Effect of glucose on assimilatory sulphate reduction in Arabidopsis thaliana roots

With the aim of analysing the relative importance of sugar supply and nitrogen nutrition for the regulation of sulphate assimilation, the regulation of adenosine 5′‐phosphosulphate reductase (APR), a key enzyme of sulphate reduction in plants, was studied. Glucose feeding experiments with Arabidopsis thaliana cultivated with and without a nitrogen source were performed. After a 38 h dark period, APR mRNA, protein, and enzymatic activity levels decreased dramatically in roots. The addition of 0.5% (w/v) glucose to the culture medium resulted in an increase of APR levels in roots (mRNA, protein and activity), comparable to those of plants kept under normal light conditions. Treatment of roots with D‐sorbitol or D‐mannitol did not increase APR activity, indicating that osmotic stress was not involved in APR regulation. The addition of O‐acetyl‐L‐serine (OAS) also quickly and transiently increased APR levels (mRNA, protein, and activity). Feeding plants with a combination of glucose and OAS resulted in a more than additive induction of APR activity. Contrary to nitrate reductase, APR was also increased by glucose in N‐deficient plants, indicating that this effect was independent of nitrate assimilation. [35S]‐sulphate feeding experiments showed that the addition of glucose to dark‐treated roots resulted in an increased incorporation of [35S] into thiols and proteins, which corresponded to the increased levels of APR activity. Under N‐deficient conditions, glucose also increased thiol labelling, but did not increase the incorporation of label into proteins. These results demonstrate that (i) exogenously supplied glucose can replace the function of photoassimilates in roots; (ii) APR is subject to co‐ordinated metabolic control by carbon metabolism; (iii) positive sugar signalling overrides negative signalling from nitrate assimilation in APR regulation. Furthermore, signals originating from nitrogen and carbon metabolism regulate APR synergistically.

Life-long growth of Quercus ilex L. at natural CO2 springs acclimates sulphur, nitrogen and carbohydrate metabolism of the progeny to elevated pCO2

The aim of the present study was to analyse whether offspring of mature Quercus ilex trees grown under life-long elevated pCO2 show alterations in the physiological response to elevated pCO2 in comparison with those originating from mature trees grown at current ambient pCO2. To investigate changes in C- (for changes in photosynthesis, biomass and lignin see Polle, McKee & Blaschke Plant, Cell and Environment 24, 1075–1083, 2001), N-, and S-metabolism soluble sugar, soluble non-proteinogenic nitrogen compounds (TSNN), nitrate reductase (NR), thiols, adenosine 5′-phosphosulphate (APS) reductase, and anions were analysed. For this purpose Q. ilex seedlings were grown from acorns of mother tree stands at a natural spring site (elevated pCO2) and a control site (ambient pCO2) of the Laiatico spring, Central Italy. Short-term elevated pCO2 exposure of the offspring of control oaks lead to higher sugar contents in stem tissues, to a reduced TSNN content in leaves, and basipetal stem tissues, to diminished thiol contents in all tissues analysed, and to reduced APS reductase activity in both, leaves and roots. Most of the components of C-, N- and S-metabolism including APS reductase activity which were reduced due to short-term elevated pCO2 exposure were recovered by life-long growth under elevated pCO2 in the offspring of spring oaks. Still TSNN contents in phloem exudates increased, nitrate contents in lateral roots and glutathione in leaves and phloem exudates remained reduced in these plants. The present results demonstrated that metabolic adaptations of Q. ilex mother trees to elevated pCO2 can be passed to the next generation. Short- and long-term effects on source-to-sink relation and physiological and genetic acclimation to elevated pCO2 are discussed.

PREPARATION AND CHARACTERIZATION OF FAD DEPENDENT NADPH CYTOCHROME P-450 REDUCTASE (FLAVOPROTEINS, APOFLAVOPROTEIN)

