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Xu X, Song F, Zhang G, Ma L, Yang N. Proteomic insights into the response of Halomonas sp. MNB13 to excess Mn(Ⅱ) and the role of H 2S in Mn(Ⅱ) resistance. ENVIRONMENTAL RESEARCH 2024; 246:118157. [PMID: 38199468 DOI: 10.1016/j.envres.2024.118157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/23/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Halomonas spp. are moderately halophilic bacteria with the ability to tolerate various heavy metals. However, the role of basic cellular metabolism, particularly amino acid metabolism, has not been investigated in Halomonas spp. under excess Mn(Ⅱ). The strain Halomonas sp. MNB13 was isolated from a deep-sea ferromanganese nodule and can tolerate 80 mM Mn(Ⅱ). To comprehensively explore the mechanisms underlying its resistance to excess Mn(Ⅱ), we conducted a comparative proteome analysis. The data revealed that both 10 mM and 50 mM Mn(Ⅱ) significantly up-regulated the expression of proteins involved in Mn(Ⅱ) transport (MntE), oxidative stress response (alkyl hydroperoxide reductase and the Suf system), and amino acid metabolism (arginine, cysteine, methionine, and phenylalanine). We further investigated the role of cysteine metabolism in Mn(Ⅱ) resistance by examining the function of its downstream product, H2S. Consistent with the up-regulation of cysteine desulfurase, we detected an elevated level of H2S in Halomonas sp. MNB13 cells under Mn(Ⅱ) stress, along with increased intracellular levels of H2O2 and O2•-. Upon exogenous addition of H2S, we observed a significant restoration of the growth of Halomonas sp. MNB13. Moreover, we identified decreased intracellular levels of H2O2 and O2•- in MNB13 cells, which coincided with a decreased formation of Mn-oxides during cultivation. In contrast, in cultures containing NaHS, the residual Mn(Ⅱ) levels were higher than in cultures without NaHS. Therefore, H2S improves Mn(Ⅱ) tolerance by eliminating intracellular reactive oxygen species rather than decreasing Mn(Ⅱ) concentration in solution. Our findings indicate that cysteine metabolism, particularly the intermediate H2S, plays a pivotal role in Mn(Ⅱ) resistance by mitigating the damage caused by reactive oxygen species. These findings provide new insights into the amino acid mechanisms associated with Mn(Ⅱ) resistance in bacteria.
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Affiliation(s)
- Xiuli Xu
- School of Ocean Sciences, China University of Geosciences, 29 Xueyuan Road, Beijing, 100083, China
| | - Fuhang Song
- School of Light Industry, Beijing Technology and Business University, 11 Fucheng Road, Beijing, 100048, China
| | - Guoliang Zhang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Linlin Ma
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, 4111, Australia
| | - Na Yang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.
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Synthesizing glycine betaine via choline oxidation pathway as an osmoprotectant strategy in Haloferacales. Gene 2022; 847:146886. [PMID: 36108788 DOI: 10.1016/j.gene.2022.146886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/21/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022]
Abstract
The accumulation of organic compatible solutes, such as glycine betaine, is one of the osmoprotective strategies used by halophilic archaea to adapt to high salinity. The uptake of glycine betaine from the external environment using various transporters has been widely studied in different halophilic archaea. However, the de novo biosynthesis of glycine betaine and its distribution in halophilic archaea remain unclear. In this study, an extremely halophilic archaea strain, named Halorubrum sp. 2020YC2 and previously isolated from a salt-lake sample, was identified with complete choline oxidation pathway genes. Halorubrum sp. 2020YC2 could synthesize and accumulate 1.56-4.25 μmol per mg of protein of glycine betaine in a defined medium, with its content increasing along with increasing salinity. The intracellular content of glycine betaine remained relatively stable at different salinities when another exogenous solute such as trehalose was provided. The metabolic profile and transcriptional results strongly suggested that the intracellular glycine betaine was derived from serine, which came from the glycolytic intermediate 3-phosphoglycerate when glucose was used as the sole carbon source. Out of 205 available genomes of halophilic archaea, genes encoding the choline oxidation pathway were identified in 30 genomes, and more than half of the strains belonging to order Haloferacales contained the choline oxidation pathway. Phylogenetic analysis further indicated that this pathway evolved from halophilic Proteobacteria, and its absence in some genera indicated a possible gene loss event during evolution. The analysis of reported culture data of halophilic archaea strains eventually demonstrated that the presence of the choline oxidation pathway had no significant effects on the adaptation of Haloferacales to high salinity habitats. Therefore, the de novo biosynthesis of glycine betaine via the choline oxidation pathway could be an auxiliary osmoprotective strategy in halophilic archaea.
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Shi J, Xia C, Tian Q, Zeng X, Wu Z, Guo Y, Pan D. Untargeted metabolomics based on LC–MS to elucidate the mechanism underlying nitrite degradation by Limosilactobacillus fermentum RC4. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gagliano MC, Sampara P, Plugge CM, Temmink H, Sudmalis D, Ziels RM. Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes. Appl Environ Microbiol 2022; 88:e0244921. [PMID: 35477253 PMCID: PMC9128505 DOI: 10.1128/aem.02449-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 12/15/2022] Open
Abstract
Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na+). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as Nε-acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments. IMPORTANCE Using genome-centric metagenomics, we discovered a new Methanothrix harundinacea subspecies that appears to be a halotolerant acetoclastic methanogen with the flexibility for adaptation in the anaerobic digestion process both at low (5 g/L Na+) and high salinity conditions (20 g/L Na+). Annotation of the recovered M. harundinacea genome revealed salinity stress-related functions, including the modification of EPS glycoconjugates and the production of compatible solutes. This is the first study reporting these genomic features within a Methanothrix sp., a milestone further supporting previous studies that identified M. harundinacea as a key-driver in anaerobic granulation under high salinity stress.
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Affiliation(s)
- Maria Cristina Gagliano
- Wetsus – European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Pranav Sampara
- Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Caroline M. Plugge
- Wetsus – European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hardy Temmink
- Wetsus – European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
- Department of Environmental Technology, Wageningen University and Research, Wageningen, the Netherlands
| | - Dainis Sudmalis
- Department of Environmental Technology, Wageningen University and Research, Wageningen, the Netherlands
| | - Ryan M. Ziels
- Civil Engineering, University of British Columbia, Vancouver, British Columbia, Canada
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Investigations of Dimethylglycine, Glycine Betaine, and Ectoine Uptake by a Betaine-Carnitine-Choline Transporter Family Transporter with Diverse Substrate Specificity in Vibrio Species. J Bacteriol 2020; 202:JB.00314-20. [PMID: 32817090 DOI: 10.1128/jb.00314-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023] Open
Abstract
Fluctuations in osmolarity are one of the most prevalent stresses to which bacteria must adapt, both hypo- and hyperosmotic conditions. Most bacteria cope with high osmolarity by accumulating compatible solutes (osmolytes) in the cytoplasm to maintain the turgor pressure of the cell. Vibrio parahaemolyticus, a halophile, utilizes at least six compatible solute transporters for the uptake of osmolytes: two ABC family ProU transporters and four betaine-carnitine-choline transporter (BCCT) family transporters. The full range of compatible solutes transported by this species has yet to be determined. Using an osmolyte phenotypic microarray plate for growth analyses, we expanded the known osmolytes used by V. parahaemolyticus to include N,N-dimethylglycine (DMG), among others. Growth pattern analysis of four triple-bccT mutants, possessing only one functional BCCT, indicated that BccT1 (VP1456), BccT2 (VP1723), and BccT3 (VP1905) transported DMG. BccT1 was unusual in that it could take up both compounds with methylated head groups (glycine betaine [GB], choline, and DMG) and cyclic compounds (ectoine and proline). Bioinformatics analysis identified the four coordinating amino acid residues for GB in the BccT1 protein. In silico modeling analysis demonstrated that GB, DMG, and ectoine docked in the same binding pocket in BccT1. Using site-directed mutagenesis, we showed that a strain with all four residues mutated resulted in the loss of uptake of GB, DMG, and ectoine. We showed that three of the four residues were essential for ectoine uptake, whereas only one of the residues was important for GB uptake. Overall, we have demonstrated that DMG is a highly effective compatible solute for Vibrio species and have elucidated the amino acid residues in BccT1 that are important for the coordination of GB, DMG, and ectoine transport.IMPORTANCE Vibrio parahaemolyticus possesses at least six osmolyte transporters, which allow the bacterium to adapt to high-salinity conditions. In this study, we identified several additional osmolytes that were utilized by V. parahaemolyticus We demonstrated that the compound DMG, which is present in the marine environment, was a highly effective osmolyte for Vibrio species. We determined that DMG is transported via BCCT family carriers, which have not been shown previously to take up this compound. BccT1 was a carrier for GB, DMG, and ectoine, and we identified the amino acid residues essential for the coordination of these compounds. The data suggest that for BccT1, GB is more easily accommodated than ectoine in the transporter binding pocket.
