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Bizup B, Tzounopoulos T. On the genesis and unique functions of zinc neuromodulation. J Neurophysiol 2024; 132:1241-1254. [PMID: 39196675 DOI: 10.1152/jn.00285.2024] [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: 07/05/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 08/30/2024] Open
Abstract
In addition to the essential structural and catalytic functions of zinc, evolution has adopted synaptic zinc as a neuromodulator. In the brain, synaptic zinc is released primarily from glutamatergic neurons, notably in the neocortex, hippocampus, amygdala, and auditory brainstem. In these brain areas, synaptic zinc is essential for neuronal and sensory processing fine-tuning. But what niche does zinc fill in neural signaling that other neuromodulators do not? Here, we discuss the evolutionary history of zinc as a signaling agent and its eventual adoption as an essential neuromodulator in the mammalian brain. We then attempt to describe the unique roles that zinc has carved out of the vast and diverse landscape of neuromodulators.
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Affiliation(s)
- Brandon Bizup
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Thanos Tzounopoulos
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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2
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Caetano-Anollés K, Aziz MF, Mughal F, Caetano-Anollés G. On Protein Loops, Prior Molecular States and Common Ancestors of Life. J Mol Evol 2024; 92:624-646. [PMID: 38652291 PMCID: PMC11458777 DOI: 10.1007/s00239-024-10167-y] [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: 02/05/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
The principle of continuity demands the existence of prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on the emergence and evolution of loop prototypes - the elemental architects of protein domain structure. Phylogenomic reconstruction spanning superkingdoms and viruses generated an evolutionary chronology of prototypes with six distinct evolutionary phases defining a most parsimonious evolutionary progression of cellular life. Each phase was marked by strategic prototype accumulation shaping the structures and functions of common ancestors. The last universal common ancestor (LUCA) of cells and viruses and the last universal cellular ancestor (LUCellA) defined stem lines that were structurally and functionally complex. The evolutionary saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while the pivotal LUCellA lacked essential DNA biosynthesis and modern transcription. Early proteins therefore relied on RNA for genetic information storage but appeared initially decoupled from it, hinting at transformative shifts of genetic processing. Urancestral loop types suggest advanced folding designs were present at an early evolutionary stage. An exploration of loop geometric properties revealed gradual replacement of prototypes with α-helix and β-strand bracing structures over time, paving the way for the dominance of other loop types. AlphFold2-generated atomic models of prototype accretion described patterns of fold emergence. Our findings favor a ‛processual' model of evolving stem lines aligned with Woese's vision of a communal world. This model prompts discussing the 'problem of ancestors' and the challenges that lie ahead for research in taxonomy, evolution and complexity.
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Affiliation(s)
- Kelsey Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Callout Biotech, Albuquerque, NM, 87112, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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3
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Leon F, Espinoza-Esparza JM, Deng V, Coyle MC, Espinoza S, Booth DS. Cell differentiation controls iron assimilation in a choanoflagellate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595918. [PMID: 39345370 PMCID: PMC11429873 DOI: 10.1101/2024.05.25.595918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Marine microeukaryotes have evolved diverse cellular features that link their life histories to surrounding environments. How those dynamic life histories intersect with the ecological functions of microeukaryotes remains a frontier to understand their roles in essential biogeochemical cycles1,2. Choanoflagellates, phagotrophs that cycle nutrients through filter feeding, provide models to explore this intersection, for many choanoflagellate species transition between life history stages by differentiating into distinct cell types3-6. Here we report that cell differentiation in the marine choanoflagellate Salpingoeca rosetta endows one of its cell types with the ability to utilize insoluble ferric colloids for improved growth through the expression of a cytochrome b561 iron reductase (cytb561a). This gene is an ortholog of the mammalian duodenal cytochrome b561 (DCYTB) that reduces ferric cations prior to their uptake in gut epithelia7 and is part of an iron utilization toolkit that choanoflagellates and their closest living relatives, the animals, inherited from a last common eukaryotic ancestor. In a database of oceanic metagenomes8,9, the abundance of cytb561a transcripts from choanoflagellates positively correlates with upwellings, which are a major source of ferric colloids in marine environments10. As this predominant form of iron11,12 is largely inaccessible to cell-walled microbes13,14, choanoflagellates and other phagotrophic eukaryotes may serve critical ecological roles by first acquiring ferric colloids through phagocytosis and then cycling this essential nutrient through iron utilization pathways13-15. These findings provide insight into the ecological roles choanoflagellates perform and inform reconstructions of early animal evolution where functionally distinct cell types became an integrated whole at the origin of animal multicellularity16-22.
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Affiliation(s)
- Fredrick Leon
- Chan Zuckerberg Biohub & Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine, San Francisco, CA 94143
| | - Jesus M. Espinoza-Esparza
- Chan Zuckerberg Biohub & Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine, San Francisco, CA 94143
| | - Vicki Deng
- Chan Zuckerberg Biohub & Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine, San Francisco, CA 94143
- Current Address: Department of Molecular Biosciences, University of Texas, Austin, Austin, TX 78712
| | - Maxwell C. Coyle
- Howard Hughes Medical Institute & Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Current Address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Sarah Espinoza
- Howard Hughes Medical Institute & Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David S. Booth
- Chan Zuckerberg Biohub & Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine, San Francisco, CA 94143
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4
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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024; 22:572-586. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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5
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Larson J, Tokmina-Lukaszewska M, Payne D, Spietz RL, Fausset H, Alam MG, Brekke BK, Pauley J, Hasenoehrl EJ, Shepard EM, Boyd ES, Bothner B. Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome of Methanosarcina barkeri. Appl Environ Microbiol 2024; 90:e0051624. [PMID: 39023267 PMCID: PMC11337800 DOI: 10.1128/aem.00516-24] [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: 03/21/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS2). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS-) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS2 to sustain growth. As such, medium supplied with FeS2 should lead to higher availability of transition metals when compared to medium supplied with HS-. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS- as sole S source) versus non-sulfidic (cells provided with FeS2 as sole S source) conditions impact the metalloproteome of Methanosarcina barkeri Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that M. barkeri utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS2 but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions.IMPORTANCEProteins that catalyze biochemical reactions often require transition metals that can have a high affinity for sulfur, another required element for life. Thus, the availability of metals and sulfur are intertwined and can have large impacts on an organismismal biochemistry. Methanogens often occupy anoxic, sulfide-rich (euxinic) environments that favor the precipitation of transition metals as metal sulfides, thereby creating presumed metal limitation. Recently, several methanogens have been shown to acquire iron and sulfur from pyrite, an abundant iron-sulfide mineral that was traditionally considered to be unavailable to biology. The work presented here provides new insights into the distribution of metalloproteins, and metal uptake of Methanosarcina barkeri Fusaro grown under euxinic or pyritic growth conditions. Thorough characterizations of this methanogen under different metal and sulfur conditions increase our understanding of the influence of metal availability on methanogens, and presumably other anaerobes, that inhabit euxinic environments.
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Affiliation(s)
- James Larson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L. Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Hunter Fausset
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Md Gahangir Alam
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Brooklyn K. Brekke
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jordan Pauley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Ethan J. Hasenoehrl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric M. Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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6
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Bakhtiar D, Vorechovsky I. Copper-binding proteins and exonic splicing enhancers and silencers. Metallomics 2024; 16:mfae023. [PMID: 38692844 PMCID: PMC11097207 DOI: 10.1093/mtomcs/mfae023] [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: 02/20/2024] [Accepted: 04/21/2024] [Indexed: 05/03/2024]
Abstract
Eukaryotic DNA codes not only for proteins but contains a wealth of information required for accurate splicing of messenger RNA precursors and inclusion of constitutively or alternatively spliced exons in mature transcripts. This "auxiliary" splicing code has been characterized as exonic splicing enhancers and silencers (ESE and ESS). The exact interplay between protein and splicing codes is, however, poorly understood. Here, we show that exons encoding copper-coordinating amino acids in human cuproproteins lack ESEs and/or have an excess of ESSs, yet RNA sequencing and expressed sequence tags data show that they are more efficiently included in mature transcripts by the splicing machinery than average exons. Their largely constitutive inclusion in messenger RNA is facilitated by stronger splice sites, including polypyrimidine tracts, consistent with an important role of the surrounding intron architecture in ensuring high expression of metal-binding residues during evolution. ESE/ESS profiles of codons and entire exons that code for copper-coordinating residues were very similar to those encoding residues that coordinate zinc but markedly different from those that coordinate calcium. Together, these results reveal how the traditional and auxiliary splicing motifs responded to constraints of metal coordination in proteins.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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7
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Cuevas-Zuviría B, Garcia AK, Rivier AJ, Rucker HR, Carruthers BM, Kaçar B. Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation. Mol Biol Evol 2024; 41:msae067. [PMID: 38526235 PMCID: PMC11018506 DOI: 10.1093/molbev/msae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable of biological nitrogen fixation. The G-subunit is a Paleoproterozoic-age orphan protein that appears more than 1 billion years after the origin of nitrogenases. We show that the G-subunit arose with novel nitrogenase metal dependence and the ecological expansion of nitrogen-fixing microbes following the transition in environmental metal availabilities and atmospheric oxygenation that began ∼2.5 billion years ago. We identify molecular features that suggest early G-subunit proteins mediated cofactor or protein interactions required for novel metal dependency, priming ancient nitrogenases and their hosts to exploit these newly diversified geochemical environments. We further examined the degree of functional specialization in G-subunit evolution with extant and ancestral homologs using laboratory reconstruction experiments. Our results indicate that permanent recruitment of the orphan protein depended on the prior establishment of conserved molecular features and showcase how contingent evolutionary novelties might shape ecologically important microbial innovations.