NADPH cytochrome P-450 reductase releases FMN and FAD upon dilution into slightly acidic potassium bromide. The flavins are released with positive cooperativity. Dithiothreitol protects the FAD dependent cytochrome c reductase activity against inactivation by free radicals. Behavior in potassium bromide is sensitive to changes in the pH. High performance hydroxylapatite resolved the FAD dependent reductase from holoreductase. For 96% FAD dependent reductase, the overall yield was 12%.^ High FAD dependence was matched by a low FAD content, with FAD/FMN as low as 0.015. There were three molecules of FMN for every four molecules of reductase. The aporeductase had negligible activity towards cytochrome c, ferricyanide, menadione, dichlorophenolindophenol, nitro blue tetrazolium, oxygen and acetyl pyridine adenine dinucleotide phosphate. A four minute incubation in FAD reconstituted one half to all of the specific activity, per milligram protein, of untreated reductase, depending upon the substrate. After a two hour reconstitution, the reductase eluted from hydroxylapatite at the location of holoreductase. It had little flavin dependence, was equimolar in FMN and FAD, and had nearly the specific activity (per mole flavin) of untreated reductase.^ The lack of activity and the ability of FMN to also reconstitute suggest that the redox center of FAD is essential for catalysis, rather than for structure. Dependence upon FAD is consistent with existing hypotheses for the catalytic cycle of the reductase. ^

In situ conversion of protochlorophyllide b to protochlorophyllide a in barley. Evidence for a novel role of 7-formyl reductase in the prolamellar body of etioplasts

We recently put forth a model of a protochlorophyllide (Pchlide) light-harvesting complex operative during angiosperm seedling de-etiolation (Reinbothe, C., Lebedev, N., and Reinbothe, S. (1999) Nature 397, 80–84). This model, which was based on in vitro reconstitution experiments with zinc analogs of Pchlide a and Pchlide b and the two NADPH:protochlorophyllide oxidoreductases (PORs), PORA and PORB, of barley, predicted a 5-fold excess of Pchlide b, relative to Pchlide a, in the prolamellar body of etioplasts. Recent work (Scheumann, V., Klement, H., Helfrich, M., Oster, U., Schoch, S., and Rüdiger, W. (1999) FEBS Lett. 445, 445–448), however, contradicted this model and reported that Pchlide b would not be present in etiolated plants. Here we demonstrate that Pchlide b is an abundant pigment in barley etioplasts but is rather metabolically unstable. It is rapidly converted to Pchlide a by virtue of 7-formyl reductase activity, an enzyme that had previously been implicated in the chlorophyll (Chl) b to Chl a reaction cycle. Our findings suggest that etiolated plants make use of 7-formyl reductase to fine tune the levels of Pchlide b and Pchlidea and thereby may regulate the steady-state level of light-harvesting POR-Pchlide comple

Biogeochemical indicators of elevated nitrogen deposition in semiarid Mediterranean ecosystems

Nitrogen (N) deposition has doubled the natural N inputs received by ecosystems through biological N fixation and is currently a global problem that is affecting the Mediterranean regions. We evaluated the existing relationships between increased atmospheric N deposition and biogeochemical indicators related to soil chemical factors and cryptogam species across semiarid central, southern, and eastern Spain. The cryptogam species studied were the biocrust-forming species Pleurochaete squarrosa (moss) and Cladonia foliacea (lichen). Sampling sites were chosen in Quercus coccifera (kermes oak) shrublands and Pinus halepensis (Aleppo pine) forests to cover a range of inorganic N deposition representative of the levels found in the Iberian Peninsula (between 4.4 and 8.1 kg N ha(-1) year(-1)). We extended the ambient N deposition gradient by including experimental plots to which N had been added for 3 years at rates of 10, 20, and 50 kg N ha(-1) year(-1). Overall, N deposition (extant plus simulated) increased soil inorganic N availability and caused soil acidification. Nitrogen deposition increased phosphomonoesterase (PME) enzyme activity and PME/nitrate reductase (NR) ratio in both species, whereas the NR activity was reduced only in the moss. Responses of PME and NR activities were attributed to an induced N to phosphorus imbalance and to N saturation, respectively. When only considering the ambient N deposition, soil organic C and N contents were positively related to N deposition, a response driven by pine forests. The PME/NR ratios of the moss were better predictors of N deposition rates than PME or NR activities alone in shrublands, whereas no correlation between N deposition and the lichen physiology was observed. We conclude that integrative physiological measurements, such as PME/NR ratios, measured on sensitive species such as P. squarrosa, can provide useful data for national-scale biomonitoring programs, whereas soil acidification and soil C and N storage could be useful as additional corroborating ecosystem indicators of chronic N pollution.