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CosR Is a Global Regulator of the Osmotic Stress Response with Widespread Distribution among Bacteria. Appl Environ Microbiol 2020; 86:AEM.00120-20. [PMID: 32169942 DOI: 10.1128/aem.00120-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
Bacteria accumulate small, organic compounds called compatible solutes via uptake from the environment or biosynthesis from available precursors to maintain the turgor pressure of the cell in response to osmotic stress. The halophile Vibrio parahaemolyticus has biosynthesis pathways for the compatible solutes ectoine (encoded by ectABC-asp_ect) and glycine betaine (encoded by betIBA-proXWV), four betaine-carnitine-choline transporters (encoded by bccT1 to bccT4), and a second ProU transporter (encoded by proVWX). All of these systems are osmotically inducible with the exception of bccT2 Previously, it was shown that CosR, a MarR-type regulator, was a direct repressor of ectABC-asp_ect in Vibrio species. In this study, we investigated whether CosR has a broader role in the osmotic stress response. Expression analyses demonstrated that betIBA-proXWV, bccT1, bccT3, bccT4, and proVWX are repressed in low salinity. Examination of an in-frame cosR deletion mutant showed that expression of these systems is derepressed in the mutant at low salinity compared with the wild type. DNA binding assays demonstrated that purified CosR binds directly to the regulatory region of both biosynthesis systems and four transporters. In Escherichia coli green fluorescent protein (GFP) reporter assays, we demonstrated that CosR directly represses transcription of betIBA-proXWV, bccT3, and proVWX Similar to Vibrio harveyi, we showed betIBA-proXWV was directly activated by the quorum-sensing LuxR homolog OpaR, suggesting a conserved mechanism of regulation among Vibrio species. Phylogenetic analysis demonstrated that CosR is ancestral to the Vibrionaceae family, and bioinformatics analysis showed widespread distribution among Gammaproteobacteria in general. Incidentally, in Aliivibrio fischeri, Aliivibrio finisterrensis, Aliivibrio sifiae, and Aliivibrio wodanis, an unrelated MarR-type regulator gene named ectR was clustered with ectABC-asp, which suggests the presence of another novel ectoine biosynthesis regulator. Overall, these data show that CosR is a global regulator of osmotic stress response that is widespread among bacteria.IMPORTANCE Vibrio parahaemolyticus can accumulate compatible solutes via biosynthesis and transport, which allow the cell to survive in high salinity conditions. There is little need for compatible solutes under low salinity conditions, and biosynthesis and transporter systems need to be repressed. However, the mechanism(s) of this repression is not known. In this study, we showed that CosR played a major role in the regulation of multiple compatible solute systems. Phylogenetic analysis showed that CosR is present in all members of the Vibrionaceae family as well as numerous Gammaproteobacteria Collectively, these data establish CosR as a global regulator of the osmotic stress response that is widespread in bacteria, controlling many more systems than previously demonstrated.
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7
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Sudmalis D, Millah SK, Gagliano MC, Butré CI, Plugge CM, Rijnaarts HHM, Zeeman G, Temmink H. The potential of osmolytes and their precursors to alleviate osmotic stress of anaerobic granular sludge. WATER RESEARCH 2018; 147:142-151. [PMID: 30308373 DOI: 10.1016/j.watres.2018.09.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/27/2018] [Accepted: 09/29/2018] [Indexed: 06/08/2023]
Abstract
Increasing amounts of saline (waste)water with high concentrations of organic pollutants are generated globally. In the anaerobic (waste)water treatment domain, high salt concentrations are repeatedly reported to inhibit methanogenic activity and strategies to overcome this toxicity are needed. Current research focuses on the use of potential osmolyte precursor compounds for osmotic stress alleviation in granular anaerobic sludges upon exposure to hypersalinity shocks. Glutamic acid, aspartic acid, lysine, potassium, gelatine, and tryptone were tested for their potential to alleviate osmotic stress in laboratory grown and full - scale granular sludge. The laboratory grown granular sludge was adapted to 5 (R5) and 20 (R20) g Na+/L. Full-scale granular sludge was obtained from internal circulation reactors treating tannery (waste)water with influent conductivity of 29.2 (Do) and 14.1 (Li) mS/cm. In batch experiments which focused on specific methanogenic activity (SMA), R5 granular sludge was exposed to a hypersalinity shock of 20 g Na+/L. The granular sludge of Do and Li was exposed to a hypersalinity shock of 10 g Na+/L with sodium acetate as the sole carbon source. The effects on R20 granular sludge were studied at the salinity level to which the sludge was already adapted, namely 20 g Na+/L. Dosing of glutamic acid, aspartic acid, gelatine, and tryptone resulted in increased SMA compared to only acetate fed batches. In batches with added glutamic acid, the SMA increased by 115% (Li), 35% (Do) and 9% (R20). With added aspartic acid, SMA increased by 72% (Li), 26% (Do), 12% (R5) and 7% (R20). The addition of tryptone resulted in SMA increases of 36% (R5), 17% (R20), 179% (Li), and 48% (Do), whereas added gelatine increased the SMA by 30% (R5), 14% (R20), 23% (Li), and 13% (Do). The addition of lysine, meanwhile, gave negative effects on SMA of all tested granular sludges. Potassium at sea water Na/K ratio (27.8 w/w) had a slight positive effect on SMA of Do (7.3%) and Li (10.1%), whereas at double the sea water ratio (13.9% w/w) had no pronounced positive effect. R20 granular sludge was also exposed to hyposalinity shock from 20 down to 5 g Na+/L. Glutamate and N-acetyl-β-lysine were excreted by microbial consortium in anaerobic granular sludge adapted to 20 g Na+/L upon this exposure to hyposalinity. A potential consequence when applying these results is that saline streams containing specific and hydrolysable proteins can be anaerobically treated without additional dosing of osmolytes.
