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Zhang M, Tong X, Wang W, Wang J, Qu W. Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer. J Basic Microbiol 2024; 64:e2300521. [PMID: 37988660 DOI: 10.1002/jobm.202300521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.
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Affiliation(s)
- Mengyuan Zhang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
- Zhejiang Ocean University-University of Pisa Marine Graduate School, Zhoushan, China
| | - Xiufang Tong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wenxin Wang
- Zhejiang Ocean University-University of Pisa Marine Graduate School, Zhoushan, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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2
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Duchâtellier G, Oehlert AM, Shernisky H, Pollier CGL, Swart PK, Howes B, Purkis SJ. Sedimentary porewaters record regional tectonic and climate events that perturbed a deep-sea brine pool in the Gulf of Aqaba, Red Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168804. [PMID: 38036117 DOI: 10.1016/j.scitotenv.2023.168804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
Brine pools in deep-sea environments provide unique perspectives into planetary and geological processes, extremophile microbial communities, and sedimentary records. The NEOM Brine Pool Complex was the first deep-sea brine pool system found in the Gulf of Aqaba, representing a significant extension of the geographical range and depositional setting of Red Sea brine pools. Here, we use a combination of brine pool samples collected via cast using a conductivity, temperature, depth instrument (CTD), as well as interstitial porewaters extracted from a sediment core collected in the NEOM Brine Pool to characterize the chemical composition and subsurface evolution of the brine. New results indicate that the NEOM brines and the subsurface porewaters may originate from different sources. Elemental concentrations suggest the brines in the NEOM pool are likely derived from dissolution of sub-seabed evaporites. In contrast, the sedimentary porewaters appear to have been influenced by periodic turbidite flows, generated either by earthquakes, submarine landslides, or flash floods, in which normal marine waters from the overlying Red Sea became entrained, periodically disturbing the chemistry of the brine pool. Thus, sediment porewaters beneath brine pools may record transient and dynamic changes in these deep marine depositional environments, reflecting the interplay between climate, tectonics, and sedimentation patterns along a rapidly urbanizing coastline. In concert, new results from NEOM extend the range and chemical constraints on Red Sea Brine Pools and highlight the dynamic interplay between Red Sea Deep water, dissolving evaporites, turbidites, and subsurface fluids that produce these unique depositional environments which host microbial life at the edge of habitability. In concert with sedimentological indicators, the chemistry of porewaters beneath deep-sea brine pools may present detailed records of natural hazards arising from interactions between the atmosphere, lithosphere, hydrosphere, and anthroposphere.
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Affiliation(s)
- Gaëlle Duchâtellier
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Amanda M Oehlert
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA.
| | - Hannah Shernisky
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Clément G L Pollier
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Peter K Swart
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Bolton Howes
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Sam J Purkis
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
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3
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:ijms24076491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
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Kokoulin MS, Dmitrenok PS, Romanenko LA. Structure of the Lipooligosaccharide from the Deep-Sea Marine Bacterium Idiomarina zobellii KMM 231 T, Isolated at a Depth of 4000 Meters. Mar Drugs 2022; 20:700. [PMID: 36355023 PMCID: PMC9695755 DOI: 10.3390/md20110700] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/06/2022] [Accepted: 11/06/2022] [Indexed: 05/31/2024] Open
Abstract
The structural characterization of lipopolysaccharides has critical implications for some biomedical applications, and marine bacteria are an inimitable source of new glyco-structures potentially usable in medicinal chemistry. On the other hand, lipopolysaccharides of marine Gram-negative bacteria present certain structural features that can help the understanding of the adaptation processes. The deep-sea marine Gram-negative bacterium Idiomarina zobellii KMM 231T, isolated from a seawater sample taken at a depth of 4000 m, represents an engaging microorganism to investigate in terms of its cell wall components. Here, we report the structural study of the R-type lipopolysaccharide isolated from I. zobellii KMM 231T that was achieved through a multidisciplinary approach comprising chemical analyses, NMR spectroscopy, and MALDI mass spectrometry. The lipooligosaccharide turned out to be characterized by a novel and unique pentasaccharide skeleton containing a very short mono-phosphorylated core region and comprising terminal neuraminic acid. The lipid A was revealed to be composed of a classical disaccharide backbone decorated by two phosphate groups and acylated by i13:0(3-OH) in amide linkage, i11:0 (3-OH) as primary ester-linked fatty acids, and i11:0 as a secondary acyl chain.
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Affiliation(s)
- Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159/2, Prospect 100 let Vladivostoku, Vladivostok 690022, Russia
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Yang Y, Feng Y, Li H, Xu C, Jiang S, Ma R, Wang B. Pretreatment of deep-sea bacteria for reverse flotation of magnesite tailings: cleaner production, behavior and mechanism. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.122685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Zhang M, Wang J, Zeng R, Wang D, Wang W, Tong X, Qu W. Agarose-Degrading Characteristics of a Deep-Sea Bacterium Vibrio Natriegens WPAGA4 and Its Cold-Adapted GH50 Agarase Aga3420. Mar Drugs 2022; 20:692. [PMID: 36355015 PMCID: PMC9698624 DOI: 10.3390/md20110692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/23/2023] Open
Abstract
Up until now, the characterizations of GH50 agarases from Vibrio species have rarely been reported compared to GH16 agarases. In this study, a deep-sea strain, WPAGA4, was isolated and identified as Vibrio natriegens due to the maximum similarity of its 16S rRNA gene sequence, the values of its average nucleotide identity, and through digital DNA-DNA hybridization. Two circular chromosomes in V. natriegens WPAGA4 were assembled. A total of 4561 coding genes, 37 rRNA, 131 tRNA, and 59 other non-coding RNA genes were predicted in the genome of V. natriegens WPAGA4. An agarase gene belonging to the GH50 family was annotated in the genome sequence and expressed in E. coli cells. The optimum temperature and pH of the recombinant Aga3420 (rAga3420) were 40 °C and 7.0, respectively. Neoagarobiose (NA2) was the only product during the degradation process of agarose by rAga3420. rAga3420 had a favorable stability following incubation at 10-30 °C for 50 min. The Km, Vmax, and kcat values of rAga3420 were 2.8 mg/mL, 78.1 U/mg, and 376.9 s-1, respectively. rAga3420 displayed cold-adapted properties as 59.7% and 41.2% of the relative activity remained at 10 3 °C and 0 °C, respectively. This property ensured V. natriegens WPAGA4 could degrade and metabolize the agarose in cold deep-sea environments and enables rAga3420 to be an appropriate industrial enzyme for NA2 production, with industrial potential in medical and cosmetic fields.