Sulfate reduction in higher plants: Molecular evidence for a novel 5′-adenylylsulfate reductase

Sulfate-assimilating organisms reduce inorganic sulfate for Cys biosynthesis. There are two leading hypotheses for the mechanism of sulfate reduction in higher plants. In one, adenosine 5′-phosphosulfate (APS) (5′-adenylylsulfate) sulfotransferase carries out reductive transfer of sulfate from APS to reduced glutathione. Alternatively, the mechanism may be similar to that in bacteria in which the enzyme, 3′-phosphoadenosine-5′-phosphosulfate (PAPS) reductase, catalyzes thioredoxin (Trx)-dependent reduction of PAPS. Three classes of cDNA were cloned from Arabidopsis thaliana termed APR1, -2, and -3, that functionally complement a cysH, PAPS reductase mutant strain of Escherichia coli. The coding sequence of the APR clones is homologous with PAPS reductases from microorganisms. In addition, a carboxyl-terminal domain is homologous with members of the Trx superfamily. Further genetic analysis showed that the APR clones can functionally complement a mutant strain of E. coli lacking Trx, and an APS kinase, cysC. mutant. These results suggest that the APR enzyme may be a Trx-independent APS reductase. Cell extracts of E. coli expressing APR showed Trx-independent sulfonucleotide reductase activity with a preference for APS over PAPS as a substrate. APR-mediated APS reduction is dependent on dithiothreitol, has a pH optimum of 8.5, is stimulated by high ionic strength, and is sensitive to inactivation by 5′-adenosinemonophosphate (5′-AMP). 2′-AMP, or 3′-phosphoadenosine-5′-phosphate (PAP), a competitive inhibitor of PAPS reductase, do not affect activity. The APR enzymes may be localized in different cellular compartments as evidenced by the presence of an amino-terminal transit peptide for plastid localization in APR1 and APR3 but not APR2. Southern blot analysis confirmed that the APR clones are members of a small gene family, possibly consisting of three members.

Liz1p, a Novel Fission Yeast Membrane Protein, Is Required for Normal Cell Division When Ribonucleotide Reductase Is Inhibited

Ribonucleotide reductase activity is required for generating deoxyribonucleotides for DNA replication. Schizosaccharomyces pombe cells lacking ribonucleotide reductase activity arrest during S phase of the cell cycle. In a screen for hydroxyurea-sensitive mutants in S. pombe, we have identified a gene, liz1+, which when mutated reveals an additional, previously undescribed role for ribonucleotide reductase activity during mitosis. Inactivation of ribonucleotide reductase, by either hydroxyurea or a cdc22-M45 mutation, causes liz1− cells in G2 to undergo an aberrant mitosis, resulting in chromosome missegregation and late mitotic arrest. liz1+ encodes a 514-amino acid protein with strong similarity to a family of transmembrane transporters, and localizes to the plasma membrane of the cell. These results reveal an unexpected G2/M function of ribonucleotide reductase and establish that defects in a transmembrane protein can affect cell cycle progression.

Dual pathways for regulation of root branching by nitrate

Root development is extremely sensitive to variations in nutrient supply, but the mechanisms are poorly understood. We have investigated the processes by which nitrate (NO3−), depending on its availability and distribution, can have both positive and negative effects on the development and growth of lateral roots. When Arabidopsis roots were exposed to a locally concentrated supply of NO3− there was no increase in lateral root numbers within the NO3−-rich zone, but there was a localized 2-fold increase in the mean rate of lateral root elongation, which was attributable to a corresponding increase in the rate of cell production in the lateral root meristem. Localized applications of other N sources did not stimulate lateral root elongation, consistent with previous evidence that the NO3− ion is acting as a signal rather than a nutrient. The axr4 auxin-resistant mutant was insensitive to the stimulatory effect of NO3−, suggesting an overlap between the NO3− and auxin response pathways. High rates of NO3− supply to the roots had a systemic inhibitory effect on lateral root development that acted specifically at the stage when the laterals had just emerged from the primary root, apparently delaying final activation of the lateral root meristem. A nitrate reductase-deficient mutant showed increased sensitivity to this systemic inhibitory effect, suggesting that tissue NO3− levels may play a role in generating the inhibitory signal. We present a model in which root branching is modulated by opposing signals from the plant’s internal N status and the external supply of NO3−.