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Affiliation(s)
- D Sudmalis
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands.
| | - S K Millah
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - M C Gagliano
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - C I Butré
- Laboratory of Food Chemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - C M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - H H M Rijnaarts
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - G Zeeman
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - H Temmink
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
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Sorokin DY, Merkel AY, Abbas B, Makarova KS, Rijpstra WIC, Koenen M, Sinninghe Damsté JS, Galinski EA, Koonin EV, van Loosdrecht MCM. Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. Int J Syst Evol Microbiol 2018; 68:2199-2208. [PMID: 29781801 DOI: 10.1099/ijsem.0.002810] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Methanogenic enrichments from hypersaline lakes at moderate thermophilic conditions have resulted in the cultivation of an unknown deep lineage of euryarchaeota related to the class Halobacteria. Eleven soda lake isolates and three salt lake enrichment cultures were methyl-reducing methanogens that utilize C1 methylated compounds as electron acceptors and H2 or formate as electron donors, but they were unable to grow on either substrates alone or to form methane from acetate. They are extreme halophiles, growing optimally at 4 M total Na+ and the first representatives of methanogens employing the 'salt-in' osmoprotective mechanism. The salt lake subgroup is neutrophilic, whereas the soda lake isolates are obligate alkaliphiles, with an optimum around pH 9.5. Both grow optimally at 50 °C. The genetic diversity inside the two subgroups is very low, indicating that the soda and salt lake clusters consist of a single genetic species each. The phylogenetic distance between the two subgroups is in the range of distant genera, whereas the distance to other euryarchaea is below 83 % identity of the 16S rRNA gene. These isolates and enriched methanogens, together with closely related environmental clones from hypersaline habitats (the SA1 group), form a novel class-level clade in the phylum Euryarchaeota. On the basis of distinct phenotypic and genetic properties, the soda lake isolates are classified into a new genus and species, Methanonatronarchaeum thermophilum, with the type strain AMET1T (DSM 28684T=NBRC 110805T=UNIQEM U982T), and the salt lake methanogens into a candidate genus and species 'Candidatus Methanohalarchaeum thermophilum'. These organisms are proposed to form novel family, order and class Methanonatronarchaeaceae fam. nov., Methanonatronarchaeales ord. nov. and Methanonatronarchaeia classis nov., within the phylum Euryarchaeota.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, TU Delft, The Netherlands
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ben Abbas
- Department of Biotechnology, TU Delft, The Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, and Utrecht University, The Netherlands
| | - M Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, and Utrecht University, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, and Utrecht University, The Netherlands.,Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Lai SJ, Deng YC, Lai MC. Comparison of Enzymatic Traits between Native and Recombinant Glycine Sarcosine N-Methyltransferase from Methanohalophilus portucalensis FDF1T. PLoS One 2016; 11:e0168666. [PMID: 28036340 PMCID: PMC5201303 DOI: 10.1371/journal.pone.0168666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 12/05/2016] [Indexed: 11/18/2022] Open
Abstract
The halophilic methanoarchaeon Methanohalophilus portucalensis FDF1T possesses the ability to synthesize the osmolyte betaine from its precursor, glycine, in response to extracellular salt stress through a three-step transmethylation process. Analysis of recombinant glycine sarcosine N-methyltransferase (rGSMT) and recombinant sarcosine dimethylglycine N-methyltransferase (rSDMT) from Escherichia coli indicated that betaine synthesis is rate-limited by rGSMT and is constitutively activated by rSDMT. Therefore, it is of interest to purify native GSMT from Methanohalophilus portucalensis to further compare its enzymatic characteristics and kinetics with rGSMT. In this study, native GSMT was purified through DEAE ion exchange and gel filtration chromatography with 95% purity. The enzymatic characteristics of GSMT and rGSMT showed similar trends of activities that were activated by high concentrations of monovalent cations. Both were feedback-inhibited by the end product, betaine, and competitively inhibited by S-adenosylhomocysteine (SAH). Native GSMT was 2-fold more sensitive to SAH than rGSMT. Notably, comparison of the kinetic parameters illustrated that the turnover rate of glycine methylation of GSMT was promoted by potassium ions, whereas rGSMT was activated by increasing protein-glycine binding affinity. These results suggest that GSMT and rGSMT may have different levels of post-translational modifications. Our preliminary mass spectrometry evidence indicated that there was no detectable phosphosite on GSMT after the complicated purification processes, whereas purified rGSMT still possessed 23.1% of its initial phosphorylation level. We believe that a phosphorylation-mediated modification may be involved in the regulation of this energy consuming betaine synthesis pathway during the stress response in halophilic methanoarchaea.
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Affiliation(s)
- Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Institute of Biological Chemistry, Academia Sinica. Taipei, Taiwan
| | - Yu-Chen Deng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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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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11
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Halophiles: Pharmaceutical Potential and Biotechnological Applications. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1201/b19347-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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12
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Jiang K, Xue Y, Ma Y. Identification of N(α)-acetyl-α-lysine as a probable thermolyte and its accumulation mechanism in Salinicoccus halodurans H3B36. Sci Rep 2015; 5:18518. [PMID: 26687465 PMCID: PMC4685198 DOI: 10.1038/srep18518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/30/2015] [Indexed: 11/09/2022] Open
Abstract
Salinicoccus halodurans H3B36 is a moderate halophile that was isolated from a 3.2-m-deep sediment sample in Qaidam Basin, China. Our results suggest that N(α)-acetyl-α-lysine can accumulate and act as a probable thermolyte in this strain. The accumulation mechanism and biosynthetic pathway for this rare compatible solute were also elucidated. We confirmed that the de novo synthesis pathway of N(α)-acetyl-α-lysine in this strain starts from aspartate and passes through lysine. Through RNA sequencing, we also found an 8-gene cluster (orf_1582-1589) and another gene (orf_2472) that might encode the biosynthesis of N(α)-acetyl-α-lysine in S. halodurans H3B36. Orf_192, orf_193, and orf_1259 might participate in the transportation of precursors for generating N(α)-acetyl-α-lysine under the heat stress. The transcriptome reported here also generated a global view of heat-induced changes and yielded clues for studying the regulation of N(α)-acetyl-α-lysine accumulation. Heat stress triggered a global transcriptional disturbance and generated a series of actions to adapt the strain to heat stress. Furthermore, the transcriptomic results showed that the regulon of RpoN (orf_2534) may be critical to conferring heat stress tolerance and survival to S. halodurans.
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Affiliation(s)
- Kai Jiang
- State Key Laboratory of Microbial Resources and National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources and National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources and National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Lai SJ, Lai MC, Lee RJ, Chen YH, Yen HE. Transgenic Arabidopsis expressing osmolyte glycine betaine synthesizing enzymes from halophilic methanogen promote tolerance to drought and salt stress. PLANT MOLECULAR BIOLOGY 2014; 85:429-41. [PMID: 24803410 DOI: 10.1007/s11103-014-0195-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 04/17/2014] [Indexed: 05/24/2023]
Abstract
Glycine betaine (betaine) has the highest cellular osmoprotective efficiency which does not accumulate in most glycophytes. The biosynthetic pathway for betaine in higher plants is derived from the oxidation of low-accumulating metabolite choline that limiting the ability of most plants to produce betaine. Halophilic methanoarchaeon Methanohalophilus portucalensis FDF1(T) is a model anaerobic methanogen to study the acclimation of water-deficit stresses which de novo synthesize betaine by the stepwise methylation of glycine, catalyzed by glycine sarcosine N-methyltransferase (GSMT) and sarcosine dimethylglycine N-methyltransferase. In this report, genes encoding these betaine biosynthesizing enzymes, Mpgsmt and Mpsdmt, were introduced into Arabidopsis. The homozygous Mpgsmt (G), Mpsdmt (S), and their cross, Mpgsmt and Mpsdmt (G × S) plants showed increased accumulation of betaine. Water loss from detached leaves was slower in G, S, and G × S lines than wild-type (WT). Pot-grown transgenic plants showed better growth than WT after 9 days of withholding water or irrigating with 300 mM NaCl. G, S, G × S lines also maintained higher relative water content and photosystem II activity than WT under salt stress. This suggests heterologously expressed Mpgsmt and Mpsdmt could enhance tolerance to drought and salt stress in Arabidopsis. We also found a twofold increase in quaternary ammonium compounds in salt-stressed leaves of G lines, presumably due to the activation of GSMT activity by high salinity. This study demonstrates that introducing stress-activated enzymes is a way of avoiding the divergence of primary metabolites under normal growing conditions, while also providing protection in stressful environments.
