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Waggoner EM, Djaoudi K, Diaz JM, Duhamel S. Dissolved organic phosphorus bond-class utilization by Synechococcus. FEMS Microbiol Ecol 2024; 100:fiae099. [PMID: 39003239 PMCID: PMC11319936 DOI: 10.1093/femsec/fiae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024] Open
Abstract
Dissolved organic phosphorus (DOP) contains compounds with phosphoester, phosphoanhydride, and phosphorus-carbon bonds. While DOP holds significant nutritional value for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by Synechococcus strains from open and coastal oceans. Both strains exhibited comparable growth rates when provided phosphate, a phosphoanhydride [3-polyphosphate and 45-polyphosphate], or a DOP compound with both phosphoanhydride and phosphoester bonds (adenosine 5'-triphosphate). Growth rates on phosphoesters [glucose-6-phosphate, adenosine 5'-monophosphate, bis(4-methylumbelliferyl) phosphate] were variable, and neither strain grew on selected phosphorus-carbon compounds. Both strains hydrolyzed 3-polyphosphate, then adenosine 5'-triphosphate, and lastly adenosine 5'-monophosphate, exhibiting preferential enzymatic hydrolysis of phosphoanhydride bonds. The strains' exoproteomes contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of phosphoanhydride bonds by these exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity toward the phosphoanhydride 3-polyphosphate, with varying affinities between strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition and highlight varied growth and enzymatic responses to molecular diversity within DOP bond-classes, thereby expanding our understanding of microbially mediated DOP cycling in marine ecosystems.
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Affiliation(s)
- Emily M Waggoner
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona, AZ 85721, United States
| | - Kahina Djaoudi
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona, AZ 85721, United States
| | - Julia M Diaz
- Geosciences Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, United States
| | - Solange Duhamel
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona, AZ 85721, United States
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2
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Mosna K, Jurczak K, Krężel A. Differentiated Zn(II) binding affinities in animal, plant, and bacterial metallothioneins define their zinc buffering capacity at physiological pZn. Metallomics 2023; 15:mfad061. [PMID: 37804185 PMCID: PMC10612145 DOI: 10.1093/mtomcs/mfad061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023]
Abstract
Metallothioneins (MTs) are small, Cys-rich proteins present in various but not all organisms, from bacteria to humans. They participate in zinc and copper metabolism, toxic metals detoxification, and protection against reactive species. Structurally, they contain one or multiple domains, capable of binding a variable number of metal ions. For experimental convenience, biochemical characterization of MTs is mainly performed on Cd(II)-loaded proteins, frequently omitting or limiting Zn(II) binding features and related functions. Here, by choosing 10 MTs with relatively well-characterized structures from animals, plants, and bacteria, we focused on poorly investigated Zn(II)-to-protein affinities, stability-structure relations, and the speciation of individual complexes. For that purpose, MTs were characterized in terms of stoichiometry, pH-dependent Zn(II) binding, and competition with chromogenic and fluorescent probes. To shed more light on protein folding and its relation with Zn(II) affinity, reactivity of variously Zn(II)-loaded MTs was studied by (5,5'-dithiobis(2-nitrobenzoic acid) oxidation in the presence of mild chelators. The results show that animal and plant MTs, despite their architectural differences, demonstrate the same affinities to Zn(II), varying from nano- to low picomolar range. Bacterial MTs bind Zn(II) more tightly but, importantly, with different affinities from low picomolar to low femtomolar range. The presence of weak, moderate, and tight zinc sites is related to the folding mechanisms and internal electrostatic interactions. Differentiated affinities of all MTs define their zinc buffering capacity required for Zn(II) donation and acceptance at various free Zn(II) concentrations (pZn levels). The data demonstrate critical roles of individual Zn(II)-depleted MT species in zinc buffering processes.
