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Wang Y, Luo CB, Li YQ. Biofuneling lignin-derived compounds into lipids using a newly isolated Citricoccus sp. P2. BIORESOURCE TECHNOLOGY 2023; 387:129669. [PMID: 37573985 DOI: 10.1016/j.biortech.2023.129669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Lignin-derived compounds (LDCs) bioconversion into lipids is a promising yet challenging task. This study focuses on the isolation of the ligninolytic bacterium Citricoccus sp. P2 and investigates its mechanism for producing lipids from LDCs. Although strain P2 exhibits a relatively low lignin degradation rate of 44.63%, it efficiently degrades various concentrations of LDCs. The highest degradation rate is observed when incubated with 0.6 g/L vanillic acid, 0.6 g/L syringic acid, 0.8 g/L p-coumaric acid, and 0.4 g/L phenol, resulting in respective lipid yields of 0.16 g/L, 0.13 g/L, 0.24 g/L, and 0.13 g/L. The genome of strain P2 provides insights into LDCs bioconversion into lipids and stress tolerance. Moreover, Citricoccus sp. P2 has been successfully developed a non-sterilized lipid production using its native alkali-halophilic characteristics, which significantly enhances the lipid yield. This study presents a promising platform for lipids production from LDCs and has potential to promote valorization of lignin.
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Affiliation(s)
- Yan Wang
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Chao-Bing Luo
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Yuan-Qiu Li
- College of Life Science, Leshan Normal University, Leshan 614000, China.
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2
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Liang KK. On the crucial features of a single‐file transport model for ion channels. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Kuo Kan Liang
- Department of Physics National Taiwan University Taipei Taiwan
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3
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Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria. Microbiol Spectr 2023; 11:e0411022. [PMID: 36541777 PMCID: PMC9927469 DOI: 10.1128/spectrum.04110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.
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4
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Tang H, Wang MJ, Gan XF, Li YQ. Funneling lignin-derived compounds into polyhydroxyalkanoate by Halomonas sp. Y3. BIORESOURCE TECHNOLOGY 2022; 362:127837. [PMID: 36031122 DOI: 10.1016/j.biortech.2022.127837] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Lignin-derived compounds (LDCs) biological funneling for polyhydroxyalkanoate (PHA) synthesis has been attractive but elusive. Herein, the Halomonas sp. Y3 is isolated and developed for PHA production from LDCs. Of the tested 13 LDCs, 4-hydroxybenzoic acid (4-HBA), protocatechuate (PA), catechol (CAT), and vanillic acid (VA) exhibit a hyper-degradation and production with 87.2 %, 85.8 %, 84.7 %, and 83.4 % TOC removal rate and 535.2 mg/L, 506.5 mg/L, 435.6 mg/L, and 440.8 mg/L PHA concentration, respectively. The Halomonas sp. Y3 genome is sequenced by identifying numerous genes responsible for LDCs funneling, stress response, and PHA biosynthesis. An open unsterilized fermentation with optimal conditions of pH 9.0 and NaCl 60 g/L is investigated, achieving a completely aseptic effect and significantly improved PHA production from LDCs. Overall, the results indicate that the Halomonas sp. Y3 is an ideal candidate for LDC bioconversion and exhibits a great potential to realize black liquor valorization.
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Affiliation(s)
- Hao Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Ming-Jun Wang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Xiao-Feng Gan
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Yuan-Qiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China; College of Life Sciences, Capital Normal University, Beijing 100048, China.
