1
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Wang P, Lu B, Chai X. The adaptive regulation mechanism of Anammox granule sludge under calcium ions stress: Defense modes transformation. WATER RESEARCH 2024; 263:122093. [PMID: 39096809 DOI: 10.1016/j.watres.2024.122093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/31/2024] [Accepted: 07/12/2024] [Indexed: 08/05/2024]
Abstract
Anammox granular sludge (AnGS) has received considerable attention due to its low carbon footprint (less aeration energy and carbon source consumption) and high biomass density, but growth rate and stability are still the bottlenecks of AnGS process. Calcium ion (Ca2+) is essential for the growth of anaerobic ammonium oxidation bacteria (AnAOB) and plays an important role in the formation and stability of AnGS. Response of AnGS to Ca2+ under different concentrations was comprehensively investigated by multi-spectral and metagenomics analysis in four aspects: nitrogen removal performance, surface morphology, extracellular polymeric substance (EPS) composition and characterization, and microbial community. The nitrogen removal efficiency was significantly enhanced at appropriate Ca2+ concentration (2 mmol/L), owning to the more favorable morphology and functional microbial composition of AnGS. However, the nitrogen removal performance of AnGS declined with the Ca2+concentration increased from 2 to 8 mmol/L, due to the negative effects of excess Ca2+on EPS, mass transfer efficiency, and functional microorganisms. Meanwhile, an unexpected slight "rebound" of nitrogen removal efficiency was observed at Ca2+ = 6 mmol/L and attributed to the defense mode transformation of AnGS (from "ion stabilization" to "precipitate shield" modes) against excess Ca2+ stress. Based on the findings, the response mechanism of AnGS to Ca2+ with different concentrations was established. Our results enhanced the understanding of the interaction between AnGS and Ca2+, which may be valuable for filling the theoretical gap in enhancing the granulation and stability of AnGS and providing a reference for the practical operation of the AnGS process.
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Affiliation(s)
- Pengcheng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Bin Lu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiaoli Chai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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2
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Xia F, Liu Z, Zhang Y, Li Q, Zhao M, He H, Bao Q, Chen B, He Q, Lai C, He X, Ma Z, Zhou Y. Calcium regulates the interactions between dissolved organic matter and planktonic bacteria in Erhai Lake, Yunnan Province, China. WATER RESEARCH 2024; 261:121982. [PMID: 38936236 DOI: 10.1016/j.watres.2024.121982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
In recent years, the global carbon cycle has garnered significant research attention. However, details of the intricate relationship between planktonic bacteria, hydrochemistry, and dissolved organic matter (DOM) in inland waters remain unclear, especially their effects on lake carbon sequestration. In this study, we analyzed 16S rRNA, chromophoric dissolved organic matter (CDOM), and inorganic nutrients in Erhai Lake, Yunnan Province, China. The results revealed that allochthonous DOM (C3) significantly regulated the microbial community, and that autochthonous DOM, generated via microbial mineralization (C2), was not preferred as a food source by lake bacteria, and neither was allochthonous DOM after microbial mineralization (C4). Specifically, the correlation between the fluorescence index and functional genes (FAPRPTAX) showed that the degree of utilization of DOM was a critical factor in regulating planktonic bacteria associated with the carbon cycle. Further examination of the correlation between environmental factors and planktonic bacteria revealed that Ca2+ had a regulatory influence on the community structure of planktonic bacteria, particularly those linked to the carbon cycle. Consequently, the utilization strategy of DOM by planktonic bacteria was also determined by elevated Ca2+ levels. This in turn influenced the development of specific recalcitrant autochthonous DOM within the high Ca2+ environment of Erhai Lake. These findings are significant for the exploration of the stability of DOM within karst aquatic ecosystems, offering a new perspective for the investigation of terrestrial carbon sinks.
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Affiliation(s)
- Fan Xia
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Zaihua Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
| | - Yunling Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Min Zhao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Haibo He
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Qian Bao
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610068, China
| | - Bo Chen
- Guizhou University of Finance and Economics, Guiyang 550025, China
| | - Qiufang He
- Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing 400700, China; Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Chaowei Lai
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Xuejun He
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Zhen Ma
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, CAS, Guiyang 550081, China
| | - Yongqiang Zhou
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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3
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Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. Annu Rev Biophys 2024; 53:487-510. [PMID: 38382113 DOI: 10.1146/annurev-biophys-030822-032215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.
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Affiliation(s)
- Wei-Chang Lo
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | | | - Teuta Pilizota
- School of Biological Sciences, Centre for Engineering Biology, University of Edinburgh, Edinburgh, United Kingdom;
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4
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Ahsan N, Kataya ARA, Rao RSP, Swatek KN, Wilson RS, Meyer LJ, Tovar-Mendez A, Stevenson S, Maszkowska J, Dobrowolska G, Yao Q, Xu D, Thelen JJ. Decoding Arabidopsis thaliana CPK/SnRK Superfamily Kinase Client Signaling Networks Using Peptide Library and Mass Spectrometry. PLANTS (BASEL, SWITZERLAND) 2024; 13:1481. [PMID: 38891291 PMCID: PMC11174488 DOI: 10.3390/plants13111481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/08/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Members of the calcium-dependent protein kinase (CDPK/CPK) and SNF-related protein kinase (SnRK) superfamilies are commonly found in plants and some protists. Our knowledge of client specificity of the members of this superfamily is fragmentary. As this family is represented by over 30 members in Arabidopsis thaliana, the identification of kinase-specific and overlapping client relationships is crucial to our understanding the nuances of this large family of kinases as directed towards signal transduction pathways. Herein, we used the kinase client (KiC) assay-a relative, quantitative, high-throughput mass spectrometry-based in vitro phosphorylation assay-to identify and characterize potential CPK/SnRK targets of Arabidopsis. Eight CPKs (1, 3, 6, 8, 17, 24, 28, and 32), four SnRKs (subclass 1 and 2), and PPCK1 and PPCK2 were screened against a synthetic peptide library that contains 2095 peptides and 2661 known phosphorylation sites. A total of 625 in vitro phosphorylation sites corresponding to 203 non-redundant proteins were identified. The most promiscuous kinase, CPK17, had 105 candidate target proteins, many of which had already been discovered. Sequence analysis of the identified phosphopeptides revealed four motifs: LxRxxS, RxxSxxR, RxxS, and LxxxxS, that were significantly enriched among CPK/SnRK clients. The results provide insight into both CPK- and SnRK-specific and overlapping signaling network architectures and recapitulate many known in vivo relationships validating this large-scale approach towards discovering kinase targets.
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Affiliation(s)
- Nagib Ahsan
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Chemistry and Biochemistry, Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, OK 73019, USA
| | - Amr R. A. Kataya
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - R. Shyama Prasad Rao
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Center for Bioinformatics, NITTE Deemed to be University, Mangaluru 575018, India
| | - Kirby N. Swatek
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rashaun S. Wilson
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Arvinas, Inc., New Haven, CT 06511, USA
| | - Louis J. Meyer
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Bayer Crop Science, St. Louis, MO 63141, USA
| | - Alejandro Tovar-Mendez
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Elemental Enzymes, St. Louis, MO 63132, USA
| | - Severin Stevenson
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Justyna Maszkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland (G.D.)
| | - Grazyna Dobrowolska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland (G.D.)
| | - Qiuming Yao
- Department of Electrical Engineering & Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Electrical Engineering & Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jay J. Thelen
- Division of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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Chen S, Jin Y, Yang N, Wei L, Xu D, Xu X. Improving microbial production of value-added products through the intervention of magnetic fields. BIORESOURCE TECHNOLOGY 2024; 393:130087. [PMID: 38042431 DOI: 10.1016/j.biortech.2023.130087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/17/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
The magnetic field application is emerging as an auxiliary physical strategy to facilitate rapid biomass accumulation and intracellular production of compounds. However, the underlying mechanisms and principles governing the application of magnetic fields for microbial growth and biotransformation are not yet fully understood. Therefore, a better understanding of interdisciplinary technologies integration, expanded magnetic field application, and scaled-up industrial implementation is crucial. In this review, the magnetic field characteristics, magnetic field-assisted fermentation devices, and the working mechanism of magnetic field have been reviewed comprehensively from both physical and microbiological perspectives. The review suggests that magnetic fields affect the biochemical processes in microorganisms by mediating nutrient transport across membranes, electron transfer during photosynthesis and respiration, enzyme activity and gene expression. Moreover, the recent advances in magnetic field application for microbial fermentation and conversion in biochemical, food and agricultural fields have been summarized.
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Affiliation(s)
- Sirui Chen
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China
| | - Yamei Jin
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China.
| | - Na Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China
| | - Liwen Wei
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China
| | - Dan Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China
| | - Xueming Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, PR China
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6
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Gorniak L, Bechwar J, Westermann M, Steiniger F, Wegner CE. Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph. Microbiol Spectr 2023; 11:e0086723. [PMID: 37909735 PMCID: PMC10848612 DOI: 10.1128/spectrum.00867-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Since its discovery, Ln-dependent metabolism in bacteria attracted a lot of attention due to its bio-metallurgical application potential regarding Ln recycling and circular economy. The physiological role of Ln is mostly studied dependent on presence and absence. Comparisons of how different (utilizable) Ln affect metabolism have rarely been done. We noticed unexpectedly pronounced changes in gene expression caused by different Ln supplementation. Our research suggests that strain RH AL1 distinguishes different Ln elements and that the effect of Ln reaches into many aspects of metabolism, for instance, chemotaxis, motility, and polyhydroxyalkanoate metabolism. Our findings regarding Ln accumulation suggest a distinction between individual Ln elements and provide insights relating to intracellular Ln homeostasis. Understanding comprehensively how microbes distinguish and handle different Ln elements is key for turning knowledge into application regarding Ln-centered biometallurgy.