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Affiliation(s)
- Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
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Transcription of the lysine-2,3-aminomutase gene in the kam locus of Bacillus thuringiensis subsp. kurstaki HD73 is controlled by both σ54 and σK factors. J Bacteriol 2014; 196:2934-43. [PMID: 24914178 DOI: 10.1128/jb.01675-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lysine 2,3-aminomutase (KAM; EC 5.4.3.2) catalyzes the interconversion of l-lysine and l-β-lysine. The transcription and regulation of the kam locus, including lysine-2,3-aminomutase-encoding genes, in Bacillus thuringiensis were analyzed in this study. Reverse transcription-PCR (RT-PCR) analysis revealed that this locus forms two operons: yodT (yodT-yodS-yodR-yodQ-yodP-kamR) and kamA (kamA-yokU-yozE). The transcriptional start sites (TSSs) of the kamA gene were determined using 5' rapid amplification of cDNA ends (RACE). A typical -12/-24 σ(54) binding site was identified in the promoter PkamA, which is located upstream of the kamA gene TSS. A β-galactosidase assay showed that PkamA, which directs the transcription of the kamA operon, is controlled by the σ(54) factor and is activated through the σ(54)-dependent transcriptional regulator KamR. The kamA operon is also controlled by σ(K) and regulated by the GerE protein in the late stage of sporulation. kamR and kamA mutants were prepared by homologous recombination to examine the role of the kam locus. The results showed that the sporulation rate in B. thuringiensis HD(ΔkamR) was slightly decreased compared to that in HD73, whereas that in HD(ΔkamA) was similar to that in HD73. This means that other genes regulated by KamR are important for sporulation.
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Hung CC, Lai MC. The phylogenetic analysis and putative function of lysine 2,3-aminomutase from methanoarchaea infers the potential biocatalysts for the synthesis of β-lysine. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2013; 46:1-10. [DOI: 10.1016/j.jmii.2011.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/02/2011] [Accepted: 11/24/2011] [Indexed: 10/28/2022]
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Characterization and regulation of the osmolyte betaine synthesizing enzymes GSMT and SDMT from halophilic methanogen Methanohalophilus portucalensis. PLoS One 2011; 6:e25090. [PMID: 21949863 PMCID: PMC3176816 DOI: 10.1371/journal.pone.0025090] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/26/2011] [Indexed: 11/20/2022] Open
Abstract
The halophilic methanoarchaeon Methanohalophilus portucalensis can synthesize the osmolyte betaine de novo in response to extracellular salt stress. Betaine is generated by the stepwise methylation of glycine to form sarcosine, N, N-dimethylglycine and betaine by using S-adenosyl-L-methionine (AdoMet) as the methyl donor. The complete gene cluster of Mpgsmt-sdmt was cloned from Southern hybridization and heterologous expressed in E. coli respectively. The recombinant MpGSMT and MpSDMT both retained their in vivo functional activities in E. coli BL21(DE3)RIL to synthesize and accumulate betaine and conferred elevated survival ability in betaine transport deficient mutant E. coli MKH13 under high salt stress. The dramatic activating effects of sodium and potassium ions on the in vitro methyltransferase activities of MpGSMT, but not MpSDMT or bacterial GSMT and SDMT, revealed that GSMT from halophilic methanoarchaeon possesses novel regulate mechanism in betaine biosynthesis pathway. The circular dichroism spectra showed the fluctuated peaks at 206 nm were detected in the MpGSMT under various concentrations of potassium or sodium ions. This fluctuated difference may cause by a change in the β-turn structure located at the conserved glycine- and sarcosine-binding residue Arg167 of MpGSMT. The analytical ultracentrifugation analysis indicated that the monomer MpGSMT switched to dimeric form increased from 7.6% to 70% with KCl concentration increased from 0 to 2.0 M. The level of potassium and sodium ions may modulate the substrate binding activity of MpGSMT through the conformational change. Additionally, MpGSMT showed a strong end product, betaine, inhibitory effect and was more sensitive to the inhibitor AdoHcy. The above results indicated that the first enzymatic step involved in synthesizing the osmolyte betaine in halophilic archaea, namely, GSMT, may also play a major role in coupling the salt-in and compatible solute (osmolyte) osmoadaptative strategies in halophilic methanogens for adapting to high salt environments.
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Bacterial abl-like genes: production of the archaeal osmolyte $$ {N^{\varepsilon }}{\text{ - acetyl - }}\beta {\text{ - lysine}} $$ by homologous overexpression of the yodP–kamA genes in Bacillus subtilis. Appl Microbiol Biotechnol 2011; 91:689-97. [DOI: 10.1007/s00253-011-3301-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/30/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
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18
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Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. ARCHAEA (VANCOUVER, B.C.) 2010; 2010:690737. [PMID: 21234345 PMCID: PMC3017947 DOI: 10.1155/2010/690737] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/09/2010] [Indexed: 11/17/2022]
Abstract
Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP(T) was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.
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Affiliation(s)
- Stefan Spring
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Feng Chen
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Elizabeth Saunders
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | - Natalia Ivanova
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Yun-Juan Chang
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Cynthia D. Jeffries
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Thomas Brettin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Manfred Rohde
- HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Markus Göker
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jim Bristow
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Davis Genome Center, University of California, Davis, CA 95817, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Hans-Peter Klenk
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
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Sprott GD, Ekiel I, Patel GB. Metabolic Pathways in Methanococcus jannaschii and Other Methanogenic Bacteria. Appl Environ Microbiol 2010; 59:1092-8. [PMID: 16348909 PMCID: PMC202243 DOI: 10.1128/aem.59.4.1092-1098.1993] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eleven strains of methanogenic bacteria were divided into two groups on the basis of the directionality (oxidative or reductive) of their citric acid pathways. These pathways were readily identified for most methanogens from the patterns of carbon atom labeling in glutamate, following growth in the presence of [2-C]acetate. All used noncyclic pathways, but members of the family Methanosarcinaceae were the only methanogens found to use the oxidative direction. Methanococcus jannaschii failed to incorporate carbon from acetate despite transmembrane equilibration comparable to other weak acids. This organism was devoid of detectable activities of the acetate-incorporating enzymes acetyl coenzyme A synthetase, acetate kinase, and phosphotransacetylase. However, incorporation of [1-C]-, [2-C]-, or [3-C]pyruvate during the growth of M. jannaschii was possible and resulted in labeling patterns indicative of a noncyclic citric acid pathway operating in the reductive direction to synthesize amino acids. Carbohydrates were labeled consistent with glucogenesis from pyruvate. Leucine, isoleucine, phenylalanine, lysine, formate, glycerol, and mevalonate were incorporated when supplied to the growth medium. Lysine was preferentially incorporated into the lipid fraction, suggesting a role as a phytanyl chain precursor.
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Affiliation(s)
- G D Sprott
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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20
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Robinson PM, Roberts MF. Effects of Osmolyte Precursors on the Distribution of Compatible Solutes in Methanohalophilus portucalensis. Appl Environ Microbiol 2010; 63:4032-8. [PMID: 16535715 PMCID: PMC1389271 DOI: 10.1128/aem.63.10.4032-4038.1997] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The halophilic methanogen Methanohalophilus portucalensis synthesizes three distinct zwitterions, (beta)-glutamine, N(sup(epsilon))-acetyl-(beta)-lysine (NA(beta)Lys), and glycine betaine, as osmolytes when it is grown at high concentrations of external NaCl. The selective distribution of these three species was determined by growing cells in the presence of osmolyte biosynthetic precursors. Glycine betaine is formed by the stepwise methylation of glycine. Exogenous glycine (10 mM) and sarcosine (10 mM), although internalized, do not bias the cells to accumulate any more betaine. However, exogenous N,N-dimethylglycine (10 mM) is available to the appropriate methyltransferase and the betaine generated from it suppresses the synthesis of other osmolytes. Precursors of the two zwitterionic (beta)-amino acids ((beta)-glutamate for (beta)-glutamine and (alpha)-lysine and diaminopimelate for NA(beta)Lys) have only small effects on (beta)-amino acid accumulation. The largest effect is provided by L-(alpha)-glutamine, suggesting that nitrogen assimilation is a key factor in osmolyte distribution.