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Affiliation(s)
- Mengyuan Zhang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Runying Zeng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China
| | - Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wenxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Xiufang Tong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China
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7
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Lunghi E, Cianferoni F, Corti C, Zhao Y, Manenti R, Ficetola GF, Mancinelli G. The trophic niche of subterranean populations of Speleomantes italicus. Sci Rep 2022; 12:18257. [PMID: 36309527 PMCID: PMC9617932 DOI: 10.1038/s41598-022-21819-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/04/2022] [Indexed: 12/31/2022] Open
Abstract
The determination of a species trophic niche can clarify its functional role within a food web and how prey resources are used in relation with the spatial and temporal variability of environmental conditions. This information may result particularly useful for the implementation of conservation plans of endangered species having a cryptic behaviour or living in places difficult to be surveyed. Here we present the first long-term study on the trophic niche of the Italian cave salamander Speleomantes italicus, a strictly protected facultative cave species that seasonally exploits surface environments (e.g., forested areas) as well as both natural and artificial subterranean environments. We analysed the diet variation of six populations of S. italicus inhabiting natural caves, surveyed 24 times in a full year. During the surveys, all sampled individuals were subjected to stomach flushing and the ingested prey were identified and enumerated; furthermore, salamanders' body condition was also evaluated. The results of the analyses provided the first comprehensive, year-round assessment of the diet for a Speleomantes species. Remarkable divergences in terms of trophic niche and body condition were observed between the studied populations. We found a discrepancy in the foraging activity of the populations located in different areas; specifically, the individuals that experienced sub-optimal microclimatic conditions poorly performed in foraging. Furthermore, we found temporal and spatial variability in the body condition of individuals. Our study highlighted a remarkably high spatial and temporal divergence in the trophic habits of conspecific populations, a feature that may represent one of the major factors promoting the variability of multiple population traits.
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Affiliation(s)
- Enrico Lunghi
- grid.9227.e0000000119573309Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.158820.60000 0004 1757 2611Dipartimento di Medicina clinica, sanità pubblica, scienze della vita e dell’ambiente (MESVA), University of L’Aquila, Coppito, L’Aquila Italy ,grid.8404.80000 0004 1757 2304Zoologia, “La Specola”, Museo di Storia Naurale, Università degli Studi di Firenze, Florence, Italy ,Natural Oasis, Prato, Italy ,Unione Speleologica Calenzano, Calenzano, Florence, Italy
| | - Fabio Cianferoni
- grid.8404.80000 0004 1757 2304Zoologia, “La Specola”, Museo di Storia Naurale, Università degli Studi di Firenze, Florence, Italy ,grid.5326.20000 0001 1940 4177Istituto di Ricerca Sugli Ecosistemi Terrestri (IRET), Consiglio Nazionale delle Ricerche (CNR), Sesto Fiorentino, Florence Italy
| | - Claudia Corti
- grid.8404.80000 0004 1757 2304Zoologia, “La Specola”, Museo di Storia Naurale, Università degli Studi di Firenze, Florence, Italy
| | - Yahui Zhao
- grid.9227.e0000000119573309Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Raoul Manenti
- grid.4708.b0000 0004 1757 2822Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy ,Laboratorio di Biologia Sotterranea “Enrico Pezzoli”, Parco Regionale del Monte Barro, Galbiate, Italy
| | - Gentile Francesco Ficetola
- grid.4708.b0000 0004 1757 2822Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy ,grid.450308.a0000 0004 0369 268XLaboratoire d’Écologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Giorgio Mancinelli
- grid.9906.60000 0001 2289 7785Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA), Università del Salento, Lecce, Italy ,grid.5326.20000 0001 1940 4177Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM), Consiglio Nazionale delle Ricerche (CNR), Lesina, Foggia Italy ,grid.10911.380000 0005 0387 0033CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
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8
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Deep-sea organisms research oriented by deep-sea technologies development. Sci Bull (Beijing) 2022; 67:1802-1816. [PMID: 36546066 DOI: 10.1016/j.scib.2022.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/30/2022] [Accepted: 05/05/2022] [Indexed: 01/07/2023]
Abstract
Deep-sea environment, characterized by high pressures, extremely high/low temperatures, limited photosynthesis-generated organic matter, darkness, and high levels of corrosion, is home to flourishing special ecosystems in the world. Here, we illustrate how the deep-sea equipment offers insights into the study of life in the deep sea based on the work in the past five decades. We first describe how organisms in the deep sea are studied, even though it is highly difficult to get access to such extreme environments. We then explain the role of deep-sea technologies in advancing research on the evolution of organisms in hydrothermal vents, cold seeps, seamounts, oceanic trenches, and whale falls from the following perspectives: biological diversity, mechanisms of environmental adaptation, biological evolution, and ecosystem connectivity. Finally, to better understand the function and service of deep-sea organisms, and further conserve the special creatures under anthropologic activity and climate change, we highlight the importance of innovative deep-sea technologies to promote cutting-edge research on deep-sea organisms, and note the remaining challenges and developing directions for deep-sea equipment.
