rhodopsins. Mol Biol Evol 2022; 39:6582242. [PMID: 35524714 PMCID: PMC9117797 DOI: 10.1093/molbev/msac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
For billions of years, life has continuously adapted to dynamic physical conditions near the Earth’s surface. Fossils and other preserved biosignatures in the paleontological record are the most direct evidence for reconstructing the broad historical contours of this adaptive interplay. However, biosignatures dating to Earth’s earliest history are exceedingly rare. Here, we combine phylogenetic inference of primordial rhodopsin proteins with modeled spectral features of the Precambrian Earth environment to reconstruct the paleobiological history of this essential family of photoactive transmembrane proteins. Our results suggest that ancestral microbial rhodopsins likely acted as light-driven proton pumps and were spectrally tuned toward the absorption of green light, which would have enabled their hosts to occupy depths in a water column or biofilm where UV wavelengths were attenuated. Subsequent diversification of rhodopsin functions and peak absorption frequencies was enabled by the expansion of surface ecological niches induced by the accumulation of atmospheric oxygen. Inferred ancestors retain distinct associations between extant functions and peak absorption frequencies. Our findings suggest that novel information encoded by biomolecules can be used as “paleosensors” for conditions of ancient, inhabited niches of host organisms not represented elsewhere in the paleontological record. The coupling of functional diversification and spectral tuning of this taxonomically diverse protein family underscores the utility of rhodopsins as universal testbeds for inferring remotely detectable biosignatures on inhabited planetary bodies.
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Affiliation(s)
- Cathryn D Sephus
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Evrim Fer
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary R Adam
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Edward W Schwieterman
- Blue Marble Space Institute of Science, Seattle, WA, USA.,Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA
| | - Betül Kaçar
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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9
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10
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Lewis AJO, Hegde RS. A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. BMC Biol 2021; 19:266. [PMID: 34911545 PMCID: PMC8675477 DOI: 10.1186/s12915-021-01171-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Protein transporters translocate hydrophilic segments of polypeptide across hydrophobic cell membranes. Two protein transporters are ubiquitous and date back to the last universal common ancestor: SecY and YidC. SecY consists of two pseudosymmetric halves, which together form a membrane-spanning protein-conducting channel. YidC is an asymmetric molecule with a protein-conducting hydrophilic groove that partially spans the membrane. Although both transporters mediate insertion of membrane proteins with short translocated domains, only SecY transports secretory proteins and membrane proteins with long translocated domains. The evolutionary origins of these ancient and essential transporters are not known. RESULTS The features conserved by the two halves of SecY indicate that their common ancestor was an antiparallel homodimeric channel. Structural searches with SecY's halves detect exceptional similarity with YidC homologs. The SecY halves and YidC share a fold comprising a three-helix bundle interrupted by a helical hairpin. In YidC, this hairpin is cytoplasmic and facilitates substrate delivery, whereas in SecY, it is transmembrane and forms the substrate-binding lateral gate helices. In both transporters, the three-helix bundle forms a protein-conducting hydrophilic groove delimited by a conserved hydrophobic residue. Based on these similarities, we propose that SecY originated as a YidC homolog which formed a channel by juxtaposing two hydrophilic grooves in an antiparallel homodimer. We find that archaeal YidC and its eukaryotic descendants use this same dimerisation interface to heterodimerise with a conserved partner. YidC's sufficiency for the function of simple cells is suggested by the results of reductive evolution in mitochondria and plastids, which tend to retain SecY only if they require translocation of large hydrophilic domains. CONCLUSIONS SecY and YidC share previously unrecognised similarities in sequence, structure, mechanism, and function. Our delineation of a detailed correspondence between these two essential and ancient transporters enables a deeper mechanistic understanding of how each functions. Furthermore, key differences between them help explain how SecY performs its distinctive function in the recognition and translocation of secretory proteins. The unified theory presented here explains the evolution of these features, and thus reconstructs a key step in the origin of cells.
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Affiliation(s)
- Aaron J O Lewis
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Ramanujan S Hegde
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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11
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Whitley P, Grau B, Gumbart JC, Martínez-Gil L, Mingarro I. Folding and Insertion of Transmembrane Helices at the ER. Int J Mol Sci 2021; 22:ijms222312778. [PMID: 34884581 PMCID: PMC8657811 DOI: 10.3390/ijms222312778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/16/2023] Open
Abstract
In eukaryotic cells, the endoplasmic reticulum (ER) is the entry point for newly synthesized proteins that are subsequently distributed to organelles of the endomembrane system. Some of these proteins are completely translocated into the lumen of the ER while others integrate stretches of amino acids into the greasy 30 Å wide interior of the ER membrane bilayer. It is generally accepted that to exist in this non-aqueous environment the majority of membrane integrated amino acids are primarily non-polar/hydrophobic and adopt an α-helical conformation. These stretches are typically around 20 amino acids long and are known as transmembrane (TM) helices. In this review, we will consider how transmembrane helices achieve membrane integration. We will address questions such as: Where do the stretches of amino acids fold into a helical conformation? What is/are the route/routes that these stretches take from synthesis at the ribosome to integration through the ER translocon? How do these stretches ‘know’ to integrate and in which orientation? How do marginally hydrophobic stretches of amino acids integrate and survive as transmembrane helices?
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Affiliation(s)
- Paul Whitley
- Department of Biology and Biochemistry, Centre for Regenerative Medicine, University of Bath, Bath BA2 7AY, UK;
| | - Brayan Grau
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - James C. Gumbart
- School of Physics, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Luis Martínez-Gil
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institute of Biotechnology and Biomedicine (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain; (B.G.); (L.M.-G.)
