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Li W, Huo R, Di Y, Liu C, Zhou S. Efficient nitrogen removal by the aerobic denitrifying bacterium Pseudomonas stutzeri RAS-L11 under triple stresses of high alkalinity, high salinity, and tetracycline: From performance to mechanism. BIORESOURCE TECHNOLOGY 2025; 430:132590. [PMID: 40288654 DOI: 10.1016/j.biortech.2025.132590] [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: 12/27/2024] [Revised: 03/31/2025] [Accepted: 04/24/2025] [Indexed: 04/29/2025]
Abstract
Efficient aerobic denitrification bacteria are rarely reported under triple stresses of high alkalinity, high salinity, and tetracycline. Here, strain Pseudomonas stutzeri RAS-L11 was isolated, under the optimal reaction conditions of C/N = 6, sodium acetate as carbon source, and pH 7.0-11.0. Moreover, RAS-L11 showed perfect nitrogen removal performance under dual and triple stresses. Specifically, the mean removal efficiency of total dissolved nitrogen for different medium (nitrate, nitrite, ammonia, nitrate and ammonia, and nitrite and ammonia) reached 92.35 %, 66.85 %, 71.33 %, 89.42 %, and 68.76 % under triple stresses. Nitrogen balance results indicated that biomass nitrogen accounted for a small percentage (4.48 % to 20.79 %). Furthermore, the nitrogen metabolism pathways and tetracycline, salinity, and alkaline tolerance-associated genes were also confirmed. Strain RAS-L11 achieved 42.67-70.72 % NO3--N and 83.72-88.53 % NH4+-N removal efficiencies in both sterilized and actual systems treating pharmaceutical wastewater. Our characterization of the RAS-L11 provides a reference for nitrogen removal of pharmaceutical wastewater.
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Affiliation(s)
- Wanying Li
- Hebei Key Laboratory of Pollution Prevention Biotechnology, College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Rui Huo
- Hebei Key Laboratory of Pollution Prevention Biotechnology, College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Yiling Di
- Hebei Key Laboratory of Pollution Prevention Biotechnology, College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Chun Liu
- Hebei Key Laboratory of Pollution Prevention Biotechnology, College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Shilei Zhou
- Hebei Key Laboratory of Pollution Prevention Biotechnology, College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China.
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2
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Huang Z, Yi G, Wang Q, Wang S, Xu Q, Huan C, Wang Y, Zhang W, Wang A, Liu W. Improving microbial activity in high-salt wastewater: A review of innovative approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176278. [PMID: 39278494 DOI: 10.1016/j.scitotenv.2024.176278] [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: 07/06/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/18/2024]
Abstract
The Zero discharge technology has become an important pathroute for sustainable development of high salt wastewater treatment. However, the cohabitation of organic and inorganic debris can cause serious problems such membrane clogging and the formation of hazardous impurity salts that further restrict the recovery of all salt varieties by evaporating and crystallizing. In highly salinized wastewater, biological treatments offer advantages in terms of cost and sustainability when used as a pre-treatment step to eliminate organic debris. On the other hand, high salinity is always a major obstacle to microbial diversity, abundance, and activity, which can result in low organic matter removal effectiveness or the failure of the microbial treatment system. Biofortification techniques can attenuate the negative effects of salt stress and other unfavourable conditions on microorganisms, while the regulation mechanisms of microbial and community collaboration by fortification methods have been an open question. Therefore, a comprehensive summary of the types, mechanisms, and effects of the major biofortification techniques is proposed. This review dialyzes the characteristics and sources of hypersaline wastewater and the main treatment methods. Then, the mechanisms of microbial salt tolerance are summarized and discussed based on microbial characteristics and the protective effects provided by the processes. Finally, the research and application of the main bioaugmentation methods are developed in detail, describing the characteristics, advantages and disadvantages of the different enhancement methods in their implementation. This review provides a more comprehensive perspective on the future engineering applications of bioaugmentation technology, and explores in depth the possibilities of applying biological methods to high-salinity wastewater treatment.
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Affiliation(s)
- Zongyi Huang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Genping Yi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Qiandi Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Sihui Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Qiongying Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Changan Huan
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Yuqi Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Wenzhe Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; China Testing & Certification International Group Co.,Ltd., Beijng 100024, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenzong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China.
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Zheng J, Mallon J, Lammers A, Rados T, Litschel T, Moody ERR, Ramirez-Diaz DA, Schmid A, Williams TA, Bisson-Filho AW, Garner E. Salactin, a dynamically unstable actin homolog in Haloarchaea. mBio 2023; 14:e0227223. [PMID: 37966230 PMCID: PMC10746226 DOI: 10.1128/mbio.02272-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.
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Affiliation(s)
- Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John Mallon
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Alex Lammers
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Department of Biomedical Engineering, The Biological Design Center, Boston University, Boston, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Theopi Rados
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Thomas Litschel
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Edmund R. R. Moody
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Diego A. Ramirez-Diaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy Schmid
- Department of Biology, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexandre W. Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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Cho C, Lee D, Jeong D, Kim S, Kim MK, Srinivasan S. Characterization of radiation-resistance mechanism in Spirosoma montaniterrae DY10 T in terms of transcriptional regulatory system. Sci Rep 2023; 13:4739. [PMID: 36959250 PMCID: PMC10036542 DOI: 10.1038/s41598-023-31509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
To respond to the external environmental changes for survival, bacteria regulates expression of a number of genes including transcription factors (TFs). To characterize complex biological phenomena, a biological system-level approach is necessary. Here we utilized six computational biology methods to infer regulatory network and to characterize underlying biologically mechanisms relevant to radiation-resistance. In particular, we inferred gene regulatory network (GRN) and operons of radiation-resistance bacterium Spirosoma montaniterrae DY10[Formula: see text] and identified the major regulators for radiation-resistance. Our results showed that DNA repair and reactive oxygen species (ROS) scavenging mechanisms are key processes and Crp/Fnr family transcriptional regulator works as a master regulatory TF in early response to radiation.