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9
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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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10
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Damare S, Mishra A, D'Souza-Ticlo-Diniz D, Krishnaswamy A, Raghukumar C. A deep-sea hydrogen peroxide-stable alkaline serine protease from Aspergillus flavus. 3 Biotech 2020; 10:528. [PMID: 33214975 DOI: 10.1007/s13205-020-02520-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/28/2020] [Indexed: 11/26/2022] Open
Abstract
We report here the production of an alkaline serine protease by Aspergillus flavus isolated at 5600-m depth from deep-sea sediments of the Central Indian Basin. When grown on defatted groundnut oil meal at 30 °C for 48-72 h, this fungal isolate produced 2000-2500 ACU mL-1 of alkaline protease. The purified protease had activity optima at pH 10.0 and 45 °C. It was a thiol-independent serine protease, identified as an alkaline serine protease ALP1 with a molecular mass of 42.57 kDa. The thermostability and activity of the enzyme increased at 60 °C, in the presence of additives such as sucrose, Tween 20, sorbitol, Ca2+ and glycerol and was not adversely affected by H2O2 indicating its potential as a detergent additive.
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Affiliation(s)
- Samir Damare
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004 India
| | - Abhishek Mishra
- Department of Biotechnology, Goa University, Taleigao Plateau, Goa, 403 206 India
| | - Donna D'Souza-Ticlo-Diniz
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004 India
- Present Address: Department of Microbiology, SVKM's Mithibai College of Arts, Chauhan Institute of Science and Amrutben Jivanlal College of Commerce and Economics, Vile Parle West, Mumbai, India
| | - Akhila Krishnaswamy
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004 India
| | - Chandralata Raghukumar
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004 India
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11
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Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
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Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
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12
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Xue D, Zeng X, Lin D, Yao S. Thermostable ethanol tolerant xylanase from a cold-adapted marine species Acinetobacter johnsonii. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2018.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Zhang X, Li SJ, Li JJ, Liang ZZ, Zhao CQ. Novel Natural Products from Extremophilic Fungi. Mar Drugs 2018; 16:md16060194. [PMID: 29867059 PMCID: PMC6025453 DOI: 10.3390/md16060194] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 12/19/2022] Open
Abstract
Extremophilic fungi have been found to develop unique defences to survive extremes of pressure, temperature, salinity, desiccation, and pH, leading to the biosynthesis of novel natural products with diverse biological activities. The present review focuses on new extremophilic fungal natural products published from 2005 to 2017, highlighting the chemical structures and their biological potential.
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Affiliation(s)
- Xuan Zhang
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Shou-Jie Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Jin-Jie Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Zi-Zhen Liang
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Chang-Qi Zhao
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
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14
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Kumar A, Alam A, Tripathi D, Rani M, Khatoon H, Pandey S, Ehtesham NZ, Hasnain SE. Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome. Semin Cell Dev Biol 2018; 84:147-157. [PMID: 29331642 DOI: 10.1016/j.semcdb.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/01/2017] [Accepted: 01/09/2018] [Indexed: 02/02/2023]
Abstract
The biological paradox about how extremophiles persist at extreme ecological conditions throws a fascinating picture of the enormous potential of a single cell to adapt to homeostatic conditions in order to propagate. Unicellular organisms face challenges from both environmental factors and the ecological niche provided by the host tissue. Although the existence of extremophiles and their physiological properties were known for a long time, availability of whole genome sequence has catapulted the study on mechanisms of adaptation and the underlying principles that have enabled these unique organisms to withstand evolutionary and environmental pressures. Comparative genomics has shown that extremophiles possess the unique set of genes and proteins that empower them with biochemical machinery necessary to thrive in extreme environments. The presence of these proteins safeguards the cell against a wide array of extreme conditions such as temperature, pressure, radiations, chemicals, drugs etc. An insight into these adaptive mechanisms in extremophiles may help us to devise strategies to alter the genes and proteins that may have therapeutic potential and commercial value. Here we present an overview of the various adaptations in extremophiles. We also try to explain how mycobacterium channelizes its proteome to survive in stress conditions posed by host immune system.
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Affiliation(s)
- Ashutosh Kumar
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Anwar Alam
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Deeksha Tripathi
- Department of Microbiology, Central University of Rajasthan, Bandar Sindri, Ajmer, Rajasthan, India
| | - Mamta Rani
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Hafeeza Khatoon
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India
| | - Saurabh Pandey
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Nasreen Z Ehtesham
- National Institute of Pathology, Safdarjang Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Molecular Infection and Functional Biology Lab, Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, New Delhi, India; JH-Institute of Molecular Medicine, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India.