- Correspondence: ; Tel.: +34-963543796
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12
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Nirody JA, Budin I, Rangamani P. ATP synthase: Evolution, energetics, and membrane interactions. J Gen Physiol 2021; 152:152111. [PMID: 32966553 PMCID: PMC7594442 DOI: 10.1085/jgp.201912475] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
The synthesis of ATP, life’s “universal energy currency,” is the most prevalent chemical reaction in biological systems and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP synthases, the family of enzymes that carry out this endless task, are nearly as ubiquitous as the energy-laden molecule they are responsible for making. The F-type ATP synthase (F-ATPase) is found in every domain of life and has facilitated the survival of organisms in a wide range of habitats, ranging from the deep-sea thermal vents to the human intestine. Accordingly, there has been a large amount of work dedicated toward understanding the structural and functional details of ATP synthases in a wide range of species. Less attention, however, has been paid toward integrating these advances in ATP synthase molecular biology within the context of its evolutionary history. In this review, we present an overview of several structural and functional features of the F-type ATPases that vary across taxa and are purported to be adaptive or otherwise evolutionarily significant: ion channel selectivity, rotor ring size and stoichiometry, ATPase dimeric structure and localization in the mitochondrial inner membrane, and interactions with membrane lipids. We emphasize the importance of studying these features within the context of the enzyme’s particular lipid environment. Just as the interactions between an organism and its physical environment shape its evolutionary trajectory, ATPases are impacted by the membranes within which they reside. We argue that a comprehensive understanding of the structure, function, and evolution of membrane proteins—including ATP synthase—requires such an integrative approach.
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Affiliation(s)
- Jasmine A Nirody
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY.,All Souls College, University of Oxford, Oxford, UK
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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13
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'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. Life (Basel) 2021; 11:life11070690. [PMID: 34357062 PMCID: PMC8306273 DOI: 10.3390/life11070690] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.
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14
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Britto DT, Coskun D, Kronzucker HJ. Potassium physiology from Archean to Holocene: A higher-plant perspective. JOURNAL OF PLANT PHYSIOLOGY 2021; 262:153432. [PMID: 34034042 DOI: 10.1016/j.jplph.2021.153432] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 05/27/2023]
Abstract
In this paper, we discuss biological potassium acquisition and utilization processes over an evolutionary timescale, with emphasis on modern vascular plants. The quintessential osmotic and electrical functions of the K+ ion are shown to be intimately tied to K+-transport systems and membrane energization. Several prominent themes in plant K+-transport physiology are explored in greater detail, including: (1) channel mediated K+ acquisition by roots at low external [K+]; (2) K+ loading of root xylem elements by active transport; (3) variations on the theme of K+ efflux from root cells to the extracellular environment; (4) the veracity and utility of the "affinity" concept in relation to transport systems. We close with a discussion of the importance of plant-potassium relations to our human world, and current trends in potassium nutrition from farm to table.
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Affiliation(s)
- Dev T Britto
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Devrim Coskun
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation (FSAA), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Herbert J Kronzucker
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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15
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Guo Y. Detergent-free systems for structural studies of membrane proteins. Biochem Soc Trans 2021; 49:1361-1374. [PMID: 34110369 PMCID: PMC8276625 DOI: 10.1042/bst20201080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins play vital roles in living organisms, serving as targets for most currently prescribed drugs. Membrane protein structural biology aims to provide accurate structural information to understand their mechanisms of action. The advance of membrane protein structural biology has primarily relied on detergent-based methods over the past several decades. However, detergent-based approaches have significant drawbacks because detergents often damage the native protein-lipid interactions, which are often crucial for maintaining the natural structure and function of membrane proteins. Detergent-free methods recently have emerged as alternatives with a great promise, e.g. for high-resolution structure determinations of membrane proteins in their native cell membrane lipid environments. This minireview critically examines the current status of detergent-free methods by a comparative analysis of five groups of membrane protein structures determined using detergent-free and detergent-based methods. This analysis reveals that current detergent-free systems, such as the styrene-maleic acid lipid particles (SMALP), the diisobutyl maleic acid lipid particles (DIBMALP), and the cycloalkane-modified amphiphile polymer (CyclAPol) technologies are not better than detergent-based approaches in terms of maintenance of native cell membrane lipids on the transmembrane domain and high-resolution structure determination. However, another detergent-free technology, the native cell membrane nanoparticles (NCMN) system, demonstrated improved maintenance of native cell membrane lipids with the studied membrane proteins, and produced particles that were suitable for high-resolution structural analysis. The ongoing development of new membrane-active polymers and their optimization will facilitate the maturation of these new detergent-free systems.
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Affiliation(s)
- Youzhong Guo
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23298-0540, USA
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16
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The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution. J Mol Evol 2021; 89:427-447. [PMID: 34173011 DOI: 10.1007/s00239-021-10014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 05/29/2021] [Indexed: 10/21/2022]
Abstract
The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.
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17
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McGaughey SA, Tyerman SD, Byrt CS. An algal PIP-like aquaporin facilitates water transport and ionic conductance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183661. [PMID: 34058166 DOI: 10.1016/j.bbamem.2021.183661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/30/2022]
Abstract
Aquaporins are water and solute channel proteins found throughout the kingdoms of life. Ion-conducting aquaporins (icAQPs) have been identified in both plants and animals indicating that this function may be conserved through evolution. In higher plants icAQP function has been demonstrated for isoforms from two of five aquaporin subfamilies indicating that this function could have existed before the divergence of higher plants from green algae. Here a PIP-like aquaporin from the charophytic alga Klebsormidium nitens was functionally characterised in Xenopus laevis oocytes and its expression was found to induce water and ion conductance.
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Affiliation(s)
- Samantha A McGaughey
- Division of Plant Sciences, Research School of Biology, College of Science, Australian National University, Acton, Australian Capital Territory 2601, Australia.
| | - Stephen D Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Caitlin S Byrt
- Division of Plant Sciences, Research School of Biology, College of Science, Australian National University, Acton, Australian Capital Territory 2601, Australia; ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia 5064, Australia
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18
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Abstract
Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic constraints that define possible quantitative metabolomes. We apply these constraints to a metabolic network of Escherichia coli that represents 90% of its metabolome. We show that the quantitative metabolomes allowed by the abiotic constraints are consistent with metabolomic and isotope-labeling data. We find that: (i) abiotic constraints drive the evolution of high-affinity phosphate transporters; (ii) Charge-, hydrogen- and magnesium-related constraints underlie transcriptional regulatory responses to osmotic stress; and (iii) hydrogen-ion and charge imbalance underlie transcriptional regulatory responses to acid stress. Thus, quantifying the constraints that the inorganic world imposes on living systems provides insights into their key characteristics, helps understand the outcomes of evolutionary adaptation, and should be considered as a fundamental part of theoretical biology and for understanding the constraints on evolution.
