Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically

BackgroundWhen the filamentous cyanobacterium Anabaena variabilis grows aerobically without combined nitrogen, some vegetative cells differentiate into N2-fixing heterocysts, while the other vegetative cells perform photosynthesis. Microarrays of sequences within protein-encoding genes were probed with RNA purified from extracts of vegetative cells, from isolated heterocysts, and from whole filaments to investigate transcript levels, and carbon and energy metabolism, in vegetative cells and heterocysts in phototrophic, mixotrophic, and heterotrophic cultures.ResultsHeterocysts represent only 5% to 10% of cells in the filaments. Accordingly, levels of specific transcripts in vegetative cells were with few exceptions very close to those in whole filaments and, also with few exceptions (e.g., nif1 transcripts), levels of specific transcripts in heterocysts had little effect on the overall level of those transcripts in filaments. In phototrophic, mixotrophic, and heterotrophic growth conditions, respectively, 845, 649, and 846 genes showed more than 2-fold difference (p < 0.01) in transcript levels between vegetative cells and heterocysts. Principal component analysis showed that the culture conditions tested affected transcript patterns strongly in vegetative cells but much less in heterocysts. Transcript levels of the genes involved in phycobilisome assembly, photosynthesis, and CO2 assimilation were high in vegetative cells in phototrophic conditions, and decreased when fructose was provided. Our results suggest that Gln, Glu, Ser, Gly, Cys, Thr, and Pro can be actively produced in heterocysts. Whether other protein amino acids are synthesized in heterocysts is unclear. Two possible components of a sucrose transporter were identified that were upregulated in heterocysts in two growth conditions. We consider it likely that genes with unknown function represent a larger fraction of total transcripts in heterocysts than in vegetative cells across growth conditions.ConclusionsThis study provides the first comparison of transcript levels in heterocysts and vegetative cells from heterocyst-bearing filaments of Anabaena. Although the data presented do not give a complete picture of metabolism in either type of cell, they provide a metabolic scaffold on which to build future analyses of cell-specific processes and of the interactions of the two types of cells.

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title: Genetic Analysis of Cyanobacteria
abstract: In recent years great strides have been made in developing genetic systems for the analysis of various aspects of cyanobacterial physiology and development. Transformation, electroporation and conjugation systems provide effective means for gene transfer in diverse cyanobacterial strains. Gene transfer, combined with the ability to clone and inactivate genes in cyanobacteria, has opened the door to advanced studies of photosynthesis, nitrogen fixation, heterocyst development and metabolism in these unique and important procaryotic microorganisms.

title: Effect on Heterocyst Differentiation of Nitrogen Fixation in Vegetative Cells of the Cyanobacterium Anabaena variabilisATCC 29413
abstract: Heterocysts are terminally differentiated cells of some filamentous cyanobacteria that fix nitrogen for the entire filament under oxic growth conditions. Anabaena variabilis ATCC 29413 is unusual in that it has two Mo-dependent nitrogenases; one, called Nif1, functions in heterocysts, while the second, Nif2, functions under anoxic conditions in vegetative cells. Both nitrogenases depended on expression of the global regulatory protein NtcA. It has long been thought that a product of nitrogen fixation in heterocysts plays a role in maintenance of the spaced pattern of heterocyst differentiation. This model assumes that each cell in a filament senses its own environment in terms of nitrogen sufficiency and responds accordingly in terms of differentiation. Expression of the Nif2 nitrogenase under anoxic conditions in vegetative cells was sufficient to support long-term growth of a nif1 mutant; however, that expression did not prevent differentiation of heterocysts and expression of thenif1 nitrogenase in either the nif1 mutant or the wild-type strain. This suggested that the nitrogen sufficiency of individual cells in the filament did not affect the signal that induces heterocyst differentiation. Perhaps there is a global mechanism by which the filament senses nitrogen sufficiency or insufficiency based on the external availability of fixed nitrogen. The filament would then respond by producing heterocyst differentiation signals that affect the entire filament. This does not preclude cell-to-cell signaling in the maintenance of heterocyst pattern but suggests that overall control of the process is not controlled by nitrogen insufficiency of individual cells.

title: Heterocyst Metabolism and Development
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title: Cyanobacterial heterocysts: terminal pores proposed as sites of gas exchange.
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title: Formation of glutamine from (/sup 13/N)ammonia, (/sup 13/N)dinitrogen, and (/sup 14/C)glutamate by heterocysts isolated from Anabaena cylindrica
abstract: A method is described for the isolation of metabolically active heterocysts from Anabaena cylindrica. These isolated heterocysts accounted for up to 34% of the acetylene-reducing activity of whole filaments and had a specific activity of up to 1,560 nmol of C/sub 2/H/sub 4/ formed per mg of heterocyst chlorophyll per min. Activity of glutamine synthetase was coupled to activity of nitrogenase in isolated heterocysts as shown by acetylene-inhibitable formation of (/sup 13/N)NH/sub 3/ and of amide-labeled (/sup 13/N)glutamine from (/sup 13/N)N/sub 2/. A method is also described for the production of 6-mCi amounts of (/sup 13/N)NH/sub 3/. Isolated heterocysts formed (/sup 13/N)glutamine from (/sup 13/N)NH/sub 3/ and glutamate, and (/sup 14/C)glutamine from NH/sub 3/ and (/sup 14/C)glutamate, in the presence of magnesium adenosine 5'-triphosphate. Methionine sulfoximine strongly inhibited these syntheses. Glutamate synthase is, after nitrogenase and glutamine synthetase, the third sequential enzyme involved in the assimilation of N/sub 2/ by intact filaments. However, the kinetics of solubilization of the activity of glutamate synthase during cavitation of suspensions of A. cylindrica indicated that very little, if any, of the activity of that enzyme was located in heterocysts. Concordantly, isolated heterocysts failed to form substantial amounts of radioactive glutamate from either (/supmore » 13/N)glutamine or ..cap alpha..-(/sup 14/C)ketoglutarate in the presence of other substrates and cofactors of the glutamate synthase reaction. However, they formed (/sup 14/C)glutamate rapidly from ..cap alpha..-(/sup 14/C)ketoglutarate by aminotransferase reactions, with various amino acids as the nitrogen donor. The implications of these findings with regard to the identities of the substances moving between heterocysts and vegetative cells are discussed.« less

title: Inactivation of a Heterocyst-Specific Invertase Indicates a Principal Role of Sucrose Catabolism in Heterocysts of Anabaena sp
abstract: Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that carries out N2 fixation in specialized cells called heterocysts, which exchange nutrients and regulators with the filament's vegetative cells that perform the photosynthetic fixation of CO2. The Anabaena genome carries two genes coding for alkaline/neutral invertases, invA and invB. As shown by Northern analysis, both genes were expressed monocistronically and induced under nitrogen deprivation, although induction was stronger for invB than for invA. Whereas expression of an InvA-N-GFP fusion (green fluorescent protein [GFP] fused to the N terminus of the InvA protein [InvA-N]) was homogeneous along the cyanobacterial filament, consistent with the lack of dependence on HetR, expression of an InvB-N-GFP fusion upon combined nitrogen deprivation took place mainly in differentiating and mature heterocysts. In an hetR genetic background, the InvB-N-GFP fusion was strongly expressed all along the filament. An insertional mutant of invA could grow diazotrophically but was impaired in nifHDK induction and exhibited an increased frequency of heterocysts, suggesting a regulatory role of the invertase-mediated carbon flux in vegetative cells. In contrast, an invB mutant was strongly impaired in diazotrophic growth, showing a crucial role of sucrose catabolism mediated by the InvB invertase in the heterocysts.