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15
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Chen CR, Makhatadze GI. Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding. J Phys Chem B 2017; 121:8300-8310. [PMID: 28795561 DOI: 10.1021/acs.jpcb.7b05831] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pressure is a well-known environmental stressor that can either stabilize or destabilize proteins. The volumetric change upon protein unfolding determines the effect of pressure on protein stability, where negative volume changes destabilized proteins at high pressures. High temperature often accompanies high pressure, for example, in the ocean depths near hydrothermal vents or near faults, so it is important to study the effect of temperature on the volumetric change upon unfolding. We previously detailed the magnitude and sign of the molecular determinants of volumetric change, allowing us to quantitatively predict the volumetric change upon protein unfolding. Here, we present a comprehensive analysis of the temperature dependence of the volumetric components of proteins, showing that hydration volume is the primary component that defines expansivities of the native and unfolded states and void volume only contributes slightly to the folded state expansivity.
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Affiliation(s)
- Calvin R Chen
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 8th Street, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 8th Street, Troy, New York 12180, United States
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16
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Lorenzo FD, Palmigiano A, Paciello I, Pallach M, Garozzo D, Bernardini ML, Cono VL, Yakimov MM, Molinaro A, Silipo A. The Deep-Sea Polyextremophile Halobacteroides lacunaris TB21 Rough-Type LPS: Structure and Inhibitory Activity towards Toxic LPS. Mar Drugs 2017; 15:md15070201. [PMID: 28653982 PMCID: PMC5532643 DOI: 10.3390/md15070201] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/12/2017] [Accepted: 06/22/2017] [Indexed: 11/24/2022] Open
Abstract
The structural characterization of the lipopolysaccharide (LPS) from extremophiles has important implications in several biomedical and therapeutic applications. The polyextremophile Gram-negative bacterium Halobacteroideslacunaris TB21, isolated from one of the most extreme habitats on our planet, the deep-sea hypersaline anoxic basin Thetis, represents a fascinating microorganism to investigate in terms of its LPS component. Here we report the elucidation of the full structure of the R-type LPS isolated from H. lacunaris TB21 that was attained through a multi-technique approach comprising chemical analyses, NMR spectroscopy, and Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry. Furthermore, cellular immunology studies were executed on the pure R-LPS revealing a very interesting effect on human innate immunity as an inhibitor of the toxic Escherichia coli LPS.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
| | - Angelo Palmigiano
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB-Unità di Catania, 95126 Catania, Italy.
| | - Ida Paciello
- Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, 00185 Rome, Italy.
| | - Mateusz Pallach
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
| | - Domenico Garozzo
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB-Unità di Catania, 95126 Catania, Italy.
| | - Maria-Lina Bernardini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, 00185 Rome, Italy.
| | - Violetta La Cono
- Marine Molecular Microbiology & Biotechnology, CNR-Institute for Coastal Marine Environment, 98122 Messina, Italy.
| | - Michail M Yakimov
- Marine Molecular Microbiology & Biotechnology, CNR-Institute for Coastal Marine Environment, 98122 Messina, Italy.
- Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia.
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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17
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Molecular determinant of the effects of hydrostatic pressure on protein folding stability. Nat Commun 2017; 8:14561. [PMID: 28169271 PMCID: PMC5309723 DOI: 10.1038/ncomms14561] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/09/2017] [Indexed: 11/14/2022] Open
Abstract
Hydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms (for example, piezophiles). Increase in hydrostatic pressure, much like increase in temperature, perturbs the thermodynamic equilibrium between native and unfolded states of proteins. Experimentally, it has been observed that increase in hydrostatic pressure can both increase and decrease protein stability. These observations suggest that volume changes upon protein unfolding can be both positive and negative. The molecular details of this difference in sign of volume changes have been puzzling the field for the past 50 years. Here we present a comprehensive thermodynamic model that provides in-depth analysis of the contribution of various molecular determinants to the volume changes upon protein unfolding. Comparison with experimental data shows that the model allows quantitative predictions of volume changes upon protein unfolding, thus paving the way to proteome-wide computational comparison of proteins from different extremophilic organisms. Proteins can be both stabilized and destabilized by pressure. Here the authors analyse the factors contributing to both negative and positive protein volume change upon denaturation, and shed light on the molecular determinants allowing proteins to be stable at high pressures.
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18
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Fan Z, Sun ZH, Liu Z, Chen YC, Liu HX, Li HH, Zhang WM. Dichotocejpins A-C: New Diketopiperazines from a Deep-Sea-Derived Fungus Dichotomomyces cejpii FS110. Mar Drugs 2016; 14:md14090164. [PMID: 27618072 PMCID: PMC5039535 DOI: 10.3390/md14090164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 01/07/2023] Open
Abstract
Three new diketopiperazines, dichotocejpins A–C (1–3), together with eight known analogues (4–11), were isolated from the culture of the deep-sea sediment derived fungus Dichotomomyces cejpii FS110. Their structures, including absolute configurations, were elucidated by a combination of HRESIMS, NMR, X-ray crystallography, and ECD calculations. Compounds 4–6, 10–11 showed significant cytotoxic activities against MCF-7, NCI-H460, HepG-2, and SF-268 tumor cell lines. Compound 1 exhibited excellent inhibitory activity against α-glucosidase with an IC50 of 138 μM.