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21
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Biofilm growth kinetics of a monomethylamine producing Alphaproteobacteria strain isolated from an anaerobic reactor. Anaerobe 2010; 16:19-26. [DOI: 10.1016/j.anaerobe.2009.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 04/23/2009] [Accepted: 04/29/2009] [Indexed: 11/17/2022]
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Characterization of osmolyte betaine synthesizing sarcosine dimethylglycine N-methyltransferase from Methanohalophilus portucalensis. Arch Microbiol 2009; 191:735-43. [DOI: 10.1007/s00203-009-0501-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 07/23/2009] [Accepted: 08/05/2009] [Indexed: 10/20/2022]
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23
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Kallio JP, Jänis J, Nyyssölä A, Hakulinen N, Rouvinen J. Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:805-8. [PMID: 19652345 DOI: 10.1107/s1744309109026232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 07/06/2009] [Indexed: 11/10/2022]
Abstract
Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 A resolution and the orthorhombic crystal diffracted to 1.8 A resolution.
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Affiliation(s)
- Juha Pekka Kallio
- Department of Chemistry, University of Joensuu, 80101 Joensuu, Finland
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Saum R, Mingote A, Santos H, Müller V. A novel limb in the osmoregulatory network of Methanosarcina mazei Gö1: N(epsilon)-acetyl-beta-lysine can be substituted by glutamate and alanine. Environ Microbiol 2009; 11:1056-65. [PMID: 19452593 DOI: 10.1111/j.1462-2920.2008.01826.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
N(epsilon)-acetyl-beta-lysine is a unique compatible solute found in methanogenic archaea grown at high salinities. Deletion of the genes that encode the lysine-2,3-aminomutase (ablA) and the beta-lysine acetyltransferase (ablB) abolished the production of N(epsilon)-acetyl-beta-lysine in Methanosarcina mazei Gö1. The mutant grew well at low and intermediate salinities. Interestingly, growth at high salt (800 mM NaCl) was only slowed down but not impaired demonstrating that in M. mazei Gö1 N(epsilon)-acetyl-beta-lysine is not essential for growth at high salinities. Nuclear magnetic resonance (NMR) analysis revealed an increased glutamate pool in the mutant. In addition to alpha-glutamate, a novel solute, alanine, was produced. The intracellular alanine concentration was as high as 0.36 +/- 0.05 micromol (mg protein)-1 representing up to 18% of the total solute pool at 800 mM NaCl. The cellular alanine concentration increased with the salinity of the medium and decreased in the presence of glycine betaine in the medium, indicating that alanine is used as compatible solute by M. mazei Gö1.
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Affiliation(s)
- Regina Saum
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Frankfurt am Main, Germany
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Diversity and stratification of archaea in a hypersaline microbial mat. Appl Environ Microbiol 2008; 75:1801-10. [PMID: 19114531 DOI: 10.1128/aem.01811-08] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.
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Saum SH, Müller V. Regulation of osmoadaptation in the moderate halophile Halobacillus halophilus: chloride, glutamate and switching osmolyte strategies. SALINE SYSTEMS 2008; 4:4. [PMID: 18442383 PMCID: PMC2412884 DOI: 10.1186/1746-1448-4-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 04/28/2008] [Indexed: 11/10/2022]
Abstract
The moderate halophile Halobacillus halophilus is the paradigm for chloride dependent growth in prokaryotes. Recent experiments shed light on the molecular basis of the chloride dependence that is reviewed here. In the presence of moderate salinities Halobacillus halophilus mainly accumulates glutamine and glutamate to adjust turgor. The transcription of glnA2 (encoding a glutamine synthetase) as well as the glutamine synthetase activity were identified as chloride dependent steps. Halobacillus halophilus switches its osmolyte strategy and produces proline as the main compatible solute at high salinities. Furthermore, Halobacillus halophilus also shifts its osmolyte strategy at the transition from the exponential to the stationary phase where proline is exchanged by ectoine. Glutamate was found as a "second messenger" essential for proline production. This observation leads to a new model of sensing salinity by sensing the physico-chemical properties of different anions.
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Affiliation(s)
- Stephan H Saum
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
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Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. SALINE SYSTEMS 2008; 4:2. [PMID: 18412960 PMCID: PMC2329653 DOI: 10.1186/1746-1448-4-2] [Citation(s) in RCA: 480] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 04/15/2008] [Indexed: 12/04/2022]
Abstract
Halophiles are found in all three domains of life. Within the Bacteria we know halophiles within the phyla Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, and Bacteroidetes. Within the Archaea the most salt-requiring microorganisms are found in the class Halobacteria. Halobacterium and most of its relatives require over 100–150 g/l salt for growth and structural stability. Also within the order Methanococci we encounter halophilic species. Halophiles and non-halophilic relatives are often found together in the phylogenetic tree, and many genera, families and orders have representatives with greatly different salt requirement and tolerance. A few phylogenetically coherent groups consist of halophiles only: the order Halobacteriales, family Halobacteriaceae (Euryarchaeota) and the anaerobic fermentative bacteria of the order Halanaerobiales (Firmicutes). The family Halomonadaceae (Gammaproteobacteria) almost exclusively contains halophiles. Halophilic microorganisms use two strategies to balance their cytoplasm osmotically with their medium. The first involves accumulation of molar concentrations of KCl. This strategy requires adaptation of the intracellular enzymatic machinery, as proteins should maintain their proper conformation and activity at near-saturating salt concentrations. The proteome of such organisms is highly acidic, and most proteins denature when suspended in low salt. Such microorganisms generally cannot survive in low salt media. The second strategy is to exclude salt from the cytoplasm and to synthesize and/or accumulate organic 'compatible' solutes that do not interfere with enzymatic activity. Few adaptations of the cells' proteome are needed, and organisms using the 'organic-solutes-in strategy' often adapt to a surprisingly broad salt concentration range. Most halophilic Bacteria, but also the halophilic methanogenic Archaea use such organic solutes. A variety of such solutes are known, including glycine betaine, ectoine and other amino acid derivatives, sugars and sugar alcohols. The 'high-salt-in strategy' is not limited to the Halobacteriaceae. The Halanaerobiales (Firmicutes) also accumulate salt rather than organic solutes. A third, phylogenetically unrelated organism accumulates KCl: the red extremely halophilic Salinibacter (Bacteroidetes), recently isolated from saltern crystallizer brines. Analysis of its genome showed many points of resemblance with the Halobacteriaceae, probably resulting from extensive horizontal gene transfer. The case of Salinibacter shows that more unusual types of halophiles may be waiting to be discovered.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, Hebrew University of Jerusalem, Jerusalem, Israel.
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The molecular basis of salt adaptation in Methanosarcina mazei Gö1. Arch Microbiol 2008; 190:271-9. [PMID: 18379758 DOI: 10.1007/s00203-008-0363-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 03/04/2008] [Accepted: 03/06/2008] [Indexed: 12/18/2022]
Abstract
The study on the molecular basis of salt adaptation and its regulation in archaea is still in its infancy, but genomics and functional genome analyses combined with classical biochemistry shed light on the processes conferring salt adaptation in the methanogenic archaeon Methanosarcina mazei Gö1. In this article, we will review discoveries made within the last years that will culminate in the description of the overall cellular response of M. mazei Gö1 to elevated salinities. This response includes accumulation of solutes and export of Na+ as well as potential uptake/export of K+ but also a restructuring of the cell surface.