title: Differential activities of heterocyst ferredoxin, vegetative cell ferredoxin, and flavodoxin as electron carriers in nitrogen fixation and photosynthesis in Anabaena sp.
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title: Ammonium assimilation in cyanobacteria
abstract: In cyanobacteria, after transport by specific permeases, ammonium is incorporated into carbon skeletons by the sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT). Two types of GS (GSI and GSIII) and two types of GOGAT (ferredoxin-GOGAT and NADH–GOGAT) have been characterized in cyanobacteria. The carbon skeleton substrate of the GS–GOGAT pathway is 2-oxoglutarate that is synthesized by the isocitrate dehydrogenase (IDH). In order to maintain the C–N balance and the amino acid pools homeostasis, ammonium assimilation is tightly regulated. The key regulatory point is the GS, which is controlled at transcriptional and posttranscriptional levels. The transcription factor NtcA plays a critical role regulating the expression of the GS and the IDH encoding genes. In the unicellular cyanobacterium Synechocystis sp. PCC 6803, NtcA controls also the expression of two small proteins (IF7 and IF17) that inhibit the activity of GS by direct protein–protein interaction. Cyanobacteria perceive nitrogen status by sensing the intracellular concentration of 2-oxoglutarate, a signaling metabolite that is able to modulate allosterically the function of NtcA, in vitro. In vivo, a functional dependence between NtcA and the signal transduction protein PII in controlling NtcA-dependent genes has been also shown.

title: The cell wall in heterocyst formation by Anabaena sp. PCC 7120
abstract: Filamentous cyanobacteria like Anabaena sp. PCC 7120 are able to develop a specialized cell type named heterocyst from vegetative cells in times of nitrogen starvation. Heterocyst development is controlled by the function of two master‐regulators, NtcA and HetR. This review focuses on the remodeling of the cell wall during transition from the vegetative cell to a heterocyst, including the formation of the heterocyst‐specific glycolipid layer and the heterocyst envelope polysaccharide layer. The functional assignment of genes involved therein, their genomic organization and their regulation are highlighted. Communication pathways and exchange routes for metabolites between heterocysts and vegetative cells are discussed. Further on, an overview of the heterocyst outer membrane proteome is given, together with possible functions of the identified proteins in the metabolism of heterocysts.

title: Cyanobacterial heterocysts.
abstract: Many multicellular cyanobacteria produce specialized nitrogen-fixing heterocysts. During diazotrophic growth of the model organism Anabaena (Nostoc) sp. strain PCC 7120, a regulated developmental pattern of single heterocysts separated by about 10 to 20 photosynthetic vegetative cells is maintained along filaments. Heterocyst structure and metabolic activity function together to accommodate the oxygen-sensitive process of nitrogen fixation. This article focuses on recent research on heterocyst development, including morphogenesis, transport of molecules between cells in a filament, differential gene expression, and pattern formation.

title: Compartmentalized function through cell differentiation in filamentous cyanobacteria
abstract: Within the wide biodiversity that is found in the bacterial world, Cyanobacteria represents a unique phylogenetic group that is responsible for a key metabolic process in the biosphere — oxygenic photosynthesis — and that includes representatives exhibiting complex morphologies. Many cyanobacteria are multicellular, growing as filaments of cells in which some cells can differentiate to carry out specialized functions. These differentiated cells include resistance and dispersal forms as well as a metabolically specialized form that is devoted to N2 fixation, known as the heterocyst. In this Review we address cyanobacterial intercellular communication, the supracellular structure of the cyanobacterial filament and the basic principles that govern the process of heterocyst differentiation.

title: Cellular differentiation in the cyanobacterium Nostoc punctiforme
abstract: Nostoc punctiforme is a phenotypically complex, filamentous, nitrogen-fixing cyanobacterium, whose vegetative cells can mature in four developmental directions. The particular developmental direction is determined by environmental signals. The vegetative cell cycle is maintained when nutrients are sufficient. Limitation for combined nitrogen induces the terminal differentiation of heterocysts, cells specialized for nitrogen fixation in an oxic environment. A number of unique regulatory events and genes have been identified and integrated into a working model of heterocyst differentiation. Phosphate limitation induces the transient differentiation of akinetes, spore-like cells resistant to cold and desiccation. A variety of environmental changes, both positive and negative for growth, induce the transient differentiation of hormogonia, motile filaments that function in dispersal. Initiation of the differentiation of heterocysts, akinetes and hormogonia are hypothesized to depart from the vegetative cell cycle, following separate and distinct events. N. punctiforme also forms nitrogen-fixing symbiotic associations; its plant partners influence the differentiation and behavior of hormogonia and heterocysts. N. punctiforme is genetically tractable and its genome sequence is nearly complete. Thus, the regulatory circuits of three cellular differentiation events and symbiotic interactions of N. punctiforme can be experimentally analyzed by functional genomics.

title: Heterocyst differentiation and pattern formation in cyanobacteria: a chorus of signals
abstract: Heterocyst differentiation in filamentous cyanobacteria provides an excellent prokaryotic model for studying multicellular behaviour and pattern formation. In Anabaena sp. strain PCC 7120, for example, 5–10% of the cells along each filament are induced, when deprived of combined nitrogen, to differentiate into heterocysts. Heterocysts are specialized in the fixation of N2 under oxic conditions and are semi‐regularly spaced among vegetative cells. This developmental programme leads to spatial separation of oxygen‐sensitive nitrogen fixation (by heterocysts) and oxygen‐producing photosynthesis (by vegetative cells). The interdependence between these two cell types ensures filament growth under conditions of combined‐nitrogen limitation. Multiple signals have recently been identified as necessary for the initiation of heterocyst differentiation, the formation of the heterocyst pattern and pattern maintenance. The Krebs cycle metabolite 2‐oxoglutarate (2‐OG) serves as a signal of nitrogen deprivation. Accumulation of a non‐metabolizable analogue of 2‐OG triggers the complex developmental process of heterocyst differentiation. Once heterocyst development has been initiated, interactions among the various components involved in heterocyst differentiation determine the developmental fate of each cell. The free calcium concentration is crucial to heterocyst differentiation. Lateral diffusion of the PatS peptide or a derivative of it from a developing cell may inhibit the differentiation of neighbouring cells. HetR, a protease showing DNA‐binding activity, is crucial to heterocyst differentiation and appears to be the central processor of various early signals involved in the developmental process. How the various signalling pathways are integrated and used to control heterocyst differentiation processes is a challenging question that still remains to be elucidated.

title: NrrA, a nitrogen‐responsive response regulator facilitates heterocyst development in the cyanobacterium Anabaena sp. strain PCC 7120
abstract: The heterocyst is a specialized cell for nitrogen fixation in the filamentous cyanobacteria, and its development is triggered by limitation of combined nitrogen in the medium. During heterocyst development, patterns of gene expression change dramatically. We identified seven genes encoding transcriptional regulators that were upregulated by nitrogen deprivation in Anabaena PCC 7120, using an Anabaena oligonucleotide microarray. Among them, the nrrA gene, which encodes a response regulator of the OmpR family with a DNA‐binding domain, has shown the most prominent induction after nitrogen deprivation. Expression of nrrA increased all through the filaments within 3 h of nitrogen deprivation and became higher in proheterocysts than in vegetative cells after 12 h. Sequence analysis of the promoter region of nrrA indicated that the induction of nrrA depended on NtcA, which is the global nitrogen regulator in cyanobacteria. In the nrrA deletion mutant, heterocyst development was delayed and the induction of hetR, which is the master gene in regulation of heterocyst development, was diminished up to 24 h nitrogen deprivation. It is concluded that nrrA facilitates heterocyst development.