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Affiliation(s)
- Linda Gorniak
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | - Julia Bechwar
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | | | - Frank Steiniger
- Electron Microscopy Center, Jena University Hospital, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
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7
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Agaras BC, Grossi CEM, Ulloa RM. Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits. PLANTS (BASEL, SWITZERLAND) 2023; 12:3398. [PMID: 37836138 PMCID: PMC10574481 DOI: 10.3390/plants12193398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
The role of Calcium ions (Ca2+) is extensively documented and comprehensively understood in eukaryotic organisms. Nevertheless, emerging insights, primarily derived from studies on human pathogenic bacteria, suggest that this ion also plays a pivotal role in prokaryotes. In this review, our primary focus will be on unraveling the intricate Ca2+ toolkit within prokaryotic organisms, with particular emphasis on its implications for plant growth-promoting rhizobacteria (PGPR). We undertook an in silico exploration to pinpoint and identify some of the proteins described in the existing literature, including prokaryotic Ca2+ channels, pumps, and exchangers that are responsible for regulating intracellular Calcium concentration ([Ca2+]i), along with the Calcium-binding proteins (CaBPs) that play a pivotal role in sensing and transducing this essential cation. These investigations were conducted in four distinct PGPR strains: Pseudomonas chlororaphis subsp. aurantiaca SMMP3, P. donghuensis SVBP6, Pseudomonas sp. BP01, and Methylobacterium sp. 2A, which have been isolated and characterized within our research laboratories. We also present preliminary experimental data to evaluate the influence of exogenous Ca2+ concentrations ([Ca2+]ex) on the growth dynamics of these strains.
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Affiliation(s)
- Betina Cecilia Agaras
- Laboratory of Physiology and Genetics of Plant Probiotic Bacteria (LFGBBP), Centre of Biochemistry and Microbiology of Soils, National University of Quilmes, Bernal B1876BXD, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
| | - Cecilia Eugenia María Grossi
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
| | - Rita María Ulloa
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina;
- Laboratory of Plant Signal Transduction, Institute of Genetic Engineering and Molecular Biology (INGEBI), National Scientific and Technical Research Council (CONICET), Buenos Aires C1425FQB, Argentina
- Biochemistry Department, Faculty of Exact and Natural Sciences, University of Buenos Aires (FCEN-UBA), Buenos Aires C1428EGA, Argentina
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8
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Ryder S, Pedigo J, Ojennus DD. Elucidating the Role of a Calcium-Binding Loop in an x-Prolyl Aminodipeptidase from Lb. helveticus. ACS OMEGA 2023; 8:35410-35416. [PMID: 37779945 PMCID: PMC10536834 DOI: 10.1021/acsomega.3c05639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Prolyl aminodipeptidase (PepX) is an α/β hydrolase that cleaves at penultimate N-terminal prolyl peptide bonds. The crystal structure of PepX from Lactobacillus helveticus exhibits a calcium-binding loop within the catalytic domain. The calcium-binding sequence of xDxDxDGxxD within this loop is highly conserved in PepX proteins among lactic acid bacteria, but its purpose remains unknown. Enzyme activity is not significantly affected in the presence of the metal chelator ethylenediaminetetraacetic acid (EDTA), nor in the presence of excess calcium ions. To eliminate calcium binding, D196A and D194A/D196A mutations were constructed within the conserved calcium-binding sequence motif. Enzyme activity and stability of the D196A mutant were comparable to the wild-type enzyme by colorimetric kinetic assays and protein thermal shift assays. However, the D194A/D196A mutant was inactive though it retained native-like structure and thermal stability, contradicting the EDTA and calcium titration results. This suggests calcium binding to PepX may be essential for activity.
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Affiliation(s)
- Stephanie Ryder
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
| | | | - Deanna Dahlke Ojennus
- Department of Chemistry, Whitworth
University, 300 W. Hawthorne Rd., Spokane, Washington 99251, United States
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9
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The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica. Microorganisms 2022; 11:microorganisms11010027. [PMID: 36677319 PMCID: PMC9862903 DOI: 10.3390/microorganisms11010027] [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] [Received: 11/24/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl2 L-1. When grown at a lower concentration of calcium (2 mg CaCl2 L-1) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl2 L-1 to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species.
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Cuéllar-Cruz M, Islas SR, Ramírez-Ramírez N, Pedraza-Reyes M, Moreno A. Protection of the DNA from Selected Species of Five Kingdoms in Nature by Ba(II), Sr(II), and Ca(II) Silica-Carbonates: Implications about Biogenicity and Evolving from Prebiotic Chemistry to Biological Chemistry. ACS OMEGA 2022; 7:37410-37426. [PMID: 36312347 PMCID: PMC9609056 DOI: 10.1021/acsomega.2c04170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The origin of life on Earth is associated with the Precambrian era, in which the existence of a large diversity of microbial fossils has been demonstrated. Notwithstanding, despite existing evidence of the emergence of life many unsolved questions remain. The first question could be as follows: Which was the inorganic structure that allowed isolation and conservation of the first biomolecules in the existing reduced conditions of the primigenial era? Minerals have been postulated as the ones in charge of protecting theses biomolecules against the external environment. There are calcium, barium, or strontium silica-carbonates, called biomorphs, which we propose as being one of the first inorganic structures in which biomolecules were protected from the external medium. Biomorphs are structures with different biological morphologies that are not formed by cells, but by nanocrystals; some of their morphologies resemble the microfossils found in Precambrian cherts. Even though biomorphs are unknown structures in the geological registry, their similarity with some biological forms, including some Apex fossils, could suggest them as the first "inorganic scaffold" where the first biomolecules became concentrated, conserved, aligned, and duplicated to give rise to the pioneering cell. However, it has not been documented whether biomorphs could have been the primary structures that conserved biomolecules in the Precambrian era. To attain a better understanding on whether biomorphs could have been the inorganic scaffold that existed in the primigenial Earth, the aim of this contribution is to synthesize calcium, barium, and strontium biomorphs in the presence of genomic DNA from organisms of the five kingdoms in conditions emulating the atmosphere of the Precambrian era and that CO2 concentration in conditions emulating current atmospheric conditions. Our results showed, for the first time, the formation of the kerogen signal, which is a marker of biogenicity in fossils, in the biomorphs grown in the presence of DNA. We also found the DNA to be internalized into the structure of biomorphs.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta,
C.P. 36050, Guanajuato, Mexico
| | - Selene R. Islas
- Instituto
de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, México City, 04510 Mexico
| | - Norma Ramírez-Ramírez
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta,
C.P. 36050, Guanajuato, Mexico
| | - Mario Pedraza-Reyes
- Departamento
de Biología, División de Ciencias Naturales y Exactas,
Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta,
C.P. 36050, Guanajuato, Mexico
| | - Abel Moreno
- Instituto
de Química, Universidad Nacional
Autónoma de México, Av. Universidad 3000, Ciudad Universitaria, México City 04510. Mexico
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11
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Responses of the Soil Microbial Community to Salinity Stress in Maize Fields. BIOLOGY 2021; 10:biology10111114. [PMID: 34827107 PMCID: PMC8614889 DOI: 10.3390/biology10111114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 01/13/2023]
Abstract
To investigate the diversity and structure of soil bacterial and fungal communities in saline soils, soil samples with three increasing salinity levels (S1, S2 and S3) were collected from a maize field in Yanqi, Xinjiang Province, China. The results showed that the K+, Na+, Ca2+ and Mg2+ values in the bulk soil were higher than those in the rhizosphere soil, with significant differences in S2 and S3 (p < 0.05). The enzyme activities of alkaline phosphatase (ALP), invertase, urease and catalase (CAT) were lower in the bulk soil than those in the rhizosphere. Principal coordinate analysis (PCoA) demonstrated that the soil microbial community structure exhibited significant differences between different salinized soils (p < 0.001). Data implied that the fungi were more susceptible to salinity stress than the bacteria based on the Shannon and Chao1 indexes. Mantel tests identified Ca2+, available phosphorus (AP), saturated electrical conductivity (ECe) and available kalium (AK) as the dominant environmental factors correlated with bacterial community structures (p < 0.001); and AP, urease, Ca2+ and ECe as the dominant factors correlated with fungal community structures (p < 0.001). The relative abundances of Firmicutes and Bacteroidetes showed positive correlations with the salinity gradient. Our findings regarding the bacteria having positive correlations with the level of salinization might be a useful biological indicator of microorganisms in saline soils.