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Affiliation(s)
- Changyun Cho
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dohoon Lee
- Bioinformatics Institute, Seoul National University, Seoul, 08826, Republic of Korea
- BK21 FOUR Intelligence Computing, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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Saez-Zamacona I, Grindlay G, Martínez-Espinosa RM. Evaluation of Haloferax mediterranei Strain R4 Capabilities for Cadmium Removal from Brines. Mar Drugs 2023; 21:72. [PMID: 36827113 PMCID: PMC9960891 DOI: 10.3390/md21020072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Haloferax mediterranei has revealed a high bioremediation potential for several inorganic anions (e.g., nitrates and nitrites) and metals from hypersaline waters and brines. However, it is unclear, to date, whether this microorganism allows Cd (II) bioremediation. Consequently, the main objective of this work was to assess the Cd (II) bioremediation potential of Hfx. mediterranei R4. To this end, Hfx. mediterranei cell growth rate and metal bioaccumulation were investigated using different culture media (complex, CM, and defined medium, DM) containing Cd (II) up to 1 mM. In addition, the elemental profile of the biomass (i.e., Al, Ba, Ca, Co, Cu, Fe, K, Mg, Mn, Na, Ni, Sr and Zn) has also been monitored to gain insight into the metabolic processes that may be taking place at the intracellular level for Cd (II) removal. Because of the formation of CdS precipitate, CM is not a suitable culture media for evaluating Cd bioremediation since metal concentration could not be appropriately controlled. When operating in DM, it was observed that the cell doubling time increases three times in the presence of Cd (II). Hfx. mediterranei can bioaccumulate Cd, showing the highest significant accumulation at concentrations of 0.4 mM (108 ± 12 mg Cd/g dry tissue). Finally, the presence of Cd (II) affects the content of K, Mg, Mn and Zn in the biomass, by increasing K levels up to 27 ± 18% and Mn up to 310 ± 140% and reducing Mg levels up to 55 ± 36% and Zn up to 30 ± 4%. These results suggest that different mechanisms are involved in Cd (II) tolerance by Hfx. mediterranei, resulting in increasing the cell concentration of stress-tolerant elements in the biomass (K and Mn), while lowering the concentration of elements which Cd (II) competes with (Mg and Zn), and that all affects the physiological response of the organism by decreasing its growth rate.
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Affiliation(s)
- Iraide Saez-Zamacona
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Guillermo Grindlay
- Department of Analytical Chemistry, Nutrition and Food Sciences, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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6
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Boase K, González C, Vergara E, Neira G, Holmes D, Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Front Microbiol 2022; 13:848410. [PMID: 35516430 PMCID: PMC9062700 DOI: 10.3389/fmicb.2022.848410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130T, Acidihalobacter yilgarnensis DSM 105917T, Acidihalobacter aeolianus DSM 14174T, and Acidihalobacter ferrooxydans DSM 14175T. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.
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Affiliation(s)
- Katelyn Boase
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - David Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes,
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Elizabeth Watkin,
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Chen C, Huang K, Li X, Tian H, Yu H, Huang J, Yuan H, Zhao S, Shao L. Effects of CcpA against salt stress in Lactiplantibacillus plantarum as assessed by comparative transcriptional analysis. Appl Microbiol Biotechnol 2021; 105:3691-3704. [PMID: 33852024 DOI: 10.1007/s00253-021-11276-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Lactiplantibacillus plantarum is frequently exposed to salt stress during industrial applications. Catabolite control protein (CcpA) controls the transcription of many genes, but its role in the response to salt stress remains unclear. In this study, we used transcriptome analyses to investigate differences in the logarithmic growth phases of Lactiplantibacillus plantarum ST-III and its ccpA-knockout mutant when grown with or without salt and glycine betaine (GB). The deletion of ccpA significantly affected bacterial growth under different conditions. Among the comparisons, the highest proportion of differentially expressed genes (64%) was observed in the comparison between the wild-type and ccpA mutant grown with NaCl, whereas the lowest proportion (6%) was observed in the comparison between the ccpA mutant strain cultures grown with NaCl alone or with GB together. Transcriptomic analyses showed that CcpA could regulate GB uptake, activate iron uptake, produce acetyl-CoA, and affect fatty acid composition to maintain membrane lipid homeostasis in the adaptation of high-salinity conditions. Conclusively, these results demonstrate the importance of CcpA as a master regulator of these processes in response to salt stress, and provide new insights into the complex regulatory network of lactic acid bacteria. KEY POINTS: • The absence of CcpA significantly affected growth of L. plantarum and its response to salt stress. • CcpA regulates compatible solutes absorption and ions transport to resist salt stress. • CcpA alters fatty acids composition to maintain membrane lipid homeostasis towards salt stress.