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Affiliation(s)
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alex J Rivier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Holly R Rucker
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brooke M Carruthers
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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8
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Colón-Santos S, Vázquez-Salazar A, Adams A, Campillo-Balderas JA, Hernández-Morales R, Jácome R, Muñoz-Velasco I, Rodriguez LE, Schaible MJ, Schaible GA, Szeinbaum N, Thweatt JL, Trubl G. Chapter 2: What Is Life? ASTROBIOLOGY 2024; 24:S40-S56. [PMID: 38498820 DOI: 10.1089/ast.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.
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Affiliation(s)
- Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A Schaible
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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9
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Sarasa-Buisan C, Ochoa de Alda JAG, Velázquez-Suárez C, Rubio MÁ, Gómez-Baena G, Fillat MF, Luque I. An ancient bacterial zinc acquisition system identified from a cyanobacterial exoproteome. PLoS Biol 2024; 22:e3002546. [PMID: 38466754 PMCID: PMC10957091 DOI: 10.1371/journal.pbio.3002546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 03/21/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Bacteria have developed fine-tuned responses to cope with potential zinc limitation. The Zur protein is a key player in coordinating this response in most species. Comparative proteomics conducted on the cyanobacterium Anabaena highlighted the more abundant proteins in a zur mutant compared to the wild type. Experimental evidence showed that the exoprotein ZepA mediates zinc uptake. Genomic context of the zepA gene and protein structure prediction provided additional insights on the regulation and putative function of ZepA homologs. Phylogenetic analysis suggests that ZepA represents a primordial system for zinc acquisition that has been conserved for billions of years in a handful of species from distant bacterial lineages. Furthermore, these results show that Zur may have been one of the first regulators of the FUR family to evolve, consistent with the scarcity of zinc in the ecosystems of the Archean eon.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (Bifi), Universidad de Zaragoza, Zaragoza, Spain
| | - Jesús A. G. Ochoa de Alda
- Didáctica de las Ciencias Experimentales y la Matemáticas, Universidad de Extremadura, Cáceres, Spain
| | | | - Miguel Ángel Rubio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (Bifi), Universidad de Zaragoza, Zaragoza, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
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10
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Bakhtiar D, Vondraskova K, Pengelly RJ, Chivers M, Kralovicova J, Vorechovsky I. Exonic splicing code and coordination of divalent metals in proteins. Nucleic Acids Res 2024; 52:1090-1106. [PMID: 38055834 PMCID: PMC10853796 DOI: 10.1093/nar/gkad1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving-Williams series, a universal order of relative stabilities of metal-organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position -3 relative to 3' splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon-intron architecture to ensure adequate metalloprotein expression.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Katarina Vondraskova
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Martin Chivers
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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11
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Clodoré L, Foucher F, Hickman-Lewis K, Sorieul S, Jouve J, Réfrégiers M, Collet G, Petoud S, Gratuze B, Westall F. Multi-Technique Characterization of 3.45 Ga Microfossils on Earth: A Key Approach to Detect Possible Traces of Life in Returned Samples from Mars. ASTROBIOLOGY 2024; 24:190-226. [PMID: 38393828 DOI: 10.1089/ast.2023.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The NASA Mars 2020 Perseverance rover is actively exploring Jezero crater to conduct analyses on igneous and sedimentary rock targets from outcrops located on the crater floor (Máaz and Séítah formations) and from the delta deposits, respectively. The rock samples collected during this mission will be recovered during the Mars Sample Return mission, which plans to bring samples back to Earth in the 2030s to conduct in-depth studies using sophisticated laboratory instrumentation. Some of these samples may contain traces of ancient martian life that may be particularly difficult to detect and characterize because of their morphological simplicity and subtle biogeochemical expressions. Using the volcanic sediments of the 3.45 Ga Kitty's Gap Chert (Pilbara, Australia), containing putative early life forms (chemolithotrophs) and considered as astrobiological analogues for potential early Mars organisms, we document the steps required to demonstrate the syngenicity and biogenicity of such biosignatures using multiple complementary analytical techniques to provide information at different scales of observation. These include sedimentological, petrological, mineralogical, and geochemical analyses to demonstrate macro- to microscale habitability. New approaches, some unavailable at the time of the original description of these features, are used to verify the syngenicity and biogenicity of the purported fossil chemolithotrophs. The combination of elemental (proton-induced X-ray emission spectrometry) and molecular (deep-ultraviolet and Fourier transform infrared) analyses of rock slabs, thin sections, and focused ion beam sections reveals that the carbonaceous matter present in the samples is enriched in trace metals (e.g., V, Cr, Fe, Co) and is associated with aromatic and aliphatic molecules, which strongly support its biological origin. Transmission electron microscopy observations of the carbonaceous matter documented an amorphous nanostructure interpreted to correspond to the degraded remains of microorganisms and their by-products (extracellular polymeric substances, filaments…). Nevertheless, a small fraction of carbonaceous particles has signatures that are more metamorphosed. They probably represent either reworked detrital biological or abiotic fragments of mantle origin. This study serves as an example of the analytical protocol that would be needed to optimize the detection of fossil traces of life in martian rocks.
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Affiliation(s)
- Laura Clodoré
- CNRS-Centre de Biophysique Moléculaire, Orléans, France
| | - Frédéric Foucher
- CNRS-Centre de Biophysique Moléculaire, Orléans, France
- CNRS-Conditions Extrêmes et Matériaux: Haute Température et Irradiation, Orléans, France
| | - Keyron Hickman-Lewis
- Natural History Museum, London, United Kingdom
- Dipartimento BiGeA, Università di Bologna, Bologna, Italy
| | | | - Jean Jouve
- University of Bordeaux, CNRS, IN2P3, CENBG, Gradignan, France
| | | | - Guillaume Collet
- CNRS-Centre de Biophysique Moléculaire, Orléans, France
- Chair of Cosmetology, AgroParisTech Innovation, Orléans, France
| | | | - Bernard Gratuze
- CNRS-Institut de Recherche sur les ArchéoMATériaux, Orléans, France
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12
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McGuinness KN, Fehon N, Feehan R, Miller M, Mutter AC, Rybak LA, Nam J, AbuSalim JE, Atkinson JT, Heidari H, Losada N, Kim JD, Koder RL, Lu Y, Silberg JJ, Slusky JSG, Falkowski PG, Nanda V. The energetics and evolution of oxidoreductases in deep time. Proteins 2024; 92:52-59. [PMID: 37596815 DOI: 10.1002/prot.26563] [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: 05/16/2023] [Accepted: 07/06/2023] [Indexed: 08/20/2023]
Abstract
The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation-reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation-reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.
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Affiliation(s)
- Kenneth N McGuinness
- Department of Natural Sciences, Caldwell University, Caldwell, New Jersey, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Nolan Fehon
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ryan Feehan
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA
| | - Michelle Miller
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Andrew C Mutter
- Department of Physics, The City College of New York, New York, New York, USA
| | - Laryssa A Rybak
- Department of Physics, The City College of New York, New York, New York, USA
| | - Justin Nam
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Jenna E AbuSalim
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Joshua T Atkinson
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Natalie Losada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - J Dongun Kim
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York, USA
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Jonathan J Silberg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Joanna S G Slusky
- Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
- Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
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13
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Subramanian AM, Thomson M. Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573145. [PMID: 38187750 PMCID: PMC10769378 DOI: 10.1101/2023.12.22.573145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Nature has likely sampled only a fraction of all protein sequences and structures allowed by the laws of biophysics. However, the combinatorial scale of amino-acid sequence-space has traditionally precluded substantive study of the full protein sequence-structure map. In particular, it remains unknown how much of the vast uncharted landscape of far-from-natural sequences consists of alternate ways to encode the familiar ensemble of natural folds; proteins in this category also represent an opportunity to diversify candidates for downstream applications. Here, we characterize sequence-structure mapping in far-from-natural regions of sequence-space guided by the capacity of protein language models (pLMs) to explore sequences outside their natural training data through generation. We demonstrate that pretrained generative pLMs sample a limited structural snapshot of the natural protein universe, including >350 common (sub)domain elements. Incorporating pLM, structure prediction, and structure-based search techniques, we surpass this limitation by developing a novel "foldtuning" strategy that pushes a pretrained pLM into a generative regime that maintains structural similarity to a target protein fold (e.g. TIM barrel, thioredoxin, etc) while maximizing dissimilarity to natural amino-acid sequences. We apply "foldtuning" to build a library of pLMs for >700 naturally-abundant folds in the SCOP database, accessing swaths of proteins that take familiar structures yet lie far from known sequences, spanning targets that include enzymes, immune ligands, and signaling proteins. By revealing protein sequence-structure information at scale outside of the context of evolution, we anticipate that this work will enable future systematic searches for wholly novel folds and facilitate more immediate protein design goals in catalysis and medicine.