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12
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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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13
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Meng Q, Tian X, Jiang B, Zhou L, Chen J, Zhang T. Characterization and enhanced extracellular overexpression of a new salt-activated alginate lyase. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5154-5162. [PMID: 33608926 DOI: 10.1002/jsfa.11161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/11/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Alginate lyases (EC 4.4.2.3/4.4.2.11) have been applied to produce alginate oligosaccharides, which have physiological advantages such as prebiotic and antidiabetic effects, and are of benefit in the food and pharmaceutical industries. Extracellular production of recombinant proteins in Escherichia coli presents advantages including simplified downstream processing and high productivity; however, the presence of certain signal peptides does not always ensure successful secretion, which make the extracellular production of alginate lyase in E. coli rarely reported but of great significance. RESULTS A PL7 family alginate lyase, Aly01, with its native signal peptide from Vibrio natriegens SK42.001, was identified, characterized, and extracellularly expressed in E. coli. The enzyme specifically released trisaccharide from alginate and was strictly NaCl activated. Green fluorescent protein (GFP) was fused with the Aly01 signal peptide and successfully secreted in E. coli to expand the feasibility of using this signal peptide to produce other heterologous proteins extracellularly. Through a synergistic strategy of utilizing Terrific Broth (TB) medium supplemented with 120 mmol L-1 glycine and 10 mmol L-1 calcium, the lag phase of protein secretion was reduced to 3 h from 12 h; meanwhile calcium remedied glycine-related cell growth impairment, leading to further enhancement of overall enzyme productivity, reaching a maximum of 4.55 U mL-1 . CONCLUSION A new salt-activated alginate lyase, Aly01, was identified and characterized. E. coli employed its signal peptide and extracellularly expressed both Aly01 and a GFP, which indicated the signal peptide of Aly01 could be a powerful tool for extracellular production of other heterologous proteins in E. coli. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Qing Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xinyu Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Licheng Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jingjing Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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14
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Liu X, Zarfel G, van der Weijden R, Loiskandl W, Bitschnau B, Dinkla IJT, Fuchs EC, Paulitsch-Fuchs AH. Density-dependent microbial calcium carbonate precipitation by drinking water bacteria via amino acid metabolism and biosorption. WATER RESEARCH 2021; 202:117444. [PMID: 34314923 DOI: 10.1016/j.watres.2021.117444] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Drinking water plumbing systems appear to be a unique environment for microorganisms as they contain few nutrients but a high mineral concentration. Interactions between mineral content and bacteria, such as microbial calcium carbonate precipitation (MCP) however, has not yet attracted too much attention in drinking water sector. This study aims to carefully examine MCP behavior of two drinking water bacteria species, which may potentially link scaling and biofouling processes in drinking water distribution systems. Evidence from cell density evolution, chemical parameters, and microscopy suggest that drinking water isolates can mediate CaCO3 precipitation through previously overlooked MCP mechanisms like ammonification or biosorption. The results also illustrate the active control of bacteria on the MCP process, as the calcium starts to concentrate onto cell surfaces only after reaching a certain cell density, even though the cell surfaces are shown to be the ideal location for the CaCO3 nucleation.
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Affiliation(s)
- Xiaoxia Liu
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands;; Institute of Hydraulics and Rural Water Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gernot Zarfel
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Renata van der Weijden
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands;; Sub-Department of Environmental Technology, Wageningen University, Wageningen, the Netherlands
| | - Willibald Loiskandl
- Institute of Hydraulics and Rural Water Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Brigitte Bitschnau
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, Austria
| | - Inez J T Dinkla
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
| | - Elmar C Fuchs
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands;; Optical Sciences group, Faculty of Science and Technology, University of Twente. Twente. the Netherlands.
| | - Astrid H Paulitsch-Fuchs
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria; School of Health Sciences & Social Work, Biomedical Sciences, Carinthia University of Applied Sciences, Klagenfurt, Austria
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15
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Groisman EA, Duprey A, Choi J. How the PhoP/PhoQ System Controls Virulence and Mg 2+ Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution. Microbiol Mol Biol Rev 2021; 85:e0017620. [PMID: 34191587 PMCID: PMC8483708 DOI: 10.1128/mmbr.00176-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The PhoP/PhoQ two-component system governs virulence, Mg2+ homeostasis, and resistance to a variety of antimicrobial agents, including acidic pH and cationic antimicrobial peptides, in several Gram-negative bacterial species. Best understood in Salmonella enterica serovar Typhimurium, the PhoP/PhoQ system consists o-regulated gene products alter PhoP-P amounts, even under constant inducing conditions. PhoP-P controls the abundance of hundreds of proteins both directly, by having transcriptional effects on the corresponding genes, and indirectly, by modifying the abundance, activity, or stability of other transcription factors, regulatory RNAs, protease regulators, and metabolites. The investigation of PhoP/PhoQ has uncovered novel forms of signal transduction and the physiological consequences of regulon evolution.
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Affiliation(s)
- Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jeongjoon Choi
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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16
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Burt CD, Chapman T, Bachoon D, Cabrera ML, Horacek C. The effect of an acidified-gypsum mixture on broiler litter urease-producing bacteria and nitrogen mineralization. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:889-898. [PMID: 33887809 DOI: 10.1002/jeq2.20229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Ammonia (NH3 ) volatilization from broiler (Gallus gallus domesticus) litter is a microbially mediated process that can decrease bird productivity and serves as an environmental pollutant. The release of NH3 is strongly influenced by the pH of litter. Flue-gas desulfurization gypsum (FGDG) has been suggested as a potential amendment to reduce NH3 volatilization due to the pH buffering capacity of calcium carbonate (CaCO3 ) precipitation. However, its effect on litter pH is not as pronounced as acidifying agents, such as aluminum sulfate (alum). The main objective of our study was to develop an acidified-FGDG amendment that has a more pronounced effect on litter pH and NH3 volatilization than FGDG alone. We conducted a 33-d incubation in which litter pH, NH3 volatilization, nitrogen mineralization, PLUP-ureC gene abundance, and CaCO3 precipitation were measured. Treatments in the study included: broiler litter (BL), broiler litter + 20% FGDG (BL+FGDG), broiler litter + FGDG-alum mixture (BL+FGDG+A6), broiler litter + 6% alum (BL+A6), and broiler litter + 10% alum (BL+A10). Our FGDG+alum amendment decreased litter pH (0.68 pH units) and PLUP-ureC gene abundance (>1 log) compared with FGDG alone and the control (p < .05). This led to a 25% decrease in cumulative NH3 loss after 33 d. The addition of FGDG alone did not have an effect on litter pH (p = .36) or cumulative NH3 loss (p = .29) due to a lack of significant CaCO3 precipitation. Treating litter with 6 and 10% alum was the most effective amendment for reducing pH and cumulative NH3 loss.
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Affiliation(s)
- Christopher Daniel Burt
- Dep. of Biological and Environmental Sciences, Georgia College, Herty Hall, Milledgeville, GA, 31061, USA
| | - Taylor Chapman
- Dep. of Biological and Environmental Sciences, Georgia College, Herty Hall, Milledgeville, GA, 31061, USA
| | - Dave Bachoon
- Dep. of Biological and Environmental Sciences, Georgia College, Herty Hall, Milledgeville, GA, 31061, USA
| | - Miguel L Cabrera
- Dep. of Crop and Soil Sciences, Univ. of Georgia, 3111 Miller Plant Sciences Bldg., Athens, GA, 30605, USA
| | - Christopher Horacek
- Dep. of Biological and Environmental Sciences, Georgia College, Herty Hall, Milledgeville, GA, 31061, USA
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17
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Galera-Laporta L, Comerci CJ, Garcia-Ojalvo J, Süel GM. IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria. Cell Syst 2021; 12:497-508. [PMID: 34139162 PMCID: PMC8570674 DOI: 10.1016/j.cels.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.
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Affiliation(s)
- Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colin J Comerci
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093- 0380, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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18
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Abstract
Bacteria are electrically powered organisms; cells maintain an electrical potential across their plasma membrane as a source of free energy to drive essential processes. In recent years, however, bacterial membrane potential has been increasingly recognized as dynamic. Those dynamics have been implicated in diverse physiological functions and behaviors, including cell division and cell-to-cell signaling. In eukaryotic cells, such dynamics play major roles in coupling bioelectrical stimuli to changes in internal cell states. Neuroscientists and physiologists have established detailed molecular pathways that transduce eukaryotic membrane potential dynamics to physiological and gene expression responses. We are only just beginning to explore these intracellular responses to bioelectrical activity in bacteria. In this review, we summarize progress in this area, including evidence of gene expression responses to stimuli from electrodes and mechanically induced membrane potential spikes. We argue that the combination of provocative results, missing molecular detail, and emerging tools makes the investigation of bioelectrically induced long-term intracellular responses an important and rewarding effort in the future of microbiology.
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Affiliation(s)
- Joshua M Jones
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Joseph W Larkin
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
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19
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Trabalza S, Buonaurio R, Del Pino AM, Palmerini CA, van den Burg HA, Moretti C. A Spectrofluorophotometrical Method Based on Fura-2-AM Probe to Determine Cytosolic Ca 2+ Level in Pseudomonas syringae Complex Bacterial Cells. Bio Protoc 2021; 11:e3949. [PMID: 33855111 DOI: 10.21769/bioprotoc.3949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 11/02/2022] Open
Abstract
Calcium signaling is an emerging mechanism by which bacteria respond to environmental cues. To measure the intracellular free-calcium concentration in bacterial cells, [Ca2+]i, a simple spectrofluorometric method based on the chemical probe Fura 2-acetoxy methyl ester (Fura 2-AM) is here presented using Pseudomonad bacterial cells. This is an alternative and quantitative method that can be completed in a short period of time with low costs, and it does not require the induction of heterologously expressed protein-based probes like Aequorin. Furthermore, it is possible to verify the properties of membrane channels involved in Ca2+ entry from the extracellular matrix. This method is in particular valuable for measuring [Ca2+]i in the range of 0.1-39.8 µM in small cells like those of prokaryotes.