The nitrite reductase from Pseudomonas aeruginosa: Essential role of two active-site histidines in the catalytic and structural properties

Cd1 nitrite reductase catalyzes the conversion of nitrite to NO in denitrifying bacteria. Reduction of the substrate occurs at the d1-heme site, which faces on the distal side some residues thought to be essential for substrate binding and catalysis. We report the results obtained by mutating to Ala the two invariant active site histidines, His-327 and His-369, of the enzyme from Pseudomonas aeruginosa. Both mutants have lost nitrite reductase activity but maintain the ability to reduce O2 to water. Nitrite reductase activity is impaired because of the accumulation of a catalytically inactive form, possibly because the productive displacement of NO from the ferric d1-heme iron is impaired. Moreover, the two distal His play different roles in catalysis; His-369 is absolutely essential for the stability of the Michaelis complex. The structures of both mutants show (i) the new side chain in the active site, (ii) a loss of density of Tyr-10, which slipped away with the N-terminal arm, and (iii) a large topological change in the whole c-heme domain, which is displaced 20 Å from the position occupied in the wild-type enzyme. We conclude that the two invariant His play a crucial role in the activity and the structural organization of cd1 nitrite reductase from P. aeruginosa.

Disponibilidade de níquel no sistema solo-planta: efeito de doses e saturações por bases

Por se tratar de um elemento essencial às plantas e um metal pesado ao mesmo tempo, o níquel requer atenção quanto aos aspectos da fisiologia de plantas e ambiental. Além disso, existe um intervalo estreito entre as exigências nutricionais e os teores tóxicos às plantas. Neste contexto, objetivou-se avaliar o efeito do Ni no sistema solo-planta, com foco no ciclo do N e a disponibilidade do elemento no solo, por meio de experimento em condições controladas, utilizando vasos distribuídos inteiramente ao acaso, utilizando-se esquema fatorial 2 x 5, com sete repetições cada tratamento. O primeiro fator foi constituído de duas saturações por base (50 e 70%) e o segundo de cinco doses de Ni (0; 0,1; 0,5; 1,0 e 10,0 mg dm-3 de solo). Os vasos foram preenchidos com 8 dm3 de terra e cultivados com soja [Glycine max (L.) Merrill] sucedida por girassol (Helianthus annuus L.). Os parâmetros qualitativos e quantitativos: altura de plantas (AP), diâmetro do caule (DC), número de nós (NN), estádio fenológico (EF), índice SPAD e, diâmetro do capítulo (DCap) (para girassol) foram avaliadas aos 30 e 60 dias após a emergência (d.a.e.) de cada cultivo. Plantas inteiras de soja, amostradas em quatro vasos de cada tratamento, foram coletadas no estádio R1. Na mesma ocasião foram coletadas amostras de solo da rizosfera. Em seguida, as plantas coletadas foram divididas em: folhas; raízes (nódulos na soja) e parte aérea. Foram determinados nas folhas utilizadas para diagnose em soja e girassol: os teores de macro e micronutrientes, as atividades da redutase do nitrato e da urease e as concentrações dos ácidos orgânicos: oxálico, malônico, succínico, málico, tartárico, fumárico, oxaloacético, cítrico e lático. Os mesmos ácidos orgânicos foram determinados em raízes secundárias de girassol e nódulos de soja. Foram realizadas avaliações ultraestruturais por meio de microscopia eletrônica de transmissão (MET) em raízes de girassol, e estruturais e de tonalidade em nódulos de soja, por meio de microscopia de luz. No solo, foram determinadas: atividade urease, desidrogenase, Ni total e fitodisponível pelos métodos: Mehlich-1, Mehlich-3 e DTPA. No período de maturidade fisiológica de cada cultura foi realizada a colheita das plantas dos vasos restantes para determinação de produção de grãos, teores de Ni na planta inteira e Ni e N nos grãos. Ao final dos dois experimentos foi realizada nova coleta de solo para extração sequencial de Ni. O índice SPAD em soja aos 60 d.a.e., a produção de massa seca da parte aérea da soja e da raiz de girassol foram influenciados pela saturação por bases, doses de níquel e pela a interação destes. Foram influenciados pelas saturações por base e doses de níquel (fatores isolados): para soja: AP aos 60 d.a.e., NN aos 30 e 60 d.a.e., SPAD aos 30 d.a.e.; para girassol: AP e NN aos 30 e 60 d.a.e., DC e SPAD aos 30 d.a.e. As demais variáveis avaliadas aos 30 e 60 d.a.e. foram influenciadas apenas pela saturação por bases, ou doses de Ni separadamente. As plantas de soja e girassol apresentaram maiores teores de Ni nos diferentes tecidos avaliados (exceto grãos) quando cultivadas sob V50%. A produção de grãos de soja e girassol não foi influenciada pelos tratamentos, porém o teor de N dos grãos de soja influenciado pelas doses de Ni na V70%. A atividade da enzima urease nas folhas de soja e girassol foi responsiva positivamente ao aumento das doses de Ni. Quatro dos ácidos orgânicos avaliados e o teor de N nas folhas e nos grãos foram maiores nas plantas cultivadas sob V70% com a dose de 0,5 mg dm-3 de Ni. As doses de Ni bem com as saturações por bases influenciaram diretamente o balanço de nutrientes das plantas. Os extratores Mehlich-1, Mehlich-3 e DTPA apresentaram elevado coefienciente de correlação entre a fração de Ni disponível no solo e a concentração do elemento nas plantas de soja e girassol, sendo o extrator DTPA o que apresentou maior coeficiente de correlação. O Ni apresentou distribuição variável entre as diferentes frações do solo em função dos tratamentos. Os solos dos tratamentos com saturação por bases de 70% apresentaram maior concentração de Ni ligado a carbonato, comparado aos tratamentos sob saturação por bases de 50%. A distribuição do Ni entre as frações do solo seguiu a seguinte orgem: ligado a carbonato < trocável < ligado a óxidos < matéria orgânica < residual. A saturação por bases exerceu efeito diferenciado para a atividade da urease no solo em função da cultura avaliada. Por sua vez, o Ni exerceu efeito diferenciado sobre a atividade de desidrogenase em função da cultura estudada