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Affiliation(s)
- Arjuna M Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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14
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Abdoli M, Bonardi A, Supuran CT, Žalubovskis R. Investigation of novel alkyl/benzyl (4-sulphamoylphenyl)carbamimidothioates as carbonic anhydrase inhibitors. J Enzyme Inhib Med Chem 2023; 38:2152811. [PMID: 36629134 PMCID: PMC9848269 DOI: 10.1080/14756366.2022.2152811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A library of novel alkyl/benzyl (4-sulphamoylphenyl)carbamimidothioates was synthesised by selective S-alkylation of the easily accessible 4-thioureidobenzenesulphonamide. The compounds were assayed as inhibitors of four human (h) carbonic anhydrase isoforms hCA I, II, VII, and XIII, as well as three bacterial enzymes belonging to the β-CA class, MscCA from Mammaliicoccus (Staphylococcus) sciuri and StCA1 and StCA2, from Salmonella enterica (serovar Typhimurium). Most compounds investigated here exhibited moderate to low nanomolar inhibition constants against hCA I, II, and VII. The cytosolic hCA XIII was also inhibited by these compounds, but not as effective as hCA I, II, and VII. Several compounds were very effective against MscCA and StCA1. StCA2 was less inhibited compared to MscCA and StCA1. Some compounds showed considerable selectivity for inhibiting some CA isoforms. They may thus be considered as interesting starting points for the discovery and development of novel therapeutic agents belonging to this class of enzyme inhibitors.
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Affiliation(s)
- Morteza Abdoli
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
| | - Alessandro Bonardi
- Neurofarba Department, Universita Degli Studi di Firenze, Florence, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, Universita Degli Studi di Firenze, Florence, Italy,Claudiu T. Supuran Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Universitàdegli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Raivis Žalubovskis
- Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia,Latvian Institute of Organic Synthesis, Riga, Latvia,CONTACT Raivis Žalubovskis Latvian Institute of Organic Synthesis, 21 Aizkraukles Str, Riga, LV-1006, Latvia
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15
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Lim L, Kang J, Song J. Extreme diversity of 12 cations in folding ALS-linked hSOD1 unveils novel hSOD1-dependent mechanisms for Fe 2+/Cu 2+-induced cytotoxicity. Sci Rep 2023; 13:19868. [PMID: 37964005 PMCID: PMC10645853 DOI: 10.1038/s41598-023-47338-8] [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: 09/04/2023] [Accepted: 11/12/2023] [Indexed: 11/16/2023] Open
Abstract
153-Residue copper-zinc superoxide dismutase 1 (hSOD1) is the first gene whose mutation was linked to FALS. To date, > 180 ALS-causing mutations have been identified within hSOD1, yet the underlying mechanism still remains mysterious. Mature hSOD1 is exceptionally stable constrained by a disulfide bridge to adopt a Greek-key β-barrel fold that accommodates copper/zinc cofactors. Conversely, nascent hSOD1 is unfolded and susceptible to aggregation and amyloid formation, requiring Zn2+ to initiate folding to a coexistence of folded and unfolded states. Recent studies demonstrate mutations that disrupt Zn2+-binding correlate with their ability to form toxic aggregates. Therefore, to decode the role of cations in hSOD1 folding provides not only mechanistic insights, but may bear therapeutic implications for hSOD1-linked ALS. Here by NMR, we visualized the effect of 12 cations: 8 essential for humans (Na+, K+, Ca2+, Zn2+, Mg2+, Mn2+, Cu2+, Fe2+), 3 mimicking zinc (Ni2+, Cd2+, Co2+), and environmentally abundant Al3+. Surprisingly, most cations, including Zn2+-mimics, showed negligible binding or induction for folding of nascent hSOD1. Cu2+ exhibited extensive binding to the unfolded state but led to severe aggregation. Unexpectedly, for the first time Fe2+ was deciphered to have Zn2+-like folding-inducing capacity. Zn2+ was unable to induce folding of H80S/D83S-hSOD1, while Fe2+ could. In contrast, Zn2+ could trigger folding of G93A-hSOD1, but Fe2+ failed. Notably, pre-existing Fe2+ disrupted the Zn2+-induced folding of G93A-hSOD1. Comparing with the ATP-induced folded state, our findings delineate that hSOD1 maturation requires: (1) intrinsic folding capacity encoded by the sequence; (2) specific Zn2+-coordination; (3) disulfide formation and Cu-load catalyzed by hCCS. This study unveils a previously-unknown interplay of cations in governing the initial folding of hSOD1, emphasizing the pivotal role of Zn2+ in hSOD1-related ALS and implying new hSOD1-dependent mechanisms for Cu2+/Fe2+-induced cytotoxicity, likely relevant to aging and other diseases.
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Affiliation(s)
- Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore
| | - Jian Kang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore.
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16
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Rennberger G, Branham SE, Wechter WP. Genome-Wide Association Study of Resistance to Pseudomonas syringae in the USDA Collection of Citrullus amarus. PLANT DISEASE 2023; 107:3464-3474. [PMID: 37129351 DOI: 10.1094/pdis-04-23-0795-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Pseudomonas leaf spot (PLS), caused by Pseudomonas syringae pv. syringae, is an emerging disease of watermelon in the United States with the potential to severely reduce yield under humid conditions. The genetic basis of resistance to this disease is not known and no resistant germplasm is available. Because Citrullus amarus is an important reservoir of resistance genes for the cultivated watermelon, C. lanatus, we screened the United States Department of Agriculture plant introduction collection of C. amarus for resistance to PLS. Accessions (n = 117) were phenotyped for their level of resistance to PLS in two separate tests. Accession means of percent leaf area affected ranged from 1.5 to 99.4%. The broad-sense heritability for the trait was 0.51. Whole-genome resequencing generated 2,126,759 single-nucleotide polymorphisms (SNPs) which were used to perform a genome-wide association study (GWAS) aimed at discovering molecular markers for resistance. Three different models-BLINK, FarmCPU, and MLM-were included in the GWAS analyses. BLINK and FarmCPU, which are multilocus models, found eight SNPs, located on chromosomes Ca01, Ca05, Ca06, Ca08, and Ca10, that were significantly associated with resistance to PLS. Two of these SNPs were found by both BLINK and FarmCPU. The MLM model did not detect any significant associations. BLINK and FarmCPU estimated an explained phenotypic variance of 43.6 and 28.5%, respectively, for SNP S6_19327000 and 25.0 and 26.0%, respectively, for SNP S1_33362258, the two most significant SNPs found. In total, 43 candidate genes with known involvement in disease resistance were discovered within the genomic intervals of seven of the eight peak SNPs. Eleven of the candidate genes that were found have been reported to be involved in resistance to P. syringae in other plant species. Two significant SNPs were within resistance genes previously documented to play important roles of plant resistance specific to P. syringae in other pathosystems. The SNPs identified in this study will be instrumental in finding causal genes involved in PLS resistance in watermelon and developing resistant germplasm through breeding.
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Affiliation(s)
- Gabriel Rennberger
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory, Charleston, SC 29414
| | - Sandra E Branham
- Clemson University, Department of Plant and Environmental Sciences, Coastal Research and Education Center, Charleston, SC 29414
| | - William P Wechter
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Vegetable Laboratory, Charleston, SC 29414
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17
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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18
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Janisse SE, Fernandez RL, Heffern MC. Characterizing metal-biomolecule interactions by mass spectrometry. Trends Biochem Sci 2023; 48:815-825. [PMID: 37433704 DOI: 10.1016/j.tibs.2023.06.006] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023]
Abstract
Metal micronutrients are essential for life and exist in a delicate balance to maintain an organism's health. The labile nature of metal-biomolecule interactions clouds the understanding of metal binders and metal-mediated conformational changes that are influential to health and disease. Mass spectrometry (MS)-based methods and technologies have been developed to better understand metal micronutrient dynamics in the intra- and extracellular environment. In this review, we describe the challenges associated with studying labile metals in human biology and highlight MS-based methods for the discovery and study of metal-biomolecule interactions.