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Affiliation(s)
- Karolina Mosna
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Kinga Jurczak
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
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3
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Liang Z, McCabe K, Fawcett SE, Forrer HJ, Hashihama F, Jeandel C, Marconi D, Planquette H, Saito MA, Sohm JA, Thomas RK, Letscher RT, Knapp AN. A global ocean dissolved organic phosphorus concentration database (DOPv2021). Sci Data 2022; 9:772. [PMID: 36526638 PMCID: PMC9758185 DOI: 10.1038/s41597-022-01873-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Dissolved organic phosphorus (DOP) concentration distributions in the global surface ocean inform our understanding of marine biogeochemical processes such as nitrogen fixation and primary production. The spatial distribution of DOP concentrations in the surface ocean reflect production by primary producers and consumption as an organic nutrient by phytoplankton including diazotrophs and other microbes, as well as other loss processes such as photolysis. Compared to dissolved organic carbon and nitrogen, however, relatively few marine DOP concentration measurements have been made, largely due to the lack of automated analysis techniques. Here we present a database of marine DOP concentration measurements (DOPv2021) that includes new (n = 730) and previously published (n = 3140) observations made over the last ~30 years (1990-2021), including 1751 observations in the upper 50 m. This dataset encompasses observations from all major ocean basins including the poorly represented Indian, South Pacific, and Southern Oceans and provides insight into spatial distributions of DOP in the ocean. It is also valuable for researchers who work on marine primary production and nitrogen fixation.
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Affiliation(s)
- Zhou Liang
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Kelly McCabe
- grid.214458.e0000000086837370Copperative Institute for Great Lakes Research (CIGLR), School for Environment and Sustainability, University of Michigan, Ann Arbor, MI USA
| | - Sarah E. Fawcett
- grid.7836.a0000 0004 1937 1151Department of Oceanography, Faculty of Science, University of Cape Town, Cape Town, South Africa ,grid.7836.a0000 0004 1937 1151Marine and Antarctic Research centre for Innovation and Sustainability (MARIS), University of Cape Town, Cape Town, South Africa
| | - Heather J. Forrer
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Fuminori Hashihama
- grid.412785.d0000 0001 0695 6482Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Catherine Jeandel
- grid.503277.40000 0004 0384 4620LEGOS, Université de Toulouse, CNRS, IRD, CNES, UPS, Toulouse, France
| | - Dario Marconi
- grid.16750.350000 0001 2097 5006Department of Geosciences, Princeton University, Princeton, NJ USA
| | - Hélène Planquette
- grid.463763.30000 0004 0638 0577Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - Mak A. Saito
- grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Falmouth, MA USA
| | - Jill A. Sohm
- grid.42505.360000 0001 2156 6853Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
| | - Rachel K. Thomas
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Robert T. Letscher
- grid.167436.10000 0001 2192 7145Earth Sciences & Ocean Process Analysis Laboratory, University of New Hampshire, Durham, NH USA
| | - Angela N. Knapp
- grid.255986.50000 0004 0472 0419Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
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4
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Mikhaylina A, Ksibe AZ, Wilkinson RC, Smith D, Marks E, Coverdale JPC, Fülöp V, Scanlan DJ, Blindauer CA. A single sensor controls large variations in zinc quotas in a marine cyanobacterium. Nat Chem Biol 2022; 18:869-877. [PMID: 35681030 PMCID: PMC9337993 DOI: 10.1038/s41589-022-01051-1] [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: 03/05/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022]
Abstract
Marine cyanobacteria are critical players in global nutrient cycles that crucially depend on trace metals in metalloenzymes, including zinc for CO2 fixation and phosphorus acquisition. How strains proliferating in the vast oligotrophic ocean gyres thrive at ultra-low zinc concentrations is currently unknown. Using Synechococcus sp. WH8102 as a model we show that its zinc-sensor protein Zur differs from all other known bacterial Zur proteins in overall structure and the location of its sensory zinc site. Uniquely, Synechococcus Zur activates metallothionein gene expression, which supports cellular zinc quotas spanning two orders of magnitude. Thus, a single zinc sensor facilitates growth across pico- to micromolar zinc concentrations with the bonus of banking this precious resource. The resultant ability to grow well at both ultra-low and excess zinc, together with overall lower zinc requirements, likely contribute to the broad ecological distribution of Synechococcus across the global oceans.
