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Ikeda T, Nakasugi Y, Nakagawa M, Matsuura SI, Ikeda T, Ishida T, Funabashi H, Hirota R, Kuroda A. Discovery of long-chain polyamines embedded in the biosilica on the Bacillus cereus spore coat. J Biosci Bioeng 2024; 137:254-259. [PMID: 38342665 DOI: 10.1016/j.jbiosc.2024.01.012] [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: 11/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/13/2024]
Abstract
Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification has only recently begun to be studied. We previously reported that biosilicification occurs in the gram-positive, spore-forming bacterium Bacillus cereus, and that silica is intracellularly deposited on the spore coat as a protective coating against acids, although the underlying mechanism is not yet fully understood. In eukaryotic biosilicifying organisms, such as diatoms and siliceous sponges, several relevant biomolecules are embedded in biogenic silica (biosilica). These biomolecules include peptides, proteins, and long-chain polyamines. In this study, we isolated organic compounds embedded in B. cereus biosilica to investigate the biomolecules involved in the prokaryotic biosilicification process and identified long-chain polyamines with a chemical structure of H2N-(CH2)4-[NH-(CH2)3]n-NH2 (n: up to 55). Our results demonstrate the common presence of long-chain polyamines in different evolutionary lineages of biosilicifying organisms, i.e., diatoms, siliceous sponges, and B. cereus, suggesting a common mechanism underlying eukaryotic and prokaryotic biosilicification.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Yukihide Nakasugi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Miki Nakagawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Shun-Ichi Matsuura
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takuji Ikeda
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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2
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Nemoto M, Iwaki S, Moriya H, Monden Y, Tamura T, Inagaki K, Mayama S, Obuse K. Correction to: Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:157. [PMID: 33001289 DOI: 10.1007/s10126-020-09999-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Michiko Nemoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
| | - Sayako Iwaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenji Inagaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Shigeki Mayama
- Department of Biology, Tokyo Gakugei University, Tokyo, 184-8511, Japan
| | - Kiori Obuse
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
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3
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Abstract
Polyamine oxidases (PAOs) are characterized by a broad variability in catalytic properties and subcellular localization, and impact key cellular processes in diverse organisms. In the present study, a comprehensive phylogenetic analysis was performed to understand the evolution of PAOs across the three domains of life and particularly within eukaryotes. Phylogenetic trees show that PAO-like sequences of bacteria, archaea, and eukaryotes form three distinct clades, with the exception of a few procaryotes that probably acquired a PAO gene through horizontal transfer from a eukaryotic donor. Results strongly support a common origin for archaeal PAO-like proteins and eukaryotic PAOs, as well as a shared origin between PAOs and monoamine oxidases. Within eukaryotes, four main lineages were identified that likely originated from an ancestral eukaryotic PAO before the split of the main superphyla, followed by specific gene losses in each superphylum. Plant PAOs show the highest diversity within eukaryotes and belong to three distinct clades that underwent to multiple events of gene duplication and gene loss. Peptide deletion along the evolution of plant PAOs of Clade I accounted for further diversification of function and subcellular localization. This study provides a reference for future structure-function studies and emphasizes the importance of extending comparisons among PAO subfamilies across multiple eukaryotic superphyla.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
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4
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Strategies among phytoplankton in response to alleviation of nutrient stress in a subtropical gyre. ISME JOURNAL 2019; 13:2984-2997. [PMID: 31439897 DOI: 10.1038/s41396-019-0489-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/07/2019] [Accepted: 08/02/2019] [Indexed: 11/08/2022]
Abstract
Despite generally low primary productivity and diatom abundances in oligotrophic subtropical gyres, the North Atlantic Subtropical Gyre (NASG) exhibits significant diatom-driven carbon export on an annual basis. Subsurface pulses of nutrients likely fuel brief episodes of diatom growth, but the exact mechanisms utilized by diatoms in response to these nutrient injections remain understudied within near-natural settings. Here we simulated delivery of subsurface nutrients and compare the response among eukaryotic phytoplankton using a combination of physiological techniques and metatranscriptomics. We show that eukaryotic phytoplankton groups exhibit differing levels of transcriptional responsiveness and expression of orthologous genes in response to release from nutrient limitation. In particular, strategies for use of newly delivered nutrients are distinct among phytoplankton groups. Diatoms channel new nitrate to growth-related strategies while physiological measurements and gene expression patterns of other groups suggest alternative strategies. The gene expression patterns displayed here provide insights into the cellular mechanisms that underlie diatom subsistence during chronic nitrogen-depleted conditions and growth upon nutrient delivery that can enhance carbon export from the surface ocean.