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19
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Matzke NJ, Lin A, Stone M, Baker MAB. Flagellar export apparatus and ATP synthetase: Homology evidenced by synteny predating the Last Universal Common Ancestor. Bioessays 2021; 43:e2100004. [PMID: 33998015 DOI: 10.1002/bies.202100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
We report evidence further supporting homology between proteins in the F1 FO -ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO -b + F1 -δ, F1 -α/β, and F1 -γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F1 FO -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).
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Affiliation(s)
- Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Micaella Stone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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20
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Moosmann B, Schindeldecker M, Hajieva P. Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation. Biol Chem 2021; 401:213-231. [PMID: 31318686 DOI: 10.1515/hsz-2019-0232] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.
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Affiliation(s)
- Bernd Moosmann
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Mario Schindeldecker
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
| | - Parvana Hajieva
- Cellular Adaptation Group, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany
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21
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Van Kranendonk MJ, Baumgartner R, Djokic T, Ota T, Steller L, Garbe U, Nakamura E. Elements for the Origin of Life on Land: A Deep-Time Perspective from the Pilbara Craton of Western Australia. ASTROBIOLOGY 2021; 21:39-59. [PMID: 33404294 DOI: 10.1089/ast.2019.2107] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
For decades, deep sea hydrothermal vents have been a preferred setting for the Origin of Life, but "The Water Problem" as relates to polymerization of organic molecules, together with a propensity to dilute critical prebiotic elements as well as a number of other crucial factors, suggests that a terrestrial hot spring field with the capacity for wet-dry cycling and element concentration may represent a more likely candidate. Here, we investigate a 3.5 billion-year-old, anoxic hot spring setting from the Pilbara Craton (Australia) and show that its hydrothermal veins and compositionally varied pools and springs concentrated all of the essential elements required for prebiotic chemistry (including B, Zn, Mn, and K, in addition to C, H, N, O, P, and S). Temporal variability (seasonal to decadal), together with the known propensity of hot springs for wet-dry cycling and information exchange, would lead to innovation pools with peaks of fitness for developing molecules. An inference from the chemical complexity of the Pilbara analogue is that life could perhaps get started quickly on planets with volcanoes, silicate rocks, an exposed land surface, and water, ingredients that should form the backbone in the search for life in the Universe.
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Affiliation(s)
- Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Raphael Baumgartner
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Tara Djokic
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Tsutomu Ota
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Luke Steller
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Ulf Garbe
- Australian Nuclear Science and Technology Organisation, Kirrawee, Australia
| | - Eizo Nakamura
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
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22
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Kozlova MI, Bushmakin IM, Belyaeva JD, Shalaeva DN, Dibrova DV, Cherepanov DA, Mulkidjanian AY. Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1518-1542. [PMID: 33705291 DOI: 10.1134/s0006297920120056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
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Affiliation(s)
- M I Kozlova
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - I M Bushmakin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - J D Belyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D N Shalaeva
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany.
| | - D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D A Cherepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - A Y Mulkidjanian
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
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23
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Gözen I, Dommersnes P. Biological lipid nanotubes and their potential role in evolution. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2020; 229:2843-2862. [PMID: 33224439 PMCID: PMC7666715 DOI: 10.1140/epjst/e2020-000130-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The membrane of cells and organelles are highly deformable fluid interfaces, and can take on a multitude of shapes. One distinctive and particularly interesting property of biological membranes is their ability to from long and uniform nanotubes. These nanoconduits are surprisingly omnipresent in all domains of life, from archaea, bacteria, to plants and mammals. Some of these tubes have been known for a century, while others were only recently discovered. Their designations are different in different branches of biology, e.g. they are called stromule in plants and tunneling nanotubes in mammals. The mechanical transformation of flat membranes to tubes involves typically a combination of membrane anchoring and external forces, leading to a pulling action that results in very rapid membrane nanotube formation - micrometer long tubes can form in a matter of seconds. Their radius is set by a mechanical balance of tension and bending forces. There also exists a large class of membrane nanotubes that form due to curvature inducing molecules. It seems plausible that nanotube formation and functionality in plants and animals may have been inherited from their bacterial ancestors during endosymbiotic evolution. Here we attempt to connect observations of nanotubes in different branches of biology, and outline their similarities and differences with the aim of providing a perspective on their joint functions and evolutionary origin.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318 Norway
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0315 Norway
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, 412 96 Sweden
| | - Paul Dommersnes
- Department of Physics, Norwegian University of Science and Technology, Hoegskoleringen 5, 7491 Trondheim, Norway
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24
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Abstract
The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.
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25
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Membrane proteins in magnetically aligned phospholipid polymer discs for solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183333. [PMID: 32371072 DOI: 10.1016/j.bbamem.2020.183333] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
Well-hydrated phospholipid bilayers provide a near-native environment for membrane proteins. They enable the preparation of chemically-defined samples suitable for NMR and other spectroscopic experiments that reveal the structure, dynamics, and functional interactions of the proteins at atomic resolution. The synthetic polymer styrene maleic acid (SMA) can be used to prepare detergent-free samples that form macrodiscs with diameters greater than 30 nm at room temperature, and spontaneously align in the magnetic field of an NMR spectrometer at temperatures above 35 °C. Here we show that magnetically aligned macrodiscs are particularly well suited for solid-state NMR experiments of membrane proteins because the SMA-lipid assembly both immobilizes the embedded protein and provides uniaxial order for oriented sample (OS) solid-state NMR studies. We show that aligned macrodiscs incorporating four different membrane proteins with a wide range of sizes and topological complexity yield high-resolution OS solid-state NMR spectra. The work is dedicated to Michelle Auger who made key contributions to the field of membrane and membrane protein biophysics.
