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Arthi R, Parameswari E, Dhevagi P, Janaki P, Parimaladevi R. Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33949-9. [PMID: 38877191 DOI: 10.1007/s11356-024-33949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.
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Affiliation(s)
- Ravichandran Arthi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Periyasamy Dhevagi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ponnusamy Janaki
- Nammazhvar Organic Farming Research Centre, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rathinasamy Parimaladevi
- Department of Bioenergy, Agrl. Engineering College & Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
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Xing Q, Zhang S, Tao X, Mesbah NM, Mao X, Wang H, Wiegel J, Zhao B. The polyextremophile Natranaerobius thermophilus adopts a dual adaptive strategy to long-term salinity stress, simultaneously accumulating compatible solutes and K . Appl Environ Microbiol 2024; 90:e0014524. [PMID: 38578096 PMCID: PMC11107154 DOI: 10.1128/aem.00145-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
The bacterium Natranaerobius thermophilus is an extremely halophilic alkalithermophile that can thrive under conditions of high salinity (3.3-3.9 M Na+), alkaline pH (9.5), and elevated temperature (53°C). To understand the molecular mechanisms of salt adaptation in N. thermophilus, it is essential to investigate the protein, mRNA, and key metabolite levels on a molecular basis. Based on proteome profiling of N. thermophilus under 3.1, 3.7, and 4.3 M Na+ conditions compared to 2.5 M Na+ condition, we discovered that a hybrid strategy, combining the "compatible solute" and "salt-in" mechanisms, was utilized for osmotic adjustment dur ing the long-term salinity adaptation of N. thermophilus. The mRNA level of key proteins and the intracellular content of compatible solutes and K+ support this conclusion. Specifically, N. thermophilus employs the glycine betaine ABC transporters (Opu and ProU families), Na+/solute symporters (SSS family), and glutamate and proline synthesis pathways to adapt to high salinity. The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels in N. thermophilus. Additionally, the upregulation of Na+/ K+/ H+ transporters facilitates the maintenance of intracellular K+ concentration, ensuring cellular ion homeostasis under varying salinities. Furthermore, N. thermophilus exhibits cytoplasmic acidification in response to high Na+ concentrations. The median isoelectric points of the upregulated proteins decrease with increasing salinity. Amino acid metabolism, carbohydrate and energy metabolism, membrane transport, and bacterial chemotaxis activities contribute to the adaptability of N. thermophilus under high salt stress. This study provides new data that support further elucidating the complex adaptation mechanisms of N. thermophilus under multiple extremes.IMPORTANCEThis study represents the first report of simultaneous utilization of two salt adaptation mechanisms within the Clostridia class in response to long-term salinity stress.
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Affiliation(s)
- Qinghua Xing
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
- Luo Yang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Luoyang, China
| | - Xinyi Tao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Noha M. Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Xinwei Mao
- Department of Civil Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
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Dindhoria K, Kumar R, Bhargava B, Kumar R. Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils. mSystems 2024; 9:e0105023. [PMID: 38377278 PMCID: PMC10949518 DOI: 10.1128/msystems.01050-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses. IMPORTANCE The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.
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Affiliation(s)
- Kiran Dindhoria
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raghawendra Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Bhavya Bhargava
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Zou Z, Kaothien-Nakayama P, Ogawa-Iwamura J, Nakayama H. Metabolic engineering of high-salinity-induced biosynthesis of γ-aminobutyric acid improves salt-stress tolerance in a glutamic acid-overproducing mutant of an ectoine-deficient Halomonas elongata. Appl Environ Microbiol 2024; 90:e0190523. [PMID: 38112419 PMCID: PMC10807429 DOI: 10.1128/aem.01905-23] [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: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
A moderately halophilic eubacterium, Halomonas elongata, has been used as cell factory to produce fine chemical 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine), which functions as a major osmolyte protecting the cells from high-salinity stress. To explore the possibility of using H. elongata to biosynthesize other valuable osmolytes, an ectoine-deficient salt-sensitive H. elongata deletion mutant strain KA1 (ΔectABC), which only grows well in minimal medium containing up to 3% NaCl, was subjected to an adaptive mutagenesis screening in search of mutants with restored salt tolerance. Consequently, we obtained a mutant, which tolerates 6% NaCl in minimal medium by overproducing L-glutamic acid (Glu). However, this Glu-overproducing (GOP) strain has a lower tolerance level than the wild-type H. elongata, possibly because the acidity of Glu interferes with the pH homeostasis of the cell and hinders its own cellular accumulation. Enzymatic decarboxylation of Glu to γ-aminobutyric acid (GABA) by a Glu decarboxylase (GAD) could restore cellular pH homeostasis; therefore, we introduced an engineered salt-inducible HopgadBmut gene, which encodes a wide pH-range GAD mutant, into the genome of the H. elongata GOP strain. We found that the resulting H. elongata GOP-Gad strain exhibits higher salt tolerance than the GOP strain by accumulating high concentration of GABA as an osmolyte in the cell (176.94 µmol/g cell dry weight in minimal medium containing 7% NaCl). With H. elongata OUT30018 genetic background, H. elongata GOP-Gad strain can utilize biomass-derived carbon and nitrogen compounds as its sole carbon and nitrogen sources, making it a good candidate for the development of GABA-producing cell factories.IMPORTANCEWhile the wild-type moderately halophilic H. elongata can synthesize ectoine as a high-value osmolyte via the aspartic acid metabolic pathway, a mutant H. elongata GOP strain identified in this work opens doors for the biosynthesis of alternative valuable osmolytes via glutamic acid metabolic pathway. Further metabolic engineering to install a GAD system into the H. elongata GOP strain successfully created a H. elongata GOP-Gad strain, which acquired higher tolerance to salt stress by accumulating GABA as a major osmolyte. With the ability to assimilate biomass-derived carbon and nitrogen sources and thrive in high-salinity environment, the H. elongata GOP-Gad strain can be used in the development of sustainable GABA-producing cell factories.
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Affiliation(s)
- Ziyan Zou
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Pulla Kaothien-Nakayama
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Junpei Ogawa-Iwamura
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Hideki Nakayama
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
- Institute of Integrated Science and Technology, Nagasaki University, Nagasaki, Japan
- Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Japan
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Khaleque HN, Nazem-Bokaee H, Gumulya Y, Carlson RP, Kaksonen AH. Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, Acidithiobacillus ferrooxidans ATCC 23270. Res Microbiol 2024; 175:104115. [PMID: 37572823 DOI: 10.1016/j.resmic.2023.104115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Halotolerant, acidophilic, bioleaching microorganisms are crucial to biomining operations that utilize saline water. Compatible solutes play an important role in the adaptation of these microorganisms to saline environments. Acidithiobacillus ferrooxidans ATCC 23270, an iron- and sulfur-oxidizing acidophilic bacterium, synthesizes trehalose as its native compatible solute but is still sensitive to salinity. Recently, halotolerant bioleaching bacteria were found to use ectoine as their key compatible solute. Previously, bioleaching bacteria were recalcitrant to genetic manipulation; however, recent advancements in genetic tools and techniques allow successful genetic modification of A. ferrooxidans ATCC 23270. Therefore, this study aimed to test, in silico, the effect of native and synthetic compatible solute biosynthesis by A. ferrooxidans ATCC 23270 on its growth and metabolism. Metabolic network flux modelling was used to provide a computational framework for the prediction of metabolic fluxes during production of native and synthetic compatible solutes by A. ferrooxidans ATCC 23270, in silico. Complete pathways for trehalose biosynthesis by the bacterium are proposed and captured in the updated metabolic model including a newly discovered UDP-dependent trehalose synthesis pathway. Finally, the effect of nitrogen sources on compatible solute production was simulated and showed that using nitrogen gas as the sole nitrogen source enables the ectoine-producing 'engineered' microbe to oxidize up to 20% more ferrous iron in comparison to the native microbe that only produces trehalose. Therefore, the predictive outcomes of the model have the potential to guide the design and optimization of a halotolerant strain of A. ferrooxidans ATCC 23270 for saline bioleaching operations.