title: Global Gene Expression Patterns of Nostoc punctiforme in Steady-State Dinitrogen-Grown Heterocyst-Containing Cultures and at Single Time Points during the Differentiation of Akinetes and Hormogonia
abstract: The vegetative cells of the filamentous cyanobacterium Nostoc punctiforme can differentiate into three mutually exclusive cell types: nitrogen-fixing heterocysts, spore-like akinetes, and motile hormogomium filaments. A DNA microarray consisting of 6,893 N. punctiforme genes was used to identify the global transcription patterns at single time points in the three developmental states, compared to those in ammonium-grown time zero cultures. Analysis of ammonium-grown cultures yielded a transcriptome of 2,935 genes, which is nearly twice the size of a soluble proteome. The NH4+-grown transcriptome was enriched in genes encoding core metabolic functions. A steady-state N2-grown (heterocyst-containing) culture showed differential transcription of 495 genes, 373 of which were up-regulated. The majority of the up-regulated genes were predicted from studies of heterocyst differentiation and N2 fixation; other genes are candidates for more detailed genetic analysis. Three days into the developmental process, akinetes showed a similar number of differentially expressed genes (497 genes), which were equally up- and down-regulated. The down-regulated genes were enriched in core metabolic functions, consistent with entry into a nongrowth state. There were relatively few adaptive genes up-regulated in 3-day akinetes, and there was little overlap with putative heterocyst developmental genes. There were 1,827 differentially transcribed genes in 24-h hormogonia, which was nearly fivefold greater than the number in akinete-forming or N2-fixing cultures. The majority of the up-regulated adaptive genes were genes encoding proteins for signal transduction and transcriptional regulation, which is characteristic of a motile filament that is poised to sense and respond to the environment. The greatest fraction of the 883 down-regulated genes was involved in core metabolism, also consistent with entry into a nongrowth state. The differentiation of heterocysts (steady state, N2 grown), akinetes, and hormogonia appears to involve the up-regulation of genes distinct for each state.

title: Genome-Wide and Heterocyst-Specific Circadian Gene Expression in the Filamentous Cyanobacterium Anabaena sp. Strain PCC 7120
abstract: The filamentous, heterocystous cyanobacterium Anabaena sp. strain PCC 7120 is one of the simplest multicellular organisms that show both morphological pattern formation with cell differentiation (heterocyst formation) and circadian rhythms. Therefore, it potentially provides an excellent model in which to analyze the relationship between circadian functions and multicellularity. However, detailed cyanobacterial circadian regulation has been intensively analyzed only in the unicellular species Synechococcus elongatus. In contrast to the highest-amplitude cycle in Synechococcus, we found that none of the kai genes in Anabaena showed high-amplitude expression rhythms. Nevertheless, ∼80 clock-controlled genes were identified. We constructed luciferase reporter strains to monitor the expression of some high-amplitude genes. The bioluminescence rhythms satisfied the three criteria for circadian oscillations and were nullified by genetic disruption of the kai gene cluster. In heterocysts, in which photosystem II is turned off, the metabolic and redox states are different from those in vegetative cells, although these conditions are thought to be important for circadian entrainment and timekeeping processes. Here, we demonstrate that circadian regulation is active in heterocysts, as shown by the finding that heterocyst-specific genes, such as all1427 and hesAB, are expressed in a robust circadian fashion exclusively without combined nitrogen.

title: Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation
abstract: BackgroundCyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc) sp. strain PCC 7120 (hereafter Anabaena) is a multicellular filamentous cyanobacterium that can "fix" atmospheric nitrogen into ammonia when grown in the absence of a source of combined nitrogen. Because the nitrogenase enzyme is oxygen sensitive, Anabaena forms specialized cells called heterocysts that create a microoxic environment for nitrogen fixation. We have employed directional RNA-seq to map the Anabaena transcriptome during vegetative cell growth and in response to combined-nitrogen deprivation, which induces filaments to undergo heterocyst development. Our data provide an unprecedented view of transcriptional changes in Anabaena filaments during the induction of heterocyst development and transition to diazotrophic growth.ResultsUsing the Illumina short read platform and a directional RNA-seq protocol, we obtained deep sequencing data for RNA extracted from filaments at 0, 6, 12, and 21 hours after the removal of combined nitrogen. The RNA-seq data provided information on transcript abundance and boundaries for the entire transcriptome. From these data, we detected novel antisense transcripts within the UTRs (untranslated regions) and coding regions of key genes involved in heterocyst development, suggesting that antisense RNAs may be important regulators of the nitrogen response. In addition, many 5' UTRs were longer than anticipated, sometimes extending into upstream open reading frames (ORFs), and operons often showed complex structure and regulation. Finally, many genes that had not been previously identified as being involved in heterocyst development showed regulation, providing new candidates for future studies in this model organism.ConclusionsDirectional RNA-seq data were obtained that provide comprehensive mapping of transcript boundaries and abundance for all transcribed RNAs in Anabaena filaments during the response to nitrogen deprivation. We have identified genes and noncoding RNAs that are transcriptionally regulated during heterocyst development. These data provide detailed information on the Anabaena transcriptome as filaments undergo heterocyst development and begin nitrogen fixation.

title: Quantitative shotgun proteomics of enriched heterocysts from Nostoc sp. PCC 7120 using 8-plex isobaric peptide tags.
abstract: The filamentous cyanobacterium Nostoc sp. strain PCC 7120 is capable of fixing atmospheric nitrogen. The labile nature of the core process requires the terminal differentiation of vegetative cells to form heterocysts, specialized cells with altered cellular and metabolic infrastructure to mediate the N2-fixing process. We present an investigation targeting the cellular proteomic expression of the heterocysts compared to vegetative cells of a population cultured under N2-fixing conditions. New 8-plex iTRAQ reagents were used on enriched replicate heterocyst and vegetative cells, and replicate N2-fixing and non-N2-fixing filaments to achieve accurate measurements. With this approach, we successfully identified 506 proteins, where 402 had confident quantifications. Observations provided by purified heterocyst analysis enabled the elucidation of the dominant metabolic processes between the respective cell types, while emphasis on the filaments enabled an overall comparison. The level of analysis provided by this investigation presents various tools and knowledge that are important for future development of cyanobacterial biohydrogen production.

title: Quantitative overview of N2 fixation in Nostoc punctiforme ATCC 29133 through cellular enrichments and iTRAQ shotgun proteomics.
abstract: Nostoc punctiforme ATCC 29133 is a photoautotrophic cyanobacterium with the capacity to fix atmospheric N 2. Its ability to mediate this process is similar to that described for Nostoc sp. PCC 7120, where vegetative cells differentiate into heterocysts. Quantitative proteomic investigations at both the filament level and the heterocyst level are presented using isobaric tagging technology (iTRAQ), with 721 proteins at the 95% confidence interval quantified across both studies. Observations from both experiments yielded findings confirmatory of both transcriptional studies, and published Nostoc sp. PCC 7120 iTRAQ data. N. punctiforme exhibits similar metabolic trends, though changes in a number of metabolic pathways are less pronounced than in Nostoc sp. PCC 7120. Results also suggest a number of proteins that may benefit from future investigations. These include ATP dependent Zn-proteases, N-reserve degraders and also redox balance proteins. Complementary proteomic data sets from both organisms present key precursor knowledge that is important for future cyanobacterial biohydrogen research.