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5
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Heal KR, Kellogg NA, Carlson LT, Lionheart RM, Ingalls AE. Metabolic Consequences of Cobalamin Scarcity in the Diatom Thalassiosira pseudonana as Revealed Through Metabolomics. Protist 2019; 170:328-348. [PMID: 31260945 DOI: 10.1016/j.protis.2019.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/17/2019] [Accepted: 05/19/2019] [Indexed: 02/07/2023]
Abstract
Diatoms perform an estimated 20% of global photosynthesis, form the base of the marine food web, and sequester carbon into the deep ocean through the biological pump. In some areas of the ocean, diatom growth is limited by the micronutrient cobalamin (vitamin B12), yet the biochemical ramifications of cobalamin limitation are not well understood. In a laboratory setting, we grew the diatom Thalassiosira pseudonana under replete and low cobalamin conditions to elucidate changes in metabolite pools. Using metabolomics, we show that the diatom experienced a metabolic cascade under cobalamin limitation that affected the central methionine cycle, transsulfuration pathway, and composition of osmolyte pools. In T. pseudonana, 5'-methylthioadenosine decreased under low cobalamin conditions, suggesting a disruption in the diatom's polyamine biosynthesis. Furthermore, two acylcarnitines accumulated under low cobalamin, suggesting the limited use of an adenosylcobalamin-dependent enzyme, methylmalonyl CoA mutase. Overall, these changes in metabolite pools yield insight into the metabolic consequences of cobalamin limitation in diatoms and suggest that cobalamin availability may have consequences for microbial interactions that are based on metabolite production by phytoplankton.
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Affiliation(s)
- Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Natalie A Kellogg
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Regina M Lionheart
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, USA.
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6
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Sekowska A, Ashida H, Danchin A. Revisiting the methionine salvage pathway and its paralogues. Microb Biotechnol 2019; 12:77-97. [PMID: 30306718 PMCID: PMC6302742 DOI: 10.1111/1751-7915.13324] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
Methionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet-like step that prevents methionine back degradation. Here, we describe the variation on this theme, developed across the tree of life. Oxygen appeared long after life had developed on Earth. The canonical MSP evolved from ancestors that used both predecessors of ribulose bisphosphate carboxylase oxygenase (RuBisCO) and methanethiol in intermediate steps. We document how these likely promiscuous pathways were also used to metabolize the omnipresent by-products of S-adenosylmethionine radical enzymes as well as the aromatic and isoprene skeleton of quinone electron acceptors.
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Affiliation(s)
- Agnieszka Sekowska
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
| | - Hiroki Ashida
- Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐SalpêtrièreParisFrance
- Institute of Synthetic BiologyShenzhen Institutes of Advanced StudiesShenzhenChina
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7
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Polyamines in Microalgae: Something Borrowed, Something New. Mar Drugs 2018; 17:md17010001. [PMID: 30577419 PMCID: PMC6356823 DOI: 10.3390/md17010001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023] Open
Abstract
Microalgae of different evolutionary origins are typically found in rivers, lakes, and oceans, providing more than 45% of global primary production. They provide not only a food source for animals, but also affect microbial ecosystems through symbioses with microorganisms or secretion of some metabolites. Derived from amino acids, polyamines are present in almost all types of organisms, where they play important roles in maintaining physiological functions or against stress. Microalgae can produce a variety of distinct polyamines, and the polyamine content is important to meet the physiological needs of microalgae and may also affect other species in the environment. In addition, some polyamines produced by microalgae have medical or nanotechnological applications. Previous studies on several types of microalgae have indicated that the putative polyamine metabolic pathways may be as complicated as the genomes of these organisms, which contain genes originating from plants, animals, and even bacteria. There are also several novel polyamine synthetic routes in microalgae. Understanding the nature of polyamines in microalgae will not only improve our knowledge of microalgal physiology and ecological function, but also provide valuable information for biotechnological applications.