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Affiliation(s)
- Himel Nahreen Khaleque
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment, 147 Underwood Avenue, Floreat, WA, Australia; Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia; School of Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Hadi Nazem-Bokaee
- Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia; Australian National Herbarium, National Research Collections Australia, NCMI, CSIRO, Canberra 2601, ACT, Australia.
| | - Yosephine Gumulya
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment, 147 Underwood Avenue, Floreat, WA, Australia; Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia.
| | - Ross P Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Environment, 147 Underwood Avenue, Floreat, WA, Australia; Synthetic Biology Future Science Platform, CSIRO, Canberra 2601, ACT, Australia.
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Li Q, Hu K, Mou J, Li J, Liu A, Ao X, Yang Y, He L, Chen S, Zou L, Guo M, Liu S. Insight into the acid tolerance mechanism of Acetilactobacillus jinshanensis subsp. aerogenes Z-1. Front Microbiol 2023; 14:1226031. [PMID: 37520381 PMCID: PMC10382275 DOI: 10.3389/fmicb.2023.1226031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Several lactic acid bacteria (LAB) are double-edged swords in the production of Sichuan bran vinegar; on the one hand, they are important for the flavour of the vinegar, but on the other hand, they result in vinegar deterioration because of their gas-producing features and their acid resistance. These characteristics intensify the difficulty in managing the safe production of vinegar using strains such as Acetilactobacillus jinshanensis subsp. aerogenes Z-1. Therefore, it is necessary to characterize the mechanisms underlying their acid tolerance. The results of this study showed a survival rate of 77.2% for Z-1 when exposed to pH 3.0 stress for 1 h. This strain could survive for approximately 15 days in a vinegar solution with 4% or 6% total acid content, and its growth was effectively enhanced by the addition of 10 mM of arginine (Arg). Under acidic stress, the relative content of the unsaturated fatty acid C18:1 (n-11) increased, and eight amino acids accumulated in the cells. Meanwhile, based on a transcriptome analysis, the genes glnA, carA/B, arcA, murE/F/G, fabD/H/G, DnaK, uvrA, opuA/C, fliy, ecfA2, dnaA and LuxS, mainly enriched in amino acid transport and metabolism, protein folding, DNA repair, and cell wall/membrane metabolism processes, were hypothesized to be acid resistance-related genes in Z-1. This work paves the way for further clarifying the acid tolerance mechanism of Z-1 and shares applicable perspectives for vinegar brewing.
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Affiliation(s)
- Qin Li
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Juan Mou
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Xiaolin Ao
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Li He
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingye Guo
- Sichuan Baoning Vinegar Co., Ltd, Langzhong, Sichuan, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
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Thompson J, Barr C, Babcock-Adams L, Bird L, La Cava E, Garber A, Hongoh Y, Liu M, Nealson KH, Okamoto A, Repeta D, Suzuki S, Tacto C, Tashjian M, Merino N. Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system. Front Microbiol 2023; 14:1179857. [PMID: 37520355 PMCID: PMC10373932 DOI: 10.3389/fmicb.2023.1179857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 08/01/2023] Open
Abstract
The terrestrial serpentinite-hosted ecosystem known as "The Cedars" is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars ('Paeni-Cedars'), Alishewanella sp. BS5-314 ('Ali-BS5-314'), and Anaerobacillus sp. CMMVII ('Anaero-CMMVII'). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7-10 (minimum pH tested was 7), temperatures 20-40°C, and 0-3% NaCl concentration. The addition of 10-20 mM CaCl2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10-12 and temperatures 10-40°C, with limited growth observed 1-5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9-12, with the addition of 0.01-1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.
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Affiliation(s)
- Jaclyn Thompson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Lydia Babcock-Adams
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Lina Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Eugenio La Cava
- National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Arkadiy Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mark Liu
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Daniel Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Shino Suzuki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, Sagamihara, Kanagawa, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Clarissa Tacto
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michelle Tashjian
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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Li W, Gao N, Zhang W, Feng K, Zhou K, Zhao H, He G, Liu W, Li G. Visual demonstration and prediction of the Hofmeister series based on a poly(ionic liquid) photonic array. NANOSCALE 2023. [PMID: 37194393 DOI: 10.1039/d3nr01531a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The Hofmeister effect and associated Hofmeister series (HS) are ubiquitous in physicochemical phenomena and have demonstrated fundamental importance in a myriad of fields ranging from chemistry to biology. Visualization of the HS not only helps to straightforwardly understand the underpinning mechanism, but also enables the prediction of new ion positions in the HS and directs the applications of the Hofmeister effect. Owing to the difficulties of sensing and reporting complete multiple and subtle inter- and intramolecular interactions involved in the Hofmeister effect, facile and accurate visual demonstration and prediction of the HS remain highly challenging. Herein, a poly(ionic liquid) (PIL)-based photonic array containing 6 inverse opal microspheres was rationally constructed to efficiently sense and report the ion effects of the HS. The PILs can not only directly conjugate with HS ions due to their ion-exchange properties, but also provide sufficient noncovalent binding diversity with these ions. Meanwhile, subtle PIL-ion interactions can be sensitively amplified to optical signals owing to their photonic structures. Therefore, synergistic integration of PILs and photonic structures gives rise to accurate visualization of the ion effect of the HS, as demonstrated by correctly ranking 7 common anions. More importantly, assisted by principal component analysis (PCA), the developed PIL photonic array can serve as a general platform to facilely, accurately, and robustly predict the HS positions of an unprecedented amount of important and useful anions and cations. These findings indicate that the PIL photonic platform is very promising for addressing challenges in the visual demonstration and prediction of HS and promoting a molecular-level understanding of the Hoffmeister effect.
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Affiliation(s)
- Wenyun Li
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Ning Gao
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Wanlin Zhang
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Kai Feng
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Kang Zhou
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Hongwei Zhao
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Guokang He
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Weigang Liu
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
| | - Guangtao Li
- Department of Chemistry, Key Lab of Organic Optoelectronics & Molecular Engineering, Tsinghua University, Beijing 100084, P. R. China.
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Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
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Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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10
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Orhan F, Ceyran E. Identification of novel halophilic/halotolerant bacterial species producing compatible solutes. Int Microbiol 2022; 26:219-229. [PMID: 36342583 DOI: 10.1007/s10123-022-00289-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/15/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
Ectoine and hydroxyectoine are compatible solutes with enormous potential for use in the medical and cosmetic industries. Considering the excellent osmoprotective properties of these compatible solutes, we investigate the presence of four compatible solutes (ectoine, hydroxyectoine, proline, and glutamic acid) quantitatively by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in forty-five halophilic/halotolerant bacterial isolates. We determined ectoine production by Marinibacillus sp., Nesterenkonia xinjiangensis, Halobacillus sp., Bacillus patagoniensis, Virgibacillus picturae, Halomonas neptunia, Bacillus patagoniensis, Gracilibacillus sp., Thalassobacillus devorans, Microbacterium sp., Nesterenkonia sp., and Bacillus agaradhaerens, and this production was NaCl dependent. Additionally, the production of hydroxyectoine was observed in six bacterial isolates (Nesterenkonia xinjiangensis, Halobacillus sp., Halomonas neptunia, Thalassobacillus devorans, Nesterenkonia sp., and Bacillus agaradhaerens) which was NaCl and temperature dependent. The study identified new bacterial isolates producing ectoine or hydroxyectoine. While the ectoine production in many different Bacillus members and a few Nesterenkonia have been documented before, ectoine production by Bacillus patagoniensis and Nesterenkonia xinjiangensis has not been shown so far. Further, ectoine production by a member of the genus Thalassobacillus (Thalassobacillus devorans) was demonstrated experimentally for the first time. The findings reported in the study may serve as a basis for the large-scale production of ectoine and hydroxyectoine in the future.
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Affiliation(s)
- Furkan Orhan
- Department of Molecular Biology and Genetics, Agri İbrahim Cecen University, Agri, 04200, Turkey.