title: Electron transfer protein complexes in the thylakoid membranes of heterocysts from the cyanobacterium Nostoc punctiforme.
abstract: Filamentous, heterocystous cyanobacteria are capable of nitrogen fixation and photoautotrophic growth. Nitrogen fixation takes place in heterocysts that differentiate as a result of nitrogen starvation. Heterocysts uphold a microoxic environment to avoid inactivation of nitrogenase, e.g. by downregulation of oxygenic photosynthesis. The ATP and reductant requirement for the nitrogenase reaction is considered to depend on Photosystem I, but little is known about the organization of energy converting membrane proteins in heterocysts. We have investigated the membrane proteome of heterocysts from nitrogen fixing filaments of Nostoc punctiforme sp. PCC 73102, by 2D gel electrophoresis and mass spectrometry. The membrane proteome was found to be dominated by the Photosystem I and ATP-synthase complexes. We could identify a significant amount of assembled Photosystem II complexes containing the D1, D2, CP43, CP47 and PsbO proteins from these complexes. We could also measure light-driven in vitro electron transfer from Photosystem II in heterocyst thylakoid membranes. We did not find any partially disassembled Photosystem II complexes lacking the CP43 protein. Several subunits of the NDH-1 complex were also identified. The relative amount of NDH-1M complexes was found to be higher than NDH-1L complexes, which might suggest a role for this complex in cyclic electron transfer in the heterocysts of Nostoc punctiforme.

title: Measuring multiple fluxes through plant metabolic networks.
abstract: Fluxes through metabolic networks are crucial for cell function, and a knowledge of these fluxes is essential for understanding and manipulating metabolic phenotypes. Labeling provides the key to flux measurement, and in network flux analysis the measurement of multiple fluxes allows a flux map to be superimposed on the metabolic network. The principles and practice of two complementary methods, dynamic and steady-state labeling, are described, emphasizing best practice and illustrating their contribution to network flux analysis with examples taken from the plant and microbial literature. The principal analytical methods for the detection of stable isotopes are also described, as well as the procedures for obtaining flux maps from labeling data. A series of boxes summarizing the key concepts of network flux analysis is provided for convenience.

title: Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis.
abstract: Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis of dynamic isotope labeling measurements and have applied it to determine metabolic pathway fluxes in the cyanobacterium Synechocystis sp. PCC6803. Comparison to a theoretically predicted flux map revealed inefficiencies in photosynthesis due to oxidative pentose phosphate pathway and malic enzyme activity, despite negligible photorespiration. This approach has potential to fill important gaps in our understanding of how carbon and energy flows are systemically regulated in cyanobacteria, plants, and algae.

title: Heterotrophic micro- and macrocultures of a nitrogen-fixing cyanobacterium
abstract: Anabaena variabilis can be cloned in the dark from fragments with one and few cells, with an efficiency of about 40%, on the nitrogen-free medium of Allen and Arnon solidified with 0.5% agarose and supplemented with 5 mM fructose. The organism can be grown exponentially (τ2≅36 h) in fermentor cultures in the dark, fixing N2, to a density of greater than 10 g dry weight/l.

title: Fructose uptake and influence on growth of and nitrogen fixation by Anabaena variabilis
abstract: Fructose is specifically taken up by nitrogen-fixing cultures of Anabaena variabilis in the light and lowers the doubling time from 24 to 8 h. The kinetics for both fructose-dependent growth and fructose uptake are exponential. The apparent Km for fructose uptake in N2-fixing cultures is 160 microM for cells not previously exposed to fructose and 50 microM in cells adapted to fructose. Picomolar amounts of [14C]fructose are scavenged from the medium and accumulate in filaments. Heterocysts of fructose-adapted filaments accumulate 14C from fructose within 20 min. Short-term experiments with fructose-starved cultures provide evidence that nitrogenase activity, protein, and chlorophyll content change within one generation time upon addition of fructose. In long-term experiments, the amount of fructose initially present in the medium determines heterocyst number and packed-cell volume. Photosynthetic oxygen evolution and amounts of chlorophyll decrease with exogenous fructose concentrations greater than 20 mM.

title: Chemoheterotrophic Growth of the Cyanobacterium Anabaena sp. Strain PCC 7120 Dependent on a Functional Cytochrome c Oxidase
abstract: Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium commonly used as a model organism for studying cyanobacterial cell differentiation and nitrogen fixation. For many decades, this cyanobacterium was considered an obligate photo-lithoautotroph. We now discovered that this strain is also capable of mixotrophic, photo-organoheterotrophic, and chemo-organoheterotrophic growth if high concentrations of fructose (at least 50 mM and up to 200 mM) are supplied. Glucose, a substrate used by some facultatively organoheterotrophic cyanobacteria, is not effective in Anabaena sp. PCC 7120. The gtr gene from Synechocystis sp. PCC 6803 encoding a glucose carrier was introduced into Anabaena sp. PCC 7120. Surprisingly, the new strain containing the gtr gene did not grow on glucose but was very sensitive to glucose, with a 5 mM concentration being lethal, whereas the wild-type strain tolerated 200 mM glucose. The Anabaena sp. PCC 7120 strain containing gtr can grow mixotrophically and photo-organoheterotrophically, but not chemo-organoheterotrophically with fructose. Anabaena sp. PCC 7120 contains five respiratory chains ending in five different respiratory terminal oxidases. One of these enzymes is a mitochondrial-type cytochrome c oxidase. As in almost all cyanobacteria, this enzyme is encoded by three adjacent genes called coxBAC1. When this locus was disrupted, the cells lost the capability for chemo-organoheterotrophic growth.

title: New Anabaena and Nostoc cyanophages from sewage settling ponds.
abstract: We have isolated, from sewage settling ponds, 16 cyanophages for heterocyst forming, filamentous cyanobacteria of the genera Anabaena and Nostoc. These phages fall into three groups based on morphology, host range, one-step growth curves, and restriction digests. On the basis of these criteria they can be distinguished from cyanophages A-1(L), A-4(L), N-1, and AN-10 which we received from other laboratories. Certain of the newly described phages are similar in morphology to the short-tailed LPP cyanophages, and others to the long-tailed AS cyanophages.

title: Mutations in Four Regulatory Genes Have Interrelated Effects on Heterocyst Maturation in Anabaena sp. Strain PCC 7120
abstract: Regulatory genes hepK, hepN, henR, and hepS are required for heterocyst maturation in Anabaena sp. strain PCC 7120. They presumptively encode two histidine kinases, a response regulator, and a serine/threonine kinase, respectively. To identify relationships between those genes, we compared global patterns of gene expression, at 14 h after nitrogen step-down, in corresponding mutants and in the wild-type strain. Heterocyst envelopes of mutants affected in any of those genes lack a homogeneous, polysaccharide layer. Those of a henR mutant also lack a glycolipid layer. patA, which encodes a positive effector of heterocyst differentiation, was up-regulated in all mutants except the hepK mutant, suggesting that patA expression may be inhibited by products related to heterocyst development. hepS and hepK were up-regulated if mutated and so appear to be negatively autoregulated. HepS and HenR regulated a common set of genes and so appear to belong to one regulatory system. Some nontranscriptional mechanism may account for the observation that henR mutants lack, and hepS mutants possess, a glycolipid layer, even though both mutations down-regulated genes involved in formation of the glycolipid layer. HepK and HepN also affected transcription of a common set of genes and therefore appear to share a regulatory pathway. However, the transcript abundance of other genes differed very significantly from expression in the wild-type strain in either the hepK or hepN mutant while differing very little from wild-type expression in the other of those two mutants. Therefore, hepK and hepN appear to participate also in separate pathways.