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8
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Pawolski D, Heintze C, Mey I, Steinem C, Kröger N. Reconstituting the formation of hierarchically porous silica patterns using diatom biomolecules. J Struct Biol 2018; 204:64-74. [DOI: 10.1016/j.jsb.2018.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 11/15/2022]
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9
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Evolution of biosynthetic diversity. Biochem J 2017; 474:2277-2299. [DOI: 10.1042/bcj20160823] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 12/16/2022]
Abstract
Since the emergence of the last common ancestor from which all extant life evolved, the metabolite repertoire of cells has increased and diversified. Not only has the metabolite cosmos expanded, but the ways in which the same metabolites are made have diversified. Enzymes catalyzing the same reaction have evolved independently from different protein folds; the same protein fold can produce enzymes recognizing different substrates, and enzymes performing different chemistries. Genes encoding useful enzymes can be transferred between organisms and even between the major domains of life. Organisms that live in metabolite-rich environments sometimes lose the pathways that produce those same metabolites. Fusion of different protein domains results in enzymes with novel properties. This review will consider the major evolutionary mechanisms that generate biosynthetic diversity: gene duplication (and gene loss), horizontal and endosymbiotic gene transfer, and gene fusion. It will also discuss mechanisms that lead to convergence as well as divergence. To illustrate these mechanisms, one of the original metabolisms present in the last universal common ancestor will be employed: polyamine metabolism, which is essential for the growth and cell proliferation of archaea and eukaryotes, and many bacteria.
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10
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Biosynthesis of polyamines and polyamine-containing molecules. Biochem J 2016; 473:2315-29. [DOI: 10.1042/bcj20160185] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/22/2016] [Indexed: 12/16/2022]
Abstract
Polyamines are evolutionarily ancient polycations derived from amino acids and are pervasive in all domains of life. They are essential for cell growth and proliferation in eukaryotes and are essential, important or dispensable for growth in bacteria. Polyamines present a useful scaffold to attach other moieties to, and are often incorporated into specialized metabolism. Life has evolved multiple pathways to synthesize polyamines, and structural variants of polyamines have evolved in bacteria, archaea and eukaryotes. Among the complex biosynthetic diversity, patterns of evolutionary reiteration can be distinguished, revealing evolutionary recycling of particular protein folds and enzyme chassis. The same enzyme activities have evolved from multiple protein folds, suggesting an inevitability of evolution of polyamine biosynthesis. This review discusses the different biosynthetic strategies used in life to produce diamines, triamines, tetra-amines and branched and long-chain polyamines. It also discusses the enzymes that incorporate polyamines into specialized metabolites and attempts to place polyamine biosynthesis in an evolutionary context.
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11
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Abstract
Polyamines are primordial polycations found in most cells and perform different functions in different organisms. Although polyamines are mainly known for their essential roles in cell growth and proliferation, their functions range from a critical role in cellular translation in eukaryotes and archaea, to bacterial biofilm formation and specialized roles in natural product biosynthesis. At first glance, the diversity of polyamine structures in different organisms appears chaotic; however, biosynthetic flexibility and evolutionary and ecological processes largely explain this heterogeneity. In this review, I discuss the biosynthetic, evolutionary, and physiological processes that constrain or expand polyamine structural and functional diversity.
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Affiliation(s)
- Anthony J Michael
- From the Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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12
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A role for diatom-like silicon transporters in calcifying coccolithophores. Nat Commun 2016; 7:10543. [PMID: 26842659 PMCID: PMC4742977 DOI: 10.1038/ncomms10543] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/23/2015] [Indexed: 12/16/2022] Open
Abstract
Biomineralization by marine phytoplankton, such as the silicifying diatoms and calcifying coccolithophores, plays an important role in carbon and nutrient cycling in the oceans. Silicification and calcification are distinct cellular processes with no known common mechanisms. It is thought that coccolithophores are able to outcompete diatoms in Si-depleted waters, which can contribute to the formation of coccolithophore blooms. Here we show that an expanded family of diatom-like silicon transporters (SITs) are present in both silicifying and calcifying haptophyte phytoplankton, including some globally important coccolithophores. Si is required for calcification in these coccolithophores, indicating that Si uptake contributes to the very different forms of biomineralization in diatoms and coccolithophores. Significantly, SITs and the requirement for Si are absent from highly abundant bloom-forming coccolithophores, such as Emiliania huxleyi. These very different requirements for Si in coccolithophores are likely to have major influence on their competitive interactions with diatoms and other siliceous phytoplankton.
