Topical Collection "Metabolism in Phototrophic Prokaryotes and Algae"

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A topical collection in Metabolites (ISSN 2218-1989).

Editor

Guest Editor
Dr. Dirk Steinhauser (Website)

Department Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
Phone: +49331 567 8218
Interests: metabolic diversity and evolution; systems metabolomics, synthetic biology; computational biology and bioinformatics

Topical Collection Information

Dear Colleagues,

Phototrophic prokaryotes and algae play an important role as primary producers in the global carbon and nitrogen cycle on Earth. Accordingly they have been the focus of research since many decades, especially with respect to their exploitability as a source for the production of renewable energy. Furthermore, the multitudes of secondary metabolites produced are of potential industrial importance as they can be used for pharmaceuticals against bacterial and viral infections or as food supplements just to name some. In addition, phototropic microalgae, which are of relatively simple architecture, have increasingly been used in basic research as models to study the photosynthetic processes in single cells. Still, there remain many open questions in particular regarding algal metabolism and metabolic diversity.

The ever-growing body of complete genome information of phototrophic prokaryotes and algae provides an unprecedented data source to explore their metabolic capabilities which have already led to new and surprising metabolic findings. As metabolites can be considered an important cellular response to environmental perturbations, metabolomics, in conjunction with data from genomics and post-genomics high-throughput ‘omics’ approaches, will facilitate insights into the molecular mechanisms, functions, and evolution of metabolic and associated regulatory pathways. Additionally, this will further enhance our biochemical and metabolic knowledge related to phototrophic prokaryotes and algae, provide the fundamental framework to exploit their potential usage in biotechnology and will also opened novel research avenues in both plant and non-plant systems.

Therefore this collection of Metabolites will be dedicated to the metabolism in phototrophic prokaryotes and algae. We will consider review articles as well as original research papers with special focus on any aspect of metabolism, its regulation, evolution, and diversity in these organisms. The focus can be either on a single organism or on comparative studies. Furthermore, original research article related to method improvements and development (e.g. culturing, harvesting, software development and biochemical / analytical approach) are also welcome, as such work represents the basic foundation to deepen our insight into the algal metabolism.

Dr. Dirk Steinhauser
Guest Editor

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Keywords

  • phototrophic prokaryotes and algae
  • metabolism and metabolomics
  • metabolic networks and modeling
  • metabolic diversity
  • metabolic and pathway evolution
  • primary and secondary metabolites
  • functional and comparative genomics
  • bioinformatics and systems biology
  • biochemical and analytic methods

Published Papers (17 papers)

2015

Jump to: 2014, 2013

Open AccessArticle Taxonomic and Environmental Variation of Metabolite Profiles in Marine Dinoflagellates of the Genus Symbiodinium
Metabolites 2015, 5(1), 74-99; doi:10.3390/metabo5010074
Received: 4 September 2014 / Revised: 4 February 2015 / Accepted: 9 February 2015 / Published: 16 February 2015
Cited by 5 | PDF Full-text (1548 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Microorganisms in terrestrial and marine ecosystems are essential to environmental sustainability. In the marine environment, invertebrates often depend on metabolic cooperation with their endosymbionts. Coral reefs, one of the most important marine ecosystems, are based on the symbiosis between a broad diversity [...] Read more.
Microorganisms in terrestrial and marine ecosystems are essential to environmental sustainability. In the marine environment, invertebrates often depend on metabolic cooperation with their endosymbionts. Coral reefs, one of the most important marine ecosystems, are based on the symbiosis between a broad diversity of dinoflagellates of the genus Symbiodinium and a wide phyletic diversity of hosts (i.e., cnidarian, molluscan, poriferan). This diversity is reflected in the ecology and physiology of the symbionts, yet the underlying biochemical mechanisms are still poorly understood. We examined metabolite profiles of four cultured species of Symbiodinium known to form viable symbioses with reef-building corals, S. microadriaticum (cp-type A194), S. minutum (cp-type B184), S. psygmophilum (cp-type B224) and S. trenchii (cp-type D206). Metabolite profiles were shown to differ among Symbiodinium species and were found to be affected by their physiological response to growth in different temperatures and light regimes. A combined Random Forests and Bayesian analysis revealed that the four Symbiodinium species examined primarily differed in their production of sterols and sugars, including a C29 stanol and the two sterols C28Δ5 and C28Δ5,22, as well as differences in metabolite abundances of a hexose and inositol. Inositol levels were also strongly affected by changes in temperature across all Symbiodinium species. Our results offer a detailed view of the metabolite profile characteristic of marine symbiotic dinoflagellates of the genus Symbiodinium, and identify patterns of metabolites related to several growth conditions. Full article