title: Developmental regulation and spatial pattern of expression of the structural genes for nitrogenase in the cyanobacterium Anabaena.
abstract: Depriving the cyanobacterium Anabaena of fixed nitrogen induces the differentiation of heterocysts at intervals along its filaments. To test whether the oxygen‐deficient conditions believed to prevail within mature heterocysts are sufficient, in the absence of fixed nitrogen, to elicit the expression of nitrogenase, PnifHDK was fused transcriptionally to luxAB (encoding luciferase). Expression, monitored from individual cells as light emission, was localized (with a resolution of approximately 1 micron) to differentiated cells, whether or not oxygen was present. Anabaena PCC 7118 is a heterocystless mutant strain that is known to fix nitrogen when deprived of combined nitrogen under anaerobic conditions. Three lines of evidence indicate that the mutant has retained the ability to develop a pattern despite its inability to make heterocysts. First, morphologically distinct cells appear at nonrandom intervals when filaments are starved of nitrogen. Second, these cells, like heterocysts, have little or no phycocyanin‐dependent fluorescence. Third, nitrogen‐starved filaments fragment, with fragment lengths similar to the spacing normally seen between heterocysts. Expression of PnifHDK‐luxAB was largely confined to differentiated cells in the mutant as in the wild‐type strain. These results provide evidence for a causal relationship between development and transcriptional events in Anabaena.

title: The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria.
abstract: The RNase P RNA gene (rnpB) from 10 cyanobacteria has been characterized. These new RNAs, together with the previously available ones, provide a comprehensive data set of RNase P RNA from diverse cyanobacterial lineages. All heterocystous cyanobacteria, but none of the non-heterocystous strains analyzed, contain short tandemly repeated repetitive (STRR) sequences that increase the length of helix P12. Site-directed mutagenesis experiments indicate that the STRR sequences are not required for catalytic activity in vitro. STRR sequences seem to have recently and independently invaded the RNase P RNA genes in heterocyst-forming cyanobacteria because closely related strains contain unrelated STRR sequences. Most cyanobacteria RNase P RNAs lack the sequence GGU in the loop connecting helices P15 and P16 that has been established to interact with the 3'-end CCA in precursor tRNA substrates in other bacteria. This character is shared with plastid RNase P RNA. Helix P6 is longer than usual in most cyanobacteria as well as in plastid RNase P RNA.

title: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
abstract: When running experiments that involve multiple high density oligonucleotide arrays, it is important to remove sources of variation between arrays of non-biological origin. Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations.



We present three methods of performing normalization at the probe intensity level. These methods are called complete data methods because they make use of data from all arrays in an experiment to form the normalizing relation. These algorithms are compared to two methods that make use of a baseline array: a one number scaling based algorithm and a method that uses a non-linear normalizing relation by comparing the variability and bias of an expression measure. Two publicly available datasets are used to carry out the comparisons. The simplest and quickest complete data method is found to perform favorably.


AVAILABILITY
Software implementing all three of the complete data normalization methods is available as part of the R package Affy, which is a part of the Bioconductor project http://www.bioconductor.org.



Additional figures may be found at http://www.stat.berkeley.edu/~bolstad/normalize/index.html

title: The metabotropic glutamate receptor antagonist L-2-amino-3-phosphonopropionic acid inhibits phosphoserine phosphatase.
abstract: Phosphoserine phosphatase catalyzes the final step in the major pathway of L-serine biosynthesis in brain. Using D-phosphoserine as substrate, the metabotropic glutamate receptor antagonist L-2-amino-3-phosphonopropionic acid (L-AP3) inhibits phosphoserine phosphatase partially purified from rat brain with a Ki of 151 microM. In contrast to AP3 enantioselectivity at metabotropic receptors, D-AP3 (Ki 48 microM) is more potent as an inhibitor of phosphoserine phosphatase than L-AP3, whereas DL-AP3 has intermediate potency. D-, L-, and DL-AP3 are 6- to 8-fold more potent inhibitors using D-phosphoserine rather than L-phosphoserine as substrate, suggesting that AP3 may have selectivity for isoforms of phosphoserine phosphatase which preferentially cleave D-phosphoserine. D-AP3 decreases the apparent affinity of D- and L-phosphoserine with little or no change in maximal velocity indicating that it is a competitive inhibitor of the enzyme. Whereas L-AP3 has similar potency at metabotropic glutamate receptors and phosphoserine phosphatase, D-AP3 is selective for phosphoserine phosphatase and is the most potent and only known competitive inhibitor of this enzyme.

title: Rapid, sensitive, microscale determination of phosphate in water and soil.
abstract: A rapid and sensitive analysis of inorganic and organic phosphorus (P) is needed to analyze water and soil extracts at submicromolar concentrations. The proposed method, based on the complexation of malachite green with phosphomolybdate under acidic conditions, was adapted to a 96-well microtiter plate format, and was tested for matrix interferences using 15 soils and some common extractants, including water, KCI, CaCl2, NaOH, and HCl. The accuracy of P determination was affected when CaCl2 and HCl concentrations were greater than 0.1 M and when NaOH concentration exceeded 0.4 M. Potassium chloride concentration up to 1 M did not interfere with P determination. The molar absorptivity was 46 841 M(-1) cm(-1) and the reagent blank absorbance was 0.071+/-0.003 (n = 10). At the 99% confidence limit, the method detection limit was calculated to be 0.006 mg P L(-1). Recovery of added inorganic P in different types of soils and extracts ranged between 95 and 112% with an average of 102%. The proposed microplate method allows P to be determined rapidly in a wide range of soil types and extracts and requires limited volume (20-200 microL). The procedure uses limited quantities (40 microL) of two stable reagents (>1 yr), and generates low amounts of hazardous waste.

title: A second nitrogenase in vegetative cells of a heterocyst-forming cyanobacterium.
abstract: In many filamentous cyanobacteria nitrogen fixation occurs in differentiated cells called heterocysts. Filamentous strains that do not form heterocysts may fix nitrogen in vegetative cells, primarily under anaerobic conditions. We describe here two functional Mo-dependent nitrogenases in a single organism, the cyanobacterium Anabaena variabilis. Using a lacZ reporter with a fluorescent beta-galactoside substrate for in situ localization of gene expression, we have shown that the two clusters of nif genes are expressed independently. One nitrogenase functions only in heterocysts under either aerobic or anaerobic growth conditions, whereas the second nitrogenase functions only under anaerobic conditions in vegetative cells and heterocysts. Differences between the two nif clusters suggest that the nitrogenase that is expressed in heterocysts is developmentally regulated while the other is regulated by environmental factors.

title: Independent regulation of nifHDK operon transcription and DNA rearrangement during heterocyst differentiation in the cyanobacterium Anabaena sp. strain PCC 7120
abstract: The filamentous cyanobacterium Anabaena sp. strain PCC 7120 expresses the genes required for nitrogen fixation in terminally differentiated cells called heterocysts. The nifHDK operon encodes the nitrogenase polypeptides and is expressed at high levels in heterocysts. During heterocyst differentiation, an 11-kb DNA element is excised from the nifD gene by site-specific recombination. The xisA gene, located on the 11-kb element, is required for the excision of the element. Transcription and DNA rearrangement of the nifHDK operon both occur late during heterocyst differentiation, about 18 to 24 h after induction, suggesting that the regulation of these events might be coupled. We show that heterocyst-specific transcription and DNA rearrangement of the nifHDK operon are independent of one another. Northern (RNA) analysis of the xisA mutant strain DW12-2.2, which cannot excise the nifD 11-kb element or fix nitrogen, showed that the nifH and nifD genes are transcribed on unrearranged chromosomes. The nifK gene was not transcribed in DW12-2.2, indicating that its expression is dependent on the nifH promoter and excision of the 11-kb element from the operon. A 1.68-kb DNA fragment containing the nifH promoter was deleted from the chromosome to produce the mutant strain LW1. LW1 formed heterocysts but did not grow on nitrogen-free medium and showed no transcription through nifD. Southern analysis of LW1 showed normal excision of the 11-kb element from the nifHDK operon, indicating that transcription from the nifH promoter is not required for the developmentally regulated DNA rearrangement.