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Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Ke Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Xiaohong Li
- Shanghai Customs P. R. China Technical Center For Animal, Plant And Food Inspection And Quarantine, Shanghai, People's Republic of China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Juan Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China
| | - Shanshan Zhao
- College of Agriculture, Hebei University of Engineering, Handan, People's Republic of China
| | - Li Shao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, People's Republic of China.
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8
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Enrichment of Hydrogen Oxidizing Bacteria from High Temperature and Salinity Environments. Appl Environ Microbiol 2021; 87:AEM.02439-20. [PMID: 33257312 PMCID: PMC7851685 DOI: 10.1128/aem.02439-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There is an urgent need for sustainable protein supply routes with low environmental footprint. Recently, the use of hydrogen oxidizing bacteria (HOB) as a platform for high quality microbial protein (MP) production has regained interest. This study aims to investigate the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, while maintaining a high protein content and a high quality amino acid profile. Pressure drop and hydrogen consumption were measured for 56 days to evaluate autotrophy of a total of six communities in serum flasks. Of the six communities, four were enriched under saline (0.0, 0.25, 0.5 and 1.0 mol NaCl l-1) and two under thermophilic conditions (65°C). Five communities enriched for HOB were subsequently cultivated in continuously stirred reactors under the same conditions to evaluate their potential as microbial protein producers. The protein percentages ranged from 41 to 80%. The highest protein content was obtained for the thermophilic enrichments. Amino acid profiles were comparable to protein sources commonly used for feed purposes. Members of the genus Achromobacter were found to dominate the saline enrichments while members of the genus Hydrogenibacillus were found to dominate the thermophilic enrichments. Here we show that enriching for HOB while steering the community toward low diversity and maintaining a high quality protein content can be successfully achieved, both in saline and thermophilic conditions.IMPORTANCE Alternative feed and food supply chains are required to decrease water and land use. HOB offer a promising substitute for traditional agricultural practice to produce microbial protein (MP) from residual materials and renewable energy. To safeguard product stability, the composition of the HOB community should be controlled. Defining strategies to maintain the stability of the communities is therefore key for optimization purposes. In this study, we use salt and temperature as independent conditions to stabilize the composition of the HOB communities. Based on the results presented, we conclude that HOB communities can be steered to have low diversity using the presented conditions while producing a desirable protein content with a valuable amino acid profile.
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Jeong SW, Choi YJ. Extremophilic Microorganisms for the Treatment of Toxic Pollutants in the Environment. Molecules 2020; 25:E4916. [PMID: 33114255 PMCID: PMC7660605 DOI: 10.3390/molecules25214916] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022] Open
Abstract
As concerns about the substantial effect of various hazardous toxic pollutants on the environment and public health are increasing, the development of effective and sustainable treatment methods is urgently needed. In particular, the remediation of toxic components such as radioactive waste, toxic heavy metals, and other harmful substances under extreme conditions is quite difficult due to their restricted accessibility. Thus, novel treatment methods for the removal of toxic pollutants using extremophilic microorganisms that can thrive under extreme conditions have been investigated during the past several decades. In this review, recent trends in bioremediation using extremophilic microorganisms and related approaches to develop them are reviewed, with relevant examples and perspectives.
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Affiliation(s)
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Korea;
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Flores N, Hoyos S, Venegas M, Galetović A, Zúñiga LM, Fábrega F, Paredes B, Salazar-Ardiles C, Vilo C, Ascaso C, Wierzchos J, Souza-Egipsy V, Araya JE, Batista-García RA, Gómez-Silva B. Haloterrigena sp. Strain SGH1, a Bacterioruberin-Rich, Perchlorate-Tolerant Halophilic Archaeon Isolated From Halite Microbial Communities, Atacama Desert, Chile. Front Microbiol 2020; 11:324. [PMID: 32194531 PMCID: PMC7066086 DOI: 10.3389/fmicb.2020.00324] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/14/2020] [Indexed: 11/16/2022] Open
Abstract
An extreme halophilic archaeon, strain SGH1, is a novel microorganism isolated from endolithic microbial communities colonizing halites at Salar Grande, Atacama Desert, in northern Chile. Our study provides structural, biochemical, genomic, and physiological information on this new isolate living at the edge of the physical and chemical extremes at the Atacama Desert. SGH1 is a Gram-negative, red-pigmented, non-motile unicellular coccoid organism. Under the transmission electron microscope, strain SGH1 showed an abundant electro-dense material surrounding electron-lucent globular structures resembling gas vacuoles. Strain SGH1 showed a 16S rRNA gene sequence with a close phylogenetic relationship to the extreme halophilic archaea Haloterrigena turkmenica and Haloterrigena salina and has been denominated Haloterrigena sp. strain SGH1. Strain SGH1 grew at 20-40°C (optimum 37°C), at salinities between 15 and 30% (w/v) NaCl (optimum 25%) and growth was improved by addition of 50 mM KCl and 0.5% w/v casamino acids. Growth was severely restricted at salinities below 15% NaCl and cell lysis is avoided at a minimal 10% NaCl. Maximal concentrations of magnesium chloride and sodium or magnesium perchlorates that supported SGH1 growth were 0.5 and 0.15M, respectively. Haloterrigena sp. strain SGH1 accumulates bacterioruberin (BR), a C50 xanthophyll, as the major carotenoid. Total carotenoids in strain SGH1 amounted to nearly 400 μg BR per gram of dry biomass. Nearly 80% of total carotenoids accumulated as geometric isomers of BR: all-trans-BR (50%), 5-cis-BR (15%), 9-cis-BR (10%), 13-cis-BR (4%); other carotenoids were dehydrated derivatives of BR. Carotenogenesis in SGH1 was a reversible and salt-dependent process; transferring BR-rich cells grown in 25% (w/v) NaCl to 15% (w/v) NaCl medium resulted in depigmentation, and BR content was recovered after transference and growth of unpigmented cells to high salinity medium. Methanol extracts and purified BR isomers showed an 8-9-fold higher antioxidant activity than Trolox or β-carotene. Both, plasma membrane integrity and mitochondrial membrane potential measurements under acute 18-h assays showed that purified BR isomers were non-toxic to cultured human THP-1 cells.