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26
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Sproul GD. Membranes Composed of Lipopeptides and Liponucleobases Inspired Protolife Evolution. ORIGINS LIFE EVOL B 2019; 49:241-254. [PMID: 31883067 DOI: 10.1007/s11084-019-09587-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/21/2019] [Indexed: 11/30/2022]
Abstract
Amino acids and peptides have been demonstrated to form lipoamino acids and lipopeptides under presumed prebiotic conditions, and readily form liposomes. Of the common nucleobases, adenine forms a liponucleobase even below 100 °C. Adenine as well as other nucleobases can also be derivatized with ethylene carbonate (and likely other similar compounds) onto which fatty acids can be attached. The fatty acid tails along with appropriately functionalized nucleobases provide some solubility of liponucleobases in membranes. Such membranes would provide a structure in which three of biology's major components are closely associated and available for chemical interactions. Nucleobase-to-nucleobase interactions would ensure that the liponucleobases would have a uniquely different head-group relationship than other amphiphiles within a membrane, likely forming rafts due their π-π interactions and providing surface discontinuities that could serve as catalytic sites. The π-π bond distance in aromatic compounds is typically 0.34 nm, commensurate with that of the amine to carboxylate distance in alpha amino acids. This would have provided opportunity for hydrogen bonding between amino acids and the distal primary amines or tautomeric carbonyl/hydroxyl groups of two π-bonded nucleobases. Such bonding would weaken the covalent linkages within the amino acids, making them susceptible to forming peptide bonds with an adjacent amino acid, likely a lipoamino acid or lipopeptide. Were this second lipoamino acid bound to a third π-bonded nucleobase, it could result in orientation, destabilization and peptide formation. The stacked triplet of nucleobases might constitute the primordial codon triplet from which peptides were synthesized: primordial translation.
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Affiliation(s)
- Gordon D Sproul
- University of South Carolina Beaufort (USCB), One University Blvd, Bluffton, SC, 29909; 37 Barnwell Dr, Beaufort, SC, 29907, USA.
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27
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Promotion of protocell self-assembly from mixed amphiphiles at the origin of life. Nat Ecol Evol 2019; 3:1705-1714. [PMID: 31686020 DOI: 10.1038/s41559-019-1015-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/25/2019] [Indexed: 01/01/2023]
Abstract
Vesicles formed from single-chain amphiphiles (SCAs) such as fatty acids probably played an important role in the origin of life. A major criticism of the hypothesis that life arose in an early ocean hydrothermal environment is that hot temperatures, large pH gradients, high salinity and abundant divalent cations should preclude vesicle formation. However, these arguments are based on model vesicles using 1-3 SCAs, even though Fischer-Tropsch-type synthesis under hydrothermal conditions produces a wide array of fatty acids and 1-alkanols, including abundant C10-C15 compounds. Here, we show that mixtures of these C10-C15 SCAs form vesicles in aqueous solutions between pH ~6.5 and >12 at modern seawater concentrations of NaCl, Mg2+ and Ca2+. Adding C10 isoprenoids improves vesicle stability even further. Vesicles form most readily at temperatures of ~70 °C and require salinity and strongly alkaline conditions to self-assemble. Thus, alkaline hydrothermal conditions not only permit protocell formation at the origin of life but actively favour it.
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28
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Abstract
Cells from all three domains of life on Earth utilize motile macromolecular devices that protrude from the cell surface to generate forces that allow them to swim through fluid media. Research carried out on archaea during the past decade or so has led to the recognition that, despite their common function, the motility devices of the three domains display fundamental differences in their properties and ancestry, reflecting a striking example of convergent evolution. Thus, the flagella of bacteria and the archaella of archaea employ rotary filaments that assemble from distinct subunits that do not share a common ancestor and generate torque using energy derived from distinct fuel sources, namely chemiosmotic ion gradients and FlaI motor-catalyzed ATP hydrolysis, respectively. The cilia of eukaryotes, however, assemble via kinesin-2-driven intraflagellar transport and utilize microtubules and ATP-hydrolyzing dynein motors to beat in a variety of waveforms via a sliding filament mechanism. Here, with reference to current structural and mechanistic information about these organelles, we briefly compare the evolutionary origins, assembly and tactic motility of archaella, flagella and cilia.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Jonathan M Scholey
- Department of Molecular and Cell Biology, University of California @ Davis, CA 95616, USA.
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29
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Lancet D, Segrè D, Kahana A. Twenty Years of "Lipid World": A Fertile Partnership with David Deamer. Life (Basel) 2019; 9:E77. [PMID: 31547028 PMCID: PMC6958426 DOI: 10.3390/life9040077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.
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Affiliation(s)
- Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Daniel Segrè
- Bioinformatics Program, Department of Biology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Amit Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
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30
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Proton leakage across lipid bilayers: Oxygen atoms of phospholipid ester linkers align water molecules into transmembrane water wires. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:439-451. [PMID: 30904457 DOI: 10.1016/j.bbabio.2019.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/20/2019] [Accepted: 03/10/2019] [Indexed: 12/31/2022]
Abstract
Up to half of the cellular energy gets lost owing to membrane proton leakage. The permeability of lipid bilayers to protons is by several orders of magnitude higher than to other cations, which implies efficient proton-specific passages. The nature of these passages remains obscure. By combining experimental measurements of proton flow across phosphatidylcholine vesicles, steered molecular dynamics (MD) simulations of phosphatidylcholine bilayers and kinetic modelling, we have analyzed whether protons could pass between opposite phospholipid molecules when they sporadically converge. The MD simulations showed that each time, when the phosphorus atoms of the two phosphatidylcholine molecules got closer than 1.6 nm, the eight oxygen atoms of their ester linkages could form a transmembrane 'oxygen passage' along which several water molecules aligned into a water wire. Proton permeability along such water wires would be limited by rearrangement of oxygen atoms, which could explain the experimentally shown independence of the proton permeability of pH, H2O/D2O substitution, and membrane dipole potential. We suggest that protons can cross lipid bilayers by moving along short, self-sustaining water wires supported by oxygen atoms of lipid ester linkages.