title: The KEGG resource for deciphering the genome
abstract: A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.

title: Effect of oxygen concentration on dark nitrogen fixation and respiration in cyanobacteria
abstract: Simultaneous measurements of acetylene reduction by Anabaena variabilis and the concentration of dissolved oxygen in the suspension were made using a specially designed vessel which allowed measurements under steady-state conditions. The rate of acetylene reduction in the dark increased with increasing oxygen concentrations until a maximum value was reached at 300 μM O2 (corresponding to 30% O2 in the gas phase at 35°C). This presumably results from a requirement for energy provided by respiration. Measurements of the dependence of respiration rate on dissolved oxygen concentration were made under comparable conditions using an open system to allow conditions close to steady-state to be obtained. The respiration rate of diazotrophically grown Anabaena variabilis had a dependence on oxygen concentration corresponding to the sum of two activities. These had Km values of 1.0 μM and 69 μM and values of Vmax of similar magnitude. Only the high affinity activity was observed in nitrate-grown cyanobacteria lacking heterocysts, and this presumably represent activity in the vegetative cells. The oxygen concentration dependence of the low affinity activity resembled that for the stimulation of acetylene reduction. We interpret this as the result of oxygen uptake by the heterocysts. The results are consistent with the idea that in intact filaments of cyanobacteria O2 enters heterocysts much more slowly than it enters the vegetative cells.

title: Evidence that the barrier to the penetration of oxygen into heterocysts depends upon two layers of the cell envelope
abstract: Mutants of Anabaena sp. PCC 7120 with O2-sensitive acetylene-reducing activity were studied to identify envelope components that contribute to the barrier limiting diffusion of oxygen into the heterocyst. Mutant strain EF114, deficient in a heterocyst-specific glycolipid, reduced acetylene only under strictly anaerobic conditions. Analysis of in vivo O2 uptake as a function of dissolved pO2 showed that EF114 has lost the low affinity, diffusion-limited respiratory component associated with heterocysts in wild-type filaments. The low affinity respiratory activity was also lost in EF116, a mutant in which the cohesiveness of the outer polysaccharide layer was reduced. Restoration of aerobic nitrogen fixation in a spontaneous revertant of EF116 and in a strain complemented with cosmid 41E11 was associated with restoration of the low affinity component of respiratory activity. The results provide evidence that the barrier to diffusion of gas into heterocysts depends upon both the glycolipid layer and the polysaccharide layer of the heterocyst envelope.

title: Cytochrome c oxidase genes required for nitrogenase activity and diazotrophic growth in Anabaena sp. PCC 7120
abstract: N2 fixation is an O2‐sensitive process and some filamentous diazotrophic cyanobacteria that grow performing oxygenic photosynthesis confine their N2 fixation machinery to heterocysts, specialized cells that maintain a reducing environment adequate for N2 fixation. Respiration is thought to contribute to the diazotrophic metabolism of heterocysts and the genome of the heterocyst‐forming cyanobacterium Anabaena sp. PCC 7120 bears three gene clusters putatively encoding cytochrome c oxidases. Transcript analysis of these cox gene clusters through RNA/DNA hybridization identified two cox operons, cox2 and cox3, that are induced after nitrogen step‐down in an NtcA‐ and HetR‐dependent manner and appear to be expressed specifically in heterocysts. In contrast, cox1 was expressed only in vegetative cells. Expression of cox2 and cox3 occurred at an intermediate stage (about 9 h) during the process of heterocyst development following nitrogen step‐down. Inactivation of genes in the two inducible cox operons, but not separately in either of them, strongly reduced nitrogenase activity and prevented diazotrophic growth in aerobic conditions. These results show that the nitrogen‐regulated cytochrome c oxidase‐type respiratory terminal oxidases Cox2 and Cox3 are essential for heterocyst function in Anabaena sp. PCC 7120.

title: Excision of an 11-kilobase-pair DNA element from within the nifD gene in anabaena variabilis heterocysts
abstract: The 3' region of the Anabaena variabilis nifD gene contains an 11-kilobase-pair element which is excised from the chromosome during heterocyst differentiation. We have sequenced the recombination sites which border the element in vegetative cells and the rearranged heterocyst sequences. In vegetative cells, the element was flanked by 11-base-pair direct repeats which were identical to the repeats present at the ends of the nifD element in Anabaena sp. strain PCC 7120 (Anabaena strain 7120). Although Anabaena strain 7120 and A. variabilis are quite distinct in many ways, the overall sequence similarity between the two strains for the regions sequenced was 96%. Like the Anabaena strain 7120 element, the A. variabilis element was excised in heterocysts to produce a functional nifD gene and a free circularized element which was neither amplified nor degraded. The Anabaena strain 7120 xisA gene is located at the nifK-proximal end of the nifD element and is required for excision of the element in heterocysts. The A. variabilis element also contained an xisA gene which could complement a defective Anabaena strain 7120 xisA gene. A. variabilis did not contain the equivalent of the Anabaena strain 7120 fdxN 55-kilobase-pair element.

title: Distinct and differently regulated Mo‐dependent nitrogen‐fixing systems evolved for heterocysts and vegetative cells of Anabaena variabilis ATCC 29413: characterization of the fdxH1/2 gene regions as part of the nif1/2 gene clusters
abstract: Two different fdxH genes (fdxH1, fdxH2) have been isolated from the nitrogen‐fixing, heterocyst‐forming cyanobacterium Anabaena variabilis ATCC 29413. They are part of two different nif gene clusters, nif1 and nif2. fdxH1 encodes the [2Fe—2S] ferredoxin that is known as the direct electron donor to nitrogenase in heterocysts, and is very similar to FdxH from Anabaena sp. PCC 7120. FdxH2 has more residues in common and shares its oxygen sensitivity with the single FdxH from the non‐heterocystous, filamentous cyanobacterium Plectonema boryanum PCC 73110. The latter expresses nitrogenase early ( 3–4 h) after nitrogen depletion in vegetative cells and exclusively under anaerobic conditions. fdxH2 and the nif2 genes of Anabaena 29413 are also transcribed 4 h after onset of nitrogen‐stepdown, exclusively under anaerobic growth conditions and long before functional heterocysts appear. At this time, no fdxH1 and nif1 gene transcription was observed. It occurred later and was associated with nitrogen fixation under aerobic conditions, i.e. within heterocysts. fdxH2 and nifHDK2 were not transcribed during aerobic, nitrogen‐fixing growth. In addition, neither was an fdxH2‐type gene found nor an anaerobically and early inducible Nif2 system detectable in Anabaena 7120. These data reveal that in filamentous cyanobacteria two different Nif systems have evolved based on molybdenum nitrogenases. It is concluded that a Nif2‐type system operates in vegetative cells of non‐heterocystous and some, but not all, heterocyst‐forming filamentous cyanobacteria. It is environmentally regulated by the levels of both oxygen and combined nitrogen in the habitat. To simultaneously allow for oxygen‐evolving photosynthesis and oxygen‐sensitive nitrogen fixation, the Nif1‐type system probably branched from an ancestral Nif2‐type system and has evolved for an exclusive operation within heterocysts. Accordingly, its expression has become an obligate late event in the developmental programme of heterocyst differentiation, irrespective of aerobic or anaerobic growth conditions.