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5
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Yan L, Wang C, Jiang J, Liu S, Zheng Y, Yang M, Zhang Y. Nitrate removal by alkali-resistant Pseudomonas sp. XS-18 under aerobic conditions: Performance and mechanism. BIORESOURCE TECHNOLOGY 2022; 344:126175. [PMID: 34678448 DOI: 10.1016/j.biortech.2021.126175] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
To improve poor nitrate removal by microorganisms under strong alkaline conditions, a new type of aerobic nitrification-reducing bacteria was isolated in this study. Using nitrogen balance and genome information, the capacity of Pseudomonas XS-18 to remove nitrate and the mechanism of alkali tolerance were analyzed. At pH 11.0, XS-18 could remove 12.17 mg N/(L·h) nitrate. At C/N ratios of 13.0 and 25 °C, nitrite and ammonia nitrogen were barely enriched. XS-18 could reduce nitrate through dissimilation and assimilation, and 21.74% and 77.39% of nitrate was converted into cellular components and organic nitrogen, respectively. Meanwhile, functional genes (nirBD, nasAB, gdhA, glnA, and gltBD) associated with nitrogen metabolism were determined. In addition, Na+/H+ antiporters (MnhACDEFG, PhaACDEFG, NhaCD and TrkAH) and a cell surface protein (SlpA) from the XS-18 genome, as well as compatible solutes that help stabilize intracellular pH, were also characterized. XS-18 possessed significant potential in alkaline wastewater treatment.
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Affiliation(s)
- Lilong Yan
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China.
| | - Caixu Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China
| | - Jishuang Jiang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China
| | - Shuang Liu
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China
| | - Yaoqi Zheng
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China
| | - Mengya Yang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China
| | - Ying Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030 PR China.
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6
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Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinfeder M, Schwarz J, Zechmeister T, Karst SM, Albertsen M, Nielsen PH, Wagner M, Daims H. Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira. THE ISME JOURNAL 2020; 14:2967-2979. [PMID: 32709974 PMCID: PMC7784846 DOI: 10.1038/s41396-020-0724-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/01/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.
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Affiliation(s)
- Anne Daebeler
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Max Planck Institute for Marine Microbiology, Department of Biogeochemistry, Bremen, Germany
| | - Hanna Koch
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Craig W Herbold
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela Steinfeder
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jasmin Schwarz
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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7
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Mikušević V, Schrecker M, Kolesova N, Patiño-Ruiz M, Fendler K, Hänelt I. A channel profile report of the unusual K + channel KtrB. J Gen Physiol 2019; 151:1357-1368. [PMID: 31624134 PMCID: PMC6888753 DOI: 10.1085/jgp.201912384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 09/03/2019] [Accepted: 09/27/2019] [Indexed: 11/20/2022] Open
Abstract
KtrAB is a key player in bacterial K+ uptake required for K+ homeostasis and osmoadaptation. The system is unique in structure and function. It consists of the K+-translocating channel subunit KtrB, which forms a dimer in the membrane, and the soluble regulatory subunit KtrA, which attaches to the cytoplasmic side of the dimer as an octameric ring conferring Na+ and ATP dependency to the system. Unlike most K+ channels, KtrB lacks the highly conserved T(X)GYG selectivity filter sequence. Instead, only a single glycine residue is found in each pore loop, which raises the question of how selective the ion channel is. Here, we characterized the KtrB subunit from the Gram-negative pathogen Vibrio alginolyticus by isothermal titration calorimetry, solid-supported membrane-based electrophysiology, whole-cell K+ uptake, and ACMA-based transport assays. We found that, despite its simple selectivity filter, KtrB selectively binds K+ with micromolar affinity. Rb+ and Cs+ bind with millimolar affinities. However, only K+ and the poorly binding Na+ are efficiently translocated, based on size exclusion by the gating loop. Importantly, the physiologically required K+ over Na+ selectivity is provided by the channel's high affinity for potassium, which interestingly results from the presence of the sodium ions themselves. In the presence of the KtrA subunit, sodium ions further decrease the Michaelis-Menten constant for K+ uptake from milli- to micromolar concentrations and increase the Vmax, suggesting that Na+ also facilitates channel gating. In conclusion, high binding affinity and facilitated K+ gating allow KtrAB to function as a selective K+ channel.