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31
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Abstract
Of all the macromolecular assemblies of life, the least understood is the biomembrane. This is especially true in regard to its atomic structure. Ideas on biomembranes, developed in the last 200 years, culminated in the fluid mosaic model of the membrane. In this essay, I provide a historical outline of how we arrived at our current understanding of biomembranes and the models we use to describe them. A selection of direct experimental findings on the nano-scale structure of biomembranes is taken up to discuss their physical nature, and special emphasis is put on the surprising insights that arise from atomic scale descriptions.
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Lebre PH, Cowan DA. Genomics of Alkaliphiles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:135-155. [PMID: 30796503 DOI: 10.1007/10_2018_83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alkalinicity presents a challenge for life due to a "reversed" proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an "omics" point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles. Graphical Abstract.
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Affiliation(s)
- Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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Protocells and LUCA: Transport of substances from first physicochemical principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:85-104. [PMID: 30612704 DOI: 10.1016/j.pbiomolbio.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/25/2018] [Accepted: 12/24/2018] [Indexed: 11/22/2022]
Abstract
Models of the transport of substances in protocells are considered from first physicochemical principles. Functional similarities and differences in the transport systems of archaea, cyanobacteria, E. coli, and diatoms have been analyzed. Based on the selection of the most important transport systems, a model of transport of substances through the membrane of the last universal common ancestor, LUCA, was constructed. Models of isotope separation in protocells were considered. Based on the proposed models, the difference in isotope concentrations in rocks can be predicted, which can serve as an indicator of the presence of life in the early stages of evolution. Mechanisms of energy conversion for the simplest forms of directed motion in protocells are considered. A special stage in the evolution of protocells is proposed - the minimal mobile cell.
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Kenaan A, Cheng J, Qi D, Chen D, Cui D, Song J. Physicochemical Analysis of DPPC and Photopolymerizable Liposomal Binary Mixture for Spatiotemporal Drug Release. Anal Chem 2018; 90:9487-9494. [PMID: 30009597 DOI: 10.1021/acs.analchem.8b02144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of a spatiotemporal drug delivery system with a long release profile, high loading efficiency, and robust therapeutic effects is still a challenge. Liposomal nanocarriers have secured a fortified position in the biomedical field over decades. Herein, liposomal binary mixtures of 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC) and photopolymerizable 1,2-bis(10,12-tricosadiynoyl)- sn-glycero-3-phosphocholine (DC8,9PC) phospholipids were prepared for drug delivery applications. The diacetylenic groups of DC8,9PC produce intermolecular cross-linking following UV irradiation. Exposure of the liposomal mixture to 254 nm radiation induces a pore within the lipid bilayer, expediting the release of its entrapped 5,6-carboxyfluorescein dye. The dosage and rate of the released content are highly dependent on the number and size of the induced pore. Photochemical cross-linking studies at different exposure times were reported through the analysis of UV-visible spectrophotometry, nano differential scanning calorimetry, Fourier transform infrared spectroscopy, and Raman spectroscopy. The optimal irradiation time was established after 8 min of exposure, inducing lipid cross-linking with minimal oxidative degradation, which plays an essential role in the pathogenesis of numerous diseases due to the formation of primary and secondary oxidation products, accordingly reducing the encapsulated drug therapeutic level.
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Affiliation(s)
- Ahmad Kenaan
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Daizong Qi
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Di Chen
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Centre for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P.R. China
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Darbani B, Kell DB, Borodina I. Energetic evolution of cellular Transportomes. BMC Genomics 2018; 19:418. [PMID: 29848286 PMCID: PMC5977736 DOI: 10.1186/s12864-018-4816-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Transporter proteins mediate the translocation of substances across the membranes of living cells. Many transport processes are energetically expensive and the cells use 20 to 60% of their energy to power the transportomes. We hypothesized that there may be an evolutionary selection pressure for lower energy transporters. RESULTS We performed a genome-wide analysis of the compositional reshaping of the transportomes across the kingdoms of bacteria, archaea, and eukarya. We found that the share of ABC transporters is much higher in bacteria and archaea (ca. 27% of the transportome) than in primitive eukaryotes (13%), algae and plants (10%) and in fungi and animals (5-6%). This decrease is compensated by an increased occurrence of secondary transporters and ion channels. The share of ion channels is particularly high in animals (ca. 30% of the transportome) and algae and plants with (ca. 13%), when compared to bacteria and archaea with only 6-7%. Therefore, our results show a move to a preference for the low-energy-demanding transporters (ion channels and carriers) over the more energy-costly transporter classes (ATP-dependent families, and ABCs in particular) as part of the transition from prokaryotes to eukaryotes. The transportome analysis also indicated seven bacterial species, including Neorickettsia risticii and Neorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, based on the phylogenetically restricted presence therein of clear homologues of modern mitochondrial solute carriers. CONCLUSIONS The results indicate that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. These changes have likely been important in the development of tissues performing energetically costly cellular functions.
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Affiliation(s)
- Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Dibrova DV, Konovalov KA, Perekhvatov VV, Skulachev KV, Mulkidjanian AY. COGcollator: a web server for analysis of distant relationships between homologous protein families. Biol Direct 2017; 12:29. [PMID: 29187234 PMCID: PMC5706428 DOI: 10.1186/s13062-017-0198-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/06/2017] [Indexed: 01/20/2023] Open
Abstract
Background The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs. Aim We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server. Results Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1. Reviewers This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf. Electronic supplementary material The online version of this article (10.1186/s13062-017-0198-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
| | - Kirill A Konovalov
- School of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim V Perekhvatov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Konstantin V Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Armen Y Mulkidjanian
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. .,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Department of Physics, Osnabrueck University, 49069, Osnabrueck, Germany.