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, 04200, Turkey.
| | - Ertuğrul Ceyran
- Central Research and Application Laboratory, Agri Ibrahim Cecen University, Agri, 04200, Turkey
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11
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Erkorkmaz BA, Kırtel O, Abaramak G, Nikerel E, Öner ET. UV and Chemically Induced Halomonas smyrnensis Mutants for Enhanced Levan Productivity. J Biotechnol 2022; 356:19-29. [PMID: 35914617 DOI: 10.1016/j.jbiotec.2022.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Halomonas smyrnensis AAD6T is a moderately halophilic bacterium proven to be a powerful biotechnological tool with its ability to accumulate valuable biopolymers such as levan and poly(3-hydroxybutyrate) (PHB). Levan is a fructose homopolymer with β-2,6 fructofuranosidic linkages on the polymer backbone, and its distinctive applications in various industries such as food, pharmaceutical, medical, and chemical have been well-defined. On the other hand, PHB is a promising raw material to produce biodegradable plastics. Although it was shown in our previous studies that H. smyrnensis AAD6T exhibits one of the highest conversion yields of sucrose to levan reported to date, novel strategies are required to overcome high costs of levan production. In this study, we aimed at increasing levan productivity of H. smyrnensis AAD6T cultures using random mutagenesis techniques combined (i.e., ethyl methanesulfate treatment and/or ultraviolet irradiation). After several consecutive treatments, mutant strains BAE2, BAE5 and BAE6 were selected as efficient levan producers, as BAE2 standing out as the most efficient one not only in sucrose utilization and levan production rates, but also in final PHB concentrations. The mutants' whole genome sequences were analysed to determine the mutations occurred. Several mutations in genes related to central carbon metabolism and osmoregulation were found. Our results suggest that random mutagenesis can be a facile and efficient strategy to enhance the performance of extremophiles in adverse conditions.
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Affiliation(s)
- Burak Adnan Erkorkmaz
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey; Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Onur Kırtel
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Gülbahar Abaramak
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, 34755 Istanbul, Turkey
| | - Ebru Toksoy Öner
- Industrial Biotechnology and Systems Biology Research Group-IBSB, Department of Bioengineering, Marmara University, 34722 Istanbul, Turkey.
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12
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Weingarten EA, Zee PC, Jackson CR. Microbial Communities in Saltpan Sediments Show Tolerance to Mars Analog Conditions, but Susceptibility to Chloride and Perchlorate Toxicity. ASTROBIOLOGY 2022; 22:838-850. [PMID: 35731161 PMCID: PMC9464085 DOI: 10.1089/ast.2021.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/28/2022] [Indexed: 06/15/2023]
Abstract
Brines at or near the surface of present-day Mars are a potential explanation for seasonally recurring dark streaks on the walls of craters, termed recurring slope lineae (RSL). Deliquescence and freezing point depression are possible drivers of brine stability, attributable to the high salinity observed in martian regolith including chlorides and perchlorates. Investigation of life, which may inhabit RSL, and the cellular mechanisms necessary for survival, must consider the tolerance of highly variable hydration, freeze-thaw cycles, and high osmolarity in addition to the anaerobic, oligotrophic, and irradiated environment. We propose the saltpan, an ephemeral, hypersaline wetland as an analogue for putative RSL hydrology. Saltpan sediment archaeal and bacterial communities showed tolerance of the Mars-analogous atmosphere, hydration, minerology, salinity, and temperature. Although active growth and a shift to well-adapted taxa were observed, susceptibility to low-concentration chloride and perchlorate addition suggested that such a composition was insufficient for beneficial water retention relative to added salt stress.
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Affiliation(s)
- Eric A. Weingarten
- Department of Biology, University of Mississippi, University, Mississippi, USA
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, USA
| | - Peter C. Zee
- Department of Biology, University of Mississippi, University, Mississippi, USA
| | - Colin R. Jackson
- Department of Biology, University of Mississippi, University, Mississippi, USA
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13
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Zhang T, Cui T, Cao Y, Li Y, Li F, Zhu D, Xing J. Whole genome sequencing of the halophilic Halomonas qaidamensis XH36, a novel species strain with high ectoine production. Antonie Van Leeuwenhoek 2022; 115:545-559. [PMID: 35243586 DOI: 10.1007/s10482-022-01709-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/18/2022] [Indexed: 10/18/2022]
Abstract
Here, we report the whole genome of a novel halophilic Halomonas species strain XH36 with high ectoine production potential. The genome was 3,818,310 bp in size with a GC content of 51.97%, and contained 3533 genes, 61 tRNAs and 18 rRNAs. The phylogenetic analysis using the 16s rRNA genes, the UBCGs and the TYGS database indicated that XH36 belongs to a novel Halomonas species, which we named as Halomonas qaidamensis. Osmoadaptation related genes including Na(+) and K(+) transport and compatible solute accumulation were both present in the XH36 genome, the latter of which mainly contained ectoine, 5-hydroxyectoine and betaine. HPLC validation studies showed that H. qaidamensis XH36 accumulated ectoine to cope with salt stress, and the content of ectoine could be as high as 315 mg/g CDW under 3 mol/l NaCl. Our results show that XH36 is a new promising industrial strain for ectoine production, and the genomic analysis will guide us to better understand its salt-induced osmoadaptation mechanisms, and provide theoretical references for future application research of ectoine.
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Affiliation(s)
- Tiantian Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Tianqi Cui
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Yaning Cao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Yongzhen Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Fenghui Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Derui Zhu
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China
| | - Jiangwa Xing
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, China.
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14
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Transcriptome Analysis of Halotolerant Staphylococcus saprophyticus Isolated from Korean Fermented Shrimp. Foods 2022; 11:foods11040524. [PMID: 35206000 PMCID: PMC8870806 DOI: 10.3390/foods11040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Saeu-jeotgal, a Korean fermented shrimp food, is commonly used as an ingredient for making kimchi and other side dishes. The high salinity of the jeotgal contributes to its flavor and inhibits the growth of food spoilage microorganisms. Interestingly, Staphylococcus saprophyticus was discovered to be capable of growth even after treatment with 20% NaCl. To elucidate the tolerance mechanism, a genome-wide gene expression of S. saprophyticus against 0%, 10%, and 20% NaCl was investigated by RNA sequencing. A total of 831, 1314, and 1028 differentially expressed genes (DEGs) were identified in the 0% vs. 10%, 0% vs. 20%, and 10% vs. 20% NaCl comparisons, respectively. The Clusters of Orthologous Groups analysis revealed that the DEGs were involved in amino acid transport and metabolism, transcription, and inorganic ion transport and metabolism. The functional enrichment analysis showed that the expression of the genes encoding mechanosensitive ion channels, sodium/proton antiporters, and betaine/carnitine/choline transporter family proteins was downregulated, whereas the expression of the genes encoding universal stress proteins and enzymes for glutamate, glycine, and alanine synthesis was upregulated. Therefore, these findings suggest that the S. saprophyticus isolated from the saeu-jeotgal utilizes different molecular strategies for halotolerance, with glutamate as the key molecule.
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15
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Tarai A, Li Y, Liu B, Zhang D, Li J, Yan W, Zhang J, Qu J, Yang Z. A review on recognition of tri-/tetra-analyte by using simple organic colorimetric and fluorometric probes. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Breisch J, Bendel M, Averhoff B. The choline dehydrogenase BetA of Acinetobacter baumannii: a flavoprotein responsible for osmotic stress protection. Environ Microbiol 2021; 24:1052-1061. [PMID: 34431198 DOI: 10.1111/1462-2920.15741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/22/2021] [Indexed: 11/29/2022]
Abstract
Acinetobacter baumannii is outstanding for its ability to cope with low water activities which significantly contributes to its persistence in hospital environments. The vast majority of bacteria are able to prevent loss of cellular water by amassing osmoactive compatible solutes or their precursors into the cytoplasm. One such precursor of an osmoprotectant is choline that is taken up from the environment and oxidized to the compatible solute glycine betaine. Here, we report the identification of the osmotic stress operon betIBA in A. baumannii. This operon encodes the choline oxidation pathway important for the production of the solute glycine betaine. The salt-sensitive phenotype of a betA deletion strain could not be rescued by addition of choline, which is consistent with the role of BetA in choline oxidation. We found that BetA is a choline dehydrogenase but also mediates in vitro the oxidation of glycine betaine aldehyde to glycine betaine. BetA was found to be associated with the membrane and to contain a flavin, indicative for BetA donating electrons into the respiratory chain. The choline dehydrogenase activity was not salt dependent but was stimulated by the compatible solute glutamate.