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Grochowski LL, White RH. Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea. Ann N Y Acad Sci 2007; 1125:190-214. [PMID: 18096851 DOI: 10.1196/annals.1419.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The development of an oxygenated atmosphere on earth resulted in the polarization of life into two major groups, those that could live in the presence of oxygen and those that could not-the aerobes and the anaerobes. The evolution of aerobes from the earliest anaerobic prokaryotes resulted in a variety of metabolic adaptations. Many of these adaptations center on the need to sustain oxygen-sensitive reactions and cofactors to function in the new oxygen-containing atmosphere. Still other metabolic pathways that were not sensitive to oxygen also diverged. This is likely due to the physical separation of the organisms, based on their ability to live in the presence of oxygen, which allowed for the independent evolution of the pathways. Through the study of metabolic pathways in anaerobes and comparison to the more established pathways from aerobes, insight into metabolic evolution can be gained. This, in turn, can allow for extra- polation to those metabolic pathways occurring in the Last Universal Common Ancestor (LUCA). Some of the unique and uncanonical metabolic pathways that have been identified in the archaea with emphasis on the biochemistry of an obligate anaerobic methanogen, Methanocaldococcus jannaschii are reviewed.
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Affiliation(s)
- Laura L Grochowski
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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Lai MC, Wang CC, Chuang MJ, Wu YC, Lee YC. Effects of substrate and potassium on the betaine-synthesizing enzyme glycine sarcosine dimethylglycine N-methyltransferase from a halophilic methanoarchaeon Methanohalophilus portucalensis. Res Microbiol 2006; 157:948-55. [PMID: 17098399 DOI: 10.1016/j.resmic.2006.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 07/31/2006] [Accepted: 08/29/2006] [Indexed: 10/24/2022]
Abstract
Methanohalophilus portucalensis FDF1 can synthesize the compatible solute betaine de novo through the methylation of glycine, sarcosine and dimethylglycine with the methyl group from S-adenosylmethionine. After separation by DEAE-Sephacel ion chromatography using a KCl step gradient, glycine, sarcosine and dimethylglycine methytransfer (GSDMT) activities were detected in a single peak. The estimated molecular weight of GSDMT was 240 kDa and 2-D gel analysis indicated it was separated into four subunits (52 kDa) with different pI. The PBE94 chromatofocusing column also separated GSDMT into four protein peaks A, B, C, D. Both peak B and D proteins possessed GSDMT activity, while the peak A protein only exhibited SDMT activity. The multiple methyltransferase activities of the large complex appear to be unique compared to other methyltransferases used in betaine synthesis. Further methyltransferase assays in response to different concentrations of KCl indicated that the peak D protein exhibited low GSDMT activity only when K(+) < or = 0.4 M. The peak B protein exhibited a higher GSDMT activity at 0.4 M K(+), while the peak A protein exhibited SDMT activity only at higher K(+) (0.8 M). These results suggest that the internal K(+) concentration regulates GSDMT activities and affects the net betaine accumulation in the cells.
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Affiliation(s)
- Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC.
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31
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Müller V, Spanheimer R, Santos H. Stress response by solute accumulation in archaea. Curr Opin Microbiol 2005; 8:729-36. [PMID: 16256422 DOI: 10.1016/j.mib.2005.10.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 10/12/2005] [Indexed: 10/25/2022]
Abstract
The accumulation of organic solutes is a prerequisite for osmotic adjustment of all organisms. Archaea synthesize unusual solutes such as beta-amino acids, Nepsilon-acetyl-beta-lysine, mannosylglycerate and di-myo-inositol phosphate but, as in other cells, uptake of solutes such as glycine betaine is preferred over de novo synthesis. Study of the molecular basis of osmoadaptation and its regulation in archaea is still in its infancy, but genomics and functional genome analyses combined with classical biochemistry shed light on the processes that confer osmoadaptation in archaea. Most interestingly, some solutes are not only produced in response to salt but also to temperature stress.
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Affiliation(s)
- Volker Müller
- Molecular Microbiology & Bioenergetics, Department Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60439 Frankfurt, Germany.
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32
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Roberts MF. Organic compatible solutes of halotolerant and halophilic microorganisms. SALINE SYSTEMS 2005; 1:5. [PMID: 16176595 PMCID: PMC1224877 DOI: 10.1186/1746-1448-1-5] [Citation(s) in RCA: 373] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 08/04/2005] [Indexed: 11/10/2022]
Abstract
Microorganisms that adapt to moderate and high salt environments use a variety of solutes, organic and inorganic, to counter external osmotic pressure. The organic solutes can be zwitterionic, noncharged, or anionic (along with an inorganic cation such as K(+)). The range of solutes, their diverse biosynthetic pathways, and physical properties of the solutes that effect molecular stability are reviewed.
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Affiliation(s)
- Mary F Roberts
- Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02465, USA.
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33
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Pflüger K, Baumann S, Gottschalk G, Lin W, Santos H, Müller V. Lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of Nepsilon-acetyl-beta-lysine and growth at high salinity. Appl Environ Microbiol 2004; 69:6047-55. [PMID: 14532061 PMCID: PMC201229 DOI: 10.1128/aem.69.10.6047-6055.2003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The compatible solute N(epsilon)-acetyl-beta-lysine is unique to methanogenic archaea and is produced under salt stress only. However, the molecular basis for the salt-dependent regulation of N(epsilon)-acetyl-beta-lysine formation is unknown. Genes potentially encoding lysine-2,3-aminomutase (ablA) and beta-lysine acetyltransferase (ablB), which are assumed to catalyze N(epsilon)-acetyl-beta-lysine formation from alpha-lysine, were identified on the chromosomes of the methanogenic archaea Methanosarcina mazei Gö1, Methanosarcina acetivorans, Methanosarcina barkeri, Methanococcus jannaschii, and Methanococcus maripaludis. The order of the two genes was identical in the five organisms, and the deduced proteins were very similar, indicating a high degree of conservation of structure and function. Northern blot analysis revealed that the two genes are organized in an operon (termed the abl operon) in M. mazei Gö1. Expression of the abl operon was strictly salt dependent. The abl operon was deleted in the genetically tractable M. maripaludis. Delta(abl) mutants of M. maripaludis no longer produced N(epsilon)-acetyl-beta-lysine and were incapable of growth at high salt concentrations, indicating that the abl operon is essential for N(epsilon)-acetyl-beta-lysine synthesis. These experiments revealed the first genes involved in the biosynthesis of compatible solutes in methanogens.
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Affiliation(s)
- K Pflüger
- Section of Microbiology, Department of Biology I, Ludwig-Maximilians-Universität München, 80638 Munich, Germany
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34
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Organic Compatible Solutes. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2003. [DOI: 10.1007/0-306-48053-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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35
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Abstract
The availability of water is the most important prerequisite for life of any living cell, and exposure of cells to hypersaline conditions always threatens the cells with a drastic loss of water. To re-establish the essential turgor pressure, cells increase the water activity of their cytoplasm by accumulation of compatible solutes, either by synthesis or by uptake. The ability to respond to increasing osmolality is well conserved in all three lines of descent and, here, we compare the osmoadaptive strategies of Bacteria and Archaea. The temporal sequence of events after an osmotic upshock will be discussed, with a focus on the most rapid response, notably the mechanisms of transport activation at the protein level, and different signals for osmolality will be compared. The spectrum of compatible solutes used by different organisms is rather diverse and a comparison of 'bacterial' and 'archaeal' compatible solutes will be given.