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Dibrov P, Dibrov E, Pierce GN. Na+-NQR (Na+-translocating NADH:ubiquinone oxidoreductase) as a novel target for antibiotics. FEMS Microbiol Rev 2017; 41:653-671. [PMID: 28961953 DOI: 10.1093/femsre/fux032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/17/2017] [Indexed: 01/08/2023] Open
Abstract
The recent breakthrough in structural studies on Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) from the human pathogen Vibrio cholerae creates a perspective for the systematic design of inhibitors for this unique enzyme, which is the major Na+ pump in aerobic pathogens. Widespread distribution of Na+-NQR among pathogenic species, its key role in energy metabolism, its relation to virulence in different species as well as its absence in eukaryotic cells makes this enzyme especially attractive as a target for prospective antibiotics. In this review, the major biochemical, physiological and, especially, the pharmacological aspects of Na+-NQR are discussed to assess its 'target potential' for drug development. A comparison to other primary bacterial Na+ pumps supports the contention that NQR is a first rate prospective target for a new generation of antimicrobials. A new, narrowly targeted furanone inhibitor of NQR designed in our group is presented as a molecular platform for the development of anti-NQR remedies.
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Affiliation(s)
- Pavel Dibrov
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Elena Dibrov
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, Canada.,Department of Physiology and Pathophysiology, Colleges of Medicine and Pharmacy, Faculty of Health Sciences, Winnipeg, Canada
| | - Grant N Pierce
- Institute of Cardiovascular Sciences, Albrechtsen Research Centre, St. Boniface Hospital, Winnipeg, Canada.,Department of Physiology and Pathophysiology, Colleges of Medicine and Pharmacy, Faculty of Health Sciences, Winnipeg, Canada
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Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars. ISME JOURNAL 2017; 11:2584-2598. [PMID: 28731475 DOI: 10.1038/ismej.2017.111] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 01/19/2023]
Abstract
Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.
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Abstract
Chemiosmotic coupling - the harnessing of electrochemical ion gradients across membranes to drive metabolism - is as universally conserved as the genetic code. As argued previously in these pages, such deep conservation suggests that ion gradients arose early in evolution, and might have played a role in the origin of life. Alkaline hydrothermal vents harbour pH gradients of similar polarity and magnitude to those employed by modern cells, one of many properties that make them attractive models for life's origin. Their congruence with the physiology of anaerobic autotrophs that use the acetyl CoA pathway to fix CO2 gives the alkaline vent model broad appeal to biologists. Recently, however, a paper by Baz Jackson criticized the hypothesis, concluding that natural pH gradients were unlikely to have played any role in the origin of life. Unfortunately, Jackson mainly criticized his own interpretations of the theory, not what the literature says. This counterpoint is intended to set the record straight.
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Affiliation(s)
- Nick Lane
- Department of Genetics, Evolution and Environment, University College London, London, UK
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40
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Barge LM, Branscomb E, Brucato JR, Cardoso SSS, Cartwright JHE, Danielache SO, Galante D, Kee TP, Miguel Y, Mojzsis S, Robinson KJ, Russell MJ, Simoncini E, Sobron P. Thermodynamics, Disequilibrium, Evolution: Far-From-Equilibrium Geological and Chemical Considerations for Origin-Of-Life Research. ORIGINS LIFE EVOL B 2017; 47:39-56. [PMID: 27271006 DOI: 10.1007/s11084-016-9508-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Affiliation(s)
- L M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91125, USA.
- Icy Worlds Team, NASA Astrobiology Institute, Mountain View, CA, 94043, USA.
| | - E Branscomb
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Champaign, IL, USA
| | - J R Brucato
- Astrophysical Observatory of Arcetri, Florence, Italy
| | - S S S Cardoso
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge, CB2 3RA, UK
| | - J H E Cartwright
- Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, E-18100 Armilla, Granada, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, E-18071, Granada, Spain
| | - S O Danielache
- Sophia University, Tokyo, Japan
- Earth and Life Science Institute, Tokyo Technical University, Tokyo, Japan
| | - D Galante
- Brazilian Synchrotron Light Laboratory, LNLS / CNPEM, Campinas, Brazil
| | - T P Kee
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Y Miguel
- Observatoire de Côte d'Azur, Nice, France
| | - S Mojzsis
- Department of Geological Sciences, University of Colorado, Boulder, CO, 80309-0399, USA
| | - K J Robinson
- School of Molecular Sciences and School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - M J Russell
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91125, USA
- Icy Worlds Team, NASA Astrobiology Institute, Mountain View, CA, 94043, USA
| | - E Simoncini
- Astrophysical Observatory of Arcetri, Florence, Italy
| | - P Sobron
- Carl Sagan Center, SETI Institute, Mountain View, CA, USA
- Impossible Sensing, St. Louis, MO, USA
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Novakovsky GE, Dibrova DV, Mulkidjanian AY. Phylogenomic Analysis of Type 1 NADH:Quinone Oxidoreductase. BIOCHEMISTRY (MOSCOW) 2017; 81:770-84. [PMID: 27449624 DOI: 10.1134/s0006297916070142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We performed phylogenomic analysis of the catalytic core of NADH:quinone oxidoreductases of type 1 (NDH-1). Analysis of phylogenetic trees, as constructed for the core subunits of NDH-1, revealed fundamental differences in their topologies. In the case of four putatively homologous ion-carrying membrane subunits, the trees for the NuoH and NuoN subunits contained separate archaeal clades, whereas subunits NuoL and NuoM were characterized by multiple archaeal clades spread among bacterial branches. Large, separate clades, which united sequences belonging to different archaeal subdomains, were also found for cytoplasmic subunits NuoD and NuoB, homologous to the large and small subunits of nickel-iron hydrogenases. A smaller such clade was also shown for subunit NuoC. Based on these data, we suggest that the ancestral NDH-1 complex could be present already at the stage of the Last Universal Cellular Ancestor (LUCA). Ancestral forms of membrane subunits NuoN and NuoH and cytoplasmic subunits NuoD, NuoB, and, perhaps NuoC, may have formed a membrane complex that operated as an ion-translocating membrane hydrogenase. After the complex attained the ability to reduce membrane quinones, gene duplications could yield the subunits NuoL and NuoM, which enabled translocation of additional ions.