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Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Melanie Bendel
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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17
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Chen DD, Fang BZ, Manzoor A, Liu YH, Li L, Mohamad OAA, Shu WS, Li WJ. Revealing the salinity adaptation mechanism in halotolerant bacterium Egicoccus halophilus EGI 80432 T by physiological analysis and comparative transcriptomics. Appl Microbiol Biotechnol 2021; 105:2497-2511. [PMID: 33625547 DOI: 10.1007/s00253-021-11190-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/30/2021] [Accepted: 02/17/2021] [Indexed: 02/02/2023]
Abstract
Egicoccus halophilus EGI 80432T, a halotolerant bacterium isolated from a saline-alkaline soil, belongs to a member of the class Nitriliruptoria, which exhibits high adaptability to salt environments. At present, the detailed knowledge of the salinity adaptation strategies of Nitriliruptoria was limited except for one research by using comparative genomics analysis. Here, we investigated the salinity adaptation mechanism of E. halophilus EGI 80432T by comparative physiological and transcriptomic analyses. The results of physiological analyses showed that trehalose and glutamate were accumulated by salt stress and showed the maximum at moderate salinity condition. Furthermore, the contents of histidine, threonine, proline, and ectoine were increased with increasing salt concentration. We found that both 0% and 9% NaCl conditions resulted in increased expressions of genes involved in carbohydrate and energy metabolisms, but negatively affected the Na+ efflux, iron, and molybdate transport. Moreover, the high salt condition led to enhancement of transcription of genes required for the synthesis of compatible solutes, e.g., glutamate, histidine, threonine, proline, and ectoine, which agree with the results of physiological analyses. The above results revealed that E. halophilus EGI 80432T increased inorganic ions uptake and accumulated trehalose and glutamate in response to moderate salinity condition, while the salinity adaptation strategy was changed from a "salt-in-cytoplasm" strategy to a "compatible solute" strategy under high salinity condition. The findings in this study would promote further studies in salt tolerance molecular mechanism of Nitriliruptoria and provide a theoretical support for E. halophilus EGI 80432T's application in ecological restoration.Key Points• Salt stress affected gene expressions responsible for carbohydrate and energy metabolisms of E. halophilus EGI 8042T.• E. halophilus EGI 80432T significantly accumulated compatible solutes under salt stress.• E. halophilus EGI 80432T adopted a "compatible solute" strategy to withstand high salt stress.
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Affiliation(s)
- Dai-Di Chen
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou, 510631, People's Republic of China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Ahmad Manzoor
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.,Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish, Egypt
| | - Wen-Sheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou, 510631, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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18
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Skitchenko RK, Usoltsev D, Uspenskaya M, Kajava AV, Guskov A. Census of halide-binding sites in protein structures. Bioinformatics 2020; 36:3064-3071. [PMID: 32022861 PMCID: PMC7214031 DOI: 10.1093/bioinformatics/btaa079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/02/2022] Open
Abstract
Motivation Halides are negatively charged ions of halogens, forming fluorides (F−), chlorides (Cl−), bromides (Br−) and iodides (I−). These anions are quite reactive and interact both specifically and non-specifically with proteins. Despite their ubiquitous presence and important roles in protein function, little is known about the preferences of halides binding to proteins. To address this problem, we performed the analysis of halide–protein interactions, based on the entries in the Protein Data Bank. Results We have compiled a pipeline for the quick analysis of halide-binding sites in proteins using the available software. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however, there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites, with a correlation between coordination numbers and amino acid composition. This pipeline can be used as a tool for the analysis of specific halide–protein interactions and assist phasing experiments relying on halides as anomalous scatters. Availability and implementation All data described in this article can be reproduced via complied pipeline published at https://github.com/rostkick/Halide_sites/blob/master/README.md. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Dmitrii Usoltsev
- Institute BioEngineering, ITMO University, Saint-Petersburg 197101, Russia
| | - Mayya Uspenskaya
- Institute BioEngineering, ITMO University, Saint-Petersburg 197101, Russia
| | - Andrey V Kajava
- Institute BioEngineering, ITMO University, Saint-Petersburg 197101, Russia.,Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Universite Montpellier, Montpellier 34293, France
| | - Albert Guskov
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen 9747 AG, the Netherlands
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19
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Pérez-Llano Y, Rodríguez-Pupo EC, Druzhinina IS, Chenthamara K, Cai F, Gunde-Cimerman N, Zalar P, Gostinčar C, Kostanjšek R, Folch-Mallol JL, Batista-García RA, Sánchez-Carbente MDR. Stress Reshapes the Physiological Response of Halophile Fungi to Salinity. Cells 2020; 9:E525. [PMID: 32106416 PMCID: PMC7140475 DOI: 10.3390/cells9030525] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/19/2020] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Mechanisms of cellular and molecular adaptation of fungi to salinity have been commonly drawn from halotolerant strains and few studies in basidiomycete fungi. These studies have been conducted in settings where cells are subjected to stress, either hypo- or hyperosmotic, which can be a confounding factor in describing physiological mechanisms related to salinity. (2) Methods: We have studied transcriptomic changes in Aspergillussydowii, a halophilic species, when growing in three different salinity conditions (No NaCl, 0.5 M, and 2.0 M NaCl). (3) Results: In this fungus, major physiological modifications occur under high salinity (2.0 M NaCl) and not when cultured under optimal conditions (0.5 M NaCl), suggesting that most of the mechanisms described for halophilic growth are a consequence of saline stress response and not an adaptation to saline conditions. Cell wall modifications occur exclusively at extreme salinity, with an increase in cell wall thickness and lamellar structure, which seem to involve a decrease in chitin content and an augmented content of alfa and beta-glucans. Additionally, three hydrophobin genes were differentially expressed under hypo- or hyperosmotic stress but not when the fungus grows optimally. Regarding compatible solutes, glycerol is the main compound accumulated in salt stress conditions, whereas trehalose is accumulated in the absence of salt. (4) Conclusions: Physiological responses to salinity vary greatly between optimal and high salt concentrations and are not a simple graded effect as the salt concentration increases. Our results highlight the influence of stress in reshaping the response of extremophiles to environmental challenges.
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Affiliation(s)
- Yordanis Pérez-Llano
- Center of Research on Cell Dynamics, Autonomous University of the State of Morelos, Morelos 62210, Mexico; (Y.P.-L.); (E.C.R.-P.)
| | - Eya Caridad Rodríguez-Pupo
- Center of Research on Cell Dynamics, Autonomous University of the State of Morelos, Morelos 62210, Mexico; (Y.P.-L.); (E.C.R.-P.)
| | - Irina S. Druzhinina
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, 1060 Vienna, Austria; (I.S.D.); (K.C.); (F.C.)
- Fungal Genomics Group, Nanjing Agricultural University, Nanjing 210095, China
| | - Komal Chenthamara
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, 1060 Vienna, Austria; (I.S.D.); (K.C.); (F.C.)
| | - Feng Cai
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, 1060 Vienna, Austria; (I.S.D.); (K.C.); (F.C.)
- Fungal Genomics Group, Nanjing Agricultural University, Nanjing 210095, China
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (N.G.-C.); (P.Z.); (C.G.); (R.K.)
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (N.G.-C.); (P.Z.); (C.G.); (R.K.)