2014

Jump to: 2015, 2013

Open AccessArticle Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942
Metabolites 2014, 4(3), 680-698; doi:10.3390/metabo4030680
Received: 26 February 2014 / Revised: 5 August 2014 / Accepted: 12 August 2014 / Published: 20 August 2014
Cited by 2 | PDF Full-text (853 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven [...] Read more.
The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942. Full article
Open AccessArticle Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme
Metabolites 2014, 4(3), 612-628; doi:10.3390/metabo4030612
Received: 13 June 2014 / Revised: 25 July 2014 / Accepted: 28 July 2014 / Published: 4 August 2014
Cited by 2 | PDF Full-text (399 KB) | HTML Full-text | XML Full-text
Abstract
The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher [...] Read more.
The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a glycolytic enolase [EC 4.2.1.11]. Our predicted cytosolic localization would require export of organic carbon from the plastid to provide substrate for the enolase and subsequent re-import of organic carbon back into the plastids. Further, our comparative sequence study of the enolase and its 3D-structure prediction may suggest that the N-terminal extension found in green algal enolases could be involved in regulation of the enolase activity. In summary, we propose that the enolase represents one of the crucial regulatory bottlenecks in carbon partitioning in green algae. Full article
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Open AccessCommunication Affinity Purification of O-Acetylserine(thiol)lyase from Chlorella sorokiniana by Recombinant Proteins from Arabidopsis thaliana
Metabolites 2014, 4(3), 629-639; doi:10.3390/metabo4030629
Received: 21 January 2014 / Revised: 17 July 2014 / Accepted: 28 July 2014 / Published: 4 August 2014
Cited by 4 | PDF Full-text (345 KB) | HTML Full-text | XML Full-text
Abstract
In the unicellular green alga Chlorella sorokiniana (211/8 k), the protein O-acetylserine(thiol)lyase (OASTL), representing the key-enzyme in the biosynthetic cysteine pathway, was isolated and purified to apparent homogeneity. The purification was carried out in cells grown in the presence of all [...] Read more.
In the unicellular green alga Chlorella sorokiniana (211/8 k), the protein O-acetylserine(thiol)lyase (OASTL), representing the key-enzyme in the biosynthetic cysteine pathway, was isolated and purified to apparent homogeneity. The purification was carried out in cells grown in the presence of all nutrients or in sulphate (S) deprived cells. After 24 h of S-starvation, a 17-fold increase in the specific activity of OASTL was measured. In order to enable the identification of OASTL proteins from non-model organisms such as C. sorokiniana, the recombinant his-tagged SAT5 protein from Arabidopsis thaliana was immobilized by metal chelate chromatography. OASTL proteins from C. sorokiniana were affinity purified in one step and activities were enhanced 29- and 41-fold, from S-sufficient and S-starved (24 h) cells, respectively. The successful application of SAT/OASTL interaction for purification confirms for the first time the existence of the cysteine synthase complexes in microalgae. The purified proteins have apparent molecular masses between 32–34 kDa and are thus slightly larger compared to those found in Arabidopsis thaliana and other vascular plants. The enhanced OASTL activity in S-starved cells can be attributed to increased amounts of plastidic and the emergence of cytosolic OASTL isoforms. The results provide proof-of-concept for the biochemical analysis of the cysteine synthase complex in diverse microalgal species. Full article
Open AccessArticle NblA1/A2-Dependent Homeostasis of Amino Acid Pools during Nitrogen Starvation in Synechocystis sp. PCC 6803
Metabolites 2014, 4(3), 517-531; doi:10.3390/metabo4030517
Received: 17 March 2014 / Revised: 14 June 2014 / Accepted: 23 June 2014 / Published: 30 June 2014
Cited by 5 | PDF Full-text (1682 KB) | HTML Full-text | XML Full-text
Abstract
Nutrient balance is important for photosynthetic growth and biomass production in microalgae. Here, we investigated and compared metabolic responses of amino acid pools to nitrogen and sulfur starvation in a unicellular model cyanobacterium, Synechocystis sp. PCC 6803, and its mutant nblA1/A2. [...] Read more.