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Affiliation(s)
- G E Novakovsky
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
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Emergence of Life on Earth: A Physicochemical Jigsaw Puzzle. J Mol Evol 2016; 84:1-7. [PMID: 27995274 DOI: 10.1007/s00239-016-9775-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
Abstract
We review physicochemical factors and processes that describe how cellular life can emerge from prebiotic chemical matter; they are: (1) prebiotic Earth is a multicomponent and multiphase reservoir of chemical compounds, to which (2) Earth-Moon rotations deliver two kinds of regular cycling energies: diurnal electromagnetic radiation and seawater tides. (3) Emerging colloidal phases cyclically nucleate and agglomerate in seawater and consolidate as geochemical sediments in tidal zones, creating a matrix of microspaces. (4) Some microspaces persist and retain memory from past cycles, and others re-dissolve and re-disperse back into the Earth's chemical reservoir. (5) Proto-metabolites and proto-biopolymers coevolve with and within persisting microspaces, where (6) Macromolecular crowding and other non-covalent molecular forces govern the evolution of hydrophilic, hydrophobic, and charged molecular surfaces. (7) The matrices of microspaces evolve into proto-biofilms of progenotes with rudimentary but evolving replication, transcription, and translation, enclosed in unstable cell envelopes. (8) Stabilization of cell envelopes 'crystallizes' bacteria-like genetics and metabolism with low horizontal gene transfer-life 'as we know it.' These factors and processes constitute the 'working pieces' of the jigsaw puzzle of life's emergence. They extend the concept of progenotes as the first proto-cellular life, connected backward in time to the cycling chemistries of the Earth-Moon planetary system, and forward to the ancient cell cycle of first bacteria-like organisms. Supra-macromolecular models of 'compartments first' are preferred: they facilitate macromolecular crowding-a key abiotic/biotic transition toward living states. Evolutionary models of metabolism or genetics 'first' could not have evolved in unconfined and uncrowded environments because of the diffusional drift to disorder mandated by the second law of thermodynamics.
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Two independent evolutionary routes to Na+/H+ cotransport function in membrane pyrophosphatases. Biochem J 2016; 473:3099-111. [DOI: 10.1042/bcj20160529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/03/2016] [Indexed: 11/17/2022]
Abstract
Membrane-bound pyrophosphatases (mPPases) hydrolyze pyrophosphate (PPi) to transport H+, Na+ or both and help organisms to cope with stress conditions, such as high salinity or limiting nutrients. Recent elucidation of mPPase structure and identification of subfamilies that have fully or partially switched from Na+ to H+ pumping have established mPPases as versatile models for studying the principles governing the mechanism, specificity and evolution of cation transporters. In the present study, we constructed an accurate phylogenetic map of the interface of Na+-transporting PPases (Na+-PPases) and Na+- and H+-transporting PPases (Na+,H+-PPases), which guided our experimental exploration of the variations in PPi hydrolysis and ion transport activities during evolution. Surprisingly, we identified two mPPase lineages that independently acquired physiologically significant Na+ and H+ cotransport function. Na+,H+-PPases of the first lineage transport H+ over an extended [Na+] range, but progressively lose H+ transport efficiency at high [Na+]. In contrast, H+-transport by Na+,H+-PPases of the second lineage is not inhibited by up to 100 mM Na+. With the identification of Na+,H+-PPase subtypes, the mPPases protein superfamily appears as a continuum, ranging from monospecific Na+ transporters to transporters with tunable levels of Na+ and H+ cotransport and further to monospecific H+ transporters. Our results lend credence to the concept that Na+ and H+ are transported by similar mechanisms, allowing the relative efficiencies of Na+ and H+ transport to be modulated by minor changes in protein structure during the course of adaptation to a changing environment.
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Klimchuk OI, Dibrova DV, Mulkidjanian AY. Phylogenomic analysis identifies a sodium-translocating decarboxylating oxidoreductase in thermotogae. BIOCHEMISTRY (MOSCOW) 2016; 81:481-90. [DOI: 10.1134/s0006297916050059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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45
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Dibrova DV, Galperin MY, Koonin EV, Mulkidjanian AY. Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics. BIOCHEMISTRY (MOSCOW) 2016; 80:495-516. [PMID: 26071768 DOI: 10.1134/s0006297915050016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cell cytoplasm of archaea, bacteria, and eukaryotes contains substantially more potassium than sodium, and potassium cations are specifically required for many key cellular processes, including protein synthesis. This distinct ionic composition and requirements have been attributed to the emergence of the first cells in potassium-rich habitats. Different, albeit complementary, scenarios have been proposed for the primordial potassium-rich environments based on experimental data and theoretical considerations. Specifically, building on the observation that potassium prevails over sodium in the vapor of inland geothermal systems, we have argued that the first cells could emerge in the pools and puddles at the periphery of primordial anoxic geothermal fields, where the elementary composition of the condensed vapor would resemble the internal milieu of modern cells. Marine and freshwater environments generally contain more sodium than potassium. Therefore, to invade such environments, while maintaining excess of potassium over sodium in the cytoplasm, primordial cells needed means to extrude sodium ions. The foray into new, sodium-rich habitats was the likely driving force behind the evolution of diverse redox-, light-, chemically-, or osmotically-dependent sodium export pumps and the increase of membrane tightness. Here we present a scenario that details how the interplay between several, initially independent sodium pumps might have triggered the evolution of sodium-dependent membrane bioenergetics, followed by the separate emergence of the proton-dependent bioenergetics in archaea and bacteria. We also discuss the development of systems that utilize the sodium/potassium gradient across the cell membranes.