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (N.G.-C.); (P.Z.); (C.G.); (R.K.)
| | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (N.G.-C.); (P.Z.); (C.G.); (R.K.)
| | - Jorge Luis Folch-Mallol
- Laboratory of Molecular Biology of Fungi, Center for Research on Biotechnology, Autonomous University of the State of Morelos, Morelos 62210, Mexico;
| | - Ramón Alberto Batista-García
- Center of Research on Cell Dynamics, Autonomous University of the State of Morelos, Morelos 62210, Mexico; (Y.P.-L.); (E.C.R.-P.)
| | - María del Rayo Sánchez-Carbente
- Laboratory of Molecular Biology of Fungi, Center for Research on Biotechnology, Autonomous University of the State of Morelos, Morelos 62210, Mexico;
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20
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Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies. Extremophiles 2019; 24:249-264. [PMID: 31820112 DOI: 10.1007/s00792-019-01150-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/25/2019] [Indexed: 12/22/2022]
Abstract
The group Nitriliruptoria, recently classified as a separate class of phylum Actinobacteria, has five members at present, which belong to halophilic or halotolerant Actinobacteria. Here, we sequenced the genomes of Egicoccus halophilus EGI 80432T and Egibacter rhizosphaerae EGI 80759T, and performed a comparative genomics approach to analyze the genomic differences and salt adaptation mechanisms in Nitriliruptoria. Phylogenetic analysis suggested that Euzebya tangerina F10T has a closer phylogenetic relationship to Euzebya rosea DSW09T, while genomic analysis revealed highest genomic similarity with Nitriliruptor alkaliphilus ANL-iso2T and E. halophilus EGI 80432T. Genomic differences of Nitriliruptoria were mainly observed in genome size, gene contents, and the amounts of gene in per functional categories. Furthermore, our analysis also revealed that Nitriliruptoria possess similar synthesis systems of solutes, such as trehalose, glutamine, glutamate, and proline. On the other hand, each member of Nitriliruptoria species possesses specific mechanisms, K+ influx and efflux, betaine and ectoine synthesis, and compatible solutes transport to survive in various high-salt environments.
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High ectoine production by an engineered Halomonas hydrothermalis Y2 in a reduced salinity medium. Microb Cell Fact 2019; 18:184. [PMID: 31655591 PMCID: PMC6815383 DOI: 10.1186/s12934-019-1230-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022] Open
Abstract
Background As an attracted compatible solute, 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine) showed great potentials in various field. However, lower productivity and high saline medium seriously hinder its wide applications. Results The entire ectoine metabolism, including pathways for ectoine synthesis and catabolism, was identified in the genome of an ectoine-excreting strain Halomonas hydrothermalis Y2. By in-frame deletion of genes encoding ectoine hydroxylase (EctD) and (or) ectoine hydrolase (DoeA) that responsible for ectoine catabolism, the pathways for ectoine utilization were disrupted and resulted in an obviously enhanced productivity. Using an optimized medium containing 100 g L−1 NaCl in a 500-mL flask, the double mutant of Y2/ΔectD/ΔdoeA synthesized 3.13 g L−1 ectoine after 30 h cultivation. This is much higher than that of the wild type strain (1.91 g L−1), and also exceeds the production of Y2/ΔectD (2.21 g L−1). The remarkably enhanced accumulation of ectoine by Y2/ΔectD/ΔdoeA implied a critical function of Doe pathway in the ectoine catabolism. Furthermore, to reduce the salinity of fermentation medium and overcome the wastewater treatment difficulty, mutants that lacking key Na+/H+ antiporter, Mrp and (or) NhaD2, were constructed based on strain Y2/ΔectD/ΔdoeA. As a result, the Mrp-deficient strain could synthesize equal amount of ectoine (around 7 g L−1 or 500 mg (g DCW) −1) in the medium containing lower concentration of NaCl. During a fed-batch fermentation process with 60 g L−1 NaCl stress, a maximum 10.5 g L−1 ectoine was accumulated by the Mrp-deficient strain, with a specific production of 765 mg (g DCW)−1 and a yield of 0.21 g g−1 monosodium glutamate. Conclusion The remarkably enhanced production of ectoine by Y2/ΔectD/ΔdoeA implied the critical function of Doe pathway in the ectoine catabolism. Moreover, the reduced salinity requirement of Mrp-deficient strain implied a feasible protocol for many compatible solute biosynthesis, i.e., by silencing some Na+/H+ antiporters in their halophilic producers and thus lowering the medium salinity.![]()
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The Hofmeister series: Specific ion effects in aqueous polymer solutions. J Colloid Interface Sci 2019; 555:615-635. [PMID: 31408761 DOI: 10.1016/j.jcis.2019.07.067] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022]
Abstract
Specific ion effects in aqueous polymer solutions have been under active investigation over the past few decades. The current state-of-the-art research is primarily focused on the understanding of the mechanisms through which ions interact with macromolecules and affect their solution stability. Hence, we herein first present the current opinion on the sources of ion-specific effects and review the relevant studies. This includes a summary of the molecular mechanisms through which ions can interact with polymers, quantification of the affinity of ions for the polymer surface, a thermodynamic description of the effects of salts on polymer stability, as well as a discussion on the different forces that contribute to ion-polymer interplay. Finally, we also highlight future research issues that call for further scrutiny. These include fundamental questions on the mechanisms of ion-specific effects and their correlation with polymer properties as well as a discussion on the specific ion effects in more complex systems such as mixed electrolyte solutions.
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Zhai Q, Xiao Y, Narbad A, Chen W. Comparative metabolomic analysis reveals global cadmium stress response of Lactobacillus plantarum strains. Metallomics 2019; 10:1065-1077. [PMID: 29998247 DOI: 10.1039/c8mt00095f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Our previous work demonstrated the protective effects of Lactobacillus plantarum (L. plantarum) strains against cadmium (Cd) toxicity in vivo, and also indicated that the Cd tolerance of the strains played an important role in this protection. The goal of this study was to investigate the Cd resistance mechanism of L. plantarum by liquid chromatography-mass spectrometry (LC-MS) based metabolomic analysis, with a focus on the global Cd stress response. L. plantarum CCFM8610 (strongly resistant to Cd) and L. plantarum CCFM191 (sensitive to Cd) were selected as target strains, and their metabolomic profiles with and without Cd exposure were compared. The underlying mechanisms of the intra-species distinction between CCFM8610 and CCFM191 in terms of Cd tolerance can be attributed to the following aspects: (a) CCFM8610 possesses a higher intracellular content of osmolytes; (b) CCFM8610 can induce more effective biosynthesis of extracellular polymeric substance (EPS) to sequestrate Cd;
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Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
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Khaleque HN, González C, Shafique R, Kaksonen AH, Holmes DS, Watkin ELJ. Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis. Front Microbiol 2019; 10:155. [PMID: 30853944 PMCID: PMC6396713 DOI: 10.3389/fmicb.2019.00155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130T, A. prosperus DSM 14174, A. prosperus F5 and "A. ferrooxidans" DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed Ka/Ks ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130T. Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130T and "A. ferrooxidans" DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.
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Affiliation(s)
- Himel N. Khaleque
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- CSIRO Land and Water, Floreat, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Science for Life Foundation, Santiago, Chile
| | | | | | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Science for Life Foundation, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Elizabeth L. J. Watkin
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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25
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Erkorkmaz BA, Kırtel O, Ateş Duru Ö, Toksoy Öner E. Development of a cost-effective production process for Halomonas levan. Bioprocess Biosyst Eng 2018; 41:1247-1259. [DOI: 10.1007/s00449-018-1952-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022]
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26
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Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E. Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis. Genes (Basel) 2018; 9:genes9040177. [PMID: 29565833 PMCID: PMC5924519 DOI: 10.3390/genes9040177] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Astrid Höppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
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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: 32.2] [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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28
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Kim KH, Jia B, Jeon CO. Identification of Trans-4-Hydroxy-L-Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus. Front Microbiol 2017; 8:2054. [PMID: 29104571 PMCID: PMC5655121 DOI: 10.3389/fmicb.2017.02054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
Halobacillus halophilus, a moderately halophilic bacterium, accumulates a variety of compatible solutes including glycine betaine, glutamate, glutamine, proline, and ectoine to cope with osmotic stress. Non-targeted analysis of intracellular organic compounds using 1H-NMR showed that a large amount of trans-4-hydroxy-L-proline (Hyp), which has not been reported as a compatible solute in H. halophilus, was accumulated in response to high NaCl salinity, suggesting that Hyp may be an important compatible solute in H. halophilus. Candidate genes encoding proline 4-hydroxylase (PH-4), which hydroxylates L-proline to generate Hyp, were retrieved from the genome of H. halophilus through domain searches based on the sequences of known PH-4 proteins. A gene, HBHAL_RS11735, which was annotated as a multidrug DMT transporter permease in GenBank, was identified as the PH-4 gene through protein expression analysis in Escherichia coli. The PH-4 gene constituted a transcriptional unit with a promoter and a rho-independent terminator, and it was distantly located from the proline biosynthetic gene cluster (pro operon). Transcriptional analysis showed that PH-4 gene expression was NaCl concentration-dependent, and was specifically induced by chloride anion, similar to the pro operon. Accumulation of intracellular Hyp was also observed in other bacteria, suggesting that Hyp may be a widespread compatible solute in halophilic and halotolerant bacteria.