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Affiliation(s)
- M Roesser
- Lehrstuhl für Mikrobiologie der LMU München, 80638 München, Germany
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36
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Martin DD, Ciulla RA, Robinson PM, Roberts MF. Switching osmolyte strategies: response of Methanococcus thermolithotrophicus to changes in external NaCl. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1524:1-10. [PMID: 11078952 DOI: 10.1016/s0304-4165(00)00131-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Methanococcus thermolithotrophicus, a thermophilic methanogenic archaeon, produces and accumulates beta-glutamate and L-alpha-glutamate as osmolytes when grown in media with <1 M NaCl. When the organism is adapted to grow in >1 M NaCl, a new zwitterionic solute, N(epsilon)-acetyl-beta-lysine, is synthesized and becomes the dominant osmolyte. Several techniques, including in vivo and in vitro NMR spectroscopy, HPLC analyses of ethanol extracts, and potassium atomic absorption, have been used to monitor the immediate response of M. thermolithotrophicus to osmotic stress. There is a temporal hierarchy in the response of intracellular osmolytes. Changes in intracellular K(+) occur within the first few minutes of altering the external NaCl. Upon hypoosmotic shock, K(+) is released from the cell; relatively small changes occur in the organic osmolyte pool on a longer time scale. Upon hyperosmotic shock, M. thermolithotrophicus immediately internalizes K(+), far more than would be needed stoichiometrically to balance the new salt concentration. This is followed by a decrease to a new K(+) concentration (over 10-15 min), at which point synthesis and accumulation of primarily L-alpha-glutamate occur. Once growth of the M. thermolithotrophicus culture begins, typically 30-100 min after the hyperosmotic shock, the intracellular levels of organic anions decrease and the zwitterion (N(epsilon)-acetyl-beta-lysine) begins to represent a larger fraction of the intracellular pool. The observation that N(epsilon)-acetyl-beta-lysine accumulation occurs in osmoadapted cells but not immediately after osmotic shock is consistent with the hypothesis that lysine 2,3-aminomutase, an enzyme involved in N(epsilon)-acetyl-beta-lysine synthesis, is either not present at high levels or has low activity in cells grown and adapted to lower NaCl. That lysine aminomutase specific activity is 8-fold lower in protein extracts from cells adapted to low NaCl compared to those adapted to 1.4 M NaCl supports this hypothesis.
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Affiliation(s)
- D D Martin
- Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02167, USA
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37
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Robinson P, Neelon K, Schreier HJ, Roberts MF. beta-Glutamate as a substrate for glutamine synthetase. Appl Environ Microbiol 2001; 67:4458-63. [PMID: 11571143 PMCID: PMC93190 DOI: 10.1128/aem.67.10.4458-4463.2001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conversion of beta-glutamate to beta-glutamine by archaeal and bacterial glutamine synthetase (GS) enzymes has been examined. The GS from Methanohalophilus portucalensis (which was partially purified) is capable of catalyzing the amidation of this substrate with a rate sevenfold less than the rate obtained with alpha-glutamate. Recombinant GS from the archaea Methanococcus jannaschii and Archaeoglobus fulgidus were considerably more selective for alpha-glutamate than beta-glutamate as a substrate. All the archaeal enzymes were much less selective than the two bacterial GS (from Escherichia coli and Bacillus subtilis), whose specific activities towards beta-glutamate were much smaller than rates with the alpha-isomer. These results are discussed in light of the observation that beta-glutamate is accumulated as an osmolyte in many archaea while beta-glutamine (produced by glutamine synthetase) is used as an osmolyte only in M. portucalensis.
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Affiliation(s)
- P Robinson
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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38
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Lai MC, Hong TY, Gunsalus RP. Glycine betaine transport in the obligate halophilic archaeon Methanohalophilus portucalensis. J Bacteriol 2000; 182:5020-4. [PMID: 10940053 PMCID: PMC111389 DOI: 10.1128/jb.182.17.5020-5024.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transport of the osmoprotectant glycine betaine was investigated using the glycine betaine-synthesizing microbe Methanohalophilus portucalensis (strain FDF1), since solute uptake for this class of obligate halophilic methanogenic Archaea has not been examined. Betaine uptake followed a Michaelis-Menten relationship, with an observed K(t) of 23 microM and a V(max) of 8 nmol per min per mg of protein. The transport system was highly specific for betaine: choline, proline, and dimethylglycine did not significantly compete for [(14)C]betaine uptake. The proton-conducting uncoupler 2, 4-dinitrophenol and the ATPase inhibitor N, N-dicyclohexylcarbodiimide both inhibited glycine betaine uptake. Growth of cells in the presence of 500 microM betaine resulted in faster cell growth due to the suppression of the de novo synthesis of the other compatible solutes, alpha-glutamate, beta-glutamine, and N(epsilon)-acetyl-beta-lysine. These investigations demonstrate that this model halophilic methanogen, M. portucalensis strain FDF1, possesses a high-affinity and highly specific betaine transport system that allows it to accumulate this osmoprotectant from the environment in lieu of synthesizing this or other osmoprotectants under high-salt growth conditions.
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Affiliation(s)
- M C Lai
- Department of Botany, National Chung-Hsing University, Taichung, Taiwan, Republic of China.
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39
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Nyyssola A, Kerovuo J, Kaukinen P, von Weymarn N, Reinikainen T. Extreme halophiles synthesize betaine from glycine by methylation. J Biol Chem 2000; 275:22196-201. [PMID: 10896953 DOI: 10.1074/jbc.m910111199] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycine betaine is a compatible solute, which is able to restore and maintain osmotic balance of living cells. It is synthesized and accumulated in response to abiotic stress. Betaine acts also as a methyl group donor and has a number of important applications including its use as a feed additive. The known biosynthetic pathways of betaine are universal and very well characterized. A number of enzymes catalyzing the two-step oxidation of choline to betaine have been isolated. In this work we have studied a novel betaine biosynthetic pathway in two phylogenically distant extreme halophiles, Actinopolyspora halophila and Ectothiorhodospira halochloris. We have identified a three-step series of methylation reactions from glycine to betaine, which is catalyzed by two methyltransferases, glycine sarcosine methyltransferase and sarcosine dimethylglycine methyltransferase, with partially overlapping substrate specificity. The methyltransferases from the two organisms show high sequence homology. E. halochloris methyltransferase genes were successfully expressed in Escherichia coli, and betaine accumulation and improved salt tolerance were demonstrated.
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Affiliation(s)
- A Nyyssola
- Danisco Cultor Innovation, Kantvik, Sokeritehtaantie 20, FIN-02460 Kantvik, Finland
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40
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Abstract
Examination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H2 + CO2 or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA+ and K+ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H2 + CO2 exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.
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Affiliation(s)
- A Oren
- Division of Microbial and Molecular Ecology, Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
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41
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Affiliation(s)
- Martin
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167, USA
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42
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Lai MC, Yang DR, Chuang MJ. Regulatory factors associated with synthesis of the osmolyte glycine betaine in the halophilic methanoarchaeon Methanohalophilus portucalensis. Appl Environ Microbiol 1999; 65:828-33. [PMID: 9925623 PMCID: PMC91102 DOI: 10.1128/aem.65.2.828-833.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The halophilic methanoarchaeon Methanohalophilus portucalensis can synthesize de novo and accumulate beta-glutamine, Nepsilon-acetyl-beta-lysine, and glycine betaine (betaine) as compatible solutes (osmolytes) when grown at elevated salt concentrations. Both in vivo and in vitro betaine formation assays in this study confirmed previous nuclear magnetic resonance 13C-labelling studies showing that the de novo synthesis of betaine proceeded from glycine, sarcosine, and dimethylglycine to form betaine through threefold methylation. Exogenous sarcosine (1 mM) effectively suppressed the intracellular accumulation of betaine, and a higher level of sarcosine accumulation was accompanied by a lower level of betaine synthesis. Exogenous dimethylglycine has an effect similar to that of betaine addition, which increased the intracellular pool of betaine and suppressed the levels of Nepsilon-acetyl-beta-lysine and beta-glutamine. Both in vivo and in vitro betaine formation assays with glycine as the substrate showed only sarcosine and betaine, but no dimethylglycine. Dimethylglycine was detected only when it was added as a substrate in in vitro assays. A high level of potassium (400 mM and above) was necessary for betaine formation in vitro. Interestingly, no methylamines were detected without the addition of KCl. Also, high levels of NaCl and LiCl (800 mM) favored sarcosine accumulation, while a lower level (400 mM) favored betaine synthesis. The above observations indicate that a high sarcosine level suppressed multiple methylation while dimethylglycine was rapidly converted to betaine. Also, high levels of potassium led to greater amounts of betaine, while lower levels of potassium led to greater amounts of sarcosine. This finding suggests that the intracellular levels of both sarcosine and potassium are associated with the regulation of betaine synthesis in M. portucalensis.