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Affiliation(s)
- Samuel E Janisse
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA
| | - Rebeca L Fernandez
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA
| | - Marie C Heffern
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA.
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19
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Srivastava S, Dong H, Baars O, Sheng Y. Bioavailability of mineral-associated trace metals as cofactors for nitrogen fixation by Azotobacter vinelandii. GEOBIOLOGY 2023; 21:507-519. [PMID: 36852450 DOI: 10.1111/gbi.12552] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/28/2023] [Accepted: 02/12/2023] [Indexed: 06/13/2023]
Abstract
Life on Earth depends on N2 -fixing microbes to make ammonia from atmospheric N2 gas by the nitrogenase enzyme. Most nitrogenases use Mo as a cofactor; however, V and Fe are also possible. N2 fixation was once believed to have evolved during the Archean-Proterozoic times using Fe as a cofactor. However, δ15 N values of paleo-ocean sediments suggest Mo and V cofactors despite their low concentrations in the paleo-oceans. This apparent paradox is based on an untested assumption that only soluble metals are bioavailable. In this study, laboratory experiments were performed to test the bioavailability of mineral-associated trace metals to a model N2 -fixing bacterium Azotobacter vinelandii. N2 fixation was observed when Mo in molybdenite, V in cavansite, and Fe in ferrihydrite were used as the sole sources of cofactors, but the rate of N2 fixation was greatly reduced. A physical separation between minerals and cells further reduced the rate of N2 fixation. Biochemical assays detected five siderophores, including aminochelin, azotochelin, azotobactin, protochelin, and vibrioferrin, as possible chelators to extract metals from minerals. The results of this study demonstrate that mineral-associated trace metals are bioavailable as cofactors of nitrogenases to support N2 fixation in those environments that lack soluble trace metals and may offer a partial answer to the paradox.
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Affiliation(s)
- Shreya Srivastava
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, North Carolina, Raleigh, USA
| | - Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio, USA
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20
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Harrison SA, Webb WL, Rammu H, Lane N. Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide. Life (Basel) 2023; 13:life13051177. [PMID: 37240822 DOI: 10.3390/life13051177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of many other essential biomolecules. Aspartate's prebiotic synthesis is complicated by the instability of its precursor, oxaloacetate. In this paper, we show that the use of the biologically relevant cofactor pyridoxamine, supported by metal ion catalysis, is sufficiently fast to offset oxaloacetate's degradation. Cu2+-catalysed transamination of oxaloacetate by pyridoxamine achieves around a 5% yield within 1 h, and can operate across a broad range of pH, temperature, and pressure. In addition, the synthesis of the downstream product β-alanine may also take place in the same reaction system at very low yields, directly mimicking an archaeal synthesis route. Amino group transfer supported by pyridoxal is shown to take place from aspartate to alanine, but the reverse reaction (alanine to aspartate) shows a poor yield. Overall, our results show that the nodal metabolite aspartate and related amino acids can indeed be synthesised via protometabolic pathways that foreshadow modern metabolism in the presence of the simple cofactor pyridoxamine and metal ions.
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Affiliation(s)
- Stuart A Harrison
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - William L Webb
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Hanadi Rammu
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Nick Lane
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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21
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Schmollinger S, Chen S, Merchant SS. Quantitative elemental imaging in eukaryotic algae. Metallomics 2023; 15:mfad025. [PMID: 37186252 PMCID: PMC10209819 DOI: 10.1093/mtomcs/mfad025] [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: 08/30/2022] [Accepted: 03/03/2023] [Indexed: 05/17/2023]
Abstract
All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.
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Affiliation(s)
- Stefan Schmollinger
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Si Chen
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sabeeha S Merchant
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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22
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Sweere TC, Dickson AJ, Vance D. Nickel and zinc micronutrient availability in Phanerozoic oceans. GEOBIOLOGY 2023; 21:310-322. [PMID: 36536606 DOI: 10.1111/gbi.12541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/19/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Nickel and zinc are both bio-essential micronutrients with a nutrient-like distribution in the modern ocean, but show key differences in their biological functions and geochemical behavior. Eukaryotic phytoplankton, and especially diatoms, have high Zn quotas, whereas cyanobacteria generally require relatively more Ni. Secular changes in the relative availability of these micronutrients may, therefore, have affected the evolution and diversification of phytoplankton. In this study, we use a large compilation of Ni and Zn concentration data for Phanerozoic sediments to evaluate long-term changes in Ni and Zn availability and possible links to phytoplankton evolution. Modern data suggest that organic-rich sediments capture the dissolved deep ocean Ni/Zn ratio, regardless of local depositional conditions. We use this observation to constrain Ni/Zn ratios for past oceans, based on data from the sedimentary record. This record highlights long-term changes in the relative availability of these micronutrients that can be linked to the (bio)geochemical conditions on the Earth's surface. Early Palaeozoic oceans were likely relatively Ni rich, with sedimentary Ni/Zn ratios for this interval mostly being around ~1 or higher. A comparison with Phanerozoic strontium-, carbon-, and sulfur-isotopic records suggests that the late Palaeozoic decrease in sulfidic conditions and increase in hydrothermal inputs and organic-carbon burial rates caused a shift towards more Zn-rich conditions. Mesozoic and Cenozoic sediments show relatively Zn-rich oceans for these time intervals, with sedimentary Ni/Zn ratios mostly being around ~1 or lower. These observations imply that the diversification of the dominant groups of modern eukaryotic phytoplankton occurred in relatively Zn-rich oceans and that these organisms still carry this signature in their stoichiometries. However, the Phanerozoic transition to a more Zn-rich ocean pre-dates the origin and diversification of modern eukaryotes and, therefore, this transition was likely not the main direct cause for eukaryotic diversification in the Mesozoic and Cenozoic Eras.
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Affiliation(s)
- Tim C Sweere
- Department of Earth Sciences, ETH Zürich, Zürich, Switzerland
| | - Alexander J Dickson
- Centre of Climate, Ocean and Atmosphere, Department of Earth Sciences, Royal Holloway University of London, Surrey, UK
| | - Derek Vance
- Department of Earth Sciences, ETH Zürich, Zürich, Switzerland
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23
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Sendra KM, Barwinska-Sendra A, Mackenzie ES, Baslé A, Kehl-Fie TE, Waldron KJ. An ancient metalloenzyme evolves through metal preference modulation. Nat Ecol Evol 2023; 7:732-744. [PMID: 37037909 PMCID: PMC10172142 DOI: 10.1038/s41559-023-02012-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/15/2023] [Indexed: 04/12/2023]
Abstract
Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree of life and evaluated in a single experimental system are lacking. Almost half of enzymes require metals, and metalloproteins tend to optimally utilize the physicochemical properties of a specific metal co-factor. Life must adapt to changes in metal bioavailability, including those during the transition from anoxic to oxic Earth or pathogens' exposure to nutritional immunity. These changes can challenge the ability of metalloenzymes to maintain activity, presumptively driving their evolution. Here we studied metal-preference evolution within the natural diversity of the iron/manganese superoxide dismutase (SodFM) family of reactive oxygen species scavengers. We identified and experimentally verified residues with conserved roles in determining metal preference that, when combined with an understanding of the protein's evolutionary history, improved prediction of metal utilization across the five SodFM subfamilies defined herein. By combining phylogenetics, biochemistry and structural biology, we demonstrate that SodFM metal utilization can be evolutionarily fine tuned by sliding along a scale between perfect manganese and iron specificities. Over the history of life, SodFM metal preference has been modulated multiple independent times within different evolutionary and ecological contexts, and can be changed within short evolutionary timeframes.
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Affiliation(s)
- K M Sendra
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - A Barwinska-Sendra
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - E S Mackenzie
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - A Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - T E Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - K J Waldron
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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24
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Willems P, Huang J, Messens J, Van Breusegem F. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures. Free Radic Biol Med 2023; 194:220-229. [PMID: 36493985 DOI: 10.1016/j.freeradbiomed.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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25
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Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function. Curr Opin Genet Dev 2022; 77:101987. [PMID: 36183585 DOI: 10.1016/j.gde.2022.101987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
Metal ions are potent catalysts and have been available for cellular biochemistry at all stages of evolution. Growing evidence suggests that metal catalysis was critical for the origin of the very first metabolic reactions. With approximately 80% of modern metabolic pathways being dependent on metal ions, metallocatalysis and homeostasis continue to be essential for intracellular metabolic networks and physiology. However, the genetic network that controls metal ion homeostasis and the impact of metal availability on metabolism is poorly understood. Here, we review recent work on gene and protein evolution relevant for better understanding metal ion biology and its role in metabolism. We highlight the importance of analysing the origin and evolution of enzyme catalysis in the context of catalytically relevant metal ions, summarise unanswered questions essential for developing a comprehensive understanding of metal ion homeostasis and advocate for the consideration of metal ion properties and availability in the design and directed evolution of novel enzymes and pathways.