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Affiliation(s)
- Vedrana Mikušević
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Marina Schrecker
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Natalie Kolesova
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Miyer Patiño-Ruiz
- Department of Biophysical Chemistry, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
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8
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Kale D, Spurny P, Shamayeva K, Spurna K, Kahoun D, Ganser D, Zayats V, Ludwig J. The S. cerevisiae cation translocation protein Trk1 is functional without its “long hydrophilic loop” but LHL regulates cation translocation activity and selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1476-1488. [DOI: 10.1016/j.bbamem.2019.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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9
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Wang HL, Sun L. Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields. World J Microbiol Biotechnol 2017; 33:86. [DOI: 10.1007/s11274-017-2255-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 03/31/2017] [Indexed: 01/14/2023]
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10
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Adiban J, Jamali Y, Rafii-Tabar H. Modeling ion permeation through a bacterial voltage-gated calcium channel CaVAb using molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2017; 13:208-214. [DOI: 10.1039/c6mb00690f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ca2+ion binds tightly to the center of the selectivity filter of voltage-gated calcium channels.
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Affiliation(s)
- Jamal Adiban
- Department of Medical Physics and Biomedical Engineering
- Faculty of Medicine
- Shahid Beheshti University of Medical Sciences
- Tehran
- Iran
| | - Yousef Jamali
- Department of Applied Mathematics
- School of Mathematical Sciences
- Tarbiat Modares University
- Tehran
- Iran
| | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering
- Faculty of Medicine
- Shahid Beheshti University of Medical Sciences
- Tehran
- Iran
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11
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Ariyarathna HACK, Francki MG. Phylogenetic relationships and protein modelling revealed two distinct subfamilies of group II HKT genes between crop and model grasses. Genome 2016; 59:509-17. [PMID: 27203707 DOI: 10.1139/gen-2016-0035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular evolution of large protein families in closely related species can provide useful insights on structural functional relationships. Phylogenetic analysis of the grass-specific group II HKT genes identified two distinct subfamilies, I and II. Subfamily II was represented in all species, whereas subfamily I was identified only in the small grain cereals and possibly originated from an ancestral gene duplication post divergence from the coarse grain cereal lineage. The core protein structures were highly analogous despite there being no more than 58% amino acid identity between members of the two subfamilies. Distinctly variable regions in known functional domains, however, indicated functional divergence of the two subfamilies. The subsets of codons residing external to known functional domains predicted signatures of positive Darwinian selection potentially identifying new domains of functional divergence and providing new insights on the structural function and relationships between protein members of the two subfamilies.
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Affiliation(s)
- H A Chandima K Ariyarathna
- a School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley WA 6009, Australia.,b State Agricultural Biotechnology Centre, Murdoch University, Murdoch WA 6150, Australia
| | - Michael G Francki
- b State Agricultural Biotechnology Centre, Murdoch University, Murdoch WA 6150, Australia.,c Department of Agriculture and Food Western Australia, 3 Baron Hay Ct, South Perth WA 6151, Australia
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12
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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13
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Shahzad K, Rauf M, Ahmed M, Malik ZA, Habib I, Ahmed Z, Mahmood K, Ali R, Masmoudi K, Lemtiri-Chlieh F, Gehring C, Berkowitz GA, Saeed NA. Functional characterisation of an intron retaining K(+) transporter of barley reveals intron-mediated alternate splicing. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:840-51. [PMID: 25631371 DOI: 10.1111/plb.12290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
Intron retention in transcripts and the presence of 5' and 3' splice sites within these introns mediate alternate splicing, which is widely observed in animals and plants. Here, functional characterisation of the K(+) transporter, HvHKT2;1, with stably retained introns from barley (Hordeum vulgare) in yeast (Saccharomyces cerevisiae), and transcript profiling in yeast and transgenic tobacco (Nicotiana tabacum) is presented. Expression of intron-retaining HvHKT2;1 cDNA (HvHKT2;1-i) in trk1, trk2 yeast strain defective in K(+) uptake restored growth in medium containing hygromycin in the presence of different concentrations of K(+) and mediated hypersensitivity to Na(+) . HvHKT2;1-i produces multiple transcripts via alternate splicing of two regular introns and three exons in different compositions. HKT isoforms with retained introns and exon skipping variants were detected in relative expression analysis of (i) HvHKT2;1-i in barley under native conditions, (ii) in transgenic tobacco plants constitutively expressing HvHKT2;1-i, and (iii) in trk1, trk2 yeast expressing HvHKT2;1-i under control of an inducible promoter. Mixed proportions of three HKT transcripts: HvHKT2;1-e (first exon region), HvHKT2;1-i1 (first intron) and HvHKT2;1-i2 (second intron) were observed. The variation in transcript accumulation in response to changing K(+) and Na(+) concentrations was observed in both heterologous and plant systems. These findings suggest a link between intron-retaining transcripts and different splice variants to ion homeostasis, and their possible role in salt stress.