Effects of nitrogen sources on the nitrate assimilation in Haloferax mediterranei: growth kinetics and transcriptomic analysis

The haloarchaeon Haloferax mediterranei is able to grow in a defined culture media not only in the presence of inorganic nitrogen salt but also with amino acid as the sole nitrogen source. Assimilatory nitrate and nitrite reductases, respectively, catalyze the first and second reactions. The genes involved in this process are nasA, which encodes nitrate reductase and is found within the operon nasABC, and nasD, which encodes nitrite reductase. These genes are subjected to transcriptional regulation, being repressed in the presence of ammonium and induced with either nitrate or nitrite. This type of regulation has also been described when the amino acids are used as nitrogen source in the minimal media. Furthermore, it has been observed that the microorganism growth depends on nitrogen source, obtaining the lowest growth rate in the presence of nitrate and aspartate. In this paper, we present the results of a comparative study of microorganism growth and transcriptomic analysis of the operon nasABC and gene nasD in different nitrogen sources. The results are the first ever produced in relation to amino acids as nitrogen sources within the Halobacteriaceae family.

Characterisation of chlorate reduction in the haloarchaeon Haloferax mediterranei

Background: Haloferax mediterranei is a denitrifying haloarchaeon using nitrate as a respiratory electron acceptor under anaerobic conditions in a reaction catalysed by pNarGH. Other ions such as bromate, perchlorate and chlorate can also be reduced. Methods: Hfx. mediterranei cells were grown anaerobically with nitrate as electron acceptor and chlorate reductase activity measured in whole cells and purified nitrate reductase. Results: No genes encoding (per)chlorate reductases have been detected either in the Hfx. mediterranei genome or in other haloarchaea. However, a gene encoding a chlorite dismutase that is predicted to be exported across the cytoplasmic membrane has been identified in Hfx. mediterranei genome. Cells did not grow anaerobically in presence of chlorate as the unique electron acceptor. However, cells anaerobically grown with nitrate and then transferred to chlorate-containing growth medium can grow a few generations. Chlorate reduction by the whole cells, as well as by pure pNarGH, has been characterised. No clear chlorite dismutase activity could be detected. Conclusions: Hfx. mediterranei pNarGH has its active site on the outer-face of the cytoplasmic membrane and reacts with chlorate and perchlorate. Biochemical characterisation of this enzymatic activity suggests that Hfx. mediterranei or its pure pNarGH could be of great interest for waste water treatments or to better understand biological chlorate reduction in early Earth or Martian environments. General significance: Some archaea species reduce (per)chlorate. However, results here presented as well as those recently reported by Liebensteiner and co-workers [1] suggest that complete perchlorate reduction in archaea follows different rules in terms of biological reactions.