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Affiliation(s)
- Alevtina Mikhaylina
- Department of Chemistry, University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Amira Z Ksibe
- Department of Chemistry, University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Rachael C Wilkinson
- School of Life Sciences, University of Warwick, Coventry, UK
- Swansea University Medical School, Swansea, UK
| | - Darbi Smith
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Eleanor Marks
- Department of Chemistry, University of Warwick, Coventry, UK
| | - James P C Coverdale
- Department of Chemistry, University of Warwick, Coventry, UK
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, UK
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5
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Ford BA, Sullivan GJ, Moore L, Varkey D, Zhu H, Ostrowski M, Mabbutt BC, Paulsen IT, Shah BS. Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria. Biochem Soc Trans 2021; 49:2465-2481. [PMID: 34882230 PMCID: PMC8786288 DOI: 10.1042/bst20200244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/03/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022]
Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
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Affiliation(s)
- Benjamin A. Ford
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Lisa Moore
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Deepa Varkey
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Hannah Zhu
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Martin Ostrowski
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Bridget C. Mabbutt
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bhumika S. Shah
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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6
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Cyanobacterial Extracellular Polymeric Substances for Heavy Metal Removal: A Mini Review. JOURNAL OF COMPOSITES SCIENCE 2020. [DOI: 10.3390/jcs5010001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heavy metals from various natural and anthropogenic sources are becoming a chief threat to the aquatic system owing to their toxic and lethal effect. The treatment of such contaminated wastewater is one of the prime concerns in this field. For decades, a huge array of innovative biosorbents is used for heavy metal removal. Though extensive microbes and their biomolecules have been experimented and have showed great potential but most of them have failed to have the substantial breakthrough for the practical application. The present review emphasis on the potential utilization of the cyanobacteria for the heavy metal removal along with the toxic effect imposed by the pollutant. Furthermore, the effect of significant parameters, plausible mechanistic insights of the heavy metal toxicity imposed onto the cyanobacteria is also discussed in detail. The role of extrapolymeric substances and metallothionein secreted by the microbes are also elaborated. The review was evident that the cyanobacterial species have a huge potential towards the heavy metal removal from the aqueous system ranging from very low to very high concentrations.
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7
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Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J Proteome Res 2019; 18:1461-1476. [PMID: 30702898 DOI: 10.1021/acs.jproteome.8b00761] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.
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Affiliation(s)
- Mak A Saito
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Erin M Bertrand
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Megan E Duffy
- School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - David A Gaylord
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Noelle A Held
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | | | - Robert L Hettich
- Oak Ridge National Laboratory and Microbiology Department , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Saint Paul , Minnesota 55108 , United States
| | - Michael G Janech
- College of Charleston , Charleston , South Carolina 29424 , United States
| | - Danie B Kinkade
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Dagmar H Leary
- U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Matthew R McIlvin
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Eli K Moore
- Department of Environmental Science , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Robert M Morris
- School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - Benjamin A Neely
- National Institute of Standards and Technology , Charleston , South Carolina 29412 , United States
| | - Brook L Nunn
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Jaclyn K Saunders
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States.,School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - Adam I Shepherd
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Nicholas I Symmonds
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - David A Walsh
- Department of Biology , Concordia University , Montreal , Quebec H4B 1R6 , Canada
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8
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Frischkorn KR, Haley ST, Dyhrman ST. Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N 2 Fixing Cyanobacterium Trichodesmium erythraeum. Front Microbiol 2019; 10:330. [PMID: 30891009 PMCID: PMC6411698 DOI: 10.3389/fmicb.2019.00330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/08/2019] [Indexed: 01/27/2023] Open
Abstract
The N2 fixing cyanobacterium Trichodesmium is a critically important organism in oligotrophic marine ecosystems, supplying “new” nitrogen (N) to the otherwise N-poor tropical and subtropical regions where it occurs. Low concentrations of phosphorus (P) in these regions can constrain Trichodesmium distribution and N2 fixation rates. Physiological characterization of a single species in a mixed community can be challenging, and ‘omic approaches are increasingly important tools for tracking nutritional physiology in a taxon-specific manner. As such, studies examining the dynamics of gene and protein markers of physiology (e.g., nutrient stress) are critical for the application and interpretation of such ‘omic data in situ. Here we leveraged combined transcriptomics, proteomics, and enzyme activity assays to track the physiological response of Trichodesmium erythraeum IMS101 to P deficiency and subsequent P re-supply over 72 h of sampling. P deficiency resulted in differential gene expression, protein abundance, and enzyme activity that highlighted a synchronous shift in P physiology with increases in the transcripts and corresponding proteins for hydrolyzing organic phosphorus, taking up phosphate with higher affinity, and modulating intracellular P demand. After P deficiency was alleviated, gene expression of these biomarkers was reduced to replete levels within 4 h of P amendment. A number of these gene biomarkers were adjacent to putative pho boxes and their expression patterns were similar to a sphR response regulator. Protein products of the P deficiency biomarkers were slow to decline, with 84% of the original P deficient protein set still significantly differentially expressed after 72 h. Alkaline phosphatase activity tracked with proteins for this enzyme. With the rapid turnover time of transcripts, they appear to be good biomarkers of a P stress phenotype, whereas proteins, with a slower turnover time, may better reflect cellular activities. These results highlight the importance of validating and pairing transcriptome and proteome data that can be applied to physiological studies of key species in situ.