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Affiliation(s)
- Simone Trabalza
- Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy.,Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Roberto Buonaurio
- Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
| | - Alberto M Del Pino
- Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
| | - Carlo A Palmerini
- Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Chiaraluce Moretti
- Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy
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20
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Zheng Y, Wang LB, Sun SF, Liu SY, Liu MJ, Lin J. Phylogenetic and ion-response analyses reveal a relationship between gene expansion and functional divergence in the Ca 2+/cation antiporter family in Angiosperms. PLANT MOLECULAR BIOLOGY 2021; 105:303-320. [PMID: 33123851 DOI: 10.1007/s11103-020-01088-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/21/2020] [Indexed: 05/28/2023]
Abstract
Plant CaCA superfamily genes with higher tendency to retain after WGD are more gene expression and function differentiated in ion-response. Plants and animals face different environmental stresses but share conserved Ca2+ signaling pathways, such as Ca2+/Cation transport. The Ca2+/cation antiporters superfamily (CaCAs) is an ancient and widespread family of ion-coupled cation transporters found in all kingdoms of life. We analyzed the molecular evolution progress of the family through comparative genomics and phylogenetics of CaCAs genes from plants and animals, grouping these genes into several families and clades, and identified multiple gene duplication retention events, particularly in the CAX (H+/cation exchanger), CCX (cation/Ca2+ exchanger), and NCL (Na+/Ca2+ exchanger-like) families. The tendency of duplication retention differs between families and gene clades. The gene duplication events were probably the result of whole-genome duplication (WGD) in plants and might have led to functional divergence. Tissue and ion-response expression analyses revealed that CaCAs genes with more highly differentiated expression patterns are more likely to be retained as duplicates than those with more conserved expression profiles. Phenotype of Arabidopsis thaliana mutants showed that loss of genes with a greater tendency to be retained after duplication resulted in more severe growth deficiency. CaCAs genes in salt-tolerant species tended to inherit the expression characteristics of their most recent common ancestral genes, with conservative ion-response expression. This study indicates a possible evolutionary scheme for cation transport and illustrates distinct fates and a mechanism for the evolution of gene duplicates. The increased copy numbers of genes and divergences in expression might have contributed to the divergent functions of CaCAs protein, allowing plants to cope with environmental stresses and adapt to a larger number of ecological niches.
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Affiliation(s)
- Ye Zheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Lin-Bo Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Shu-Feng Sun
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Shi-Ying Liu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Ming-Jia Liu
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Juan Lin
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China.
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21
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Wahdan SFM, Heintz-Buschart A, Sansupa C, Tanunchai B, Wu YT, Schädler M, Noll M, Purahong W, Buscot F. Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link. Front Microbiol 2021; 12:629169. [PMID: 33597941 PMCID: PMC7882529 DOI: 10.3389/fmicb.2021.629169] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,Department of Biology, Leipzig University, Leipzig, Germany.,Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Anna Heintz-Buschart
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Chakriya Sansupa
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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22
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Xue Y, Tian J, Quine TA, Powlson D, Xing K, Yang L, Kuzyakov Y, Dungait JAJ. The persistence of bacterial diversity and ecosystem multifunctionality along a disturbance intensity gradient in karst soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:142381. [PMID: 33113676 DOI: 10.1016/j.scitotenv.2020.142381] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 05/20/2023]
Abstract
Extensive, progressive rock emergence causes localized variations in soil biogeochemical and microbial properties that may influence the capacity for the regeneration of degraded karst ecosystems. It is likely that karst ecosystem recovery relies on the persistence of soil functions at the microbial scale, and we aimed to explored the role of interactions between soil bacterial taxa and identify keystone species that deliver key biogeochemical functions, i.e. carbon (C) and nutrient (nitrogen, N and phosphorus, P) cycling. We applied high-throughput sequencing and phylogenetic molecular ecological network approaches to topsoils sampled at rock-soil interfaces and adjacent bulk soil along an established gradient of land-use intensity in the Chinese Karst Critical Zone Observatory. Bacterial α-diversity was greater under increased perturbation and at the rock-soil interface compared to bulk soils under intensive cultivation. However, bacterial ecological networks were less intricate and connected fewer keystone taxa as human disturbance increased and at the rock-soil interface. Co-occurrence within the bacterial community in natural primary forest soils was 13% larger than cultivated soils. The relative abundances of keystone taxa Acidobacteria, Bacteroidetes and Chloroflexi increased with land-use intensity, while Proteobacteria, Actinobacteria and Verrucomicrobia decreased by up to 6%. In general, Bacteroidetes, Verrucomicrobia and Chlorobi were related to C-cycling, Proteobacteria, Actinobacteria and Chloroflexi were related to N-cycling, and Actinobacteria and Nitrospirae were related to both N- and P-cycling. Proteobacteria and Chlorobi affected C-cycling and multiple functionality indexes in the abandoned land. We conclude that increasing land-use intensity changed the soil bacterial community structure and decreased bacterial interactions. However, increases in α-diversity at the rock-soil interface in cultivated soils indicated that major soil functions related to biogeochemical cycling were maintained within keystone taxa in this microenvironment. Our study provides foundations to test the success of different regeneration practices in restoring soil microbial diversity and the multifunctionality of karst ecosystems.
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Affiliation(s)
- Yafang Xue
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China; Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Tian
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China; Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Timothy A Quine
- Geography, College of Life and Environmental Sciences, University of Exeter, Rennes Drive, Exeter EX4 4RJ, UK
| | - David Powlson
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Herts. AL5 2JQ, UK
| | - Kaixiong Xing
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Liyang Yang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37077, Germany; Institute of Environmental Sciences, Kazan Federal University, Kazan 420049, Russia; Agro-Technological Institute, RUDN University, Moscow 117198, Russia
| | - Jennifer A J Dungait
- Geography, College of Life and Environmental Sciences, University of Exeter, Rennes Drive, Exeter EX4 4RJ, UK
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Rojas JJ, Vargas-Lagos C, Martínez D, Oyarzún-Salazar R, Pontigo JP, Morera F, Vargas-Chacoff L. Francisella noatunensis subsp. noatunensis triggers calcium metabolism gene modulation in Eleginops maclovinus. Comp Biochem Physiol A Mol Integr Physiol 2020; 250:110805. [PMID: 32927078 DOI: 10.1016/j.cbpa.2020.110805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/10/2020] [Accepted: 09/07/2020] [Indexed: 11/30/2022]
Abstract
Francisella noatunensis subsp. noatunensis is the responsible agent of Francisellosis, a bacterial disease that affects an important amount of aquatic farmed species. Eleginops maclovinus is a fish that cohabits with salmonids cages in Chile and can also act as a vector of this bacterial disease. In the present study, we evaluated calcium metabolism in the liver of E. maclovinus injected intraperitoneally with different doses of F. noatunensis subsp. noatunensis (low 1.5 × 101, medium 1.5 × 105 and high doses 1.5 × 1010 cells/μL). Fish were sampled at 1, 3, 7, 14, 21 and 28 days post injection (dpi). No mortalities nor clinical signs were observed. Plasma calcium levels were higher in the high doses group of F. noatunensis subsp. noatunensis at day 7 and 14 compared to the control group (fish injected with bacterial medium alone). Hypercalcemic factors increased at day 14 and 21 for the medium and low dose (parathyroid hormone-related protein precursor), while vitamin D3 receptor increased its expression at times 1, 3 and 7 for the low dose. On the other hand, hypocalcemic factors such as calcitonin receptor and stanniocalcin increased its expression at time 7 and 14, respectively. Calmodulin involved in calcium storage decreased its expression during all experimental days in fish subjected to high bacterial dose. Proteins involved in calcium transport, such as L-type voltage-gated calcium channel and trpv5 increased their transcription at day 1 and 14, compared to calcium sensing-receptor and plasma membrane Ca2 +- ATPase that showed peak expression at times 14 and 28. The results suggest a clear alteration of calcium metabolism, mainly in high bacterial doses. This study provides new knowledge about the calcium metabolism in fish infected with bacteria.
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Affiliation(s)
- Juan José Rojas
- Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile.
| | - Carolina Vargas-Lagos
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile
| | - Danixa Martínez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile
| | - Ricardo Oyarzún-Salazar
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile; Universidad Austral de Chile, Puerto Montt, Chile
| | - Juan Pablo Pontigo
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt, Chile
| | - Francisco Morera
- Instituto de Farmacología y Morfofisiología, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Luis Vargas-Chacoff
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP-IDEAL, Universidad Austral de Chile, Valdivia, Chile.
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Lezhnina MM, Rochowiak W, Göhde W, Kuczius R, Kynast U. The microbial threat: Can rare earths help? JOURNAL OF BIOPHOTONICS 2020; 13:e202000068. [PMID: 32500670 DOI: 10.1002/jbio.202000068] [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: 02/28/2020] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Despite an ever increasing demand for reliable and cheap methods in the detection and quantification of microbes, surprisingly few investigations have explored or utilized the luminescence of rare earths in the microbial context, neither in conventional, that is, plating and microscopic imaging techniques, nor in advanced methods like fluorescence flow cytometry. We have thus investigated the potential of some rare earth complexes and hybrid materials for microbiological analysis. We found fairly simple procedures for internal staining (dyes inside the bacterial cell) and external staining (dyes on the cell surface). The present paper is predominantly relying on microscopic imaging and luminescence spectroscopies (excitation, emission, decay times), but also evaluates model rare earth microspheres to estimate an eventual rare earth based stain for a fast and sensitive bacteria enumeration with luminescence flow cytometry.