Effect after introducing Bacillus thuringiensis gene on nitrogen metabolism in cotton

Bacillus thuringiensis (Bt) transgenic cotton has shown changes of vegetative and reproductive growth characteristics. The objective of this study was to investigate the physiological change of nitrogen metabolism that related closely to the growth in Bt cotton cultivars. The study Was undertaken on two 131 transgenic cotton cultivars and their parents, one conventional (Xingyang822) and recurrent parent (Sumian No. 9), the other a hybrid (Kumian No. 1) and female parent (Yumian No. 1), during the 2001 and 2002 growing seasons at the Yangzhou University Farm, Yangzhou, China. In the 2001 study, The results indicated that the Bt cotton cultivars were higher than their parents in leaf total nitrogen, free amino acid and soluble protein content, greater in NR and GPT activity, and lower in protease activity, during peak square and boll developing period. The biggest increase of total nitrogen was at peak boll period, which increased by 36.01 and 18.96% for Kumian No. I and Xingyang822, respectively. There were similar results for free amino acid and soluble protein content. The results showed further in 2002 study that NR activity increased dramatically at peak square and early boll open period, the biggest increase at early boll open period, with Kumian No. I and Xingyan,822 being 87.5 and 61.4% higher than their parent, respectively, the biggest increase of GPT activity was at peak boll period, with Kumian No. I and Xingyang822 being 39.1 and 29.1% higher than their parent, respectively. However, protease activity of Bt cultivars reduced significantly before flowering and early boll open period, the biggest decrease was before flowering period, with Kumian No. I being more than 30%, Xingyang822 being 26.5% at peak square period. Moreover, the boll total nitrogen content reduced sharply. The results suggest that the Bt cotton cultivars have higher intensity of leaf nitrogen metabolism than their parent, especially during square and boll development period. It is disadvantage for square development and earlier boll maturity under high nitrogen condition. The cultural practice should aim at reducing leaf nitrogen metabolic strength and keep the balance of vegetative and reproductive growth. (C) 2003 Elsevier B.V. All rights reserved.

Dimethylsulfide dehydrogenase from rhodovulum sulfidophilum: EPR spectroscopy and biochemical analysis reveal its place in the DMSO reductase family of molybdenum enzymes

Dimethylsulfide (DMS) dehydrogenase catalyses the oxidation of DMS to dimethylsulfoxide. The purified enzyme has three subunits of Mr = 94, 38 and 32 kDa and has an optical spectrum dominated by a b-type cytochrome. The metal ion and nucleotide analysis revealed 0.5 g-atom Mo, 9.8 g-atom Fe and 1.96 mol GMP per tool of enzyme. Taken together, these data indicate that DMS dehydrogenase contains a bis(MGD)Mo cofactor. A comparison of the Nterminal amino acid sequence of DMS dehydrogenase revealed that the Mo-containing ct-subunit was most closely related to the c~-subunits of nitrate reductase (NarG) and selenate reductase (SerA). Similarly, the [~-subunit of DMS dehydrogenase was most closely related to the [3-subunits of nitrate reductase (NarH) and selenate reductase (SerB). Variable temperature X-band EPR spectra (120-2K) of 'as isolated' DMS dehydrogenase showed resonances arising from multiple redox centres, Mo(V), [3Fe-4S] +, [4Fe-4S] ÷. A pH dependent EPR study of the Mo(V) centre in lH20 and 2H20 reveals the presence of three Mo(V) species in equilibrium, Mo(V)-OH2, Mo(V)-X and Mo(V)-OH. Between pH6 and 8.2 the dominant species is Mo(V)-OH2 and Mo(V)-X is a minor component. X is probably the anion, chloride. Comparison of the rhombicity and anisotropy parameters for the Mo(V) species in DMS dehydrogenase with other Mo(V) centres in metalloproteins showed that it was most similar to the low pH nitrite spectrum of E. coli nitrate reductase (NarGHI). The spin Hamiltonian parameters (2.0158, 1.8870, 1.8620) for the [4Fe-4S] + cluster suggests the presence of histidine (N) coordination to iron in this cluster. It is suggested that this unusual [Fe-S] cluster may be associated with a histidine-cysteine rich sequence at the N-terminus of the ct-subunit of DMS dehydrogenase.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.