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26
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Enzingmüller-Bleyl TC, Boden JS, Herrmann AJ, Ebel KW, Sánchez-Baracaldo P, Frankenberg-Dinkel N, Gehringer MM. On the trail of iron uptake in ancestral Cyanobacteria on early Earth. GEOBIOLOGY 2022; 20:776-789. [PMID: 35906866 DOI: 10.1111/gbi.12515] [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: 05/16/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacteria oxygenated Earth's atmosphere ~2.4 billion years ago, during the Great Oxygenation Event (GOE), through oxygenic photosynthesis. Their high iron requirement was presumably met by high levels of Fe(II) in the anoxic Archean environment. We found that many deeply branching Cyanobacteria, including two Gloeobacter and four Pseudanabaena spp., cannot synthesize the Fe(II) specific transporter, FeoB. Phylogenetic and relaxed molecular clock analyses find evidence that FeoB and the Fe(III) transporters, cFTR1 and FutB, were present in Proterozoic, but not earlier Archaean lineages of Cyanobacteria. Furthermore Pseudanabaena sp. PCC7367, an early diverging marine, benthic strain grown under simulated Archean conditions, constitutively expressed cftr1, even after the addition of Fe(II). Our genetic profiling suggests that, prior to the GOE, ancestral Cyanobacteria may have utilized alternative metal iron transporters such as ZIP, NRAMP, or FicI, and possibly also scavenged exogenous siderophore bound Fe(III), as they only acquired the necessary Fe(II) and Fe(III) transporters during the Proterozoic. Given that Cyanobacteria arose 3.3-3.6 billion years ago, it is possible that limitations in iron uptake may have contributed to the delay in their expansion during the Archean, and hence the oxygenation of the early Earth.
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Affiliation(s)
| | - Joanne S Boden
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, UK
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, UK
| | - Achim J Herrmann
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Katharina W Ebel
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | | | - Michelle M Gehringer
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
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27
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Valenti R, Jabłońska J, Tawfik DS. Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin. Protein Sci 2022; 31:e4423. [PMID: 36173172 PMCID: PMC9490801 DOI: 10.1002/pro.4423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the "ancestors" are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.
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Affiliation(s)
- Rosario Valenti
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Jagoda Jabłońska
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Dan S. Tawfik
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
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28
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Liu D, Gao Z, Li J, Yao Q, Tan W, Xing W, Lu Z. Effects of cadmium stress on the morphology, physiology, cellular ultrastructure, and BvHIPP24 gene expression of sugar beet ( Beta vulgaris L.). INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2022; 25:455-465. [PMID: 35771710 DOI: 10.1080/15226514.2022.2090496] [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] [Indexed: 06/15/2023]
Abstract
To clarify the mechanism of the response of sugar beet (Beta vulgaris L.) to cadmium (Cd) stress, this study investigated changes in the phenotype, physiological indexes, and subcellular structure of B. vulgaris under Cd treatment and the transcriptional pattern of the BvHIPP24 gene (a heavy metal-associated isoprenylated plant protein involved in heavy metal detoxification). The plant height and shoot and root growth of B. vulgaris seedlings were inhibited to some extent under 0.5 and 1 mM Cd, with gradually wilting and yellowing of leaves and dark brown roots. When the Cd concentration was increased, malondialdehyde content and the activities of peroxidase, superoxide dismutase, and glutathione S-transferase increased differentially. qPCR indicated that the expression of BvHIPP24 was induced by different concentrations of Cd. Although transmission electron microscopy revealed damage to nuclei, mitochondria, and chloroplasts, B. vulgaris exhibited strong adaptability to 0.5 mM Cd according to a comprehensive analysis using the membership function. The results showed that B. vulgaris may reduce cell damage and improve its Cd tolerance by regulating functional gene expression and antioxidant enzymes. This study increases our understanding of the Cd-tolerance mechanism of B. vulgaris and provides insights into the use of B. vulgaris in Cd bioremediation.
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Affiliation(s)
- Dali Liu
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Zhuo Gao
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Jiajia Li
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Qi Yao
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
- Key Laboratory of Molecular Biology, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Wenbo Tan
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Wang Xing
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Zhenqiang Lu
- Key Laboratory of Molecular Biology, School of Life Sciences, Heilongjiang University, Harbin, China
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29
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Pengelly RJ, Bakhtiar D, Borovská I, Královičová J, Vořechovský I. Exonic splicing code and protein binding sites for calcium. Nucleic Acids Res 2022; 50:5493-5512. [PMID: 35474482 PMCID: PMC9177970 DOI: 10.1093/nar/gkac270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/12/2022] Open
Abstract
Auxilliary splicing sequences in exons, known as enhancers (ESEs) and silencers (ESSs), have been subject to strong selection pressures at the RNA and protein level. The protein component of this splicing code is substantial, recently estimated at ∼50% of the total information within ESEs, but remains poorly understood. The ESE/ESS profiles were previously associated with the Irving-Williams (I-W) stability series for divalent metals, suggesting that the ESE/ESS evolution was shaped by metal binding sites. Here, we have examined splicing activities of exonic sequences that encode protein binding sites for Ca2+, a weak binder in the I-W affinity order. We found that predicted exon inclusion levels for the EF-hand motifs and for Ca2+-binding residues in nonEF-hand proteins were higher than for average exons. For canonical EF-hands, the increase was centred on the EF-hand chelation loop and, in particular, on Ca2+-coordinating residues, with a 1>12>3∼5>9 hierarchy in the 12-codon loop consensus and usage bias at codons 1 and 12. The same hierarchy but a lower increase was observed for noncanonical EF-hands, except for S100 proteins. EF-hand loops preferentially accumulated exon splits in two clusters, one located in their N-terminal halves and the other around codon 12. Using splicing assays and published crosslinking and immunoprecipitation data, we identify candidate trans-acting factors that preferentially bind conserved GA-rich motifs encoding negatively charged amino acids in the loops. Together, these data provide evidence for the high capacity of codons for Ca2+-coordinating residues to be retained in mature transcripts, facilitating their exon-level expansion during eukaryotic evolution.
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Affiliation(s)
- Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Jana Královičová
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
- Slovak Academy of Sciences, Institute of Zoology, 845 06 Bratislava, Slovak Republic
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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30
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Polar algae flaunt their zinc assets. Nat Ecol Evol 2022; 6:851-852. [PMID: 35654897 DOI: 10.1038/s41559-022-01721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Abstract
SignificanceZinc deficiency in the human population, a major public health concern, can also be a consequence of nutritional deficiency in protein uptake. The discovery that tryptophan metabolites 3-hydroxykynurenine and xanthurenic acid are major zinc-binding ligands in insect cells establishes the kynurenine pathway as a regulator of systemic zinc homeostasis. Many biological processes influenced by zinc and the kynurenine pathway, including the regulation of innate and acquired immune responses to viral infections, have not been studied in light of the direct molecular links revealed in this study.
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32
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Clemens S. The cell biology of zinc. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1688-1698. [PMID: 34727160 DOI: 10.1093/jxb/erab481] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Nearly 10% of all plant proteins belong to the zinc (Zn) proteome. They require Zn either for catalysis or as a structural element. Most of the protein-bound Zn in eukaryotic cells is found in the cytosol. The fundamental differences between transition metal cations in the stability of their complexes with organic ligands, as described by the Irving-Williams series, necessitate buffering of cytosolic Zn (the 'free Zn' pool) in the picomolar range (i.e. ~6 orders of magnitude lower than the total cellular concentration). Various metabolites and peptides, including nicotianamine, glutathione, and phytochelatins, serve as Zn buffers. They are hypothesized to supply Zn to enzymes, transporters, or the recently identified sensor proteins. Zn2+ acquisition is mediated by ZRT/IRT-like proteins. Metal tolerance proteins transport Zn2+ into vacuoles and the endoplasmic reticulum, the major Zn storage sites. Heavy metal ATPase-dependent efflux of Zn2+ is another mechanism to control cytosolic Zn. Spatially controlled Zn2+ influx or release from intracellular stores would result in dynamic modulation of cellular Zn pools, which may directly influence protein-protein interactions or the activities of enzymes involved in signaling cascades. Possible regulatory roles of such changes, as recently elucidated in mammalian cells, are discussed.