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Affiliation(s)
| | | | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, South Korea
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Draft Genome Sequences of Tetragenococcus muriaticus Strains 3MR10-3 and PMC-11-5 Isolated from Thai Fish Sauce during Natural Fermentation. GENOME ANNOUNCEMENTS 2017; 5:5/15/e00198-17. [PMID: 28408690 PMCID: PMC5391428 DOI: 10.1128/genomea.00198-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tetragenococcus muriaticus strains 3MR10-3 and PMC-11-5 are homofermentative halophilic lactic acid bacteria isolated from Thai fish sauce during natural fermentation. Their draft genomes were sequenced. Our interest in these organisms is related to their impact on fish sauce flavor and their high osmotolerance.
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Trivedi VD, Bharadwaj A, Varunjikar MS, Singha AK, Upadhyay P, Gautam K, Phale PS. Insights into metabolism and sodium chloride adaptability of carbaryl degrading halotolerant Pseudomonas sp. strain C7. Arch Microbiol 2017; 199:907-916. [PMID: 28374062 DOI: 10.1007/s00203-017-1363-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/11/2017] [Accepted: 03/15/2017] [Indexed: 11/25/2022]
Abstract
Pseudomonas sp. strain C7 isolated from sediment of Thane creek near Mumbai, India, showed the ability to grow on glucose and carbaryl in the presence of 7.5 and 3.5% of NaCl, respectively. It also showed good growth in the absence of NaCl indicating the strain to be halotolerant. Increasing salt concentration impacted the growth on carbaryl; however, the specific activity of various enzymes involved in the metabolism remained unaffected. Among various enzymes, 1-naphthol 2-hydroxylase was found to be sensitive to chloride as compared to carbaryl hydrolase and gentisate 1,2-dioxygenase. The intracellular concentration of Cl- ions remained constant (6-8 mM) for cells grown on carbaryl either in the presence or absence of NaCl. Thus the ability to adapt to the increasing concentration of NaCl is probably by employing chloride efflux pump and/or increase in the concentration of osmolytes as mechanism for halotolerance. The halotolerant nature of the strain will be beneficial to remediate carbaryl from saline agriculture fields, ecosystems and wastewaters.
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Affiliation(s)
- Vikas D Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Anahita Bharadwaj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Madhushri S Varunjikar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Arminder K Singha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Priya Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Kamini Gautam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, Goh KM. Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses. Sci Rep 2016; 6:33660. [PMID: 27641516 PMCID: PMC5027565 DOI: 10.1038/srep33660] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/31/2016] [Indexed: 11/21/2022] Open
Abstract
Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.
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Affiliation(s)
- Amira Suriaty Yaakop
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81300 Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Yan Lue Lim
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Siew-Kim Lee
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Fazilah Abd Manan
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81300 Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81300 Skudai, Johor, Malaysia
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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Chuang MY, Tsai WC, Kuo TY, Chen HM, Chen WJ. Comparative proteome analysis reveals proteins involved in salt adaptation in Photobacterium damselae subsp. piscicida. J Basic Microbiol 2016; 56:1234-1243. [PMID: 27282981 DOI: 10.1002/jobm.201600091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/16/2016] [Indexed: 11/07/2022]
Abstract
Proteomic approaches were applied to investigate whether Photobacterium damselae subsp. piscicida (Phdp) can directly sense and respond to growth conditions under different salinities, 0.85% and 3.5% NaCl concentrations, mimicking the osmotic conditions in host and marine water bodies, respectively. Proteins significantly altered were analyzed by two-dimensional gel electrophoresis (2-DE), liquid chromatography-electrospray ionization-quadrupole-time-of-flight tandem mass spectrometry (LC-ESI-Q-TOF MS/MS) and bioinformatics analysis, thus resulting in 16 outer membrane proteins (OMPs), 12 inner membrane proteins (IMPs), and 20 cytoplasmic proteins (CPs). Quantitative real-time PCR was also applied to monitor the mRNA expression level of these target proteins. Cluster of orthologous groups of protein (COG) analysis revealed that when shifting from 3.5% to 0.85% salinity, the majority of the up-regulated proteins were involved in posttranslational modification, protein turnover, and chaperones, while the down-regulated proteins were mainly related to energy production and conversion, compatible solutes (carbohydrates, amino acids and their derivatives) biogenesis and transport. Differentially expressed proteins identified in the current study could be used to elucidate the salt adaptation mechanisms of Phdp during their transition between host cells and the marine habitats.
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Affiliation(s)
- Min-Yuan Chuang
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Wei-Chen Tsai
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Tsun-Yung Kuo
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Han-Min Chen
- Department of Life Science, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Wei-Jung Chen
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
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Abbamondi GR, Suner S, Cutignano A, Grauso L, Nicolaus B, Toksoy Oner E, Tommonaro G. Identification of N-Hexadecanoyl-L-homoserine lactone (C16-AHL) as signal molecule in halophilic bacterium Halomonas smyrnensis AAD6. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1206-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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35
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Zhang Y, Li Y, Zhang Y, Wang Z, Zhao M, Su N, Zhang T, Chen L, Wei W, Luo J, Zhou Y, Xu Y, Xu P, Li W, Tao Y. Quantitative Proteomics Reveals Membrane Protein-Mediated Hypersaline Sensitivity and Adaptation in Halophilic Nocardiopsis xinjiangensis. J Proteome Res 2015; 15:68-85. [DOI: 10.1021/acs.jproteome.5b00526] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yao Zhang
- Institute
of Microbiology, Chinese Academy of Science, Beijing 100101, China
- State
Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant
Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanchang Li
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yongguang Zhang
- Key
Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang
Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, China
| | - Zhiqiang Wang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry
of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, P. R. China
| | - Mingzhi Zhao
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Na Su
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Tao Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Lingsheng Chen
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- State
Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, P. R. China
| | - Wei Wei
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Jing Luo
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Key
Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang
Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanxia Zhou
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Hebei
Province Key Lab of Research and Application on Microbial Diversity,
College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Yongru Xu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- State
Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, P. R. China
| | - Ping Xu
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Engineering Research Center for Protein Drugs, National Center for
Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry
of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, P. R. China
- Anhui Medical University, Hefei, Anhui 230032, P. R. China
| | - Wenjun Li
- State
Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant
Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, China
- Key
Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang
Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, China
- Key
Laboratory of Microbial Diversity in Southwest China, Ministry of
Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, China
| | - Yong Tao
- Institute
of Microbiology, Chinese Academy of Science, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Joghee NN, Jayaraman G. Biochemical changes induced by salt stress in halotolerant bacterial isolates are media dependent as well as species specific. Prep Biochem Biotechnol 2014; 46:8-14. [DOI: 10.1080/10826068.2014.970689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Shiyan A, Thompson M, Köcher S, Tausendschön M, Santos H, Hänelt I, Müller V. Glutamine synthetase 2 is not essential for biosynthesis of compatible solutes in Halobacillus halophilus. Front Microbiol 2014; 5:168. [PMID: 24782854 PMCID: PMC3995056 DOI: 10.3389/fmicb.2014.00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/27/2014] [Indexed: 11/13/2022] Open
Abstract
Halobacillus halophilus, a moderately halophilic bacterium isolated from salt marshes, produces various compatible solutes to cope with osmotic stress. Glutamate and glutamine are dominant compatible solutes at mild salinities. Glutamine synthetase activity in cell suspensions of Halobacillus halophilus wild type was shown to be salt dependent and chloride modulated. A possible candidate to catalyze glutamine synthesis is glutamine synthetase A2, whose transcription is stimulated by chloride. To address the role of GlnA2 in the biosynthesis of the osmolytes glutamate and glutamine, a deletion mutant (ΔglnA2) was generated and characterized in detail. We compared the pool of compatible solutes and performed transcriptional analyses of the principal genes controlling the solute production in the wild type strain and the deletion mutant. These measurements did not confirm the hypothesized role of GlnA2 in the osmolyte production. Most likely the presence of another, yet to be identified enzyme has the main contribution in the measured activity in crude extracts and probably determines the total chloride-modulated profile. The role of GlnA2 remains to be elucidated.