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Affiliation(s)
- Marina M Lezhnina
- Quantum Analysis GmbH, Münster, Germany
- Institute for Optical Technologies, Münster University of Applied Sciences, Steinfurt, Germany
| | - Weronika Rochowiak
- Institute for Optical Technologies, Münster University of Applied Sciences, Steinfurt, Germany
| | | | - Rauni Kuczius
- Mikrobiologisches Labor Dr. Michael Lohmeyer GmbH, Münster, Germany
| | - Ulrich Kynast
- Institute for Optical Technologies, Münster University of Applied Sciences, Steinfurt, Germany
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25
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Jalil A, Asim MH, Nazir I, Matuszczak B, Bernkop-Schnürch A. Self-emulsifying drug delivery systems containing hydrophobic ion pairs of polymyxin B and agaric acid: A decisive strategy for enhanced antimicrobial activity. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Aerobic and anaerobic removal of lead and mercury via calcium carbonate precipitation mediated by statistically optimized nitrate reductases. Sci Rep 2020; 10:4029. [PMID: 32132620 PMCID: PMC7055279 DOI: 10.1038/s41598-020-60951-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/11/2020] [Indexed: 01/18/2023] Open
Abstract
The nonbiodegradability nature of heavy metals renders them resident in food chain and subsequently, destructing the entire ecosystem. Therefore, this study aimed to employ nitrate reduction-driven calcium carbonate precipitation in remediation of lead and mercury aerobically and anaerobically by Proteus mirabilis 10B, for the first time. Initially, Plackett-Burman design was employed to screen of 16 independent variables for their significances on periplasmic (NAP) and membrane-bound (NAR) nitrate reductases. The levels for five significant variables and their interaction effects were further optimized by central composite design. The maximum activities of NAP and NAR recorded 2450 and 3050 U/mL by 2-fold enhancement, comparing with non-optimized medium. Under aerobic and anaerobic optimized remediation conditions, the changes in media chemistry revealed positive correlation among bacterial growth, nitrate reductase activity, pH, NO3- and NO2- consumption and removal of Ca2+, Pb2+ and Hg2+. Subsequently, the remediated precipitates were subjected to mineralogical analysis; energy dispersive X-ray patterns exhibited characteristic peaks of C, O and Ca in addition to Pb and Hg. Scanning electron microscope depicted the presence of bacterial imprints and protrusions on rough and smooth surface bioliths. However, X-ray diffraction indicated entrapment of PbCO3, Pb2O, CaPbO3, Hg and Hg2O in calcite lattice. Interestingly, such approach is feasible, efficient, cost-effective and ecofriendly for heavy metals remediation.
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Schrecker M, Wunnicke D, Hänelt I. How RCK domains regulate gating of K+ channels. Biol Chem 2020; 400:1303-1322. [PMID: 31361596 DOI: 10.1515/hsz-2019-0153] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/02/2019] [Indexed: 11/15/2022]
Abstract
Potassium channels play a crucial role in the physiology of all living organisms. They maintain the membrane potential and are involved in electrical signaling, pH homeostasis, cell-cell communication and survival under osmotic stress. Many prokaryotic potassium channels and members of the eukaryotic Slo channels are regulated by tethered cytoplasmic domains or associated soluble proteins, which belong to the family of regulator of potassium conductance (RCK). RCK domains and subunits form octameric rings, which control ion gating. For years, a common regulatory mechanism was suggested: ligand-induced conformational changes in the octameric ring would pull open a gate in the pore via flexible linkers. Consistently, ligand-dependent conformational changes were described for various RCK gating rings. Yet, recent structural and functional data of complete ion channels uncovered that the following signal transduction to the pore domains is divers. The different RCK-regulated ion channels show remarkably heterogeneous mechanisms with neither the connection from the RCK domain to the pore nor the gate being conserved. Some channels even lack the flexible linkers, while in others the gate cannot easily be assigned. In this review we compare available structures of RCK-gated potassium channels, highlight the similarities and differences of channel gating, and delineate existing inconsistencies.
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Affiliation(s)
- Marina Schrecker
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt Main, Germany
| | - Dorith Wunnicke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt Main, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt Main, Germany
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28
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Scheel RA, Fusi AD, Min BC, Thomas CM, Ramarao BV, Nomura CT. Increased Production of the Value-Added Biopolymers Poly( R-3-Hydroxyalkanoate) and Poly(γ-Glutamic Acid) From Hydrolyzed Paper Recycling Waste Fines. Front Bioeng Biotechnol 2019; 7:409. [PMID: 31921814 PMCID: PMC6930151 DOI: 10.3389/fbioe.2019.00409] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/27/2019] [Indexed: 11/25/2022] Open
Abstract
Reject fines, a waste stream of short lignocellulosic fibers produced from paper linerboard recycling, are a cellulose-rich paper mill byproduct that can be hydrolyzed enzymatically into fermentable sugars. In this study, the use of hydrolyzed reject fines as a carbon source for bacterial biosynthesis of poly(R-3-hydroxyalkanoate) (PHA) and poly(γ-glutamic acid) (PGA) was investigated. Recombinant Escherichia coli harboring PHA biosynthesis genes were cultivated with purified sugars or crude hydrolysate to produce both poly(R-3-hydroxybutyrate) (PHB) homopolymer and medium chain length-containing copolymer (PHB-co-MCL). Wild-type Bacillus licheniformis WX-02 were cultivated with crude hydrolysate to produce PGA. Both PHB and short chain-length-co-medium chain-length (SCL-co-MCL) PHA yields from crude hydrolysate were a 2-fold improvement over purified sugars, and the MCL monomer fraction was decreased slightly in copolymers produced from crude hydrolysate. PGA yield from crude hydrolysate was similarly increased 2-fold. The results suggest that sugars from hydrolyzed reject fines are a viable carbon source for PHA and PGA biosynthesis. The use of crude hydrolysate is not only possible but beneficial for biopolymer production, eliminating the need for costly separation and purification techniques. This study demonstrates the potential to divert a lignocellulosic waste stream into valuable biomaterials, mitigating the environmental impacts of solid waste disposal.
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Affiliation(s)
- Ryan A Scheel
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Alexander D Fusi
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Byeong C Min
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Christopher M Thomas
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Bandaru V Ramarao
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Christopher T Nomura
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States.,Center for Applied Microbiology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
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29
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Jalil A, Asim MH, Akkus ZB, Schoenthaler M, Matuszczak B, Bernkop-Schnürch A. Self-emulsifying drug delivery systems comprising chlorhexidine and alkyl-EDTA: A novel approach for augmented antimicrobial activity. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Moretti C, Trabalza S, Granieri L, Caballo‐Ponce E, Devescovi G, Del Pino AM, Ramos C, Venturi V, van den Burg HA, Buonaurio R, Palmerini CA. A Na + /Ca 2+ exchanger of the olive pathogen Pseudomonas savastanoi pv. savastanoi is critical for its virulence. MOLECULAR PLANT PATHOLOGY 2019; 20:716-730. [PMID: 30912619 PMCID: PMC6637891 DOI: 10.1111/mpp.12787] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In a number of compatible plant-bacterium interactions, a rise in apoplastic Ca2+ levels is observed, suggesting that Ca2+ represents an important environmental clue, as reported for bacteria infecting mammalians. We demonstrate that Ca2+ entry in Pseudomonas savastanoi pv. savastanoi (Psav) strain DAPP-PG 722 is mediated by a Na+ /Ca2+ exchanger critical for virulence. Using the fluorescent Ca2+ probe Fura 2-AM, we demonstrate that Ca2+ enters Psav cells foremost when they experience low levels of energy, a situation mimicking the apoplastic fluid. In fact, Ca2+ entry was suppressed in the presence of high concentrations of glucose, fructose, sucrose or adenosine triphosphate (ATP). Since Ca2+ entry was inhibited by nifedipine and LiCl, we conclude that the channel for Ca2+ entry is a Na+ /Ca2+ exchanger. In silico analysis of the Psav DAPP-PG 722 genome revealed the presence of a single gene coding for a Na+ /Ca2+ exchanger (cneA), which is a widely conserved and ancestral gene within the P. syringae complex based on gene phylogeny. Mutation of cneA compromised not only Ca2+ entry, but also compromised the Hypersensitive response (HR) in tobacco leaves and blocked the ability to induce knots in olive stems. The expression of both pathogenicity (hrpL, hrpA and iaaM) and virulence (ptz) genes was reduced in this Psav-cneA mutant. Complementation of the Psav-cneA mutation restored both Ca2+ entry and pathogenicity in olive plants, but failed to restore the HR in tobacco leaves. In conclusion, Ca2+ entry acts as a 'host signal' that allows and promotes Psav pathogenicity on olive plants.