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Affiliation(s)
- Stephan Clemens
- Department of Plant Physiology and Faculty of Life Science: Food, Nutrition and Health, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
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33
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Subirana MA, Riemschneider S, Hause G, Dobritzsch D, Schaumlöffel D, Herzberg M. High spatial resolution imaging of subcellular macro and trace element distribution during phagocytosis. Metallomics 2022; 14:6530650. [PMID: 35179212 DOI: 10.1093/mtomcs/mfac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022]
Abstract
The bioavailability of trace elements in the course of evolution had an essential influence on the emergence of life itself. This is reflected in the co-evolution between eukaryotes and prokaryotes. In this study, the influence and cellular distribution of bioelements during phagocytosis at the host-pathogen interface was investigated using high-resolution nanoscale secondary ion mass spectrometry (NanoSIMS) and quantitative inductively coupled plasma mass spectrometry (ICP-MS). In the eukaryotic murine macrophages (RAW 264.7 cell line), the cellular Fe / Zn ratio was found to be balanced, whereas the dominance of iron in the prokaryotic cells of the pathogen Salmonella enterica Serovar Enteritidis was about 90% compared to zinc. This confirms the evolutionary increased zinc requirement of the eukaryotic animal cell. Using NanoSIMS, the Cs+ primary ion source allowed high spatial resolution mapping of cell morphology down to subcellular level. At a comparable resolution, several low abundant trace elements could be mapped during phagocytosis with a RF plasma O- primary ion source. An enrichment of copper and nickel could be detected in the prokaryotic cells. Surprisingly, an accumulation of cobalt in the area of nuclear envelope was observed indicating an interesting but still unknown distribution of this trace element in murine macrophages.
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Affiliation(s)
- Maria Angels Subirana
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France
| | - Sina Riemschneider
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103 Leipzig, Germany
| | - Gerd Hause
- Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Dirk Dobritzsch
- Martin-Luther-University Halle-Wittenberg, Core Facility - Proteomic Mass Spectrometry, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Dirk Schaumlöffel
- CNRS, Université de Pau et des Pays de l'Adour, E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254, 64000 Pau, France.,Peoples' Friendship University of Russia (RUDN University), Mklukho-Maklaya str. 6, 117198 Moscow, Russia
| | - Martin Herzberg
- Martin-Luther-University Halle-Wittenberg, Institute for Biology/Microbiology, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany
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34
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Bromberg Y, Aptekmann AA, Mahlich Y, Cook L, Senn S, Miller M, Nanda V, Ferreiro DU, Falkowski PG. Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. SCIENCE ADVANCES 2022; 8:eabj3984. [PMID: 35030025 PMCID: PMC8759750 DOI: 10.1126/sciadv.abj3984] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/22/2021] [Indexed: 06/07/2023]
Abstract
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago.Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life. [A. I. Oparin (1)]
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Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Ariel A. Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Yannick Mahlich
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Linda Cook
- Program in Applied and Computational Math, Princeton University, Princeton, NJ 08540, USA
| | - Stefan Senn
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Maximillian Miller
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, and Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Diego U. Ferreiro
- Protein Physiology Lab, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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35
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Uraguchi S, Nagai K, Naruse F, Otsuka Y, Ohshiro Y, Nakamura R, Takanezawa Y, Kiyono M. Development of affinity bead-based in vitro metal-ligand binding assay reveals dominant cadmium affinity of thiol-rich small peptides phytochelatins beyond glutathione. Metallomics 2021; 13:6445037. [PMID: 34850059 DOI: 10.1093/mtomcs/mfab068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/17/2021] [Indexed: 11/12/2022]
Abstract
For a better understanding of metal-ligand interaction and its function in cells, we developed an easy, sensitive, and high-throughput method to quantify ligand-metal(loid) binding affinity under physiological conditions by combining ligand-attached affinity beads and inductively coupled plasma-optical emission spectrometry (ICP-OES). Glutathione (GSH) and two phytochelatins (PC2 and PC3, small peptides with different numbers of free thiols) were employed as model ligands and attached to hydrophilic beads. The principle of the assay resembles that of affinity purification of proteins in biochemistry: metals binding to the ligand on the beads and the rest in the buffer are separated by a spin column and quantified by ICP-OES. The binding assay using the GSH-attached beads and various metal(loid)s suggested the different affinity of the metal-GSH interactions, in accordance with the order of the Irving-Williams series and the reported stability constants. The binding assay using PC2 or PC3-attached beads suggested positive binding between PCs and Ni(II), Cu(II), Zn(II), Cd(II), and As(III) in accordance with the number of thiols in PC2 and PC3. We then conducted the competition assay using Cd(II), Mn(II), Fe(II), Cu(II), and Zn(II), and the results suggested a better binding affinity of PC2 with Cd(II) than with the essential metals. Another competition assay using PC2 and GSH suggested a robust binding affinity between PCs and Cd(II) compared to GSH and Cd(II). These results suggested the dominance of PC-Cd complex formation in vitro, supporting the physiological importance of PCs for the detoxification of cadmium in vivo. We also discuss the potential application of the assay.
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Affiliation(s)
- Shimpei Uraguchi
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kenichiro Nagai
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Fumii Naruse
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yuto Otsuka
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yuka Ohshiro
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Ryosuke Nakamura
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yasukazu Takanezawa
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Masako Kiyono
- Department of Public Health, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Abstract
Iron is an irreplaceable component of proteins and enzyme systems required for life. This need for iron is a well-characterized evolutionary mechanism for genetic selection. However, there is limited consideration of how iron bioavailability, initially determined by planetary accretion but fluctuating considerably at global scale over geological time frames, has shaped the biosphere. We describe influences of iron on planetary habitability from formation events >4 Gya and initiation of biochemistry from geochemistry through oxygenation of the atmosphere to current host–pathogen dynamics. By determining the iron and transition element distribution within the terrestrial planets, planetary core formation is a constraint on both the crustal composition and the longevity of surface water, hence a planet’s habitability. As such, stellar compositions, combined with metallic core-mass fraction, may be an observable characteristic of exoplanets that relates to their ability to support life. On Earth, the stepwise rise of atmospheric oxygen effectively removed gigatons of soluble ferrous iron from habitats, generating evolutionary pressures. Phagocytic, infectious, and symbiotic behaviors, dating from around the Great Oxygenation Event, refocused iron acquisition onto biotic sources, while eukaryotic multicellularity allows iron recycling within an organism. These developments allow life to more efficiently utilize a scarce but vital nutrient. Initiation of terrestrial life benefitted from the biochemical properties of abundant mantle/crustal iron, but the subsequent loss of iron bioavailability may have been an equally important driver of compensatory diversity. This latter concept may have relevance for the predicted future increase in iron deficiency across the food chain caused by elevated atmospheric CO2.
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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38
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Li H, Yang Y, Zhang D, Li Y, Zhang H, Luo J, Jones KC. Evaluating the simulated toxicities of metal mixtures and hydrocarbons using the alkane degrading bioreporter Acinetobacter baylyi ADPWH_recA. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126471. [PMID: 34216972 DOI: 10.1016/j.jhazmat.2021.126471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Oil spillages lead to the formation of hydrocarbon and metal mixtures possessing effects on alkane-degrading bacteria that are responsible for the bioremediation of oil-contaminated soils and waters. Studies of bacterial responses to the mixture of petroleum and metal can inform appropriate strategies for bioremediation. We employed a luminescent bioreporter Acinetobacter baylyi ADPWH_recA with alkane degradation capability to evaluate the combined effects from heavy metals (Cd, Pb and Cu) and alkanes (dodecane, tetradecane, hexadecane and octadecane). Bioluminescent ratios of ADPWH_recA in single Cd or Pb treatments ranged from 0.25 to 1.98, indicating both genotoxicity and cytotoxicity of these two metals, while ratios < 1.0 postexposure to Cu showed its cytotoxic impacts on ADPWH_recA bioreporter. Metal mixtures exhibited enhanced antagonistic effects (Ti>4.0) determined by the Toxic Unit model. With 100 mg/L alkane, the morbidity of ADPWH-recA reduced to < 20%, showing the inhibition of alkanes on Cd toxicity. Exposed to the metal mixture containing 10 mg/L Cu, the weak binding affinity of Cu with alkanes contributed to a high morbidity of > 85% in ADPWH_recA cells. This study provides a new way to understand the toxicity of mixture contaminants, which can help to optimize treatment efficiencies of bacterial remediation for oil contamination.
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Affiliation(s)
- Hanbing Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; Key Laboratory of Beijing on Regional Air Pollution Control, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100086, China
| | - Yanying Li
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Hao Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Jun Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Kevin C Jones
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK.