Nutrient balance is important for photosynthetic growth and biomass production in microalgae. Here, we investigated and compared metabolic responses of amino acid pools to nitrogen and sulfur starvation in a unicellular model cyanobacterium, Synechocystis sp. PCC 6803, and its mutant nblA1/A2. It is known that NblA1/A2-dependent and -independent breakdown of abundant photosynthetic phycobiliproteins and other cellular proteins supply nutrients to the organism. However, the contribution of the NblA1/A2-dependent nutrient supply to amino acid pool homeostasis has not been studied. Our study demonstrates that changes in the pool size of many amino acids during nitrogen starvation can be categorized as NblA1/A2-dependent (Gln, Glu, glutathione, Gly, Ile, Leu, Met, Phe, Pro, Ser, Thr, Tyr and Val) and NblA1/A2-independent (Ala, Asn, Lys, and Trp). We also report unique changes in amino acid pool sizes during sulfur starvation in wild type and the mutant and found a generally marked increase in the Lys pool in cyanobacteria during nutrient starvation. In conclusion, the NblA1/A2-dependent protein turnover contributes to the maintenance of many amino acid pools during nitrogen starvation. Full article
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Open AccessReview Surveillance of C-Allocation in Microalgal Cells
Metabolites 2014, 4(2), 453-464; doi:10.3390/metabo4020453
Received: 29 April 2014 / Revised: 6 June 2014 / Accepted: 9 June 2014 / Published: 19 June 2014
Cited by 4 | PDF Full-text (317 KB) | HTML Full-text | XML Full-text
Abstract
When microalgae are exposed to changing environmental conditions, e.g., light-dark cycles or oscillations in nutrient availability (CO2, nitrogen, phosphate or silicate) they respond with metabolic changes in the carbon allocation pattern. Short time regulations in the time range of few [...] Read more.
When microalgae are exposed to changing environmental conditions, e.g., light-dark cycles or oscillations in nutrient availability (CO2, nitrogen, phosphate or silicate) they respond with metabolic changes in the carbon allocation pattern. Short time regulations in the time range of few seconds to minutes can be mirrored best by mass spectroscopy based metabolomics. However, these snap shots do not reflect the alterations in the carbon flow to the cellular macromolecules like protein, carbohydrate or lipid. In this review it is shown how the combination of FTIR spectroscopy and Chla-in-vivo-fluorescence based electron transport rates can reveal changes in the metabolic flux rates of carbon during a shift of the environmental conditions. The review will demonstrate in which time range FTIR spectroscopy can deliver significant information and how FTIR spectroscopy data can synergistically support metabolome analysis by mass-spectroscopy. Full article
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Open AccessArticle Biotechnological Screening of Microalgal and Cyanobacterial Strains for Biogas Production and Antibacterial and Antifungal Effects
Metabolites 2014, 4(2), 373-393; doi:10.3390/metabo4020373
Received: 17 March 2014 / Revised: 26 April 2014 / Accepted: 29 April 2014 / Published: 15 May 2014
Cited by 4 | PDF Full-text (274 KB) | HTML Full-text | XML Full-text
Abstract
Microalgae and cyanobacteria represent a valuable natural resource for the generation of a large variety of chemical substances that are of interest for medical research, can be used as additives in cosmetics and food production, or as an energy source in biogas [...] Read more.
Microalgae and cyanobacteria represent a valuable natural resource for the generation of a large variety of chemical substances that are of interest for medical research, can be used as additives in cosmetics and food production, or as an energy source in biogas plants. The variety of potential agents and the use of microalgae and cyanobacteria biomass for the production of these substances are little investigated and not exploited for the market. Due to the enormous biodiversity of microalgae and cyanobacteria, they hold great promise for novel products. In this study, we investigated a large number of microalgal and cyanobacterial strains from the Culture Collection of Algae at Göttingen University (SAG) with regard to their biomass and biogas production, as well antibacterial and antifungal effects. Our results demonstrated that microalgae and cyanobacteria are able to generate a large number of economically-interesting substances in different quantities dependent on strain type. The distribution and quantity of some of these components were found to reflect phylogenetic relationships at the level of classes. In addition, between closely related species and even among multiple isolates of the same species, the productivity may be rather variable. Full article
Open AccessArticle Contrasting Strategies of Photosynthetic Energy Utilization Drive Lifestyle Strategies in Ecologically Important Picoeukaryotes
Metabolites 2014, 4(2), 260-280; doi:10.3390/metabo4020260
Received: 20 February 2014 / Revised: 9 April 2014 / Accepted: 23 April 2014 / Published: 29 April 2014
Cited by 5 | PDF Full-text (479 KB) | HTML Full-text | XML Full-text
Abstract