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Affiliation(s)
- Nataly Flores
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Sebastián Hoyos
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Mauricio Venegas
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Alexandra Galetović
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Lidia M. Zúñiga
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisca Fábrega
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Bernardo Paredes
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Camila Salazar-Ardiles
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Claudia Vilo
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Carmen Ascaso
- Department Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences – Spanish National Research Council, Madrid, Spain
| | - Jacek Wierzchos
- Department Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences – Spanish National Research Council, Madrid, Spain
| | - Virginia Souza-Egipsy
- Department of Macromolecular Physics, Institute of Material Structure – Spanish National Research Council, Madrid, Spain
| | - Jorge E. Araya
- Laboratory of Molecular Parasitology, Department of Medical Technology and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Benito Gómez-Silva
- Laboratory of Biochemistry, Biomedical Department and Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
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A potassium chloride to glycine betaine osmoprotectant switch in the extreme halophile Halorhodospira halophila. Sci Rep 2020; 10:3383. [PMID: 32098991 PMCID: PMC7042295 DOI: 10.1038/s41598-020-59231-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
Halophiles utilize two distinct osmoprotection strategies. The accumulation of organic compatible solutes such as glycine betaine does not perturb the functioning of cytoplasmic components, but represents a large investment of energy and carbon. KCl is an energetically attractive alternative osmoprotectant, but requires genome-wide modifications to establish a highly acidic proteome. Most extreme halophiles are optimized for the use of one of these two strategies. Here we examine the extremely halophilic Proteobacterium Halorhodospira halophila and report that medium K+ concentration dramatically alters its osmoprotectant use. When grown in hypersaline media containing substantial K+ concentrations, H. halophila accumulates molar concentrations of KCl. However, at limiting K+ concentrations the organism switches to glycine betaine as its major osmoprotectant. In contrast, the closely related organism Halorhodospira halochloris is limited to using compatible solutes. H. halophila performs both de novo synthesis and uptake of glycine betaine, matching the biosynthesis and transport systems encoded in its genome. The medium K+ concentration (~10 mM) at which the KCl to glycine betaine osmoprotectant switch in H. halophila occurs is near the K+ content of the lake from which it was isolated, supporting an ecological relevance of this osmoprotectant strategy.
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12
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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: 14] [Impact Index Per Article: 2.8] [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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13
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Pfeiffer F, Losensky G, Marchfelder A, Habermann B, Dyall‐Smith M. Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754 T ) and the laboratory strains R1 and NRC-1. Microbiologyopen 2020; 9:e974. [PMID: 31797576 PMCID: PMC7002104 DOI: 10.1002/mbo3.974] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/04/2023] Open
Abstract
Halobacterium salinarum is an extremely halophilic archaeon that is widely distributed in hypersaline environments and was originally isolated as a spoilage organism of salted fish and hides. The type strain 91-R6 (DSM 3754T ) has seldom been studied and its genome sequence has only recently been determined by our group. The exact relationship between the type strain and two widely used model strains, NRC-1 and R1, has not been described before. The genome of Hbt. salinarum strain 91-R6 consists of a chromosome (2.17 Mb) and two large plasmids (148 and 102 kb, with 39,230 bp being duplicated). Cytosine residues are methylated (m4 C) within CTAG motifs. The genomes of type and laboratory strains are closely related, their chromosomes sharing average nucleotide identity (ANIb) values of 98% and in silico DNA-DNA hybridization (DDH) values of 95%. The chromosomes are completely colinear, do not show genome rearrangement, and matching segments show <1% sequence difference. Among the strain-specific sequences are three large chromosomal replacement regions (>10 kb). The well-studied AT-rich island (61 kb) of the laboratory strains is replaced by a distinct AT-rich sequence (47 kb) in 91-R6. Another large replacement (91-R6: 78 kb, R1: 44 kb) codes for distinct homologs of proteins involved in motility and N-glycosylation. Most (107 kb) of plasmid pHSAL1 (91-R6) is very closely related to part of plasmid pHS3 (R1) and codes for essential genes (e.g. arginine-tRNA ligase and the pyrimidine biosynthesis enzyme aspartate carbamoyltransferase). Part of pHS3 (42.5 kb total) is closely related to the largest strain-specific sequence (164 kb) in the type strain chromosome. Genome sequencing unraveled the close relationship between the Hbt. salinarum type strain and two well-studied laboratory strains at the DNA and protein levels. Although an independent isolate, the type strain shows a remarkably low evolutionary difference to the laboratory strains.