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Affiliation(s)
- M C Lai
- Department of Botany, National Chung-Hsing University, Taichung, Taiwan, Republic of China.
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43
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Chen L, Spiliotis ET, Roberts MF. Biosynthesis of Di-myo-inositol-1,1'-phosphate, a novel osmolyte in hyperthermophilic archaea. J Bacteriol 1998; 180:3785-92. [PMID: 9683472 PMCID: PMC107359 DOI: 10.1128/jb.180.15.3785-3792.1998] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Biosynthesis of di-myo-inositol-1,1'-phosphate (DIP) is proposed to occur with myo-inositol and myo-inositol 1-phosphate (I-1-P) used as precursors. Activation of the I-1-P with CTP and condensation of the resultant CDP-inositol (CDP-I) with myo-inositol then generates DIP. The sole known biosynthetic pathway of inositol in all organisms is the conversion of D-glucose-6-phosphate to myo-inositol. This conversion requires two key enzymes: L-I-1-P synthase and I-1-P phosphatase. Enzymatic assays using 31P nuclear magnetic resonance spectroscopy as well as a colorimetric assay for inorganic phosphate have confirmed the occurrence of L-I-1-P synthase and a moderately specific I-1-P phosphatase. The enzymatic reaction that couples CDP-I with myo-inositol to generate DIP has also been detected in Methanococcus igneus. 13C labeling studies with [2,3-13C]pyruvate and [3-13C]pyruvate were used to examine this pathway in M. igneus. Label distribution in DIP was consistent with inositol units formed from glucose-6-phosphate, but the label in the glucose moiety was scrambled via transketolase and transaldolase activities of the pentose phosphate pathway.
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Affiliation(s)
- L Chen
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167, USA
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44
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da Costa MS, Santos H, Galinski EA. An overview of the role and diversity of compatible solutes in Bacteria and Archaea. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1998; 61:117-53. [PMID: 9670799 DOI: 10.1007/bfb0102291] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The accumulation of compatible solutes is a prerequisite for the adaptation of microorganisms to osmotic stress imposed by salt or organic solutes. Two types of strategies exist to cope with high external solute concentrations; one strategy is found in the extremely halophilic Archaea of the family Halobacteriaceae and the Bacteria of the order Haloanaerobiales involving the accumulation of inorganic ions. The other strategy of osmoadaptation involves the accumulation of specific organic solutes and is found in the vast majority of microorganisms. The organic osmolytes range from sugars, polyols, amino acids and their respective derivatives, ectoines and betaines. The diversity of these organic solutes has increased in the past few years as more organisms, especially thermophilic and hyperthermophilic Bacteria and Archaea, have been examined. The term compatible solute can also be applied to solutes that protect macromolecules and cells against stresses such as high temperature, desiccation and freezing. The mechanisms by which compatible solutes protect enzymes, cell components and cells are still a long way from being thoroughly elucidated, but there is a growing interest in the utilization of these solutes to protect macromolecules and cells from heating, freezing and desiccation.
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Affiliation(s)
- M S da Costa
- Departamento de Bioquímica, Universidade de Coimbra, Portugal.
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45
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46
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47
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Choquet CG, Richards JC, Patel GB, Sprott GD. Ribose biosynthesis in methanogenic bacteria. Arch Microbiol 1994. [DOI: 10.1007/bf00307768] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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48
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Ciulla R, Clougherty C, Belay N, Krishnan S, Zhou C, Byrd D, Roberts MF. Halotolerance of Methanobacterium thermoautotrophicum delta H and Marburg. J Bacteriol 1994; 176:3177-87. [PMID: 8195071 PMCID: PMC205486 DOI: 10.1128/jb.176.11.3177-3187.1994] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Methanobacterium thermoautotrophicum delta H and Marburg were adapted to grow in medium containing up to 0.65 M NaCl. From 0.01 to 0.5 M NaCl, there was a lag before cell growth which increased with increasing external NaCl. The effect of NaCl on methane production was not significant once the cells began to grow. Intracellular solutes were monitored by nuclear magnetic resonance (NMR) spectroscopy as a function of osmotic stress. In the delta H strain, the major intracellular small organic solutes, cyclic-2,3-diphosphoglycerate and glutamate, increased at most twofold between 0.01 and 0.4 M NaCl and decreased when the external NaCl was 0.5 M. M. thermoautotrophicum Marburg similarly showed a decrease in solute (cyclic-2,3-diphosphoglycerate, 1,3,4,6-tetracarboxyhexane, and L-alpha-glutamate) concentrations for cells grown in medium containing > 0.5 M NaCl. At 0.65 M NaCl, a new organic solute, which was visible in only trace amounts at the lower NaCl concentrations, became the dominant solute. Intracellular potassium in the delta H strain, detected by atomic absorption and 39K NMR, was roughly constant between 0.01 and 0.4 M and then decreased as the external NaCl increased further. The high intracellular K+ was balanced by the negative charges of the organic osmolytes. At the higher external salt concentrations, it is suggested that Na+ and possibly Cl- ions are internalized to provide osmotic balance. A striking difference of strain Marburg from strain delta H was that yeast extract facilitated growth in high-NaCl-containing medium. The yeast extract supplied only trace NMR-detectable solutes (e.g., betaine) but had a large effect on endogenous glutamate levels, which were significantly decreased. Exogenous choline and glycine, instead of yeast extract, also aided growth in NaCl-containing media. Both solutes were internalized with the choline converted to betaine; the contribution to osmotic balance of these species was 20 to 25% of the total small-molecule pool. These results indicate that M. thermoautotrophicum shows little changes in its internal solutes over a wide range of external NaCl. Furthermore, they illustrate the considerable differences in physiology in the delta H and Marburg strains of this organism.
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Affiliation(s)
- R Ciulla
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167-3860
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49
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Compatible solutes of halophilic eubacteria: molecular principles, water-solute interaction, stress protection. ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf01955150] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Lai MC, Gunsalus RP. Glycine betaine and potassium ion are the major compatible solutes in the extremely halophilic methanogen Methanohalophilus strain Z7302. J Bacteriol 1992; 174:7474-7. [PMID: 1429470 PMCID: PMC207447 DOI: 10.1128/jb.174.22.7474-7477.1992] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Methanohalophilus strain Z7302 was previously isolated from a hypersaline environment and grows over a range of NaCl concentrations from 1.7 to 4.4 M. We examined the relationships between cell growth rate, cell volume, and intracellular solute concentrations with increasing salinity. This extremely halophilic methanogen synthesized three zwitterionic compounds, beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine, and also accumulated potassium ion as compatible solutes to balance the external and internal osmotic pressures. Potassium and glycine betaine were the predominant compatible solutes when Methanohalophilus strain Z7302 was grown at high external NaCl concentrations and approached intracellular levels of 3 and 4 M, respectively.
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Affiliation(s)
- M C Lai
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles 90024
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