The efficiency with which absorbed light is converted to net growth is a key property for estimating global carbon production. We previously showed that, despite considerable evolutionary distance, Dunaliella tertiolecta (Chlorophyceae) and Thalassiosira weissflogii (Bacillariophyceae) share a common strategy of photosynthetic energy [...] Read more.
The efficiency with which absorbed light is converted to net growth is a key property for estimating global carbon production. We previously showed that, despite considerable evolutionary distance, Dunaliella tertiolecta (Chlorophyceae) and Thalassiosira weissflogii (Bacillariophyceae) share a common strategy of photosynthetic energy utilization and nearly identical light energy conversion efficiencies. These findings suggested that a single model might be appropriate for describing relationships between measures of phytoplankton production. This conclusion was further evaluated for Ostreococcus tauri RCC1558 and Micromonas pusilla RCC299 (Chlorophyta, Prasinophyceae), two picoeukaryotes with contrasting geographic distributions and swimming abilities. Nutrient-dependent photosynthetic efficiencies in O. tauri were similar to the previously studied larger algae. Specifically, absorption-normalized gross oxygen and carbon production and net carbon production were independent of nutrient limited growth rate. In contrast, all measures of photosynthetic efficiency were strongly dependent on nutrient availability in M. pusilla. This marked difference was accompanied by a diminished relationship between Chla:C and nutrient limited growth rate and a remarkably greater efficiency of gross-to-net energy conversion than the other organisms studied. These results suggest that the cost-benefit of decoupling pigment concentration from nutrient availability enables motile organisms to rapidly exploit more frequent encounters with micro-scale nutrient patches in open ocean environments. Full article
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Open AccessArticle Effects of Inorganic Carbon Limitation on the Metabolome of the Synechocystis sp. PCC 6803 Mutant Defective in glnB Encoding the Central Regulator PII of Cyanobacterial C/N Acclimation
Metabolites 2014, 4(2), 232-247; doi:10.3390/metabo4020232
Received: 27 February 2014 / Revised: 14 April 2014 / Accepted: 16 April 2014 / Published: 22 April 2014
Cited by 6 | PDF Full-text (993 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Non-diazotrophic strains such as the model Synechocystis sp. PCC 6803 depend on a balanced uptake and assimilation of inorganic carbon and nitrogen sources. The internal C/N ratio is sensed via the PII protein (GlnB). [...] Read more.
Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Non-diazotrophic strains such as the model Synechocystis sp. PCC 6803 depend on a balanced uptake and assimilation of inorganic carbon and nitrogen sources. The internal C/N ratio is sensed via the PII protein (GlnB). We analyzed metabolic changes of the DglnB mutant of Synechocystis sp. PCC 6803 under different CO2 availability. The identified metabolites provided a snapshot of the central C/N metabolism. Cells of the DglnB mutant shifted to carbon-limiting conditions, i.e. a decreased C/N ratio, showed changes in intermediates of the sugar storage and particularly of the tricarboxylic acid cycle, arginine, and glutamate metabolism. The changes of the metabolome support the notion that the PII protein is primarily regulating the N-metabolism whereas the changes in C-metabolism are probably secondary effects of the PII deletion. Full article
Open AccessReview Rationales and Approaches for Studying Metabolism in Eukaryotic Microalgae
Metabolites 2014, 4(2), 184-217; doi:10.3390/metabo4020184
Received: 7 February 2014 / Revised: 23 March 2014 / Accepted: 25 March 2014 / Published: 11 April 2014
Cited by 6 | PDF Full-text (890 KB) | HTML Full-text | XML Full-text
Abstract
The generation of efficient production strains is essential for the use of eukaryotic microalgae for biofuel production. Systems biology approaches including metabolite profiling on promising microalgal strains, will provide a better understanding of their metabolic networks, which is crucial for metabolic engineering [...] Read more.
The generation of efficient production strains is essential for the use of eukaryotic microalgae for biofuel production. Systems biology approaches including metabolite profiling on promising microalgal strains, will provide a better understanding of their metabolic networks, which is crucial for metabolic engineering efforts. Chlamydomonas reinhardtii represents a suited model system for this purpose. We give an overview to genetically amenable microalgal strains with the potential for biofuel production and provide a critical review of currently used protocols for metabolite profiling on Chlamydomonas. We provide our own experimental data to underpin the validity of the conclusions drawn. Full article