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13
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Low-Molecular-Weight Metabolites from Diatoms: Structures, Biological Roles and Biosynthesis. Mar Drugs 2015; 13:3672-709. [PMID: 26065408 PMCID: PMC4483651 DOI: 10.3390/md13063672] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/05/2015] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
Diatoms are abundant and important biological components of the marine environment that biosynthesize diverse natural products. These microalgae are rich in various lipids, carotenoids, sterols and isoprenoids, some of them containing toxins and other metabolites. Several groups of diatom natural products have attracted great interest due to their potential practical application as energy sources (biofuel), valuable food constituents, and prospective materials for nanotechnology. In addition, hydrocarbons, which are used in climate reconstruction, polyamines which participate in biomineralization, new apoptotic agents against tumor cells, attractants and deterrents that regulate the biochemical communications between marine species in seawaters have also been isolated from diatoms. However, chemical studies on these microalgae are complicated by difficulties, connected with obtaining their biomass, and the influence of nutrients and contaminators in their environment as well as by seasonal and climatic factors on the biosynthesis of the corresponding natural products. Overall, the number of chemically studied diatoms is lower than that of other algae, but further studies, particularly those connected with improvements in the isolation and structure elucidation technique as well as the genomics of diatoms, promise both to increase the number of studied species with isolated biologically active natural products and to provide a clearer perception of their biosynthesis.
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14
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Li B, Kim SH, Zhang Y, Hanfrey CC, Elliott KA, Ealick SE, Michael AJ. Different polyamine pathways from bacteria have replaced eukaryotic spermidine biosynthesis in ciliates Tetrahymena thermophila and Paramecium tetaurelia. Mol Microbiol 2015; 97:791-807. [PMID: 25994085 DOI: 10.1111/mmi.13066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 11/28/2022]
Abstract
The polyamine spermidine is absolutely required for growth and cell proliferation in eukaryotes, due to its role in post-translational modification of essential translation elongation factor eIF5A, mediated by deoxyhypusine synthase. We have found that free-living ciliates Tetrahymena and Paramecium lost the eukaryotic genes encoding spermidine biosynthesis: S-adenosylmethionine decarboxylase (AdoMetDC) and spermidine synthase (SpdSyn). In Tetrahymena, they were replaced by a gene encoding a fusion protein of bacterial AdoMetDC and SpdSyn, present as three copies. In Paramecium, a bacterial homospermidine synthase replaced the eukaryotic genes. Individual AdoMetDC-SpdSyn fusion protein paralogues from Tetrahymena exhibit undetectable AdoMetDC activity; however, when two paralogous fusion proteins are mixed, AdoMetDC activity is restored and spermidine is synthesized. Structural modelling indicates a functional active site is reconstituted by sharing critical residues from two defective protomers across the heteromer interface. Paramecium was found to accumulate homospermidine, suggesting it replaces spermidine for growth. To test this concept, a budding yeast spermidine auxotrophic strain was found to grow almost normally with homospermidine instead of spermidine. Biosynthesis of spermidine analogue aminopropylcadaverine, but not exogenously provided norspermidine, correlated with some growth. Finally, we found that diverse single-celled eukaryotic parasites and multicellular metazoan Schistosoma worms have lost the spermidine biosynthetic pathway but retain deoxyhypusine synthase.
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Affiliation(s)
- Bin Li
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sok Ho Kim
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Anthony J Michael
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
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15
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Ahou A, Martignago D, Alabdallah O, Tavazza R, Stano P, Macone A, Pivato M, Masi A, Rambla JL, Vera-Sirera F, Angelini R, Federico R, Tavladoraki P. A plant spermine oxidase/dehydrogenase regulated by the proteasome and polyamines. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1585-603. [PMID: 24550437 DOI: 10.1093/jxb/eru016] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyamine oxidases (PAOs) are flavin-dependent enzymes involved in polyamine catabolism. In Arabidopsis five PAO genes (AtPAO1-AtPAO5) have been identified which present some common characteristics, but also important differences in primary structure, substrate specificity, subcellular localization, and tissue-specific expression pattern, differences which may suggest distinct physiological roles. In the present work, AtPAO5, the only so far uncharacterized AtPAO which is specifically expressed in the vascular system, was partially purified from 35S::AtPAO5-6His Arabidopsis transgenic plants and biochemically characterized. Data presented here allow AtPAO5 to be classified as a spermine dehydrogenase. It is also shown that AtPAO5 oxidizes the polyamines spermine, thermospermine, and N(1)-acetylspermine, the latter being the best in vitro substrate of the recombinant enzyme. AtPAO5 also oxidizes these polyamines in vivo, as was evidenced by analysis of polyamine levels in the 35S::AtPAO5-6His Arabidopsis transgenic plants, as well as in a loss-of-function atpao5 mutant. Furthermore, subcellular localization studies indicate that AtPAO5 is a cytosolic protein undergoing proteasomal control. Positive regulation of AtPAO5 expression by polyamines at the transcriptional and post-transcriptional level is also shown. These data provide new insights into the catalytic properties of the PAO gene family and the complex regulatory network controlling polyamine metabolism.