title: Isolation and characterization of the VnfEN genes of the cyanobacterium Anabaena variabilis
abstract: The filamentous cyanobacterium Anabaena variabilis fixes nitrogen in the presence of vanadium (V) and in the absence of molybdenum (Mo), using a V-dependent nitrogenase (V-nitrogenase) encoded by the vnfDGK genes. Downstream from these genes are two genes that are similar to the vnfEN genes of Azotobacter vinelandii. Like the vnfDGK genes, the vnfEN genes were transcribed in the absence of Mo, whether or not V was present. A mutant with an insertion in the vnfN gene lacked V-nitrogenase activity; thus, the vnfEN genes were essential for the V-nitrogenase system in A. variabilis. Growth and acetylene reduction assays with wild-type and mutant strains suggested that the V-nitrogenase reduced dinitrogen better than acetylene. The similarity of the vnfEN genes of A. variabilis and A. vinelandii was not strong. The vnfEN genes of A. variabilis showed greater similarity to the vnfDK genes just upstream than to the A. vinelandii vnfEN genes. Sequence comparisons provide support for the idea that if the vnf genes were transferred laterally among bacterial strains, the vnf cluster was not transferred intact. It appears likely that the structural genes were transferred before a duplication event led to the evolution of the vnfEN genes independently in the two strains. The divergence of the vnfEN genes from the vnfDK genes suggests that this duplication, and hence the transfer of vnf genes, was an ancient event.

title: KEGG: Kyoto Encyclopedia of Genes and Genomes
abstract: KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).

title: KEGG for integration and interpretation of large-scale molecular data sets
abstract: Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ or http://www.kegg.jp/) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem. Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the KEGG Orthology system. Here we report KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets. We also report a variant of the KEGG mapping procedure to extend the knowledge base, where different types of data and knowledge, such as disease genes and drug targets, are integrated as part of the KEGG molecular networks. Finally, we describe recent enhancements to the KEGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.

title: Control of phycobiliprotein proteolysis and heterocyst differentiation in Anabaena
abstract: Phycobiliprotein degradation can be initiated in cultures of the cyanobacterium Anabaena by removal of combined nitrogen from the medium. Certain strains of Anabaena differentiate cells specialized for aerobic nitrogen fixation (heterocysts) under such conditions. We describe here a procedure for the preparation of extracts from heterocysts or vegetative cells that contain an activity capable of degrading only the phycobiliproteins in a mixture of soluble Anabaena proteins in vitro. This activity increased under nitrogen starvation conditions or in ammonia-replete cultures treated with the glutamine synthetase inhibitor methionine sulfoximine. The increase in activity induced by nitrogen starvation was prevented by chloramphenicol or by carbon starvation. Under all these conditions, phycobiliprotein degradative activity assayed in vitro was correlated with the loss of phycobiliprotein absorbance in vivo. Finally, starvation of a met auxotroph of Anabaena for methionine (in the presence of ammonia) did not induce phycobiliprotein degradation in vivo or the increase in proteinase activity. Together with direct measurements of ppGpp, these results indicate that proteolysis in Anabaena is not controlled by compounds associated with the stringent response in Escherichia coli. Since the increase in proteinase activity appears to be regulated by the same variables that control heterocyst differentiation, the activity should provide a useful biochemical marker for the early events of differentiation.

title: Calcium-dependent protease of the cyanobacterium Anabaena: molecular cloning and expression of the gene in Escherichia coli, sequencing and site-directed mutagenesis
abstract: SummaryIt has been suggested that a calcium-dependent intracellular protease of the cyanobacterium, Anabaena sp., participates in the differentiation of heterocysts, cells that are specialized for fixation of N2. Clones of the structural gene (designated prcA) for this protease from Anabaena variabilis strain ATCC 29413 and Anabaena sp. strain PCC 7120 were identified via their expression in Escherichia coli. The prcA gene from A. variabilis was sequenced. The genes of both strains, mutated by insertion of a drug resistance cassette, were returned to these same strains of Anabaena on suicide plasmids. The method of sacB-mediated positive selection for double recombinants was used to achieve replacement of the wild-type prcA genes by the mutated forms. The resulting mutants, which lacked Ca2+-dependent protease activity, were not impaired in heterocyst formation and grew on N2 as sole nitrogen source.

title: Alanine Dehydrogenase Activity Is Required for Adequate Progression of Phycobilisome Degradation during Nitrogen Starvation in Synechococcus elongatus PCC 7942
abstract: Degradation of the cyanobacterial light-harvesting antenna, the phycobilisome, is a general acclimation response that is observed under various stress conditions. In this study we identified a novel mutant of Synechococcus elongatus PCC 7942 that exhibits impaired phycobilisome degradation specifically during nitrogen starvation, unlike previously described mutants, which exhibit aberrant degradation under nitrogen, sulfur, and phosphorus starvation conditions. The phenotype of the new mutant, AldΩ, results from inactivation of ald (encoding alanine dehydrogenase). AldΩ is deficient in transcription induction of a number of genes during nitrogen starvation. These genes include the “general nutrient stress-related” genes, nblA and nblC, the products of which are essential for phycobilisome degradation. Furthermore, transcripts of several specific nitrogen-responsive genes accumulate at lower levels in AldΩ than in the wild-type strain. In contrast, ald inactivation did not decrease the accumulation of transcripts during sulfur starvation. Transcription of ald is induced upon nitrogen starvation, which is consistent with the ability of wild-type cells to maintain a low cellular content of alanine under these conditions. Unlike wild-type cells, AldΩ accumulates alanine upon nitrogen starvation. Our analyses suggest that alanine dehydrogenase activity is necessary for an adequate cellular response to nitrogen starvation. Decomposition of alanine may be required to provide a sufficient amount of ammonia. Furthermore, the accumulated alanine, or a related metabolite, may interfere with the cues that modulate acclimation during nitrogen starvation. Taken together, our results provide novel information regarding cellular responses to nitrogen starvation and suggest that mechanisms related to nitrogen-specific responses are involved in modulation of a general acclimation process.

title: Carbon and nitrogen fixation and metabolite exchange in and between individual cells of Anabaena oscillarioides
abstract: Filamentous nitrogen fixing cyanobacteria are key players in global nutrient cycling, but the relationship between CO2- and N2-fixation and intercellular exchange of these elements remains poorly understood in many genera. Using high-resolution nanometer-scale secondary ion mass spectrometry (NanoSIMS) in conjunction with enriched H13CO3− and 15N2 incubations of Anabaena oscillarioides, we imaged the cellular distributions of C, N and P and 13C and 15N enrichments at multiple time points during a diurnal cycle as proxies for C and N assimilation. The temporal and spatial distributions of the newly fixed C and N were highly heterogeneous at both the intra- and inter-cellular scale, and indicative of regions performing active assimilation and biosynthesis. Subcellular components such as the neck region of heterocycts, cell division septae and putative cyanophycin granules were clearly identifiable by their elemental composition. Newly fixed nitrogen was rapidly exported from heterocysts and was evenly allocated among vegetative cells, with the exception of the most remote vegetative cells between heterocysts, which were N limited based on lower 15N enrichment. Preexisting functional heterocysts had the lowest levels of 13C and 15N enrichment, while heterocysts that were inferred to have differentiated during the experiment had higher levels of enrichment. This innovative approach, combining stable isotope labeling and NanoSIMS elemental and isotopic imaging, allows characterization of cellular development (division, heterocyst differentiation), changes in individual cell composition and cellular roles in metabolite exchange.

title: Transport of basic amino acids by the dinitrogen-fixing cyanobacterium Anabaena PCC 7120.
abstract: Two transport systems for L-arginine were evident in Anabaena sp. strain PCC 7120: a high-affinity one (Km, 1.7 microM) that accumulated arginine within the cells through an energy-requiring process and another one that exhibited low affinity for L-arginine (Km, 0.75 mM) and was unable to accumulate the substrate. Both systems were inhibited by L-canavanine, L-lysine, and L-ornithine. Two systems were also evident for L-lysine uptake (Km, 1.9 and 110 microM, respectively). After selection for resistance to canavanine or hydroxylysine, independent mutants were isolated which were impaired in the high-affinity uptake of arginine and lysine. A common permease appears, therefore, to be involved in the high-affinity transport of these basic amino acids. Both the high- and the low-affinity systems can contribute to the growth of Anabaena sp. on L-arginine. However, arginine did not effectively repress either nitrogenase or nitrate reductase.