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Affiliation(s)
- K Shahzad
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - M Rauf
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - M Ahmed
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Z A Malik
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - I Habib
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Z Ahmed
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - K Mahmood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - R Ali
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, Storrs, CT, USA
| | - K Masmoudi
- International Centre for Biosaline Agriculture (ICBA), Dubai, UAE
| | - F Lemtiri-Chlieh
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - C Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - G A Berkowitz
- Agricultural Biotechnology Laboratory, Department of Plant Science, University of Connecticut, Storrs, CT, USA
| | - N A Saeed
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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14
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Kuang Q, Purhonen P, Hebert H. Structure of potassium channels. Cell Mol Life Sci 2015; 72:3677-93. [PMID: 26070303 PMCID: PMC4565861 DOI: 10.1007/s00018-015-1948-5] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 12/25/2022]
Abstract
Potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. Since the first atomic structure of a prokaryotic potassium channel (KcsA, a channel from Streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. In this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming domain only (KcsA), voltage-gated, inwardly rectifying, tandem pore domain, and ligand-gated ones. The general properties shared by all potassium channels are introduced first, followed by specific features in each class. Our purpose is to help readers to grasp the basic concepts, to be familiar with the property of the different domains, and to understand the structure and function of the potassium channels better.
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Affiliation(s)
- Qie Kuang
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden.
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden.
| | - Pasi Purhonen
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden
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15
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Sonawane KD, Barage SH. Structural analysis of membrane-bound hECE-1 dimer using molecular modeling techniques: insights into conformational changes and Aβ1–42 peptide binding. Amino Acids 2014; 47:543-59. [DOI: 10.1007/s00726-014-1887-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
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Levin EJ, Zhou M. Recent progress on the structure and function of the TrkH/KtrB ion channel. Curr Opin Struct Biol 2014; 27:95-101. [PMID: 25011047 DOI: 10.1016/j.sbi.2014.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Abstract
Members of the Superfamily of K(+) Transporters (SKT) are integral membrane proteins that mediate the uptake of ions into non-animal cells. Although these proteins are homologous to the well-characterized K(+) channel family, relatively little was known about their transport and gating mechanisms until the recent determination of crystal structures for two SKT proteins, TrkH and KtrB. These structures reveal that the SKT proteins are channels, containing a flexible loop in the middle of the permeation pathway that may act as a gate. Two different conformational changes have been observed for the associated gating rings, suggesting different mechanisms of regulation by the binding of nucleotides.
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Affiliation(s)
- Elena J Levin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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17
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Shirvanyants D, Ramachandran S, Mei Y, Xu L, Meissner G, Dokholyan NV. Pore dynamics and conductance of RyR1 transmembrane domain. Biophys J 2014; 106:2375-84. [PMID: 24896116 PMCID: PMC4052289 DOI: 10.1016/j.bpj.2014.04.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/17/2014] [Indexed: 11/25/2022] Open
Abstract
Ryanodine receptors (RyR) are calcium release channels, playing a major role in the regulation of muscular contraction. Mutations in skeletal muscle RyR (RyR1) are associated with congenital diseases such as malignant hyperthermia and central core disease (CCD). The absence of high-resolution structures of RyR1 has limited our understanding of channel function and disease mechanisms at the molecular level. Previously, we have reported a hypothetical structure of the RyR1 pore-forming region, obtained by homology modeling and supported by mutational scans, electrophysiological measurements, and cryo-electron microscopy. Here, we utilize the expanded model encompassing six transmembrane helices to calculate the RyR1 pore region conductance, to analyze its structural stability, and to hypothesize the mechanism of the Ile4897 CCD-associated mutation. The calculated conductance of the wild-type RyR1 suggests that the proposed pore structure can sustain ion currents measured in single-channel experiments. We observe a stable pore structure on timescales of 0.2 μs, with multiple cations occupying the selectivity filter and cytosolic vestibule, but not the inner chamber. We further suggest that stability of the selectivity filter critically depends on the interactions between the I4897 residue and several hydrophobic residues of the neighboring subunit. Loss of these interactions in the case of polar substitution I4897T results in destabilization of the selectivity filter, a possible cause of the CCD-specific reduced Ca(2+) conductance.