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Affiliation(s)
- Zhen Fan
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
| | - Zhang-Hua Sun
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
| | - Zhong Liu
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Yu-Chan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
| | - Hong-Xin Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
| | - Hao-Hua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
| | - Wei-Min Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
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19
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Dichotocejpins A–C: New Diketopiperazines from a Deep-Sea-Derived Fungus Dichotomomyces cejpii FS110. Mar Drugs 2016. [DOI: 10.3390/md14090164 pmid: 276180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Domagal-Goldman SD, Wright KE, Adamala K, Arina de la Rubia L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud ME, Paulino-Lima IG, Singer K, Walther-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, Imari Walker S, Wong T. The Astrobiology Primer v2.0. ASTROBIOLOGY 2016; 16:561-653. [PMID: 27532777 PMCID: PMC5008114 DOI: 10.1089/ast.2015.1460] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/06/2016] [Indexed: 05/09/2023]
Affiliation(s)
- Shawn D Domagal-Goldman
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland, USA
- 2 Virtual Planetary Laboratory , Seattle, Washington, USA
| | - Katherine E Wright
- 3 University of Colorado at Boulder , Colorado, USA
- 4 Present address: UK Space Agency, UK
| | - Katarzyna Adamala
- 5 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota, USA
| | | | - Jade Bond
- 7 Department of Physics, University of New South Wales , Sydney, Australia
| | | | | | - Kennda Lynch
- 10 Division of Biological Sciences, University of Montana , Missoula, Montana, USA
| | - Marie-Eve Naud
- 11 Institute for research on exoplanets (iREx) , Université de Montréal, Montréal, Canada
| | - Ivan G Paulino-Lima
- 12 Universities Space Research Association , Mountain View, California, USA
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | - Kelsi Singer
- 14 Southwest Research Institute , Boulder, Colorado, USA
| | | | - Ximena C Abrevaya
- 16 Instituto de Astronomía y Física del Espacio (IAFE) , UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rika Anderson
- 17 Department of Biology, Carleton College , Northfield, Minnesota, USA
| | - Giada Arney
- 18 University of Washington Astronomy Department and Astrobiology Program , Seattle, Washington, USA
| | - Dimitra Atri
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Jeff S Bowman
- 19 Lamont-Doherty Earth Observatory, Columbia University , Palisades, New York, USA
| | | | | | - Regina Carns
- 22 Polar Science Center, Applied Physics Laboratory, University of Washington , Seattle, Washington, USA
| | - Aditya Chopra
- 23 Planetary Science Institute, Research School of Earth Sciences, Research School of Astronomy and Astrophysics, The Australian National University , Canberra, Australia
| | - Jesse Colangelo-Lillis
- 24 Earth and Planetary Science, McGill University , and the McGill Space Institute, Montréal, Canada
| | | | - Julia DeMarines
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Carie Frantz
- 27 Department of Geosciences, Weber State University , Ogden, Utah, USA
| | - Eduardo de la Fuente
- 28 IAM-Departamento de Fisica, CUCEI , Universidad de Guadalajara, Guadalajara, México
| | - Douglas Galante
- 29 Brazilian Synchrotron Light Laboratory , Campinas, Brazil
| | - Jennifer Glass
- 30 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia , USA
| | | | | | - Colin Goldblatt
- 33 School of Earth and Ocean Sciences, University of Victoria , Victoria, Canada
| | - Rachel Horak
- 34 American Society for Microbiology , Washington, DC, USA
| | | | - Betül Kaçar
- 36 Harvard University , Organismic and Evolutionary Biology, Cambridge, Massachusetts, USA
| | - Akos Kereszturi
- 37 Research Centre for Astronomy and Earth Sciences , Hungarian Academy of Sciences, Budapest, Hungary
| | - Emily Knowles
- 38 Johnson & Wales University , Denver, Colorado, USA
| | - Paul Mayeur
- 39 Rensselaer Polytechnic Institute , Troy, New York, USA
| | - Shawn McGlynn
- 40 Earth Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
| | - Yamila Miguel
- 41 Laboratoire Lagrange, UMR 7293, Université Nice Sophia Antipolis , CNRS, Observatoire de la Côte d'Azur, Nice, France
| | | | - Catherine Neish
- 43 Department of Earth Sciences, The University of Western Ontario , London, Canada
| | - Lena Noack
- 44 Royal Observatory of Belgium , Brussels, Belgium
| | - Sarah Rugheimer
- 45 Department of Astronomy, Harvard University , Cambridge, Massachusetts, USA
- 46 University of St. Andrews , St. Andrews, UK
| | - Eva E Stüeken
- 47 University of Washington , Seattle, Washington, USA
- 48 University of California , Riverside, California, USA
| | | | - Sara Imari Walker
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
- 50 School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University , Tempe, Arizona, USA
| | - Teresa Wong
- 51 Department of Earth and Planetary Sciences, Washington University in St. Louis , St. Louis, Missouri, USA
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21
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Pandharipande PP, Makhatadze GI. Applications of pressure perturbation calorimetry to study factors contributing to the volume changes upon protein unfolding. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1860:1036-1042. [PMID: 26341789 DOI: 10.1016/j.bbagen.2015.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 08/28/2015] [Accepted: 08/30/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Pressure perturbation calorimetry (PPC) is a biophysical method that allows direct determination of the volume changes upon conformational transitions in macromolecules. SCOPE OF THIS REVIEW This review provides novel details of the use of PPC to analyze unfolding transitions in proteins. The emphasis is made on the data analysis as well as on the validation of different structural factors that define the volume changes upon unfolding. Four case studies are presented that show the application of these concepts to various protein systems. MAJOR CONCLUSIONS The major conclusions are: 1. Knowledge of the thermodynamic parameters for heat induced unfolding facilitates the analysis of the PPC profiles. 2. The changes in the thermal expansion coefficient upon unfolding appear to be temperature dependent.3.Substitutions on the protein surface have negligible effects on the volume changes upon protein unfolding. 4. Structural plasticity of proteins defines the position dependent effect of amino acid substitutions of the residues buried in the native state. 5. Small proteins have positive volume changes upon unfolding which suggests difference in balance between the cavity/void volume in the native state and the hydration volume changes upon unfolding as compared to the large proteins that have negative volume changes. GENERAL SIGNIFICANCE The information provided here gives a better understanding and deeper insight into the role played by various factors in defining the volume changes upon protein unfolding.