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Affiliation(s)
- Chiaraluce Moretti
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Simone Trabalza
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Letizia Granieri
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Eloy Caballo‐Ponce
- Instituto de Hortofruticultura Subtropical y Mediterránea La MayoraUniversidad de Málaga‐Consejo Superior de Investigaciones Científicas (IHSM‐UMACSIC)Área de GenéticaMálagaSpain
| | - Giulia Devescovi
- Bacteriology Group, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Alberto Marco Del Pino
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Cayo Ramos
- Bacteriology Group, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Vittorio Venturi
- Bacteriology Group, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Harrold A. van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS)University of AmsterdamAmsterdamNetherlands
| | - Roberto Buonaurio
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
| | - Carlo Alberto Palmerini
- Department of Agricultural, Food and Environmental ScienceUniversity of PerugiaBorgo XX Giugno 74, Perugia06121Italy
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31
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A novel Ca 2+-binding protein influences photosynthetic electron transport in Anabaena sp. PCC 7120. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:519-532. [PMID: 31034800 DOI: 10.1016/j.bbabio.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022]
Abstract
Ca2+ is a potent signalling molecule that regulates many cellular processes. In cyanobacteria, Ca2+ has been linked to cell growth, stress response and photosynthesis, and to the development of specialist heterocyst cells in certain nitrogen-fixing species. Despite this, the pathways of Ca2+ signal transduction in cyanobacteria are poorly understood, and very few protein components are known. The current study describes a previously unreported Ca2+-binding protein which was called the Ca2+ Sensor EF-hand (CSE), which is conserved in filamentous, nitrogen-fixing cyanobacteria. CSE is shown to bind Ca2+, which induces a conformational change in the protein structure. Poor growth of a strain of Anabaena sp. PCC 7120 overexpressing CSE was attributed to diminished photosynthetic performance. Transcriptomics, biophysics and proteomics analyses revealed modifications in the light-harvesting phycobilisome and photosynthetic reaction centre protein complexes.
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32
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Lee YS, Park W. Enhanced calcium carbonate-biofilm complex formation by alkali-generating Lysinibacillus boronitolerans YS11 and alkaliphilic Bacillus sp. AK13. AMB Express 2019; 9:49. [PMID: 30976947 PMCID: PMC6459448 DOI: 10.1186/s13568-019-0773-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Microbially induced calcium carbonate (CaCO3) precipitation (MICP) is a process where microbes induce condition favorable for CaCO3 formation through metabolic activities by increasing the pH or carbonate ions when calcium is near. The molecular and ecological basis of CaCO3 precipitating (CCP) bacteria has been poorly illuminated. Here, we showed that increased pH levels by deamination of amino acids is a driving force toward MICP using alkalitolerant Lysinibacillus boronitolerans YS11 as a model species of non-ureolytic CCP bacteria. This alkaline generation also facilitates the growth of neighboring alkaliphilic Bacillus sp. AK13, which could alter characteristics of MICP by changing the size and shape of CaCO3 minerals. Furthermore, we showed CaCO3 that precipitates earlier in an experiment modifies membrane rigidity of YS11 strain via upregulation of branched chain fatty acid synthesis. This work closely examines MICP conditions by deamination and the effect of MICP on cell membrane rigidity and crystal formation for the first time.
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33
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Kalwasińska A, Deja-Sikora E, Szabó A, Felföldi T, Kosobucki P, Brzezinska MS, Walczak M. Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:842-854. [PMID: 30481711 DOI: 10.1016/j.scitotenv.2018.11.246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3-25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.
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Affiliation(s)
- Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland.
| | - Edyta Deja-Sikora
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland; Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, PázmányPéterstny. 1/c. H-1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, PázmányPéterstny. 1/c. H-1117 Budapest, Hungary
| | - Przemysław Kosobucki
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Maciej Walczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
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Tal N, Rudnick-Glick S, Grinberg I, Natan M, Banin E, Margel S. Engineering of a New Bisphosphonate Monomer and Nanoparticles of Narrow Size Distribution for Antibacterial Applications. ACS OMEGA 2018; 3:1458-1469. [PMID: 30023805 PMCID: PMC6044825 DOI: 10.1021/acsomega.7b01686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
In recent years, many bacteria have developed resistance to commonly used antibiotics. It is well-known that calcium is essential for bacterial function and cell wall stability. Bisphosphonates (BPs) have high affinity to calcium ions and are effective calcium chelators. Therefore, BPs could potentially be used as antibacterial agents. This article provides a detailed description regarding the synthesis of a unique BP vinylic monomer MA-Glu-BP (methacrylate glutamate bisphosphonate) and polyMA-Glu-BP nanoparticles (NPs) for antibacterial applications. polyMA-Glu-BP NPs were synthesized by dispersion copolymerization of the MA-Glu-BP monomer with the primary amino monomer N-(3-aminopropyl)methacrylamide hydrochloride (APMA) and the cross-linker monomer tetra ethylene glycol diacrylate, to form cross-linked NPs with a narrow size distribution. The size and size distribution of polyMA-Glu-BP NPs were controlled by changing various polymerization parameters. Near-infrared fluorescent polyMA-Glu-BP NPs were prepared by covalent binding of the dye cyanine7 N-hydroxysuccinimide to the primary amino groups belonging to the APMA monomeric units on the polyMA-Glu-BP NPs. The affinity of the near-infrared fluorescent polyMA-Glu-BP NPs toward calcium was demonstrated in vitro by a coral model. Cytotoxicity, cell uptake, and antibacterial properties of the polyMA-Glu-BP NPs against two common bacterial pathogens representing Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, and two representing Gram-positive bacteria, Listeria innocua and Staphylococcus aureus, were then demonstrated.
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Affiliation(s)
- Nimrod Tal
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Safra Rudnick-Glick
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Igor Grinberg
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Natan
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ehud Banin
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shlomo Margel
- The Institute of Nanotechnology
and Advanced Materials, Department
of Chemistry, and The Mina and Everard Goodman Faculty of Life Sciences, The Institute
for Advanced Materials and Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
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35
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Xue L, Ren H, Li S, Leng X, Yao X. Soil Bacterial Community Structure and Co-occurrence Pattern during Vegetation Restoration in Karst Rocky Desertification Area. Front Microbiol 2017; 8:2377. [PMID: 29250053 PMCID: PMC5717032 DOI: 10.3389/fmicb.2017.02377] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
Vegetation restoration has been widely used in karst rocky desertification (KRD) areas of southwestern China, but the response of microbial community to revegetation has not been well characterized. We investigated the diversity, structure, and co-occurrence patterns of bacterial communities in soils of five vegetation types (grassland, shrubbery, secondary forest, pure plantation and mixed plantation) in KRD area using high-throughput sequencing of the 16S rRNA gene. Bray-Curtis dissimilarity analysis revealed that 15 bacterial community samples were clustered into five groups that corresponded very well to the five vegetation types. Shannon diversity was positively correlated with pH and Ca2+ content but negatively correlated with organic carbon, total nitrogen, and soil moisture. Redundancy analysis indicated that soil pH, Ca2+ content, organic carbon, total nitrogen, and soil moisture jointly influenced bacterial community structure. Co-occurrence network analysis revealed non-random assembly patterns of bacterial composition in the soils. Bryobacter, GR-WP33-30, and Rhizomicrobium were identified as keystone genera in co-occurrence network. These results indicate that diverse soil physicochemical properties and potential interactions among taxa during vegetation restoration may jointly affect the bacterial community structure in KRD regions.
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Affiliation(s)
- Liang Xue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Huadong Ren
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Sheng Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Xiuhui Leng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
- Observation and Research Station for Rock Desert Ecosystem, Puding, China
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Burt CD, Cabrera ML, Rothrock MJ, Kissel DE. Flue-gas desulfurization gypsum effects on urea-degrading bacteria and ammonia volatilization from broiler litter. Poult Sci 2017; 96:2676-2683. [PMID: 28482091 DOI: 10.3382/ps/pex044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 02/02/2017] [Indexed: 11/20/2022] Open
Abstract
A major concern of the broiler industry is the volatilization of ammonia (NH3) from the mixture of bedding material and broiler excretion that covers the floor of broiler houses. Gypsum has been proposed as a litter amendment to reduce NH3 volatilization, but reports of NH3 abatement vary among studies and the mechanism responsible for decreasing NH3 volatilization is not well understood. The goal of this study was to evaluate the effect of adding 20 or 40% flue-gas desulfurization gypsum (FGDG) to broiler litter on pH, electrical conductivity (EC), water potential, urea-degrading bacteria abundance, NH3 and carbon dioxide (CO2) evolution, and nitrogen (N) mineralization in several 21-d experiments. The addition of FGDG to broiler litter increased EC by 24 to 33% (P < 0.0001), decreased urea-degrading bacteria by 48 to 57% (P = 0.0001) and increased N mineralization by 10 to 11% (P = 0.0001) as compared to litters not amended with FGDG. Furthermore, the addition of FGDG to broiler litter decreased NH3 volatilization by 18 to 28% (P < 0.0001), potentially resulting from the significantly lower litter pH values compared to un-amended litter (P < 0.0001). Findings of this study indicate that amending broiler litter with 20% FGDG can decrease NH3 volatilization and increase the fertlizer value of broiler litter.