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Affiliation(s)
- Abdellah Ahou
- Department of Science, University 'ROMA TRE', Rome, Italy
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16
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Bridoux MC, Ingalls AE. Diatom microfossils from cretaceous and eocene sediments contain native silica precipitating long-chain polyamines. GEOBIOLOGY 2013; 11:215-23. [PMID: 23418943 DOI: 10.1111/gbi.12028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 01/04/2013] [Indexed: 05/12/2023]
Abstract
Organic molecules from known biological sources (biomarkers) that are preserved over geological time are critical tools in the study of past conditions and events on earth. Polar molecules are typically recycled rapidly in marine environments and do not survive burial within aquatic sediments in unambiguously recognizable form. As such, geological biomarkers are formed almost exclusively from precursor biomolecules that have been altered, limiting their utility as paleoproxies. Here, we report that nitrogen-rich aliphatic long-chain polyamines (LCPAs), biosynthesized by diatoms in species-specific assemblages for the precipitation of nanopatterned siliceous cell walls (frustules), are preserved unaltered in the oldest available diatom fossils dating to the Lower Cretaceous (early Albian, 115-110 Ma). We further show that the cumulative LCPA pool accounts for 60% of the total C and 80% of the total N preserved in the Cretaceous age sediments. We suggest that silica glass formation by diatoms constitutes an important preservation mechanism for source-specific, polar biomolecules, protecting them indefinitely by encapsulation within the silicified frustule. LCPAs are a unique, source-specific carbon and nitrogen archive of diatom biomass, offering a promising tool for reconstruction of global cycles of carbon and nitrogen over geological timescales.
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Affiliation(s)
- M C Bridoux
- School of Oceanography, University of Washington, Seattle, WA, USA.
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17
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Marron AO, Alston MJ, Heavens D, Akam M, Caccamo M, Holland PWH, Walker G. A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates. Proc Biol Sci 2013; 280:20122543. [PMID: 23407828 PMCID: PMC3574361 DOI: 10.1098/rspb.2012.2543] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/17/2013] [Indexed: 11/12/2022] Open
Abstract
Biosilicification is widespread across the eukaryotes and requires concentration of silicon in intracellular vesicles. Knowledge of the molecular mechanisms underlying this process remains limited, with unrelated silicon-transporting proteins found in the eukaryotic clades previously studied. Here, we report the identification of silicon transporter (SIT)-type genes from the siliceous loricate choanoflagellates Stephanoeca diplocostata and Diaphanoeca grandis. Until now, the SIT gene family has been identified only in diatoms and other siliceous stramenopiles, which are distantly related to choanoflagellates among the eukaryotes. This is the first evidence of similarity between SITs from different eukaryotic supergroups. Phylogenetic analysis indicates that choanoflagellate and stramenopile SITs form distinct monophyletic groups. The absence of putative SIT genes in any other eukaryotic groups, including non-siliceous choanoflagellates, leads us to propose that SIT genes underwent a lateral gene transfer event between stramenopiles and loricate choanoflagellates. We suggest that the incorporation of a foreign SIT gene into the stramenopile or choanoflagellate genome resulted in a major metabolic change: the acquisition of biomineralized silica structures. This hypothesis implies that biosilicification has evolved multiple times independently in the eukaryotes, and paves the way for a better understanding of the biochemical basis of silicon transport through identification of conserved sequence motifs.