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Affiliation(s)
- Friedhelm Pfeiffer
- Computational Biology GroupMax‐Planck‐Institute of BiochemistryMartinsriedGermany
| | - Gerald Losensky
- Microbiology and ArchaeaDepartment of BiologyTechnische Universität DarmstadtDarmstadtGermany
| | | | - Bianca Habermann
- Computational Biology GroupMax‐Planck‐Institute of BiochemistryMartinsriedGermany
- CNRSIBDM UMR 7288Aix Marseille UniversitéMarseilleFrance
| | - Mike Dyall‐Smith
- Computational Biology GroupMax‐Planck‐Institute of BiochemistryMartinsriedGermany
- Veterinary BiosciencesFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVic.Australia
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14
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Müller WJ, Smit MS, van Heerden E, Capes MD, DasSarma S. Complex Effects of Cytochrome P450 Monooxygenase on Purple Membrane and Bacterioruberin Production in an Extremely Halophilic Archaeon: Genetic, Phenotypic, and Transcriptomic Analyses. Front Microbiol 2018; 9:2563. [PMID: 30416496 PMCID: PMC6212597 DOI: 10.3389/fmicb.2018.02563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/08/2018] [Indexed: 12/30/2022] Open
Abstract
Halophilic archaea are known to produce a diverse array of pigments for phototrophy and photoprotection. The aim of this paper was to determine the role of a Halobacterium gene encoding the predicted cytochrome P450 monooxygenase (CYP174A1) in pigment synthesis through a combined genetic, phenotypic, and transcriptomic approach. We report on the observed phenotype changes [increased bacterioruberin levels and the loss of purple membrane (PM)] between the Halobacterium salinarum R1 and its CYP174A1-deletion mutant. In addition, we report on the whole-genome DNA microarray analysis, which supports the phenotype of PM loss. This work expands our understanding of the bop-gene regulon, and its relation to carotenoid biosynthesis, and sheds light on our broader understanding of the role (s) of CYP174A1 in archaeal pigment synthesis. To date, this is the first study in which the physiological role of any cytochrome P450 monooxygenase (CYP450) in extremely halophilic archaea has been reported.
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Affiliation(s)
- Walter J Müller
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Martha S Smit
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Esta van Heerden
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Melinda D Capes
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD, United States
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15
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In silico and experimental improvement of bacteriorhodopsin production in Halobacterium salinarum R1 by increasing DNA-binding affinity of Bat through Q661R/Q665R substitutions in HTH motif. Extremophiles 2018; 23:59-67. [PMID: 30350225 DOI: 10.1007/s00792-018-1060-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
DNA-binding motif of bacterioopsin activator (Bat) protein is a Helix-Turn-Helix motif, which binds to bop promoter and induces bacterioopsin (Bop) expression under light and low oxygen tension. Bacterioopsin is linked to retinal to produce bacteriorhodopsin (BR), which in turn supplies energy source in Halobacterium salinarum. In this study, effect of Bat HTH motif-promoter DNA interaction on bacterioopsin (Bop) expression was investigated using in silico and experimental approaches. Molecular docking showed that the most stable DNA-protein complex was generated by Q661R/Q665R mutant. Based on the in silico analysis, HTH motif was mutated using site-directed mutagenesis and Hbt. salinarum recombinant strains were developed by introduction of mutant bat genes. Double positively charged amino acid substitutions (Q661R/Q665R) in second helix of HTH motif increased whereas deletion of this region decreased BR production. However, other single substitutions (Q665R and Q661H) did not change BR production. These findings represent key role of HTH motif stability for DNA binding and regulation of bacterioopsin (Bop) expression and bacteriorhodopsin (BR) production independent of environmental condition.
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16
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Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 2018. [DOI: 10.1093/femsre/fuy009] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 1, SI-1000 Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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17
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McMillan LJ, Hwang S, Farah RE, Koh J, Chen S, Maupin-Furlow JA. Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses. Environ Microbiol 2017; 20:385-401. [PMID: 29194950 DOI: 10.1111/1462-2920.14014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023]
Abstract
Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here, we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of 13 C/15 N-lysine and 13 C-arginine such that each peptide derived from trypsin digestion was labelled. This strain was found amenable to multiplex SILAC by case study of responses to oxidative stress by hypochlorite. A total of 2565 proteins was identified by LC-MS/MS analysis (q-value ≤ 0.01) that accounted for 64% of the theoretical proteome. Of these, 176 proteins were altered at least 1.5-fold (p-value < 0.05) in abundance during hypochlorite stress. Many of the differential proteins were of unknown function. Those of known function included transcription factor homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons. Thus, SILAC is found to be an ideal method for quantitative proteomics of archaea that holds promise to unravel gene function.
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Affiliation(s)
- Lana J McMillan
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Sungmin Hwang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rawan E Farah
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Sixue Chen
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.,Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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18
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Reitter JN, Cousin CE, Nicastri MC, Jaramillo MV, Mills KV. Salt-Dependent Conditional Protein Splicing of an Intein from Halobacterium salinarum. Biochemistry 2016; 55:1279-82. [PMID: 26913597 DOI: 10.1021/acs.biochem.6b00128] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An intein from Halobacterium salinarum can be isolated as an unspliced precursor protein with exogenous exteins after Escherichia coli overexpression. The intein promotes protein splicing and uncoupled N-terminal cleavage in vitro, conditional on incubation with NaCl or KCl at concentrations of >1.5 M. The protein splicing reaction also is conditional on reduction of a disulfide bond between two active site cysteines. Conditional protein splicing under these relatively mild conditions may lead to advances in intein-based biotechnology applications and hints at the possibility that this H. salinarum intein could serve as a switch to control extein activity under physiologically relevant conditions.