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Affiliation(s)
- Pranav P Pandharipande
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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22
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A Continuous Culture System for Assessing Microbial Activities in the Piezosphere. Appl Environ Microbiol 2015. [PMID: 26209666 DOI: 10.1128/aem.01215-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere.
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23
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Li H, Voutilainen S, Ojamo H, Turunen O. Stability and activity of Dictyoglomus thermophilum GH11 xylanase and its disulphide mutant at high pressure and temperature. Enzyme Microb Technol 2015; 70:66-71. [DOI: 10.1016/j.enzmictec.2014.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023]
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Bai J, Liu D, Yu S, Proksch P, Lin W. Amicoumacins from the marine-derived bacterium Bacillus sp. with the inhibition of NO production. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.09.100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Niu S, Liu D, Hu X, Proksch P, Shao Z, Lin W. Spiromastixones A-O, antibacterial chlorodepsidones from a deep-sea-derived Spiromastix sp. fungus. JOURNAL OF NATURAL PRODUCTS 2014; 77:1021-1030. [PMID: 24571273 DOI: 10.1021/np5000457] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fifteen new depsidone-based analogues named spiromastixones A-O (1-15) were isolated from the fermentation broth of a deep-sea Spiromastix sp. fungus. Their structures were elucidated on the basis of extensive NMR and mass spectroscopic analysis in association with chemical conversion. Spiromastixones A-O are classified into two subtypes based on the orientation of ring C relative to ring A, while the n-propyl substituents on rings A and C are rarely seen in natural products. Most analogues are substituted by various numbers of chlorine atoms. All compounds exhibited significant inhibition against Gram-positive bacteria including Staphylococcus aureus, Bacillus thuringiensis, and Bacillus subtilis with MIC values ranging from 0.125 to 8.0 μg/mL. In addition, compounds 6-10 displayed potent inhibitory effects against methicillin-resistant bacterial strains of S. aureus (MRSA) and S. epidermidis (MRSE), while 10 also inhibited the growth of the vancomycin-resistant bacteria Enterococcus faecalis and E. faecium (VRE). The structure-activity relationships are discussed.
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Affiliation(s)
- Siwen Niu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University , Beijing, 100191, People's Republic of China
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Nikolic N, Smole Z, Krisko A. Proteomic properties reveal phyloecological clusters of Archaea. PLoS One 2012; 7:e48231. [PMID: 23133575 PMCID: PMC3485053 DOI: 10.1371/journal.pone.0048231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 09/28/2012] [Indexed: 11/18/2022] Open
Abstract
In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.
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Affiliation(s)
- Nela Nikolic
- Mediterranean Institute for Life Sciences, Split, Croatia
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag, Duebendorf, Switzerland
| | - Zlatko Smole
- Mediterranean Institute for Life Sciences, Split, Croatia
- Institute of Cell Biology, ETH Zurich, Zurich, Switzerland
| | - Anita Krisko
- Mediterranean Institute for Life Sciences, Split, Croatia
- * E-mail:
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Rosenbaum E, Gabel F, Durá MA, Finet S, Cléry-Barraud C, Masson P, Franzetti B. Effects of hydrostatic pressure on the quaternary structure and enzymatic activity of a large peptidase complex from Pyrococcus horikoshii. Arch Biochem Biophys 2011; 517:104-10. [PMID: 21896270 DOI: 10.1016/j.abb.2011.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 07/31/2011] [Indexed: 10/17/2022]
Abstract
While molecular adaptation to high temperature has been extensively studied, the effect of hydrostatic pressure on protein structure and enzymatic activity is still poorly understood. We have studied the influence of pressure on both the quaternary structure and enzymatic activity of the dodecameric TET3 peptidase from Pyrococcus horikoshii. Small angle X-ray scattering (SAXS) revealed a high robustness of the oligomer under high pressure of up to 300 MPa at 25°C as well as at 90°C. The enzymatic activity of TET3 was enhanced by pressure up to 180 MPa. From the pressure behavior of the different rate-constants we have determined the volume changes associated with substrate binding and catalysis. Based on these results we propose that a change in the rate-limiting step occurs around 180 MPa.
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Affiliation(s)
- Eva Rosenbaum
- Group Extremophiles and Large Molecular Assemblies (ELMA), CEA, Institut de Biologie Structurale, Grenoble, France
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Marine biocatalysts: enzymatic features and applications. Mar Drugs 2011; 9:478-499. [PMID: 21731544 PMCID: PMC3124967 DOI: 10.3390/md9040478] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 02/28/2011] [Accepted: 03/23/2011] [Indexed: 11/21/2022] Open
Abstract
In several recent reports related to biocatalysis the enormous pool of biodiversity found in marine ecosystems is considered a profitable natural reservoir for acquiring an inventory of useful biocatalysts. These enzymes are characterized by well-known habitat-related features such as salt tolerance, hyperthermostability, barophilicity and cold adaptivity. In addition, their novel chemical and stereochemical characteristics increase the interest of biocatalysis practitioners both in academia and research industry. In this review, starting from the analysis of these featuring habitat-related properties, important examples of marine enzymes in biocatalysis will be reported. Completion of this report is devoted to the analysis of novel chemical and stereochemical biodiversity offered by marine biocatalysts with particular emphasis on current or potential applications of these enzymes in chemical and pharmaceutical fields. The analysis of literature cited here and the many published patent applications concerning the use of marine enzymes supports the view that these biocatalysts are just waiting to be discovered, reflecting the importance of the marine environment. The potential of this habitat should be thoroughly explored and possibly the way to access useful biocatalysts should avoid destructive large-scale collections of marine biomass for enzyme production. These two aspects are day by day increasing in interest and a future increase in the use of marine enzymes in biocatalysis should be expected.