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Affiliation(s)
- Alan O Marron
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
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Bertrand EM, Allen AE. Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton. Front Microbiol 2012; 3:375. [PMID: 23091473 PMCID: PMC3476827 DOI: 10.3389/fmicb.2012.00375] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/02/2012] [Indexed: 01/22/2023] Open
Abstract
While nitrogen availability is known to limit primary production in large parts of the ocean, vitamin starvation amongst eukaryotic phytoplankton is becoming increasingly recognized as an oceanographically relevant phenomenon. Cobalamin (B(12)) and thiamine (B(1)) auxotrophy are widespread throughout eukaryotic phytoplankton, with over 50% of cultured isolates requiring B(12) and 20% requiring B(1). The frequency of vitamin auxotrophy in harmful algal bloom species is even higher. Instances of colimitation between nitrogen and B vitamins have been observed in marine environments, and interactions between these nutrients have been shown to impact phytoplankton species composition. This review surveys available data, including relevant gene expression patterns, to evaluate the potential for interactive effects of nitrogen and vitamin B(12) and B(1) starvation in eukaryotic phytoplankton. B(12) plays essential roles in amino acid and one-carbon metabolism, while B(1) is important for primary carbohydrate and amino acid metabolism and likely useful as an anti-oxidant. Here we will focus on three potential metabolic interconnections between vitamin, nitrogen, and sulfur metabolism that may have ramifications for the role of vitamin and nitrogen scarcities in driving ocean productivity and species composition. These include: (1) B(12), B(1), and N starvation impacts on osmolyte and antioxidant production, (2) B(12) and B(1) starvation impacts on polyamine biosynthesis, and (3) influence of B(12) and B(1) starvation on the diatom urea cycle and amino acid recycling through impacts on the citric acid cycle. We evaluate evidence for these interconnections and identify oceanographic contexts in which each may impact rates of primary production and phytoplankton community composition. Major implications include that B(12) and B(1) deprivation may impair the ability of phytoplankton to recover from nitrogen starvation and that changes in vitamin and nitrogen availability may synergistically impact harmful algal bloom formation.
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Affiliation(s)
- Erin M Bertrand
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute San Diego, CA, USA
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Takano A, Kakehi JI, Takahashi T. Thermospermine is not a minor polyamine in the plant kingdom. PLANT & CELL PHYSIOLOGY 2012; 53:606-16. [PMID: 22366038 DOI: 10.1093/pcp/pcs019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Thermospermine is a structural isomer of spermine, which is one of the polyamines studied extensively in the past, and is produced from spermidine by the action of thermospermine synthase encoded by a gene named ACAULIS5 (ACL5) in plants. According to recent genome sequencing analyses, ACL5-like genes are widely distributed throughout the plant kingdom. In Arabidopsis, ACL5 is expressed specifically during xylem formation from procambial cells to differentiating xylem vessels. Loss-of-function mutants of ACL5 display overproliferation of xylem vessels along with severe dwarfism, suggesting that thermospermine plays a role in the repression of xylem differentiation. Studies of suppressor mutants of acl5 that recover the wild-type phenotype in the absence of thermospermine suggest that thermospermine acts on the translation of specific mRNAs containing upstream open reading frames (uORFs). Thermospermine is a novel type of plant growth regulator and may also serve in the control of wood biomass production.
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Affiliation(s)
- Ayaka Takano
- Division of Bioscience, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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Otzen D. The role of proteins in biosilicification. SCIENTIFICA 2012; 2012:867562. [PMID: 24278750 PMCID: PMC3820600 DOI: 10.6064/2012/867562] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/24/2012] [Indexed: 05/19/2023]
Abstract
Although the use of silicon dioxide (silica) as a constituent of living organisms is mainly restricted to diatoms and sponges, the ways in which this process is controlled by nature continue to inspire and fascinate. Both diatoms and sponges carry out biosilificiation using an organic matrix but they adopt very different strategies. Diatoms use small and heavily modified peptides called silaffins, where the most characteristic feature is a modulation of charge by attaching long chain polyamines (LCPAs) to lysine groups. Free LCPAs can also cooperate with silaffins. Sponges use the enzyme silicatein which is homologous to the cysteine protease cathepsin. Both classes of proteins form higher-order structures which act both as structural templates and mechanistic catalysts for the polycondensation reaction. In both cases, additional proteins are continuously being discovered which modulate the process further. This paper concentrates on the role of these proteins in the biosilification process as well as in various applications, highlighting areas where focus on specific protein properties may provide further insight. The field of biosilification is a crossroads of different disciplines, where insight into the energetics and mechanisms of molecular self-assembly combine with fundamental biology, complex multicomponent colloidal systems, and an impressive array of potential technological applications.
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Affiliation(s)
- Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Center for Insoluble Protein Structures (inSPIN), and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- *Daniel Otzen:
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