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Affiliation(s)
- Julie N Reitter
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Christopher E Cousin
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Michael C Nicastri
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Mario V Jaramillo
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
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19
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Charlesworth J, P. Burns B. Extremophilic adaptations and biotechnological applications in diverse environments. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.3.251] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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20
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The rad2 gene of haloarchaeum Halobacterium salinarum is functional in the repair of ultraviolet light induced DNA photoproducts. Microbiol Res 2015; 173:44-9. [PMID: 25801970 DOI: 10.1016/j.micres.2015.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 01/27/2015] [Accepted: 01/31/2015] [Indexed: 11/21/2022]
Abstract
There are a lot of bacterial and eukaryotic DNA repair gene homologs among sequenced archaeal genomes but there is little information about DNA repair mechanisms and the interaction of involved repair proteins. In order to study DNA repair mechanisms in the third domain of life, we studied these processes in the model archaeon, Halobacterium salinarum. H. salinarum has homologs of eukaryotic nucleotide excision repair genes such as rad2 gene. A functional analysis of rad2 was performed by knocking down of this gene. We introduced an antisense RNA expression vector into the cells and the sensitivity of transformants against ultraviolet light exposure was measured to determine whether rad2 gene performs any role in the repair of the DNA lesions induced by UV light or not. Our data suggests that rad2 is functional in this pathway and knocked down strains were unable to completely repair the UV induced DNA damages. In this study, for the first time antisense RNA is used for functional analysis of a gene in H. salinarum and it is shown that antisense RNA could be used as a reliable genetic tool for understanding of the archaeal genetics.
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21
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Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation. Appl Environ Microbiol 2014; 80:1821-31. [PMID: 24413600 DOI: 10.1128/aem.03280-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain "ecological memory" of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms.
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22
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Hilbers F, Eggers R, Pradela K, Friedrich K, Herkenhoff-Hesselmann B, Becker E, Deckers-Hebestreit G. Subunit δ is the key player for assembly of the H(+)-translocating unit of Escherichia coli F(O)F1 ATP synthase. J Biol Chem 2013; 288:25880-25894. [PMID: 23864656 DOI: 10.1074/jbc.m113.484675] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ATP synthase (F(O)F1) of Escherichia coli couples the translocation of protons across the cytoplasmic membrane to the synthesis or hydrolysis of ATP. This nanomotor is composed of the rotor c10γε and the stator ab2α3β3δ. To study the assembly of this multimeric enzyme complex consisting of membrane-integral as well as peripheral hydrophilic subunits, we combined nearest neighbor analyses by intermolecular disulfide bond formation or purification of partially assembled F(O)F1 complexes by affinity chromatography with the use of mutants synthesizing different sets of F(O)F1 subunits. Together with a time-delayed in vivo assembly system, the results demonstrate that F(O)F1 is assembled in a modular way via subcomplexes, thereby preventing the formation of a functional H(+)-translocating unit as intermediate product. Surprisingly, during the biogenesis of F(O)F1, F1 subunit δ is the key player in generating stable F(O). Subunit δ serves as clamp between ab2 and c10α3β3γε and guarantees that the open H(+) channel is concomitantly assembled within coupled F(O)F1 to maintain the low membrane proton permeability essential for viability, a general prerequisite for the assembly of multimeric H(+)-translocating enzymes.
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Affiliation(s)
- Florian Hilbers
- From the Department of Microbiology, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Ruth Eggers
- From the Department of Microbiology, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Kamila Pradela
- From the Department of Microbiology, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Kathleen Friedrich
- From the Department of Microbiology, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | | | - Elisabeth Becker
- From the Department of Microbiology, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Gabriele Deckers-Hebestreit
- From the Department of Microbiology, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany.
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23
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Time-delayed in vivo assembly of subunit a into preformed Escherichia coli FoF1 ATP synthase. J Bacteriol 2013; 195:4074-84. [PMID: 23836871 DOI: 10.1128/jb.00468-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Escherichia coli F(O)F(1) ATP synthase, a rotary nanomachine, is composed of eight different subunits in a α3β3γδεab2c10 stoichiometry. Whereas F(O)F(1) has been studied in detail with regard to its structure and function, much less is known about how this multisubunit enzyme complex is assembled. Single-subunit atp deletion mutants are known to be arrested in assembly, thus leading to formation of partially assembled subcomplexes. To determine whether those subcomplexes are preserved in a stable standby mode, a time-delayed in vivo assembly system was developed. To establish this approach, we targeted the time-delayed assembly of membrane-integrated subunit a into preformed F(O)F(1) lacking subunit a (F(O)F(1)-a) which is known to form stable subcomplexes in vitro. Two expression systems (araBADp and T7p-laco) were adjusted to provide compatible, mutually independent, and sufficiently stringent induction and repression regimens. In detail, all structural atp genes except atpB (encoding subunit a) were expressed under the control of araBADp and induced by arabinose. Following synthesis of F(O)F(1)-a during growth, expression was repressed by glucose/d-fucose, and degradation of atp mRNA controlled by real-time reverse transcription-PCR. A time-delayed expression of atpB under T7p-laco control was subsequently induced in trans by addition of isopropyl-β-d-thiogalactopyranoside. Formation of fully assembled, and functional, F(O)F(1) complexes was verified. This demonstrates that all subunits of F(O)F(1)-a remain in a stable preformed state capable to integrate subunit a as the last subunit. The results reveal that the approach presented here can be applied as a general method to study the assembly of heteromultimeric protein complexes in vivo.