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Affiliation(s)
- David Shirvanyants
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Srinivas Ramachandran
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Yingwu Mei
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Le Xu
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Gerhard Meissner
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina.
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina.
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18
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Adaptation in Haloalkaliphiles and Natronophilic Bacteria. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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21
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Furini S, Domene C. Nonselective conduction in a mutated NaK channel with three cation-binding sites. Biophys J 2012. [PMID: 23200044 DOI: 10.1016/j.bpj.2012.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The NaK channel is a cation-selective protein with similar permeability for K(+) and Na(+) ions. Crystallographic structures are available for the wild-type and mutated NaK channels with different numbers of cation-binding sites. We have performed a comparison between the potentials of mean force governing the translocation of K(+) ions and mixtures of one Na(+) and three K(+) ions in a mutated NaK channel with only three cation-binding sites (NaK-CNG). Since NaK-CNG is not selective for K(+) over Na(+), analysis of its multi-ion potential energy surfaces can provide clues about how selectivity originates. Comparison of the potentials of mean force of NaK-CNG and K(+)-selective channels yields observations that strongly suggest that the number of contiguous ion binding sites in a single-file mechanism is the key determinant of the channel's selectivity properties, as already proposed by experimental studies. We conclude that the presence of four binding sites in K(+)-selective channels is essential for highly selective and efficient permeation of K(+) ions, and that a key difference between K(+)-selective and nonselective channels is the absence/presence of a binding site for Na(+) ions at the boundary between S2 and S3 in the context of multi-ion permeation events.
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Affiliation(s)
- Simone Furini
- Department of Medical Surgery and Bioengineering, University of Siena, Siena, Italy
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22
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A two-staged model of Na+ exclusion in rice explained by 3D modeling of HKT transporters and alternative splicing. PLoS One 2012; 7:e39865. [PMID: 22808069 PMCID: PMC3394774 DOI: 10.1371/journal.pone.0039865] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/28/2012] [Indexed: 11/19/2022] Open
Abstract
The HKT family of Na(+) and Na(+)/K(+) transporters is implicated in plant salinity tolerance. Amongst these transporters, the cereal HKT1;4 and HKT1;5 are responsible for Na(+) exclusion from photosynthetic tissues, a key mechanism for plant salinity tolerance. It has been suggested that Na(+) is retrieved from the xylem transpiration stream either in the root or the leaf sheath, protecting the leaf blades from excessive Na(+) accumulation. However, direct evidence for this scenario is scarce. Comparative modeling and evaluation of rice (Oryza sativa) HKT-transporters based on the recent crystal structure of the bacterial TrkH K(+) transporter allowed to reconcile transcriptomic and physiological data. For OsHKT1;5, both transcript abundance and protein structural features within the selectivity filter could control shoot Na(+) accumulation in a range of rice varieties. For OsHKT1;4, alternative splicing of transcript and the anatomical complexity of the sheath needed to be taken into account. Thus, Na(+) accumulation in a specific leaf blade seems to be regulated by abundance of a correctly spliced OsHKT1;4 transcript in a corresponding sheath. Overall, allelic variation of leaf blade Na(+) accumulation can be explained by a complex interplay of gene transcription, alternative splicing and protein structure.
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