2013

Jump to: 2015, 2014

Open AccessReview Multiple Roles of Photosynthetic and Sunscreen Pigments in Cyanobacteria Focusing on the Oxidative Stress
Metabolites 2013, 3(2), 463-483; doi:10.3390/metabo3020463
Received: 8 February 2013 / Revised: 7 May 2013 / Accepted: 22 May 2013 / Published: 30 May 2013
Cited by 11 | PDF Full-text (306 KB) | HTML Full-text | XML Full-text
Abstract
Cyanobacteria have two types of sunscreen pigments, scytonemin and mycosporine-like amino acids (MAAs). These secondary metabolites are thought to play multiple roles against several environmental stresses such as UV radiation and desiccation. Not only the large molar absorption coefficients of these sunscreen [...] Read more.
Cyanobacteria have two types of sunscreen pigments, scytonemin and mycosporine-like amino acids (MAAs). These secondary metabolites are thought to play multiple roles against several environmental stresses such as UV radiation and desiccation. Not only the large molar absorption coefficients of these sunscreen pigments, but also their antioxidative properties may be necessary for the protection of biological molecules against the oxidative damages induced by UV radiation. The antioxidant activity and vitrification property of these pigments are thought to be requisite for the desiccation and rehydration processes in anhydrobiotes. In this review, the multiple roles of photosynthetic pigments and sunscreen pigments on stress resistance, especially from the viewpoint of their structures, biosynthetic pathway, and in vitro studies of their antioxidant activity, will be discussed. Full article
Open AccessReview The Central Carbon and Energy Metabolism of Marine Diatoms
Metabolites 2013, 3(2), 325-346; doi:10.3390/metabo3020325
Received: 4 March 2013 / Revised: 25 April 2013 / Accepted: 25 April 2013 / Published: 7 May 2013
Cited by 10 | PDF Full-text (732 KB) | HTML Full-text | XML Full-text
Abstract
Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic [...] Read more.
Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved. Full article
Open AccessReview Amino Acid Biosynthesis Pathways in Diatoms
Metabolites 2013, 3(2), 294-311; doi:10.3390/metabo3020294
Received: 14 January 2013 / Revised: 4 April 2013 / Accepted: 8 April 2013 / Published: 18 April 2013
Cited by 4 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Amino acids are not only building blocks for proteins but serve as precursors for the synthesis of many metabolites with multiple functions in growth and other biological processes of a living organism. The biosynthesis of amino acids is tightly connected with central [...] Read more.
Amino acids are not only building blocks for proteins but serve as precursors for the synthesis of many metabolites with multiple functions in growth and other biological processes of a living organism. The biosynthesis of amino acids is tightly connected with central carbon, nitrogen and sulfur metabolism. Recent publication of genome sequences for two diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum created an opportunity for extensive studies on the structure of these metabolic pathways. Based on sequence homology found in the analyzed diatomal genes, the biosynthesis of amino acids in diatoms seems to be similar to higher plants. However, one of the most striking differences between the pathways in plants and in diatomas is that the latter possess and utilize the urea cycle. It serves as an important anaplerotic pathway for carbon fixation into amino acids and other N-containing compounds, which are essential for diatom growth and contribute to their high productivity. Full article
Open AccessArticle Gas-Chromatography Mass-Spectrometry (GC-MS) Based Metabolite Profiling Reveals Mannitol as a Major Storage Carbohydrate in the Coccolithophorid Alga Emiliania huxleyi
Metabolites 2013, 3(1), 168-184; doi:10.3390/metabo3010168