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Jones EG, Lineweaver CH. To what extent does terrestrial life "follow the water"? ASTROBIOLOGY 2010; 10:349-361. [PMID: 20446874 DOI: 10.1089/ast.2009.0428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Terrestrial life is known to require liquid water, but not all terrestrial water is inhabited. Thus, liquid water is a necessary, but not sufficient, condition for life. To quantify the terrestrial limits on the habitability of water and help identify the factors that make some terrestrial water uninhabited, we present empirical pressure-temperature (P-T) phase diagrams of water, Earth, and terrestrial life. Eighty-eight percent of the volume of Earth where liquid water exists is not known to host life. This potentially uninhabited terrestrial liquid water includes (i) hot and deep regions of Earth where some combination of high temperature (T > 122 degrees C) and restrictions on pore space, nutrients, and energy is the limiting factor and (ii) cold and near-surface regions of Earth, such as brine inclusions and thin films in ice and permafrost (depths less than approximately 1 km), where low temperatures (T < -40 degrees C), low water activity (a(w) < 0.6), or both are the limiting factors. If the known limits of terrestrial life do not change significantly, these limits represent important constraints on our biosphere and, potentially, on others, since approximately 4 billion years of evolution have not allowed life to adapt to a large fraction of the volume of Earth where liquid water exists.
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Affiliation(s)
- Eriita G Jones
- Planetary Sciences Institute, Research School of Astronomy and Astrophysics and the Research School of Earth Sciences, Australian National University, Canberra, Australia.
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Morozkina EV, Slutskaya ES, Fedorova TV, Tugay TI, Golubeva LI, Koroleva OV. Extremophilic microorganisms: Biochemical adaptation and biotechnological application (review). APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810010011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bass D, Howe A, Brown N, Barton H, Demidova M, Michelle H, Li L, Sanders H, Watkinson SC, Willcock S, Richards TA. Yeast forms dominate fungal diversity in the deep oceans. Proc Biol Sci 2008; 274:3069-77. [PMID: 17939990 DOI: 10.1098/rspb.2007.1067] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fungi are the principal degraders of biomass in most terrestrial ecosystems. In contrast to surface environments, deep-sea environmental gene libraries have suggested that fungi are rare and non-diverse in high-pressure marine environments. Here, we report the diversity of fungi from 11 deep-sea samples from around the world representing depths from 1,500 to 4,000 m (146-388 atm) and two shallower water column samples (250 and 500m). We sequenced 239 clones from 10 fungal-specific 18S rRNA gene libraries constructed from these samples, from which we detected only 18 fungal 18S-types in deep-sea samples. Our phylogenetic analyses show that a total of only 32 fungal 18S-types have so far been recovered from deep-sea habitats, and our results suggest that fungi, in general, are relatively rare in the deep-sea habitats we sampled. The fungal diversity detected suggests that deep-sea environments host an evolutionarily diverse array of fungi dominated by groups of distantly related yeasts, although four putative filamentous fungal 18S-types were detected. The majority of our new sequences branch close to known fungi found in surface environments. This pattern contradicts the proposal that deep-sea and hydrothermal vent habitats represent ancient ecosystems, and demonstrates a history of frequent dispersal between terrestrial and deep-sea habitats.
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Affiliation(s)
- David Bass
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
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Chiu KH, Huang HW, Mok HK. Differential proteome analysis of hagfish dental and somatic skeletal muscles. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:689-700. [PMID: 17965921 DOI: 10.1007/s10126-007-9020-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2006] [Revised: 04/16/2007] [Accepted: 04/17/2007] [Indexed: 05/25/2023]
Abstract
Hagfish, the plesiomorphic sister group of all vertebrates, are deep-sea scavengers. The large musculus (m.) longitudinalis linguae (dental muscle) is a specialized element of the feeding apparatus that facilitates the efficient ingestion of food. In this article, we compare the protein expression in hagfish dental and somatic (the m. parietalis) skeletal muscles via two-dimensional gel electrophoresis and mass spectrometry in order to characterize the former muscle. Of the 500 proteins screened, 24 were identified with significant differential expression between these muscles. The proteins that were overexpressed in the dental muscle compared to the somatic muscle were troponin C (TnC), glycogen phosphorylase, beta-enolase, fructose-bisphosphate aldolase A (aldolase A), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In contrast, myosin light chain 1 (MLC 1) and creatine kinase (CK) were over-expressed in the somatic muscle relative to the dental muscle. These results suggest that these two muscles have different energy sources and contractile properties and provide an initial representative map for comparative studies of muscle-protein expression in low craniates.
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Affiliation(s)
- Kuo-Hsun Chiu
- Institute of Marine Biology, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
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Tan C, Song H, Niemi J, You L. A synthetic biology challenge: making cells compute. MOLECULAR BIOSYSTEMS 2007; 3:343-53. [PMID: 17460793 DOI: 10.1039/b618473c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Advances in biology and engineering have enabled the reprogramming of cells with well-defined functions, leading to the emergence of synthetic biology. Early successes in this nascent field suggest its potential to impact diverse areas. Here, we examine the feasibility of engineering circuits for cell-based computation. We illustrate the basic concepts by describing the mapping of several computational problems to engineered gene circuits. Revolving around these examples and past studies, we discuss technologies and computational methods available to design, test, and optimize gene circuits. We conclude with discussion of challenges involved in a typical design cycle, as well as those specific to cellular computation.