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Affiliation(s)
- Kyle R Frischkorn
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.,Lamont-Doherty Earth Observatory, Palisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Palisades, NY, United States
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.,Lamont-Doherty Earth Observatory, Palisades, NY, United States
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9
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Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120. mSystems 2017; 2:mSystems00008-17. [PMID: 28593196 PMCID: PMC5451487 DOI: 10.1128/msystems.00008-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022] Open
Abstract
Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57% of the theoretical proteome, were identified-the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes (P value of <0.05) were observed for 408 proteins, with the majority of proteins (92.4%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins PII and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to global primary production and playing a prominent role in biogeochemical cycles. Here we study the effects of extreme nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism. Quantitative proteomics allowed an accurate quantification of the Prochlorococcus proteome, finding three main responses to nitrogen limitation: upregulation of nitrogen assimilation-related proteins, including transporters; downregulation of ribosome proteins; and induction of the photosystem II cyclic electron flow. This suggests that nitrogen limitation affects a range of metabolic processes far wider than initially believed, with the ultimate goal of saving nitrogen and maximizing the nitrogen uptake and assimilation capabilities of the cell.
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10
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Browning TJ, Achterberg EP, Yong JC, Rapp I, Utermann C, Engel A, Moore CM. Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic. Nat Commun 2017; 8:15465. [PMID: 28524880 PMCID: PMC5454538 DOI: 10.1038/ncomms15465] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/31/2017] [Indexed: 11/12/2022] Open
Abstract
In certain regions of the predominantly nitrogen limited ocean, microbes can become co-limited by phosphorus. Within such regions, a proportion of the dissolved organic phosphorus pool can be accessed by microbes employing a variety of alkaline phosphatase (APase) enzymes. In contrast to the PhoA family of APases that utilize zinc as a cofactor, the recent discovery of iron as a cofactor in the more widespread PhoX and PhoD implies the potential for a biochemically dependant interplay between oceanic zinc, iron and phosphorus cycles. Here we demonstrate enhanced natural community APase activity following iron amendment within the low zinc and moderately low iron Western North Atlantic. In contrast we find no evidence for trace metal limitation of APase activity beneath the Saharan dust plume in the Eastern Atlantic. Such intermittent iron limitation of microbial phosphorus acquisition provides an additional facet in the argument for iron controlling the coupling between oceanic nitrogen and phosphorus cycles.