Received: 1 February 2013 / Revised: 1 March 2013 / Accepted: 1 March 2013 / Published: 11 March 2013
Cited by 6 | PDF Full-text (372 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Algae are divergent organisms having a wide variety of evolutional histories. Although most of them share photosynthetic activity, their pathways of primary carbon metabolism are rather diverse among species. Here we developed a method for gas chromatography-mass spectroscopy (GC-MS) based metabolite profiling [...] Read more.
Algae are divergent organisms having a wide variety of evolutional histories. Although most of them share photosynthetic activity, their pathways of primary carbon metabolism are rather diverse among species. Here we developed a method for gas chromatography-mass spectroscopy (GC-MS) based metabolite profiling for the coccolithophorid alga Emiliania huxleyi, which is one of the most abundant microalgae in the ocean, in order to gain an overview of the pathway of primary metabolism within this alga. Following method optimization, twenty-six metabolites could be detected by this method. Whilst most proteogenic amino acids were detected, no peaks corresponding to malate and fumarate were found. The metabolite profile of E. huxleyi was, however, characterized by a prominent accumulation of mannitol reaching in excess of 14 nmol 106 cells−1. Similarly, the accumulation of the 13C label during short term H13CO3 feeding revealed a massive redistribution of label into mannitol as well as rapid but saturating label accumulation into glucose and several amino acids including aspartate, glycine and serine. These results provide support to previous work suggesting that this species adopts C3 photosynthesis and that mannitol functions as a carbon store in E. huxleyi. Full article
Open AccessArticle Isolation and Expression of a cDNA Encoding Methylmalonic Aciduria Type A Protein from Euglena gracilis Z
Metabolites 2013, 3(1), 144-154; doi:10.3390/metabo3010144
Received: 27 December 2012 / Revised: 6 February 2013 / Accepted: 7 February 2013 / Published: 18 February 2013
PDF Full-text (487 KB) | HTML Full-text | XML Full-text
Abstract
In animals, cobalamin (Cbl) is a cofactor for methionine synthase and methylmalonyl-CoA mutase (MCM), which utilizes methylcobalamin and 5′-deoxyadenosylcobalamin (AdoCbl), respectively. The cblA complementation class of inborn errors of Cbl metabolism in humans is one of three known disorders that affect AdoCbl [...] Read more.
In animals, cobalamin (Cbl) is a cofactor for methionine synthase and methylmalonyl-CoA mutase (MCM), which utilizes methylcobalamin and 5′-deoxyadenosylcobalamin (AdoCbl), respectively. The cblA complementation class of inborn errors of Cbl metabolism in humans is one of three known disorders that affect AdoCbl synthesis. The gene responsible for cblA has been identified in humans (MMAA) as well as its homolog (meaB) in Methylobacterium extorquens. Recently, it has been reported that human MMAA plays an important role in the protection and reactivation of MCM in vitro. However, the physiological function of MMAA is largely unknown. In the present study, we isolated the cDNA encoding MMAA from Euglena gracilis Z, a photosynthetic flagellate. The deduced amino acid sequence of the cDNA shows 79%, 79%, 79% and 80% similarity to human, mouse, Danio rerio MMAAs and M. extorquens MeaB, respectively. The level of the MCM transcript was higher in Cbl-deficient cultures of E. gracilis than in those supplemented with Cbl. In contrast, no significant differences were observed in the levels of the MMAA transcript under the same two conditions. No significant difference in MCM activity was observed between Escherichia coli that expressed either MCM together with MMAA or expressed MCM alone. Full article
Open AccessArticle Metabolic Changes in Synechocystis PCC6803 upon Nitrogen-Starvation: Excess NADPH Sustains Polyhydroxybutyrate Accumulation