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Affiliation(s)
- Christopher D Burt
- Dep. Crop and Soil Sciences, Univ. of Georgia, 3111 Miller Plant Sciences Bldg., Athens, GA 30605
| | - Miguel L Cabrera
- Dep. Crop and Soil Sciences, Univ. of Georgia, 3111 Miller Plant Sciences Bldg., Athens, GA 30605
| | - Michael J Rothrock
- USDA-ARS U.S. National Poultry Research Center, 950 College Station Rd., Athens, GA 30605
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Zhu Y, Ma N, Jin W, Wu S, Sun C. Genomic and Transcriptomic Insights into Calcium Carbonate Biomineralization by Marine Actinobacterium Brevibacterium linens BS258. Front Microbiol 2017; 8:602. [PMID: 28428780 PMCID: PMC5382220 DOI: 10.3389/fmicb.2017.00602] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/23/2017] [Indexed: 01/31/2023] Open
Abstract
Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca2+ concentration. To disclose the mechanisms of biomineralization, the genome of B. linens BS258 was further completely sequenced. Interestingly, the expression of three carbonic anhydrases was significantly up-regulated along with the increase of Ca2+ concentration and the extent of calcite dissolution. Moreover, transcriptome analyses revealed that increasing concentration of Ca2+ induced KEGG pathways including quorum sensing (QS) in B. linens BS258. Notably, most up-regulated genes related to QS were found to encode peptide/nickel ABC transporters, which suggested that nickel uptake and its associated urease stimulation were essential to boost CaCO3 biomineralization. Within the genome of B. linens BS258, there are both cadmium and lead resistance gene clusters. Therefore, the sequestration abilities of Cd2+ and Pb2+ by B. linens BS258 were checked. Consistently, Pb2+ and Cd2+ could be effectively sequestered with the precipitation of calcite by B. linens BS258. To our knowledge, this is the first study investigating the microbial CaCO3 biomineralization from both genomic and transcriptomic insights, which paves the way to disclose the relationships among bacterial metabolisms and the biomineralization.
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Affiliation(s)
- Yuying Zhu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- College of Earth Science, University of Chinese Academy of SciencesBeijing, China
| | - Ning Ma
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- College of Earth Science, University of Chinese Academy of SciencesBeijing, China
| | - Weihua Jin
- College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Shimei Wu
- College of Life Sciences, Qingdao UniversityQingdao, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
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38
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Pateraki C, Patsalou M, Vlysidis A, Kopsahelis N, Webb C, Koutinas AA, Koutinas M. Actinobacillus succinogenes : Advances on succinic acid production and prospects for development of integrated biorefineries. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Walter J, Lynch F, Battchikova N, Aro EM, Gollan PJ. Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3997-4008. [PMID: 27012282 PMCID: PMC4915528 DOI: 10.1093/jxb/erw112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Calcium is integral to the perception, communication and adjustment of cellular responses to environmental changes. However, the role of Ca(2+) in fine-tuning cellular responses of wild-type cyanobacteria under favourable growth conditions has not been examined. In this study, extracellular Ca(2+) has been altered, and changes in the whole transcriptome of Anabaena sp. PCC 7120 have been evaluated under conditions replete of carbon and combined nitrogen. Ca(2+) induced differential expression of many genes driving primary cellular metabolism, with transcriptional regulation of carbon- and nitrogen-related processes responding with opposing trends. However, physiological effects of these transcriptional responses on biomass accumulation, biomass composition, and photosynthetic activity over the 24h period following Ca(2+) adjustment were found to be minor. It is well known that intracellular carbon:nitrogen balance is integral to optimal cell growth and that Ca(2+) plays an important role in the response of heterocystous cyanobacteria to combined-nitrogen deprivation. This work adds to the current knowledge by demonstrating a signalling role of Ca(2+) for making sensitive transcriptional adjustments required for optimal growth under non-limiting conditions.
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Affiliation(s)
- Julia Walter
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Fiona Lynch
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
| | - Peter J Gollan
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland
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40
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Parker JK, Chen H, McCarty SE, Liu LY, De La Fuente L. Calcium transcriptionally regulates the biofilm machinery of Xylella fastidiosa to promote continued biofilm development in batch cultures. Environ Microbiol 2016; 18:1620-34. [PMID: 26913481 DOI: 10.1111/1462-2920.13242] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/21/2016] [Indexed: 11/29/2022]
Abstract
The functions of calcium (Ca) in bacteria are less characterized than in eukaryotes, where its role has been studied extensively. The plant-pathogenic bacterium Xylella fastidiosa has several virulence features that are enhanced by increased Ca concentrations, including biofilm formation. However, the specific mechanisms driving modulation of this feature are unclear. Characterization of biofilm formation over time showed that 4 mM Ca supplementation produced denser biofilms that were still developing at 96 h, while biofilm in non-supplemented media had reached the dispersal stage by 72 h. To identify changes in global gene expression in X. fastidiosa grown in supplemental Ca, RNA-Seq of batch culture biofilm cells was conducted at three 24-h time intervals. Results indicate that a variety of genes are differentially expressed in response to Ca, including genes related to attachment, motility, exopolysaccharide synthesis, biofilm formation, peptidoglycan synthesis, regulatory functions, iron homeostasis, and phages. Collectively, results demonstrate that Ca supplementation induces a transcriptional response that promotes continued biofilm development, while biofilm cells in nonsupplemented media are driven towards dispersion of cells from the biofilm structure. These results have important implications for disease progression in planta, where xylem sap is the source of Ca and other nutrients for X. fastidiosa.
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Affiliation(s)
- Jennifer K Parker
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL
| | - Hongyu Chen
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL
| | - Sara E McCarty
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL
| | - Lawrence Y Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL
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Tian QQ, Liang L, Zhu MJ. Enhanced biohydrogen production from sugarcane bagasse by Clostridium thermocellum supplemented with CaCO3. BIORESOURCE TECHNOLOGY 2015; 197:422-8. [PMID: 26356113 DOI: 10.1016/j.biortech.2015.08.111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/21/2015] [Accepted: 08/22/2015] [Indexed: 05/23/2023]
Abstract
Clostridium thermocellum ATCC 27405 was used to degrade sugarcane bagasse (SCB) directly for hydrogen production, which was significantly enhanced by supplementing medium with CaCO3. The effect of CaCO3 concentration on the hydrogen production was investigated. The hydrogen production was significantly enhanced with the CaCO3 concentration increased from 10mM to 20mM. However, with the CaCO3 concentration further increased from 20mM to 100mM, the hydrogen production didn't increase further. Under the optimal CaCO3 concentration of 20mM, the hydrogen production reached 97.83±5.19mmol/L from 2% sodium hydroxide-pretreated SCB, a 116.72% increase over the control (45.14±1.03mmol/L), and the yield of hydrogen production reached 4.89mmol H2/g SCBadded. Additionally, CaCO3 promoted the biodegradation of SCB and the growth of C. thermocellum. The stimulatory effects of CaCO3 on biohydrogen production are mainly attributed to the buffering capacity of carbonate. The study provides a novel strategy to enhance biohydrogen production from lignocellulose.
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Affiliation(s)
- Qing-Qing Tian
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou 510006, People's Republic of China
| | - Lei Liang
- Guangzhou Sugarcane Industry Research Institute, Guangzhou 510316, People's Republic of China
| | - Ming-Jun Zhu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou 510006, People's Republic of China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China.
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Singh S, Mishra AK. Unraveling of cross talk between Ca(2+) and ROS regulating enzymes in Anabaena 7120 and ntcA mutant. J Basic Microbiol 2015; 56:762-78. [PMID: 26374944 DOI: 10.1002/jobm.201500326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/09/2015] [Indexed: 01/25/2023]
Abstract
In order to understand a cross talk between Ca(2+) and ROS regulating enzymes and the possible involvement of ntcA gene, Anabaena sp. PCC 7120 and its derivative ntcA mutant grown in varied levels of calcium chloride (0, 1, 10, and 100 mM) have been investigated. Scanning Electron Microscopy showed abnormal structure formation at high calcium concentration (100 mM) both in wild type and mutant. Fv /Fm values suggested that 100 mM calcium concentration was detrimental for photosynthetic apparatus. SOD, catalase, APX, GR, and peroxidase activity were found to be maximum for 100 mM and minimum for 1 mM of exogenously supplied calcium salt. NADPH contents were higher for wild type than mutant. RAPD-PCR and SDS-PAGE analysis revealed a difference in DNA as well as proteome pattern with changes in calcium chloride regime. Prominent bands of approximately 70, 33, 21, and 14 kDa expressed in the wild type served as the marker polypeptide bands under calcium supplementation. Results suggest that higher levels of calcium ion disturb the cellular homeostasis generating ROS, thereby inducing enhanced levels of antioxidative enzymes. Further, data also suggests possible involvement of ntcA gene in cross talk between calcium ion and ROS regulating enzymes.
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Affiliation(s)
- Savita Singh
- Department of Botany, Laboratory of Microbial Genetics, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Department of Botany, Laboratory of Microbial Genetics, Banaras Hindu University, Varanasi, India
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Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine. BIOMED RESEARCH INTERNATIONAL 2015; 2015:816102. [PMID: 26273646 PMCID: PMC4529937 DOI: 10.1155/2015/816102] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/08/2015] [Accepted: 03/09/2015] [Indexed: 11/25/2022]
Abstract
The precipitation of calcium carbonate and calcium sulphate by isolated bacteria from seawater and real brine obtained in a desalination plant growth in culture media containing seawater and brine as mineral sources has been studied. However, only bioprecipitation was detected when the bacteria were grown in media with added organic matter. Biomineralization process started rapidly, crystal formation taking place in the beginning a few days after inoculation of media; roughly 90% of total cultivated bacteria showed. Six major colonies with carbonate precipitation capacity dominated bacterial community structure cultivated in heterotrophic platable bacteria medium. Taxonomic identification of these six strains through partial 16S rRNA gene sequences showed their affiliation with Gram-positive Bacillus and Virgibacillus genera. These strains were able to form calcium carbonate minerals, which precipitated as calcite and aragonite crystals and showed bacterial fingerprints or bacteria calcification. Also, carbonic anhydrase activity was observed in three of these isolated bacteria. The results of this research suggest that microbiota isolated from sea water and brine is capable of precipitation of carbonate biominerals, which can occur in situ with mediation of organic matter concentrations. Moreover, calcium carbonate precipitation ability of this microbiota could be of importance in bioremediation of CO2 and calcium in certain environments.