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24
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Deole R, Challacombe J, Raiford DW, Hoff WD. An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content. J Biol Chem 2012; 288:581-8. [PMID: 23144460 DOI: 10.1074/jbc.m112.420505] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Halophilic archaea accumulate molar concentrations of KCl in their cytoplasm as an osmoprotectant and have evolved highly acidic proteomes that function only at high salinity. We examined osmoprotection in the photosynthetic Proteobacteria Halorhodospira halophila and Halorhodospira halochloris. Genome sequencing and isoelectric focusing gel electrophoresis showed that the proteome of H. halophila is acidic. In line with this finding, H. halophila accumulated molar concentrations of KCl when grown in high salt medium as detected by x-ray microanalysis and plasma emission spectrometry. This result extends the taxonomic range of organisms using KCl as a main osmoprotectant to the Proteobacteria. The closely related organism H. halochloris does not exhibit an acidic proteome, matching its inability to accumulate K(+). This observation indicates recent evolutionary changes in the osmoprotection strategy of these organisms. Upon growth of H. halophila in low salt medium, its cytoplasmic K(+) content matches that of Escherichia coli, revealing an acidic proteome that can function in the absence of high cytoplasmic salt concentrations. These findings necessitate a reassessment of two central aspects of theories for understanding extreme halophiles. First, we conclude that proteome acidity is not driven by stabilizing interactions between K(+) ions and acidic side chains but by the need for maintaining sufficient solvation and hydration of the protein surface at high salinity through strongly hydrated carboxylates. Second, we propose that obligate protein halophilicity is a non-adaptive property resulting from genetic drift in which constructive neutral evolution progressively incorporates weakly stabilizing K(+)-binding sites on an increasingly acidic protein surface.
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Affiliation(s)
- Ratnakar Deole
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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25
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Feng J, Liu B, Zhang Z, Ren Y, Li Y, Gan F, Huang Y, Chen X, Shen P, Wang L, Tang B, Tang XF. The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements. PLoS One 2012; 7:e41621. [PMID: 22911826 PMCID: PMC3402447 DOI: 10.1371/journal.pone.0041621] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Accepted: 06/22/2012] [Indexed: 11/19/2022] Open
Abstract
Natrinema sp. J7-2 is an extreme haloarchaeon capable of growing on synthetic media without amino acid supplements. Here we report the complete genome sequence of Natrinema sp. J7-2 which is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid pJ7-I. This is the first complete genome sequence of a member of the genus Natrinema. We demonstrate that Natrinema sp. J7-2 can use gluconate, glycerol, or acetate as the sole carbon source and that its genome encodes complete metabolic pathways for assimilating these substrates. The biosynthetic pathways for all 20 amino acids have been reconstructed, and we discuss a possible evolutionary relationship between the haloarchaeal arginine synthetic pathway and the bacterial lysine synthetic pathway. The genome harbors the genes for assimilation of ammonium and nitrite, but not nitrate, and has a denitrification pathway to reduce nitrite to N2O. Comparative genomic analysis suggests that most sequenced haloarchaea employ the TrkAH system, rather than the Kdp system, to actively uptake potassium. The genomic analysis also reveals that one of the three CRISPR loci in the Natrinema sp. J7-2 chromosome is located in an integrative genetic element and is probably propagated via horizontal gene transfer (HGT). Finally, our phylogenetic analysis of haloarchaeal genomes provides clues about evolutionary relationships of haloarchaea.
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Affiliation(s)
- Jie Feng
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Ziqian Zhang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yan Ren
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yang Li
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Fei Gan
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yuping Huang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Xiangdong Chen
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Ping Shen
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China
| | - Bing Tang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
- * E-mail: (BT); (X-FT)
| | - Xiao-Feng Tang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
- * E-mail: (BT); (X-FT)
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Kixmüller D, Greie JC. An ATP-driven potassium pump promotes long-term survival of Halobacterium salinarum within salt crystals. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:234-241. [PMID: 23757278 DOI: 10.1111/j.1758-2229.2012.00326.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many extremely halophilic archaea belonging to the Halobacteriales have remarkable longevity. They are even known to persist for millions of years within fluid inclusions of salt crystals. However, the key systems responsible for this remarkable ability and the underlying physiological mechanisms have not yet been deciphered. This study revealed that the ATP-dependent K(+) uptake system KdpFABC of Halobacterium salinarum is essential for survival under desiccation and salt crystal inclusion and, thus, can be identified as at least one of these systems in this organism. The presence of the kdp genes promoted survival of H. salinarum entombed in halite, compared with cells in which these genes were deleted. Expression of the kdp operon was found to be induced already under desiccating conditions without halite entombment. The morphology of cells included in halite resembled that of cells grown under potassium limitation. Therefore, a steady potassium supply, even under unfavourable energetic conditions, plays a key role in long-term survival and desiccation tolerance.