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Affiliation(s)
- Anna Shiyan
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Melanie Thompson
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Saskia Köcher
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Michaela Tausendschön
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Inga Hänelt
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
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Widderich N, Höppner A, Pittelkow M, Heider J, Smits SHJ, Bremer E. Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. PLoS One 2014; 9:e93809. [PMID: 24714029 PMCID: PMC3979721 DOI: 10.1371/journal.pone.0093809] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Ectoine and hydroxyectoine are well-recognized members of the compatible solutes and are widely employed by microorganisms as osmostress protectants. The EctABC enzymes catalyze the synthesis of ectoine from the precursor L-aspartate-β-semialdehyde. A subgroup of the ectoine producers can convert ectoine into 5-hydroxyectoine through a region-selective and stereospecific hydroxylation reaction. This compatible solute possesses stress-protective and function-preserving properties different from those of ectoine. Hydroxylation of ectoine is carried out by the EctD protein, a member of the non-heme-containing iron (II) and 2-oxoglutarate-dependent dioxygenase superfamily. We used the signature enzymes for ectoine (EctC) and hydroxyectoine (EctD) synthesis in database searches to assess the taxonomic distribution of potential ectoine and hydroxyectoine producers. Among 6428 microbial genomes inspected, 440 species are predicted to produce ectoine and of these, 272 are predicted to synthesize hydroxyectoine as well. Ectoine and hydroxyectoine genes are found almost exclusively in Bacteria. The genome context of the ect genes was explored to identify proteins that are functionally associated with the synthesis of ectoines; the specialized aspartokinase Ask_Ect and the regulatory protein EctR. This comprehensive in silico analysis was coupled with the biochemical characterization of ectoine hydroxylases from microorganisms that can colonize habitats with extremes in salinity (Halomonas elongata), pH (Alkalilimnicola ehrlichii, Acidiphilium cryptum), or temperature (Sphingopyxis alaskensis, Paenibacillus lautus) or that produce hydroxyectoine very efficiently over ectoine (Pseudomonas stutzeri). These six ectoine hydroxylases all possess similar kinetic parameters for their substrates but exhibit different temperature stabilities and differ in their tolerance to salts. We also report the crystal structure of the Virgibacillus salexigens EctD protein in its apo-form, thereby revealing that the iron-free structure exists already in a pre-set configuration to incorporate the iron catalyst. Collectively, our work defines the taxonomic distribution and salient biochemical properties of the ectoine hydroxylase protein family and contributes to the understanding of its structure.
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Affiliation(s)
- Nils Widderich
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Emeritus Group R.K. Thauer, Marburg, Germany
| | - Astrid Höppner
- X-Ray Facility and Crystal Farm, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marco Pittelkow
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- * E-mail: (SHGS); (EB)
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (SHGS); (EB)
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Dynamic metabolic and transcriptional profiling of Rhodococcus sp. strain YYL during the degradation of tetrahydrofuran. Appl Environ Microbiol 2014; 80:2656-64. [PMID: 24532074 DOI: 10.1128/aem.04131-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Although tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD(+), and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through (1)H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms.
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40
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Vajda J, Mueller E, Bahret E. Dual salt mixtures in mixed mode chromatography with an immobilized tryptophan ligand influence the removal of aggregated monoclonal antibodies. Biotechnol J 2014; 9:555-65. [DOI: 10.1002/biot.201300230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 11/29/2013] [Accepted: 12/09/2013] [Indexed: 11/11/2022]
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41
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López-Pérez M, Ghai R, Leon MJ, Rodríguez-Olmos Á, Copa-Patiño JL, Soliveri J, Sanchez-Porro C, Ventosa A, Rodriguez-Valera F. Genomes of "Spiribacter", a streamlined, successful halophilic bacterium. BMC Genomics 2013; 14:787. [PMID: 24225341 PMCID: PMC3832224 DOI: 10.1186/1471-2164-14-787] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/11/2013] [Indexed: 11/25/2022] Open
Abstract
Background Thalassosaline waters produced by the concentration of seawater are widespread and common extreme aquatic habitats. Their salinity varies from that of sea water (ca. 3.5%) to saturation for NaCl (ca. 37%). Obviously the microbiota varies dramatically throughout this range. Recent metagenomic analysis of intermediate salinity waters (19%) indicated the presence of an abundant and yet undescribed gamma-proteobacterium. Two strains belonging to this group have been isolated from saltern ponds of intermediate salinity in two Spanish salterns and were named “Spiribacter”. Results The genomes of two isolates of “Spiribacter” have been fully sequenced and assembled. The analysis of metagenomic datasets indicates that microbes of this genus are widespread worldwide in medium salinity habitats representing the first ecologically defined moderate halophile. The genomes indicate that the two isolates belong to different species within the same genus. Both genomes are streamlined with high coding densities, have few regulatory mechanisms and no motility or chemotactic behavior. Metabolically they are heterotrophs with a subgroup II xanthorhodopsin as an additional energy source when light is available. Conclusions This is the first bacterium that has been proven by culture independent approaches to be prevalent in hypersaline habitats of intermediate salinity (half a way between the sea and NaCl saturation). Predictions from the proteome and analysis of transporter genes, together with a complete ectoine biosynthesis gene cluster are consistent with these microbes having the salt-out-organic-compatible solutes type of osmoregulation. All these features are also consistent with a well-adapted fully planktonic microbe while other halophiles with more complex genomes such as Salinibacter ruber might have particle associated microniches.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain.
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Guesmi A, Ettoumi B, El Hidri D, Essanaa J, Cherif H, Mapelli F, Marasco R, Rolli E, Boudabous A, Cherif A. Uneven distribution of Halobacillus trueperi species in arid natural saline systems of Southern Tunisian Sahara. MICROBIAL ECOLOGY 2013; 66:831-839. [PMID: 23949950 DOI: 10.1007/s00248-013-0274-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 07/28/2013] [Indexed: 06/02/2023]
Abstract
The genetic diversity of a collection of 336 spore-forming isolates recovered from five salt-saturated brines and soils (Chott and Sebkhas) mainly located in the hyper-arid regions of the southern Tunisian Sahara has been assessed. Requirements and abilities for growth at a wide range of salinities\ showed that 44.3 % of the isolates were extremely halotolerant, 23 % were moderate halotolerant, and 32.7 % were strict halophiles, indicating that they are adapted to thrive in these saline ecosystems. A wide genetic diversity was documented based on 16S-23S rRNA internal transcribed spacer fingerprinting profiles (ITS) and 16S rRNA gene sequences that clustered the strains into seven genera: Bacillus, Gracilibacillus, Halobacillus, Oceanobacillus, Paenibacillus, Pontibacillus, and Virgibacillus. Halobacillus trueperi was the most encountered species in all the sites and presented a large intraspecific diversity with a multiplicity of ITS types. The most frequent ITS type included 42 isolates that were chosen for assessing of the intraspecific diversity by BOX-PCR fingerprinting. A high intraspecific microdiversity was documented by 14 BOX-PCR genotypes whose distribution correlated with the strain geographic origin. Interestingly, H. trueperi isolates presented an uneven geographic distribution among sites with the highest frequency of isolation from the coastal sites, suggesting a marine rather than terrestrial origin of the strains. The high frequency and diversity of H. trueperi suggest that it is a major ecosystem-adapted microbial component of the Tunisian Sahara harsh saline systems of marine origin.