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44
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Awad WA, Smorodchenko A, Hess C, Aschenbach JR, Molnár A, Dublecz K, Khayal B, Pohl EE, Hess M. Increased intracellular calcium level and impaired nutrient absorption are important pathogenicity traits in the chicken intestinal epithelium during Campylobacter jejuni colonization. Appl Microbiol Biotechnol 2015; 99:6431-41. [PMID: 25825050 DOI: 10.1007/s00253-015-6543-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 02/08/2023]
Abstract
Although a high number of chickens carry Campylobacter jejuni, the mechanistic action of colonization in the intestine is still poorly understood. The current study was therefore designed to investigate the effects of C. jejuni on glucose uptake, amino acids availability in digesta, and intracellular calcium [Ca(2+)]i signaling in the intestines of broiler chickens. For this, we compared: control birds (n = 60) and C. jejuni-infected birds (n = 60; infected orally with 1 × 10(8) CFU of C. jejuni NCTC 12744 at 14 days of age). Our results showed that glucose uptake was reduced due to C. jejuni infection in isolated jejunal, but not in cecal mucosa at 14 days postinfection (dpi). The decrease in intestinal glucose absorption coincided with a decrease in body weight gain during the 2-week post-infectious period. A reduction in the amount of the amino acids (serine, proline, valine, leucine, phenylalanine, arginine, histidine, and lysine) in ileal digesta of the infected birds at 2 and/or 7 dpi was found, indicating that Campylobacter utilizes amino acids as a carbon source for their multiplication. Applying the cell-permeable Ca(2+) indicator Fluo-4 and two-photon microscopy, we revealed that [Ca(2+)]i was increased in the jejunal and cecal mucosa of infected birds. The muscarinic agonist carbachol induced an increase in [Ca(2+)]i in jejunum and cecum mucosa of control chickens, a response absent in the mucosa of infected chickens, demonstrating that the modulation of [Ca(2+)]i by Campylobacter might be involved in facilitating the necessary cytoskeletal rearrangements that occur during the bacterial invasion of epithelial cells. In conclusion, this study demonstrates the multifaceted interactions of C. jejuni with the gastrointestinal mucosa of broiler chickens. For the first time, it could be shown that a Campylobacter infection could interfere with intracellular Ca(2+) signaling and nutrient absorption in the small intestine with consequences on intestinal function, performance, and Campylobacter colonization. Altogether, these findings indicate that Campylobacter is not entirely a commensal and can be recognized as an important factor contributing to an impaired chicken gut health.
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Affiliation(s)
- Wageha A Awad
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria,
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45
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Plattner H, Verkhratsky A. The ancient roots of calcium signalling evolutionary tree. Cell Calcium 2015; 57:123-32. [DOI: 10.1016/j.ceca.2014.12.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/05/2014] [Indexed: 12/26/2022]
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46
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Tessaro LWE, Murugan NJ, Persinger MA. Bacterial growth rates are influenced by cellular characteristics of individual species when immersed in electromagnetic fields. Microbiol Res 2015; 172:26-33. [PMID: 25721476 DOI: 10.1016/j.micres.2014.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
Previous studies have shown that exposure to extremely low-frequency electromagnetic fields (ELF-EMFs) have negative effects on the rate of growth of bacteria. In the present study, two Gram-positive and two Gram-negative species were exposed to six magnetic field conditions in broth cultures. Three variations of the 'Thomas' pulsed frequency-modulated pattern; a strong-static "puck" magnet upwards of 5000G in intensity; a pair of these magnets rotating opposite one another at ∼30rpm; and finally a strong dynamic magnetic field generator termed the 'Resonator' with an average intensity of 250μT were used. Growth rate was discerned by optical density (OD) measurements every hour at 600nm. ELF-EMF conditions significantly affected the rates of growth of the bacterial cultures, while the two static magnetic field conditions were not statistically significant. Most interestingly, the 'Resonator' dynamic magnetic field increased the rates of growth of three species (Staphylococcus epidermidis, Staphylococcus aureus, and Escherichia coli), while slowing the growth of one (Serratia marcescens). We suggest that these effects are due to individual biophysical characteristics of the bacterial species.
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Affiliation(s)
- Lucas W E Tessaro
- Behavioural Neuroscience Program, Laurentian University, Sudbury, Ontario, Canada P3E 2C6; Department of Biology, Laurentian University, Sudbury, Ontario, Canada P3E 2C6.
| | - Nirosha J Murugan
- Behavioural Neuroscience Program, Laurentian University, Sudbury, Ontario, Canada P3E 2C6; Department of Biology, Laurentian University, Sudbury, Ontario, Canada P3E 2C6
| | - Michael A Persinger
- Behavioural Neuroscience Program, Laurentian University, Sudbury, Ontario, Canada P3E 2C6; Department of Biology, Laurentian University, Sudbury, Ontario, Canada P3E 2C6.
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47
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Rad B, Haxton TK, Shon A, Shin SH, Whitelam S, Ajo-Franklin CM. Ion-specific control of the self-assembly dynamics of a nanostructured protein lattice. ACS NANO 2015; 9:180-90. [PMID: 25494454 PMCID: PMC4310639 DOI: 10.1021/nn502992x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/10/2014] [Indexed: 05/22/2023]
Abstract
Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca(2+). These diagrams revealed a localized region of optimum yield of nanosheets at intermediate Ca(2+) concentration. Replacement of Mg(2+) or Ba(2+) for Ca(2+) indicates that Ca(2+) acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca(2+) bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. Our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.
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Affiliation(s)
- Behzad Rad
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Thomas K. Haxton
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Albert Shon
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California 94720-1462, United States
| | - Seong-Ho Shin
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Department of Chemistry, UC Berkeley, Berkeley, California 94720-1460, United States
| | - Stephen Whitelam
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Caroline M. Ajo-Franklin
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Address correspondence to
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48
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Srivastava S, Bharti RK, Thakur IS. Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:1499-1511. [PMID: 25163561 DOI: 10.1007/s11356-014-3442-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/11/2014] [Indexed: 06/03/2023]
Abstract
Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO3 respectively. These six isolates were tested for sequestration of carbon dioxide by (14)C metabolic labeling of NaH(14)CO3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH(14)CO3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm(-1). Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.
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Affiliation(s)
- Shaili Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India,
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49
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Calcium binding proteins and calcium signaling in prokaryotes. Cell Calcium 2014; 57:151-65. [PMID: 25555683 DOI: 10.1016/j.ceca.2014.12.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding β-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.
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50
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Norris V, Reusch RN, Igarashi K, Root-Bernstein R. Molecular complementarity between simple, universal molecules and ions limited phenotype space in the precursors of cells. Biol Direct 2014; 10:28. [PMID: 25470982 PMCID: PMC4264330 DOI: 10.1186/s13062-014-0028-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/24/2014] [Indexed: 01/29/2023] Open
Abstract
Background Fundamental problems faced by the protocells and their modern descendants include how to go from one phenotypic state to another; escape from a basin of attraction in the space of phenotypes; reconcile conflicting growth and survival strategies (and thereby live on ‘the scales of equilibria’); and create a coherent, reproducible phenotype from a multitude of constituents. Presentation of the hypothesis The solutions to these problems are likely to be found with the organic and inorganic molecules and inorganic ions that constituted protocells, which we term SUMIs for Simple Universal Molecules and Ions. These SUMIs probably included polyphosphate (PolyP) as a source of energy and of phosphate; poly-(R)-3-hydroxybutyrate (PHB) as a source of carbon and as a transporter in association with PolyP; polyamines as a source of nitrogen; lipids as precursors of membranes; as well as peptides, nucleic acids, and calcium. Here, we explore the hypothesis that the direct interactions between PHB, PolyP, polyamines and lipids – modulated by calcium – played a central role in solving the fundamental problems faced by early and modern cells. Testing the hypothesis We review evidence that SUMIs (1) were abundant and available to protocells; (2) are widespread in modern cells; (3) interact with one another and other cellular constituents to create structures with new functions surprisingly similar to those of proteins and RNA; (4) are essential to creating coherent phenotypes in modern bacteria. SUMIs are therefore natural candidates for reducing the immensity of phenotype space and making the transition from a “primordial soup” to living cells. Implications of the hypothesis We discuss the relevance of the SUMIs and their interactions to the ideas of molecular complementarity, composomes (molecular aggregates with hereditary properties based on molecular complementarity), and a prebiotic ecology of co-evolving populations of composomes. In particular, we propose that SUMIs might limit the initial phenotype space of composomes in a coherent way. As examples, we propose that acidocalcisomes arose from interactions and self-selection among SUMIs and that the phosphorylation of proteins in modern cells had its origin in the covalent modification of proteins by PHB. Reviewers This article was reviewed by Doron Lancet and Kepa Ruiz-Mirazo.
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