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Affiliation(s)
- D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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46
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Laskowski M, Augustynek B, Kulawiak B, Koprowski P, Bednarczyk P, Jarmuszkiewicz W, Szewczyk A. What do we not know about mitochondrial potassium channels? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1247-1257. [PMID: 26951942 DOI: 10.1016/j.bbabio.2016.03.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 01/14/2023]
Abstract
In this review, we summarize our knowledge about mitochondrial potassium channels, with a special focus on unanswered questions in this field. The following potassium channels have been well described in the inner mitochondrial membrane: ATP-regulated potassium channel, Ca(2+)-activated potassium channel, the voltage-gated Kv1.3 potassium channel, and the two-pore domain TASK-3 potassium channel. The primary functional roles of these channels include regulation of mitochondrial respiration and the alteration of membrane potential. Additionally, they modulate the mitochondrial matrix volume and the synthesis of reactive oxygen species by mitochondria. Mitochondrial potassium channels are believed to contribute to cytoprotection and cell death. In this paper, we discuss fundamental issues concerning mitochondrial potassium channels: their molecular identity, channel pharmacology and functional properties. Attention will be given to the current problems present in our understanding of the nature of mitochondrial potassium channels. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Michał Laskowski
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Bartłomiej Augustynek
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Bogusz Kulawiak
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Piotr Koprowski
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Piotr Bednarczyk
- Department of Biophysics, Warsaw University of Life Sciences - SGGW, 159 Nowoursynowska St., 02-776 Warsaw, Poland
| | - Wieslawa Jarmuszkiewicz
- Laboratory of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Adam Szewczyk
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland.
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Nadeau VG, Deber CM. Structural impact of proline mutations in the loop region of an ancestral membrane protein. Biopolymers 2016; 106:37-42. [DOI: 10.1002/bip.22765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Vincent G. Nadeau
- Program in Molecular Structure & Function; Research Institute, Hospital for Sick Children; Toronto, M5G 1X8 Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto, M5S 1A8 Ontario Canada
| | - Charles M. Deber
- Program in Molecular Structure & Function; Research Institute, Hospital for Sick Children; Toronto, M5G 1X8 Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto, M5S 1A8 Ontario Canada
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48
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Ray S, Kassan A, Busija AR, Rangamani P, Patel HH. The plasma membrane as a capacitor for energy and metabolism. Am J Physiol Cell Physiol 2015; 310:C181-92. [PMID: 26771520 DOI: 10.1152/ajpcell.00087.2015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
When considering which components of the cell are the most critical to function and physiology, we naturally focus on the nucleus, the mitochondria that regulate energy and apoptotic signaling, or other organelles such as the endoplasmic reticulum, Golgi, ribosomes, etc. Few people will suggest that the membrane is the most critical element of a cell in terms of function and physiology. Those that consider the membrane critical will point to its obvious barrier function regulated by the lipid bilayer and numerous ion channels that regulate homeostatic gradients. What becomes evident upon closer inspection is that not all membranes are created equal and that there are lipid-rich microdomains that serve as platforms of signaling and a means of communication with the intracellular environment. In this review, we explore the evolution of membranes, focus on lipid-rich microdomains, and advance the novel concept that membranes serve as "capacitors for energy and metabolism." Within this framework, the membrane then is the primary and critical regulator of stress and disease adaptation of the cell.
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Affiliation(s)
- Supriyo Ray
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Anesthesiology, University of California, San Diego, La Jolla, California; and
| | - Adam Kassan
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Anesthesiology, University of California, San Diego, La Jolla, California; and
| | - Anna R Busija
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Anesthesiology, University of California, San Diego, La Jolla, California; and
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California
| | - Hemal H Patel
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California; Department of Anesthesiology, University of California, San Diego, La Jolla, California; and
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49
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Makarova KS, Galperin MY, Koonin EV. Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems. Biochimie 2015; 118:302-12. [PMID: 25583072 PMCID: PMC5898192 DOI: 10.1016/j.biochi.2015.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/02/2015] [Indexed: 01/03/2023]
Abstract
A systematic comparative genomic analysis of all archaeal membrane proteins that have been projected to the last archaeal common ancestor gene set led to the identification of several novel components of predicted secretion, membrane remodeling, and protein glycosylation systems. Among other findings, most crenarchaea have been shown to encode highly diverged orthologs of the membrane insertase YidC, which is nearly universal in bacteria, eukaryotes, and euryarchaea. We also identified a vast family of archaeal proteins, including the C-terminal domain of N-glycosylation protein AglD, as membrane flippases homologous to the flippase domain of bacterial multipeptide resistance factor MprF, a bifunctional lysylphosphatidylglycerol synthase and flippase. Additionally, several proteins were predicted to function as membrane transporters. The results of this work, combined with our previous analyses, reveal an unexpected diversity of putative archaeal membrane-associated functional systems that remain to be functionally characterized. A more general conclusion from this work is that the currently available collection of archaeal (and bacterial) genomes could be sufficient to identify (almost) all widespread functional modules and develop experimentally testable predictions of their functions.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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50
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César-Razquin A, Snijder B, Frappier-Brinton T, Isserlin R, Gyimesi G, Bai X, Reithmeier RA, Hepworth D, Hediger MA, Edwards AM, Superti-Furga G. A Call for Systematic Research on Solute Carriers. Cell 2015; 162:478-87. [PMID: 26232220 DOI: 10.1016/j.cell.2015.07.022] [Citation(s) in RCA: 381] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 01/10/2023]
Abstract
Solute carrier (SLC) membrane transport proteins control essential physiological functions, including nutrient uptake, ion transport, and waste removal. SLCs interact with several important drugs, and a quarter of the more than 400 SLC genes are associated with human diseases. Yet, compared to other gene families of similar stature, SLCs are relatively understudied. The time is right for a systematic attack on SLC structure, specificity, and function, taking into account kinship and expression, as well as the dependencies that arise from the common metabolic space.
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Affiliation(s)
- Adrián César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Berend Snijder
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine and Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, 3012 Bern, Switzerland
| | - Xiaoyun Bai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
| | | | - David Hepworth
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine and Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, 3012 Bern, Switzerland.
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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