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Affiliation(s)
- Cheemeng Tan
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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Xu Y, Miao L, Li XC, Xiao X, Qian PY. Antibacterial and antilarval activity of deep-sea bacteria from sediments of the West Pacific Ocean. BIOFOULING 2007; 23:131-7. [PMID: 17453737 DOI: 10.1080/08927010701219323] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Deep-sea microorganisms are a new source of bioactive compounds. In this study, crude ethyl acetate extracts of 176 strains of deep-sea bacteria, isolated from sediments of the West Pacific Ocean, were screened for their antibacterial activity against four test bacterial strains isolated from marine biofilms. Of these, 28 deep-sea bacterial strains exhibited antibacterial activity against one or more of the bacteria tested. Active deep-sea bacterial strains belonged mainly to the genera of Pseudomonas, Psychrobacter and Halomonas. Additionally, antilarval activity of 56 deep-sea bacterial strains was screened using Balanus amphitrite larvae. Seven bacterial strains produced metabolites that had strong inhibitive effects on larval settlement. None of these metabolites showed significant toxicity. The crude extract of one deep-sea Streptomyces strain could completely inhibit larval settlement at a concentration of 25 microg ml(-1).
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Affiliation(s)
- Ying Xu
- Department of Biology/Coastal Marine Laboratory, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong
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Debashish G, Malay S, Barindra S, Joydeep M. Marine enzymes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 96:189-218. [PMID: 16566092 DOI: 10.1007/b135785] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Marine enzyme biotechnology can offer novel biocatalysts with properties like high salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and ease in large-scale cultivation. This review deals with the research and development work done on the occurrence, molecular biology, and bioprocessing of marine enzymes during the last decade. Exotic locations have been accessed for the search of novel enzymes. Scientists have isolated proteases and carbohydrases from deep sea hydrothermal vents. Cold active metabolic enzymes from psychrophilic marine microorganisms have received considerable research attention. Marine symbiont microorganisms growing in association with animals and plants were shown to produce enzymes of commercial interest. Microorganisms isolated from sediment and seawater have been the most widely studied, proteases, carbohydrases, and peroxidases being noteworthy. Enzymes from marine animals and plants were primarily studied for their metabolic roles, though proteases and peroxidases have found industrial applications. Novel techniques in molecular biology applied to assess the diversity of chitinases, nitrate, nitrite, ammonia-metabolizing, and pollutant-degrading enzymes are discussed. Genes encoding chitinases, proteases, and carbohydrases from microbial and animal sources have been cloned and characterized. Research on the bioprocessing of marine-derived enzymes, however, has been scanty, focusing mainly on the application of solid-state fermentation to the production of enzymes from microbial sources.
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Affiliation(s)
- Ghosh Debashish
- Environmental Science Programme and Department of Life Science & Biotechnology, Jadavpur University, 700 032 Kolkata, India
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Affiliation(s)
- Antonio D Molina-García
- Department of Engineering, Instituto del Frío, C.S.I.C., José Antonio Novais, 10, Ciudad Universitaria, 28040 Madrid, Spain.
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Abstract
Extremophiles thrive in ice, boiling water, acid, the water core of nuclear reactors, salt crystals, and toxic waste and in a range of other extreme habitats that were previously thought to be inhospitable for life. Extremophiles include representatives of all three domains (Bacteria, Archaea, and Eucarya); however, the majority are microorganisms, and a high proportion of these are Archaea. Knowledge of extremophile habitats is expanding the number and types of extraterrestrial locations that may be targeted for exploration. In addition, contemporary biological studies are being fueled by the increasing availability of genome sequences and associated functional studies of extremophiles. This is leading to the identification of new biomarkers, an accurate assessment of cellular evolution, insight into the ability of microorganisms to survive in meteorites and during periods of global extinction, and knowledge of how to process and examine environmental samples to detect viable life forms. This paper evaluates extremophiles and extreme environments in the context of astrobiology and the search for extraterrestrial life.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Abstract
The industrial application of enzymes that can withstand harsh conditions has greatly increased over the past decade. This is mainly a result of the discovery of novel enzymes from extremophilic microorganisms. Recent advances in the study of extremozymes point to the acceleration of this trend. In particular, enzymes from thermophilic organisms have found the most practical commercial use to date because of their overall inherent stability. This has also led to a greater understanding of stability factors involved in adaptation of these enzymes to their unusual environments.
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Abstract
Each recent report of liquid water existing elsewhere in the Solar System has reverberated through the international press and excited the imagination of humankind. Why? Because in the past few decades we have come to realize that where there is liquid water on Earth, virtually no matter what the physical conditions, there is life. What we previously thought of as insurmountable physical and chemical barriers to life, we now see as yet another niche harbouring 'extremophiles'. This realization, coupled with new data on the survival of microbes in the space environment and modelling of the potential for transfer of life between celestial bodies, suggests that life could be more common than previously thought. Here we examine critically what it means to be an extremophile, and the implications of this for evolution, biotechnology and especially the search for life in the Universe.
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Affiliation(s)
- L J Rothschild
- NASA Ames Research Center, Moffett Field, California 94035-1000, USA.
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