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Wu Z, Liu D, Yue N, Song H, Luo J, Zhang Z. PDF1.5 Enhances Adaptation to Low Nitrogen Levels and Cadmium Stress. Int J Mol Sci 2021; 22:ijms221910455. [PMID: 34638794 PMCID: PMC8509053 DOI: 10.3390/ijms221910455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/17/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Environmental acclimation ability plays a key role in plant growth, although the mechanism remains unclear. Here, we determined the involvement of Arabidopsis thaliana PLANT DEFENSIN 1 gene AtPDF1.5 in the adaptation to low nitrogen (LN) levels and cadmium (Cd) stress. Histochemical analysis revealed that AtPDF1.5 was mainly expressed in the nodes and carpopodium and was significantly induced in plants exposed to LN conditions and Cd stress. Subcellular localization analysis revealed that AtPDF1.5 was cell wall- and cytoplasm-localized. AtPDF1.5 overexpression significantly enhanced adaptation to LN and Cd stress and enhanced the distribution of metallic elements. The functional disruption of AtPDF1.5 reduced adaptations to LN and Cd stress and impaired metal distribution. Under LN conditions, the nitrate transporter AtNRT1.5 expression was upregulated. Nitrate transporter AtNRT1.8 expression was downregulated when AtPDF1.5 was overexpressed, resulting in enhanced transport of NO3- to shoots. In response to Cd treatment, AtPDF1.5 regulated the expression of metal transporter genes AtHMP07, AtNRAMP4, AtNRAMP1, and AtHIPP3, resulting in higher Cd accumulation in the shoots. We conclude that AtPDF1.5 is involved in the processing or transmission of signal substances and plays an important role in the remediation of Cd pollution and LN adaptation.
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Affiliation(s)
- Zhimin Wu
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 410128, China; (Z.W.); (D.L.); (N.Y.); (H.S.)
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410221, China
| | - Dong Liu
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 410128, China; (Z.W.); (D.L.); (N.Y.); (H.S.)
- National Centre of Oilseed Crops Improvement, Hunan Branch, Changsha 410128, China
| | - Ningyan Yue
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 410128, China; (Z.W.); (D.L.); (N.Y.); (H.S.)
- National Centre of Oilseed Crops Improvement, Hunan Branch, Changsha 410128, China
| | - Haixing Song
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 410128, China; (Z.W.); (D.L.); (N.Y.); (H.S.)
- National Centre of Oilseed Crops Improvement, Hunan Branch, Changsha 410128, China
| | - Jinsong Luo
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 410128, China; (Z.W.); (D.L.); (N.Y.); (H.S.)
- National Centre of Oilseed Crops Improvement, Hunan Branch, Changsha 410128, China
- Correspondence: (J.L.); (Z.Z.)
| | - Zhenhua Zhang
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha 410128, China; (Z.W.); (D.L.); (N.Y.); (H.S.)
- National Centre of Oilseed Crops Improvement, Hunan Branch, Changsha 410128, China
- Correspondence: (J.L.); (Z.Z.)
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41
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Abstract
The ancestors of cyanobacteria generated Earth's first biogenic molecular oxygen, but how they dealt with oxidative stress remains unconstrained. Here we investigate when superoxide dismutase enzymes (SODs) capable of removing superoxide free radicals evolved and estimate when Cyanobacteria originated. Our Bayesian molecular clocks, calibrated with microfossils, predict that stem Cyanobacteria arose 3300-3600 million years ago. Shortly afterwards, we find phylogenetic evidence that ancestral cyanobacteria used SODs with copper and zinc cofactors (CuZnSOD) during the Archaean. By the Paleoproterozoic, they became genetically capable of using iron, nickel, and manganese as cofactors (FeSOD, NiSOD, and MnSOD respectively). The evolution of NiSOD is particularly intriguing because it corresponds with cyanobacteria's invasion of the open ocean. Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) now demonstrate that marine geochemical records alone may not predict patterns of metal usage by phototrophs from freshwater and terrestrial habitats.
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42
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Tostevin R, Snow JT, Zhang Q, Tosca NJ, Rickaby REM. The influence of elevated SiO 2 (aq) on intracellular silica uptake and microbial metabolism. GEOBIOLOGY 2021; 19:421-433. [PMID: 33838079 DOI: 10.1111/gbi.12442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/12/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Microbes are known to accumulate intracellular SiO2 (aq) up to 100s of mmol/l from modern seawater (SiO2 (aq) <100 µmol/l), despite having no known nutrient requirement for Si. Before the evolution of siliceous skeletons, marine silica concentrations were likely an order of magnitude higher than the modern ocean, raising the possibility that intracellular SiO2 (aq) accumulation interfered with normal cellular function in non-silicifying algae. Yet, because few culturing studies have isolated the effects of SiO2 (aq) at high concentration, the potential impact of elevated marine silica on early microbial evolution is unknown. Here, we test the influence of elevated SiO2 (aq) on eukaryotic algae, as well as a prokaryote species. Our results demonstrate that under SiO2 (aq) concentrations relevant to ancient seawater, intracellular Si accumulates to concentrations comparable to those found in siliceous algae such as diatoms. In addition, all eukaryotic algae showed a statistically significant response to the high-Si treatment, including reduced average cell sizes and/or a reduction in the maximum growth rate. In contrast, there was no consistent response to the high-Si treatment by the prokaryote species. Our results highlight the possibility that elevated marine SiO2 (aq) may have been an environmental stressor during early eukaryotic evolution.
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Affiliation(s)
- Rosalie Tostevin
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
- Department of Earth Science, University of Oxford, Oxford, UK
| | - Joseph T Snow
- Department of Earth Science, University of Oxford, Oxford, UK
| | - Qiong Zhang
- Department of Earth Science, University of Oxford, Oxford, UK
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43
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Smith HH, Hyde AS, Simkus DN, Libby E, Maurer SE, Graham HV, Kempes CP, Sherwood Lollar B, Chou L, Ellington AD, Fricke GM, Girguis PR, Grefenstette NM, Pozarycki CI, House CH, Johnson SS. The Grayness of the Origin of Life. Life (Basel) 2021; 11:498. [PMID: 34072344 PMCID: PMC8226951 DOI: 10.3390/life11060498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 12/05/2022] Open
Abstract
In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.
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Affiliation(s)
- Hillary H. Smith
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew S. Hyde
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Danielle N. Simkus
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | - Eric Libby
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
- Icelab, Umeå University, 90187 Umeå, Sweden
| | - Sarah E. Maurer
- Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT 06050, USA;
| | - Heather V. Graham
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | | | | | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - G. Matthew Fricke
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87108, USA;
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;
| | - Natalie M. Grefenstette
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Chad I. Pozarycki
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Christopher H. House
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Science, Technology and International Affairs Program, Georgetown University, Washington, DC 20057, USA
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44
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Wright GSA. Bacterial evolutionary precursors of eukaryotic copper-zinc superoxide dismutases. Mol Biol Evol 2021; 38:3789-3803. [PMID: 34021750 PMCID: PMC8382915 DOI: 10.1093/molbev/msab157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
Internalization of a bacteria by an archaeal cell expedited eukaryotic evolution. An important feature of the species that diversified into the great variety of eukaryotic life visible today was the ability to combat oxidative stress with a copper–zinc superoxide dismutase (CuZnSOD) enzyme activated by a specific, high-affinity copper chaperone. Adoption of a single protein interface that facilitates homodimerization and heterodimerization was essential; however, its evolution has been difficult to rationalize given the structural differences between bacterial and eukaryotic enzymes. In contrast, no consistent strategy for the maturation of periplasmic bacterial CuZnSODs has emerged. Here, 34 CuZnSODs are described that closely resemble the eukaryotic form but originate predominantly from aquatic bacteria. Crystal structures of a Bacteroidetes bacterium CuZnSOD portray both prokaryotic and eukaryotic characteristics and propose a mechanism for self-catalyzed disulfide maturation. Unification of a bacterial but eukaryotic-like CuZnSOD along with a ferredoxin-fold MXCXXC copper-binding domain within a single polypeptide created the advanced copper delivery system for CuZnSODs exemplified by the human copper chaperone for superoxide dismutase-1. The development of this system facilitated evolution of large and compartmentalized cells following endosymbiotic eukaryogenesis.