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Affiliation(s)
- T. J. Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - E. P. Achterberg
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - J. C. Yong
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - I. Rapp
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - C. Utermann
- Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24106, Germany
| | - A. Engel
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - C. M. Moore
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, UK
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11
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Giner-Lamia J, Pereira SB, Bovea-Marco M, Futschik ME, Tamagnini P, Oliveira P. Extracellular Proteins: Novel Key Components of Metal Resistance in Cyanobacteria? Front Microbiol 2016; 7:878. [PMID: 27375598 PMCID: PMC4894872 DOI: 10.3389/fmicb.2016.00878] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/24/2016] [Indexed: 11/13/2022] Open
Abstract
Metals are essential for all living organisms and required for fundamental biochemical processes. However, when in excess, metals can turn into highly-toxic agents able to disrupt cell membranes, alter enzymatic activities, and damage DNA. Metal concentrations are therefore tightly controlled inside cells, particularly in cyanobacteria. Cyanobacteria are ecologically relevant prokaryotes that perform oxygenic photosynthesis and can be found in many different marine and freshwater ecosystems, including environments contaminated with heavy metals. As their photosynthetic machinery imposes high demands for metals, homeostasis of these micronutrients has been widely studied in cyanobacteria. So far, most studies have focused on how cells are capable of controlling their internal metal pools, with a strong bias toward the analysis of intracellular processes. Ultrastructure, modulation of physiology, dynamic changes in transcription and protein levels have been studied, but what takes place in the extracellular environment when cells are exposed to an unbalanced metal availability remains largely unknown. The interest in studying the subset of proteins present in the extracellular space has only recently begun and the identification and functional analysis of the cyanobacterial exoproteomes are just emerging. Remarkably, metal-related proteins such as the copper-chaperone CopM or the iron-binding protein FutA2 have already been identified outside the cell. With this perspective, we aim to raise the awareness that metal-resistance mechanisms are not yet fully known and hope to motivate future studies assessing the role of extracellular proteins on bacterial metal homeostasis, with a special focus on cyanobacteria.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, Centro de Ciências do Mar, Universidade do AlgarveFaro, Portugal; Center for Biomedical Research, Universidade do AlgarveFaro, Portugal
| | - Sara B Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal
| | | | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, Centro de Ciências do Mar, Universidade do AlgarveFaro, Portugal; Center for Biomedical Research, Universidade do AlgarveFaro, Portugal
| | - Paula Tamagnini
- Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal; Faculdade de Ciências, Departamento de Biologia, Universidade do PortoPorto, Portugal
| | - Paulo Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do PortoPorto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do PortoPorto, Portugal
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12
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Roy SK, Cho SW, Kwon SJ, Kamal AHM, Kim SW, Oh MW, Lee MS, Chung KY, Xin Z, Woo SH. Morpho-Physiological and Proteome Level Responses to Cadmium Stress in Sorghum. PLoS One 2016; 11:e0150431. [PMID: 26919231 PMCID: PMC4769174 DOI: 10.1371/journal.pone.0150431] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/12/2016] [Indexed: 11/18/2022] Open
Abstract
Cadmium (Cd) stress may cause serious morphological and physiological abnormalities in addition to altering the proteome in plants. The present study was performed to explore Cd-induced morpho-physiological alterations and their potential associated mechanisms in Sorghum bicolor leaves at the protein level. Ten-day-old sorghum seedlings were exposed to different concentrations (0, 100, and 150 μM) of CdCl2, and different morpho-physiological responses were recorded. The effects of Cd exposure on protein expression patterns in S. bicolor were investigated using two-dimensional gel electrophoresis (2-DE) in samples derived from the leaves of both control and Cd-treated seedlings. The observed morphological changes revealed that the plants treated with Cd displayed dramatically altered shoot lengths, fresh weights and relative water content. In addition, the concentration of Cd was markedly increased by treatment with Cd, and the amount of Cd taken up by the shoots was significantly and directly correlated with the applied concentration of Cd. Using the 2-DE method, a total of 33 differentially expressed protein spots were analyzed using MALDI-TOF/TOF MS. Of these, treatment with Cd resulted in significant increases in 15 proteins and decreases in 18 proteins. Major changes were absorbed in the levels of proteins known to be involved in carbohydrate metabolism, transcriptional regulation, translation and stress responses. Proteomic results revealed that Cd stress had an inhibitory effect on carbon fixation, ATP production and the regulation of protein synthesis. Our study provides insights into the integrated molecular mechanisms involved in responses to Cd and the effects of Cd on the growth and physiological characteristics of sorghum seedlings. We have aimed to provide a reference describing the mechanisms involved in heavy metal damage to plants.