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Affiliation(s)
- Amel Guesmi
- Laboratoire MBA, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire, 2092, Tunis, Tunisia
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Sand M, Stahl J, Waclawska I, Ziegler C, Averhoff B. Identification of an osmo-dependent and an osmo-independent choline transporter inAcinetobacter baylyi: implications in osmostress protection and metabolic adaptation. Environ Microbiol 2013; 16:1490-502. [DOI: 10.1111/1462-2920.12188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/04/2013] [Accepted: 06/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Miriam Sand
- Molecular Microbiology & Bioenergetics; Institute of Molecular Biosciences; Johann Wolfgang Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Julia Stahl
- Molecular Microbiology & Bioenergetics; Institute of Molecular Biosciences; Johann Wolfgang Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Izabela Waclawska
- Department of Structural Biology; Max-Planck-Institute of Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Christine Ziegler
- Department of Structural Biology; Max-Planck-Institute of Biophysics; Max-von-Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics; Institute of Molecular Biosciences; Johann Wolfgang Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
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Biosynthesis of the osmoprotectant ectoine, but not glycine betaine, is critical for survival of osmotically stressed Vibrio parahaemolyticus cells. Appl Environ Microbiol 2013; 79:5038-49. [PMID: 23770911 DOI: 10.1128/aem.01008-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio parahaemolyticus is a halophile present in marine and estuarine environments, ecosystems characterized by fluctuations in salinity and temperature. One strategy to thrive in such environments is the synthesis and/or uptake of compatible solutes. The V. parahaemolyticus genome contains biosynthesis systems for both ectoine and glycine betaine, which are known to act as compatible solutes in other species. We showed that V. parahaemolyticus had a 6% NaCl tolerance when grown in M9 minimal medium with 0.4% glucose (M9G) with a >5-h lag phase. By using (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR) analysis, we determined that cells synthesized ectoine and glutamate in a NaCl-dependent manner. The most effective compatible solutes as measured by a reduction in lag-phase growth in M9G with 6% NaCl (M9G 6% NaCl) were in the order glycine betaine > choline > proline = glutamate > ectoine. However, V. parahaemolyticus could use glutamate or proline as the sole carbon source, but not ectoine or glycine betaine, which suggests that these are bona fide compatible solutes. Expression analysis showed that the ectA and betA genes were more highly expressed in log-phase cells, and expression of both genes was induced by NaCl up-shock. Under all conditions examined, the ectA gene was more highly expressed than the betA gene. Analysis of in-frame deletions in betA and ectB and in a double mutant showed that the ectB mutant was defective for growth, and this defect was rescued by the addition of glycine betaine, proline, ectoine, and glutamate, indicating that these compounds are compatible solutes for this species. The presence of both synthesis systems was the predominant distribution pattern among members of the Vibrionaceae family, suggesting this is the ancestral state.
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Bioenergetics of the moderately halophilic bacterium Halobacillus halophilus: composition and regulation of the respiratory chain. Appl Environ Microbiol 2013; 79:3839-46. [PMID: 23584768 DOI: 10.1128/aem.00855-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In their natural environments, moderately halophilic bacteria are confronted not only with high salinities but also with low oxygen tensions due to the high salinities. The growth of H. halophilus is strictly aerobic. To analyze the dependence of respiration on the NaCl concentration and oxygen availability of the medium, resting cell experiments were performed. The respiration rates were dependent on the NaCl concentration of the growth medium, as well as on the NaCl concentration of the assay buffer, indicating regulation on the transcriptional and the activity level. Respiration was accompanied by the generation of an electrochemical proton potential (Δμ(H+)) across the cytoplasmic membrane whose magnitude was dependent on the external pH. Genes encoding proteins involved in respiration and Δμ(H+) generation, such as a noncoupled NADH dehydrogenase (NDH-2), complex II, and complex III, were identified in the genome. In addition, genes encoding five different terminal oxidases are present. Inhibitor profiling revealed the presence of NDH-2 and complex III, but the nature of the oxidases could not be resolved using this approach. Expression analysis demonstrated that all the different terminal oxidases were indeed expressed, but by far the most prominent was cta, encoding cytochrome caa3 oxidase. The expression of all of the different oxidase genes increased at high NaCl concentrations, and the transcript levels of cta and qox (encoding cytochrome aa3 oxidase) also increased at low oxygen concentrations. These data culminate in a model of the composition and variation of the respiratory chain of H. halophilus.
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Molecular Mechanisms of Adaptation of the Moderately Halophilic Bacterium Halobacillis halophilus to Its Environment. Life (Basel) 2013; 3:234-43. [PMID: 25371341 PMCID: PMC4187189 DOI: 10.3390/life3010234] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/02/2013] [Accepted: 02/05/2013] [Indexed: 11/16/2022] Open
Abstract
The capability of osmoadaptation is a prerequisite of organisms that live in an environment with changing salinities. Halobacillus halophilus is a moderately halophilic bacterium that grows between 0.4 and 3 M NaCl by accumulating both chloride and compatible solutes as osmolytes. Chloride is absolutely essential for growth and, moreover, was shown to modulate gene expression and activity of enzymes involved in osmoadaptation. The synthesis of different compatible solutes is strictly salinity- and growth phase-dependent. This unique hybrid strategy of H. halophilus will be reviewed here taking into account the recently published genome sequence. Based on identified genes we will speculate about possible scenarios of the synthesis of compatible solutes and the uptake of potassium ion which would complete our knowledge of the fine-tuned osmoregulation and intracellular osmolyte balance in H. halophilus.
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Sand M, Mingote AI, Santos H, Müller V, Averhoff B. Mannitol, a compatible solute synthesized by Acinetobacter baylyi in a two-step pathway including a salt-induced and salt-dependent mannitol-1-phosphate dehydrogenase. Environ Microbiol 2013; 15:2187-97. [PMID: 23414076 DOI: 10.1111/1462-2920.12090] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 11/29/2022]
Abstract
The nutritionally versatile and naturally competent soil bacterium Acinetobacter baylyi copes with salt stress by the accumulation of compatible solutes. NMR analyses revealed that cells amassed glutamate and the rather unusual sugar alcohol mannitol upon an increase of the external NaCl concentration. To unravel the path of mannitol biosynthesis, the genome was inspected for genes potentially involved in its biosynthesis. A gene encoding a potential mannitol-1-phosphate dehydrogenase (mtlD) was identified in the genome of A. baylyi. Expression of mtlD was highly induced at high salinity. mtlD was overexpressed and the purified protein indeed produced mannitol-1-phosphate from fructose-6-phosphate. The enzyme preferred NADPH over NADH and the specific activity of fructose-6-phosphate reduction with NADPH was 130 U mg(-1) . Enzymatic activity was strictly salt-dependent. Deletion of mtlD resulted in a complete loss of salt-dependent mannitol biosynthesis. We provide clear evidence that osmo-induced synthesis of the compatible solute mannitol is by a two-step pathway and that the mannitol-1-phosphate dehydrogenase mediating the first step of this pathway is regulated by salinity on the transcriptional as well as on the activity level.
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Affiliation(s)
- Miriam Sand
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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48
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Polyextremophiles and the Constraints for Terrestrial Habitability. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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49
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Copeland E, Choy N, Gabani P, Singh OV. Biosynthesis of Extremolytes: Radiation Resistance and Biotechnological Implications. Extremophiles 2012. [DOI: 10.1002/9781118394144.ch15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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50
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Lopalco P, Angelini R, Lobasso S, Köcher S, Thompson M, Müller V, Corcelli A. Adjusting membrane lipids under salt stress: the case of the moderate halophilic organism Halobacillus halophilus. Environ Microbiol 2012; 15:1078-87. [PMID: 22970819 DOI: 10.1111/j.1462-2920.2012.02870.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 11/28/2022]
Abstract
The lipid composition of Halobacillus halophilus was investigated by combined thin-layer chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analyses of the total lipid extract. Main polar lipids were found to be sulfoquinovosyldiacylglycerol and phosphatidylglycerol, while cardiolipin was a minor lipid together with phosphatidic acid, alanyl-phosphatidylglycerol and two not yet fully identified lipid components. In addition the analyses of residual lipids, associated with denatured proteins after the lipid extraction, revealed the presence of significant amounts of cardiolipin, indicating that it is a not readily extractable phospholipid. Post decay source mass spectrometry analyses allowed the determination of acyl chains of main lipid components. On increasing the culture medium salinity, an increase in the shorter chains and the presence of chain unsaturations were observed. These changes in the lipid core structures might compensate for the increase in packing and rigidity of phospholipid and sulfoglycolipid polar heads in high-salt medium, therefore contributing to the homeostasis of membrane fluidity and permeability in salt stress conditions.
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Affiliation(s)
- Patrizia Lopalco
- Institute for Microelectronics and Microsystems, National Research Council (IMM-CNR), Lecce, Italy
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