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Affiliation(s)
- Gareth S A Wright
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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45
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Kuznetsov AV, Vainer VI, Volkova YM, Kartashov LE. Motility disorders and disintegration into separate cells of Trichoplax sp. H2 in the presence of Zn 2+ ions and L-cysteine molecules: A systems approach. Biosystems 2021; 206:104444. [PMID: 34023485 DOI: 10.1016/j.biosystems.2021.104444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 01/01/2023]
Abstract
Placozoa remain an ancient multicellular system with a dynamic body structure where calcium ions carry out a primary role in maintaining the integrity of the entire animal. Zinc ions can compete with calcium ions adsorption. We studied the effect of zinc ions and l-cysteine molecules on the interaction of Trichoplax sp. H2 cells. The regularity of formless motion was diminished in the presence of 20-25 μM of Zn2+ ions leading to the formation of branching animal forms. Locomotor ciliated cells moved chaotically and independently of each other leaving the Trichoplax body and opening a network of fiber cells. Application of 100 μM cysteine resulted in dissociation of the plate into separate cells. The combined chemical treatment shifted the effect in a random sample of animals toward disintegration, i.e. initially leading to disorder of collective cell movement and then to total body fragmentation. Two dissociation patterns of Trichoplax plate as "expanding ring" and "bicycle wheel" were revealed. Analysis of the interaction of Ca2+ and Zn2+ ions with cadherin showed that more than half (54%) of the amino acid residues with which Ca2+ and Zn2+ ions bind are common. The contact interaction of cells covered by the cadherin molecules is important for the coordinated movements of Trichoplax organism, while zinc ions are capable to break junctions between the cells. The involvement of other players, for example, l-cysteine in the regulation of Ca2+-dependent adhesion may be critical leading to the typical dissociation of Trichoplax body like in a calcium-free environment. A hypothesis about the essential role of calcium ions in the emergence of Metazoa ancestor is proposed.
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Affiliation(s)
- A V Kuznetsov
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia.
| | - V I Vainer
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia
| | - Yu M Volkova
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia
| | - L E Kartashov
- A.O. Kovalevsky Institute of Biology of the Southern Seas RAS, Leninsky Avenue 38, Moscow, 119991, Russia
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Angulo-Bejarano PI, Puente-Rivera J, Cruz-Ortega R. Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:635. [PMID: 33801570 PMCID: PMC8066251 DOI: 10.3390/plants10040635] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Worldwide, the effects of metal and metalloid toxicity are increasing, mainly due to anthropogenic causes. Soil contamination ranks among the most important factors, since it affects crop yield, and the metals/metalloids can enter the food chain and undergo biomagnification, having concomitant effects on human health and alterations to the environment. Plants have developed complex mechanisms to overcome these biotic and abiotic stresses during evolution. Metals and metalloids exert several effects on plants generated by elements such as Zn, Cu, Al, Pb, Cd, and As, among others. The main strategies involve hyperaccumulation, tolerance, exclusion, and chelation with organic molecules. Recent studies in the omics era have increased knowledge on the plant genome and transcriptome plasticity to defend against these stimuli. The aim of the present review is to summarize relevant findings on the mechanisms by which plants take up, accumulate, transport, tolerate, and respond to this metal/metalloid stress. We also address some of the potential applications of biotechnology to improve plant tolerance or increase accumulation.
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Affiliation(s)
- Paola I. Angulo-Bejarano
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, 275, Ciudad Universitaria D.F. Circuito Exterior s/n Anexo al Jardín Botánico Exterior, México City 04510, Mexico; (P.I.A.-B.); (J.P.-R.)
- School of Engineering and Sciences, Centre of Bioengineering, Tecnologico de Monterrey, Queretaro 21620, Mexico
| | - Jonathan Puente-Rivera
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, 275, Ciudad Universitaria D.F. Circuito Exterior s/n Anexo al Jardín Botánico Exterior, México City 04510, Mexico; (P.I.A.-B.); (J.P.-R.)
| | - Rocío Cruz-Ortega
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, 275, Ciudad Universitaria D.F. Circuito Exterior s/n Anexo al Jardín Botánico Exterior, México City 04510, Mexico; (P.I.A.-B.); (J.P.-R.)
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47
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Královičová J, Borovská I, Pengelly R, Lee E, Abaffy P, Šindelka R, Grutzner F, Vořechovský I. Restriction of an intron size en route to endothermy. Nucleic Acids Res 2021; 49:2460-2487. [PMID: 33550394 PMCID: PMC7969005 DOI: 10.1093/nar/gkab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 11/15/2022] Open
Abstract
Ca2+-insensitive and -sensitive E1 subunits of the 2-oxoglutarate dehydrogenase complex (OGDHC) regulate tissue-specific NADH and ATP supply by mutually exclusive OGDH exons 4a and 4b. Here we show that their splicing is enforced by distant lariat branch points (dBPs) located near the 5' splice site of the intervening intron. dBPs restrict the intron length and prevent transposon insertions, which can introduce or eliminate dBP competitors. The size restriction was imposed by a single dominant dBP in anamniotes that expanded into a conserved constellation of four dBP adenines in amniotes. The amniote clusters exhibit taxon-specific usage of individual dBPs, reflecting accessibility of their extended motifs within a stable RNA hairpin rather than U2 snRNA:dBP base-pairing. The dBP expansion took place in early terrestrial species and was followed by a uridine enrichment of large downstream polypyrimidine tracts in mammals. The dBP-protected megatracts permit reciprocal regulation of exon 4a and 4b by uridine-binding proteins, including TIA-1/TIAR and PUF60, which promote U1 and U2 snRNP recruitment to the 5' splice site and BP, respectively, but do not significantly alter the relative dBP usage. We further show that codons for residues critically contributing to protein binding sites for Ca2+ and other divalent metals confer the exon inclusion order that mirrors the Irving-Williams affinity series, linking the evolution of auxiliary splicing motifs in exons to metallome constraints. Finally, we hypothesize that the dBP-driven selection for Ca2+-dependent ATP provision by E1 facilitated evolution of endothermy by optimizing the aerobic scope in target tissues.
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Affiliation(s)
- Jana Královičová
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben Pengelly
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
| | - Eunice Lee
- School of Biological Sciences, University of Adelaide, Adelaide 5005, SA, Australia
| | - Pavel Abaffy
- Czech Academy of Sciences, Institute of Biotechnology, 25250 Vestec, Czech Republic
| | - Radek Šindelka
- Czech Academy of Sciences, Institute of Biotechnology, 25250 Vestec, Czech Republic
| | - Frank Grutzner
- School of Biological Sciences, University of Adelaide, Adelaide 5005, SA, Australia
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
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Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:958-972. [PMID: 33631428 PMCID: PMC9402790 DOI: 10.1016/j.gpb.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/23/2019] [Accepted: 06/06/2019] [Indexed: 12/01/2022]
Abstract
Trace elements are required by all organisms, which are key components of many enzymes catalyzing important biological reactions. Many trace element-dependent proteins have been characterized; however, little is known about their occurrence in microbial communities in diverse environments, especially the global marine ecosystem. Moreover, the relationships between trace element utilization and different types of environmental stressors are unclear. In this study, we used metagenomic data from the Global Ocean Sampling expedition project to identify the biogeographic distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, cobalt, nickel, and selenium) in a variety of marine and non-marine aquatic samples. More than 56,000 metalloprotein and selenoprotein genes corresponding to nearly 100 families were predicted, becoming the largest dataset of marine metalloprotein and selenoprotein genes reported to date. In addition, samples with enriched or depleted metalloprotein/selenoprotein genes were identified, suggesting an active or inactive usage of these micronutrients in various sites. Further analysis of interactions among the elements showed significant correlations between some of them, especially those between nickel and selenium/copper. Finally, investigation of the relationships between environmental conditions and metalloprotein/selenoprotein families revealed that many environmental factors might contribute to the evolution of different metalloprotein and/or selenoprotein genes in the marine microbial world. Our data provide new insights into the utilization and biological roles of these trace elements in extant marine microbes, and might also be helpful for the understanding of how these organisms have adapted to their local environments.
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Yu J, Yang J, Seok C, Song WJ. Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes. Chem Sci 2021; 12:5091-5101. [PMID: 34168770 PMCID: PMC8179601 DOI: 10.1039/d0sc06823c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Directed evolution has provided us with great opportunities and prospects in the synthesis of tailor-made proteins. It, however, often requires at least mid to high throughput screening, necessitating more effective strategies for laboratory evolution. We herein demonstrate that protein symmetry can be a versatile criterion for searching for promising hotspots for the directed evolution of de novo oligomeric enzymes. The randomization of symmetry-related residues located at the rotational axes of artificial metallo-β-lactamase yields drastic effects on catalytic activities, whereas that of non-symmetry-related, yet, proximal residues to the active site results in negligible perturbations. Structural and biochemical analysis of the positive hits indicates that seemingly trivial mutations at symmetry-related spots yield significant alterations in overall structures, metal-coordination geometry, and chemical environments of active sites. Our work implicates that numerous artificially designed and natural oligomeric proteins might have evolutionary advantages of propagating beneficial mutations using their global symmetry. Symmetry-related residues located at the rotational axes can be promising hotspots for the evolution of de novo oligomeric enzymes even though they are distantly located from the active site pocket.![]()
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Affiliation(s)
- Jaeseung Yu
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Jinsol Yang
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Chaok Seok
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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50
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Furukawa Y. Good and Bad of Cu/Zn-Superoxide Dismutase Controlled by Metal Ions and Disulfide Bonds. CHEM LETT 2021. [DOI: 10.1246/cl.200770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yoshiaki Furukawa
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku, Kanagawa 223-8522, Japan
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