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Affiliation(s)
- Swapan Kumar Roy
- Department of Crop Science, Chungbuk National University, Cheong-ju, Korea
| | - Seong-Woo Cho
- Division of Rice Research, National Institute of Crop Science, Rural Development Administration, Suwon, Korea
| | - Soo Jeong Kwon
- Department of Crop Science, Chungbuk National University, Cheong-ju, Korea
| | - Abu Hena Mostafa Kamal
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Sang-Woo Kim
- Department of Crop Science, Chungbuk National University, Cheong-ju, Korea
| | - Myeong-Won Oh
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju, Korea
| | - Moon-Soon Lee
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheong-ju, Korea
| | - Keun-Yook Chung
- Department of Environmental & Biological Chemistry, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, 3810 4th Street, Lubbock, TX, United States of America
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Korea
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13
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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14
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Christie-Oleza JA, Armengaud J, Guerin P, Scanlan DJ. Functional distinctness in the exoproteomes of marine Synechococcus. Environ Microbiol 2015; 17:3781-94. [PMID: 25727668 PMCID: PMC4949707 DOI: 10.1111/1462-2920.12822] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 12/31/2022]
Abstract
The exported protein fraction of an organism may reflect its life strategy and, ultimately, the way it is perceived by the outside world. Bioinformatic prediction of the exported pan‐proteome of Prochlorococcus and Synechococcus lineages demonstrated that (i) this fraction of the encoded proteome had a much higher incidence of lineage‐specific proteins than the cytosolic fraction (57% and 73% homologue incidence respectively) and (ii) exported proteins are largely uncharacterized to date (54%) compared with proteins from the cytosolic fraction (35%). This suggests that the genomic and functional diversity of these organisms lies largely in the diverse pool of novel functions these organisms export to/through their membranes playing a key role in community diversification, e.g. for niche partitioning or evading predation. Experimental exoproteome analysis of marine Synechococcus showed transport systems for inorganic nutrients, an interesting array of strain‐specific exoproteins involved in mutualistic or hostile interactions (i.e. hemolysins, pilins, adhesins), and exoenzymes with a potential mixotrophic goal (i.e. exoproteases and chitinases). We also show how these organisms can remodel their exoproteome, i.e. by increasing the repertoire of interaction proteins when grown in the presence of a heterotroph or decrease exposure to prey when grown in the dark. Finally, our data indicate that heterotrophic bacteria can feed on the exoproteome of Synechococcus.
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Affiliation(s)
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Technological Innovations for Detection and Diagnostic', Bagnols-sur-Cèze, F-30207, France
| | - Philippe Guerin
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Technological Innovations for Detection and Diagnostic', Bagnols-sur-Cèze, F-30207, France
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Hernández-Prieto MA, Semeniuk TA, Futschik ME. Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. Front Genet 2014; 5:191. [PMID: 25071821 PMCID: PMC4079066 DOI: 10.3389/fgene.2014.00191] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/11/2014] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteria are essential primary producers in marine ecosystems, playing an important role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and metagenomic projects have generated large amounts of genetic data for cyanobacteria. This wealth of data provides researchers with a new basis for the study of molecular adaptation, ecology and evolution of cyanobacteria, as well as for developing biotechnological applications. It also facilitates the use of multiplex techniques, i.e., expression profiling by high-throughput technologies such as microarrays, RNA-seq, and proteomics. However, exploration and analysis of these data is challenging, and often requires advanced computational methods. Also, they need to be integrated into our existing framework of knowledge to use them to draw reliable biological conclusions. Here, systems biology provides important tools. Especially, the construction and analysis of molecular networks has emerged as a powerful systems-level framework, with which to integrate such data, and to better understand biological relevant processes in these organisms. In this review, we provide an overview of the advances and experimental approaches undertaken using multiplex data from genomic, transcriptomic, proteomic, and metabolomic studies in cyanobacteria. Furthermore, we summarize currently available web-based tools dedicated to cyanobacteria, i.e., CyanoBase, CyanoEXpress, ProPortal, Cyanorak, CyanoBIKE, and CINPER. Finally, we present a case study for the freshwater model cyanobacteria, Synechocystis sp. PCC6803, to show the power of meta-analysis, and the potential to extrapolate acquired knowledge to the ecologically important marine cyanobacteria genus, Prochlorococcus.
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Affiliation(s)
| | - Trudi A Semeniuk
- Systems Biology and Bioinformatics Laboratory, IBB-CBME, University of Algarve Faro, Portugal
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, IBB-CBME, University of Algarve Faro, Portugal ; Centre of Marine Sciences, University of Algarve Faro, Portugal
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