Metabolites 2013, 3(1), 101-118; doi:10.3390/metabo3010101
Received: 20 December 2012 / Revised: 28 January 2013 / Accepted: 30 January 2013 / Published: 6 February 2013
Cited by 13 | PDF Full-text (568 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Polyhydroxybutyrate (PHB) is a common carbon storage polymer among heterotrophic bacteria. It is also accumulated in some photoautotrophic cyanobacteria; however, the knowledge of how PHB accumulation is regulated in this group is limited. PHB synthesis in Synechocystis sp. PCC 6803 is [...] Read more.
Polyhydroxybutyrate (PHB) is a common carbon storage polymer among heterotrophic bacteria. It is also accumulated in some photoautotrophic cyanobacteria; however, the knowledge of how PHB accumulation is regulated in this group is limited. PHB synthesis in Synechocystis sp. PCC 6803 is initiated once macronutrients like phosphorus or nitrogen are limiting. We have previously reported a mutation in the gene sll0783 that impairs PHB accumulation in this cyanobacterium upon nitrogen starvation. In this study we present data which explain the observed phenotype. We investigated differences in intracellular localization of PHB synthase, metabolism, and the NADPH pool between wild type and mutant. Localization of PHB synthase was not impaired in the sll0783 mutant; however, metabolome analysis revealed a difference in sorbitol levels, indicating a more oxidizing intracellular environment than in the wild type. We confirmed this by directly measuring the NADPH/NADP ratio and by altering the intracellular redox state of wild type and sll0783 mutant. We were able to physiologically complement the mutant phenotype of diminished PHB synthase activity by making the intracellular environment more reducing. Our data illustrate that the NADPH pool is an important factor for regulation of PHB biosynthesis and metabolism, which is also of interest for potential biotechnological applications. Full article
Open AccessReview Recent Applications of Metabolomics Toward Cyanobacteria
Metabolites 2013, 3(1), 72-100; doi:10.3390/metabo3010072
Received: 20 December 2012 / Revised: 23 January 2013 / Accepted: 23 January 2013 / Published: 4 February 2013
Cited by 19 | PDF Full-text (1291 KB) | HTML Full-text | XML Full-text
Abstract
Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the “omics” techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror [...] Read more.
Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the “omics” techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror cellular metabolism and its flexibility under diverse conditions. Traditionally, small sets of metabolites are quantified in targeted metabolome approaches. The development of separation technologies coupled to mass-spectroscopy- or nuclear-magnetic-resonance-based identification of low molecular mass molecules presently allows the profiling of hundreds of metabolites of diverse chemical nature. Metabolome analysis was applied to characterize changes in the cyanobacterial primary metabolism under diverse environmental conditions or in defined mutants. The resulting lists of metabolites and their steady state concentrations in combination with transcriptomics can be used in system biology approaches. The application of stable isotopes in fluxomics, i.e. the quantitative estimation of carbon and nitrogen fluxes through the biochemical network, has only rarely been applied to cyanobacteria, but particularly this technique will allow the making of kinetic models of cyanobacterial systems. The further application of metabolomics in the concert of other “omics” technologies will not only broaden our knowledge, but will also certainly strengthen the base for the biotechnological application of cyanobacteria. Full article

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

 

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