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Affiliation(s)
- Dorthe Kixmüller
- Department for Biology/Chemistry, University of Osnabrück, 49069 Osnabrück, Germany
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Construction and characterization of a gradually inducible expression vector for Halobacterium salinarum, based on the kdp promoter. Appl Environ Microbiol 2012; 78:2100-5. [PMID: 22287001 DOI: 10.1128/aem.07155-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gradually inducible expression vectors which are governed by variations of growth conditions are powerful tools for gene expression of conditionally lethal mutants. Furthermore, controlled expression allows monitoring of overproduction of proteins at various stages in their expressing hosts. For Halobacterium salinarum, which is often used as a paradigm for halophilic archaea, such an inducible expression system is not available to date. Here we show that the kdp promoter (Pkdp), which facilitates gene expression upon K(+) limitation, can be used to establish such a system for molecular applications. Pkdp features a rather high expression rate, with an approximately 50-fold increase that can be easily varied by K(+) concentrations in the growth medium. Besides the construction of an expression vector, our work describes the characterization of expression patterns and, thus, offers a gradually inducible expression system to the scientific community.
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Archaeal transcriptional regulation of the prokaryotic KdpFABC complex mediating K+ uptake in H. salinarum. Extremophiles 2011; 15:643-52. [DOI: 10.1007/s00792-011-0395-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
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Hänelt I, Tholema N, Kröning N, Vor der Brüggen M, Wunnicke D, Bakker EP. KtrB, a member of the superfamily of K+ transporters. Eur J Cell Biol 2011; 90:696-704. [DOI: 10.1016/j.ejcb.2011.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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30
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Irzik K, Pfrötzschner J, Goss T, Ahnert F, Haupt M, Greie JC. The KdpC subunit of the Escherichia coli K+-transporting KdpB P-type ATPase acts as a catalytic chaperone. FEBS J 2011; 278:3041-53. [PMID: 21711450 DOI: 10.1111/j.1742-4658.2011.08224.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Bacteria and Archaea, high-affinity potassium uptake is mediated by the ATP-driven KdpFABC complex. On the basis of the biochemical properties of the ATP-hydrolyzing subunit KdpB, the transport complex is classified as type IA P-type ATPase. However, the KdpA subunit, which promotes K(+) transport, clearly resembles a potassium channel, such that the KdpFABC complex represents a chimera of ion pumps and ion channels. In the present study, we demonstrate that the blending of these two groups of transporters in KdpFABC also entails a nucleotide-binding mechanism in which the KdpC subunit acts as a catalytic chaperone. This mechanism is found neither in P-type ATPases nor in ion channels, although parallels are found in ABC transporters. In the latter, the ATP nucleotide is coordinated by the LSGGQ signature motif via double hydrogen bonds at a conserved glutamine residue, which is also present in KdpC. High-affinity nucleotide binding to the KdpFABC complex was dependent on the presence of this conserved glutamine residue in KdpC. In addition, both ATP binding to KdpC and ATP hydrolysis activity of KdpFABC were sensitive to the accessibility, presence or absence of the hydroxyl groups at the ribose moiety of the nucleotide. Furthermore, the KdpC subunit was shown to interact with the nucleotide-binding loop of KdpB in an ATP-dependent manner around the ATP-binding pocket, thereby increasing the ATP-binding affinity by the formation of a transient KdpB/KdpC/ATP ternary complex.
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Affiliation(s)
- Kristina Irzik
- Fachbereich Biologie/Chemie, Universität Osnabrück, Osnabrück, Germany
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Ebrahimie E, Ebrahimi M, Sarvestani NR, Ebrahimi M. Protein attributes contribute to halo-stability, bioinformatics approach. SALINE SYSTEMS 2011; 7:1. [PMID: 21592393 PMCID: PMC3117752 DOI: 10.1186/1746-1448-7-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Accepted: 05/18/2011] [Indexed: 12/05/2022]
Abstract
Halophile proteins can tolerate high salt concentrations. Understanding halophilicity features is the first step toward engineering halostable crops. To this end, we examined protein features contributing to the halo-toleration of halophilic organisms. We compared more than 850 features for halophilic and non-halophilic proteins with various screening, clustering, decision tree, and generalized rule induction models to search for patterns that code for halo-toleration. Up to 251 protein attributes selected by various attribute weighting algorithms as important features contribute to halo-stability; from them 14 attributes selected by 90% of models and the count of hydrogen gained the highest value (1.0) in 70% of attribute weighting models, showing the importance of this attribute in feature selection modeling. The other attributes mostly were the frequencies of di-peptides. No changes were found in the numbers of groups when K-Means and TwoStep clustering modeling were performed on datasets with or without feature selection filtering. Although the depths of induced trees were not high, the accuracies of trees were higher than 94% and the frequency of hydrophobic residues pointed as the most important feature to build trees. The performance evaluation of decision tree models had the same values and the best correctness percentage recorded with the Exhaustive CHAID and CHAID models. We did not find any significant difference in the percent of correctness, performance evaluation, and mean correctness of various decision tree models with or without feature selection. For the first time, we analyzed the performance of different screening, clustering, and decision tree algorithms for discriminating halophilic and non-halophilic proteins and the results showed that amino acid composition can be used to discriminate between halo-tolerant and halo-sensitive proteins.
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Affiliation(s)
- Esmaeil Ebrahimie
- Bioinformatics Research Group, Green Research Center, Qom University, Qom, Iran.
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