title: Amino acid transport systems required for diazotrophic growth in the cyanobacterium Anabaena sp. strain PCC 7120
abstract: Uptake of 16 amino acids by the filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was characterized with regard to kinetic parameters of transport, intracellular accumulation of the transported amino acids, and sensitivity of the transport process to energy metabolism inhibitors. Mutants resistant to certain toxic analogs of some amino acids were isolated that were impaired in amino acid transport. Results obtained in this study, together with those reported previously (A. Herrero and E. Flores,  1990), suggest that there are at least five amino acid transport systems in strain PCC 7120: one high-affinity, active system for basic amino acids; one low-affinity, passive system for basic amino acids; two high-affinity, active systems with overlapping, but not identical, specificities for neutral amino acids; and one putative system for acidic amino acids. Some of the amino acid transport mutants were impaired in diazotrophic growth. These mutants were unable to develop a normal percentage of heterocysts and normal nitrogenase activity in response to nitrogen stepdown. Putative roles for the amino acid transport systems in uptake of extracellular amino acids, recapture of amino acids that have leaked from the cells, and intercellular transfer of amino acids in the filaments of Anabaena sp. strain PCC 7120 are discussed.

title: ABC‐type neutral amino acid permease N‐I is required for optimal diazotrophic growth and is repressed in the heterocysts of Anabaena sp. strain PCC 7120
abstract: Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can fix N2 in differentiated cells called heterocysts. The products of Anabaena open reading frames (ORFs) all1046, all1047, all1284, alr1834 and all2912 were identified as putative elements of a neutral amino acid permease. Anabaena mutants of these ORFs were strongly affected (1–12% of the wild‐type activity) in the transport of Pro, Phe, Leu and Gly and also impaired (17–30% of the wild‐type activity) in the transport of Ala and Ser. These results identified those ORFs as the nat genes encoding the N‐I neutral amino acid permease. According to amino acid sequence homologies, natA (all1046) and natE (all2912) encode ATPases, natC (all1047) and natD (all1284) encode transmembrane proteins, and natB (alr1834) encodes a periplasmic substrate‐binding protein of an ABC‐type uptake transporter. The natA, natC, natD and natE mutants showed defects in Gln and His uptake that were not observed in the natB mutant suggesting that NatB is not a binding protein for Gln or His. The nat mutants released hydrophobic amino acids to the medium, and amino acid release took place at higher levels in cultures incubated in the absence of combined N than in the presence of nitrate. Alanine was the amino acid released at highest levels, and its release was impaired in a mutant unable to develop heterocysts. The nat mutants were also impaired in diazotrophic growth, with natA, natC, natD and natE mutants showing more severe defects than the natB mutant. Expression of natA and natC, which constitute an operon, natCA, as well as of natB was studied and found to take place in vegetative cells but not in the heterocysts. These results indicate that the N‐I permease is necessary for normal growth of Anabaena sp. strain PCC 7120 on N2, and that this permease has a role in the diazotrophic filament specifically in the vegetative cells.

title: ABC‐type amino acid uptake transporters Bgt and N‐II of Anabaena sp. strain PCC 7120 share an ATPase subunit and are expressed in vegetative cells and heterocysts
abstract: Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can fix N2 in differentiated cells called heterocysts. Anabaena open reading frames alr4167 and alr3187 encode, respectively, an ATPase subunit, BgtA, and a composite protein bearing periplasmic substrate‐binding and transmembrane domains, BgtB, of an ABC‐type high‐affinity basic amino acid uptake transporter (Bgt). Open reading frame alr4167 is clustered with open reading frames alr4164, alr4165 and alr4166 that encode a periplasmic substrate‐binding protein, NatF, and transmembrane proteins NatG and NatH respectively. The NatF, NatG, NatH and BgtA proteins constitute an ABC‐type uptake transporter for acidic and neutral polar amino acids (N‐II). The Bgt and N‐II transport systems thus share the ATPase subunit, BgtA. These transporters together with the previously characterized ABC‐type uptake transporter for proline and hydrophobic amino acids (N‐I) account for more than 98% of the amino acid transport activity exhibited by Anabaena sp. strain PCC 7120. In contrast to N‐I that is expressed only in vegetative cells, the Bgt and N‐II systems are present in both vegetative cells and heterocysts. Whereas Bgt is dispensable for diazotrophic growth, N‐II appears to contribute together with N‐I to the diazotrophic physiology of this cyanobacterium.

title: Mechanism of intercellular molecular exchange in heterocyst‐forming cyanobacteria
abstract: Heterocyst‐forming filamentous cyanobacteria are true multicellular prokaryotes, in which heterocysts and vegetative cells have complementary metabolism and are mutually dependent. The mechanism for metabolite exchange between cells has remained unclear. To gain insight into the mechanism and kinetics of metabolite exchange, we introduced calcein, a 623‐Da fluorophore, into the Anabaena cytoplasm. We used fluorescence recovery after photobleaching to quantify rapid diffusion of this molecule between the cytoplasms of all the cells in the filament. This indicates nonspecific intercellular channels allowing the movement of molecules from cytoplasm to cytoplasm. We quantify rates of molecular exchange as filaments adapt to diazotrophic growth. Exchange among vegetative cells becomes faster as filaments differentiate, becoming considerably faster than exchange with heterocysts. Slower exchange is probably a price paid to maintain a microaerobic environment in the heterocyst. We show that the slower exchange is partly due to the presence of cyanophycin polar nodules in heterocysts. The phenotype of a null mutant identifies FraG (SepJ), a membrane protein localised at the cell–cell interface, as a strong candidate for the channel‐forming protein.

title: FraC/FraD‐dependent intercellular molecular exchange in the filaments of a heterocyst‐forming cyanobacterium, Anabaena sp.
abstract: The filamentous, heterocyst‐forming cyanobacteria are multicellular organisms in which two different cell types, the CO2‐fixing vegetative cells and the N2‐fixing heterocysts, exchange nutrients and regulators. In Anabaena sp. strain PCC 7120, inactivation of sepJ or genes in the fraC operon (fraC, fraD and fraE) produce filament fragmentation. SepJ, FraC and FraD are cytoplasmic membrane proteins located in the filament's intercellular septa that are needed for intercellular exchange of the fluorescent tracer calcein (622 Da). Transmission electron microscopy showed an alteration in the heterocyst cytoplasmic membrane at the vegetative cell‐heterocyst septa in ΔfraC and ΔfraD mutants. Immunogold labelling of FraD confirmed its localization in the intercellular septa and clearly showed the presence of part of the protein between the cytoplasmic membranes of the adjacent cells. This localization seemed to be affected in the ΔfraC mutant but was not impaired in a ΔsepJ mutant. Intercellular transfer of a smaller fluorescent tracer, 5‐carboxyfluorescein (374 Da), was largely impaired in ΔfraC, ΔfraD and double ΔfraC‐ΔfraD mutants, but much less in the ΔsepJ mutant. These results show the existence in the Anabaena filaments of a FraC/FraD‐dependent intercellular molecular exchange that does not require SepJ.

title: Outer membrane continuity and septosome formation between vegetative cells in the filaments of Anabaena sp. PCC 7120
abstract: Anabaena sp. PCC 7120 is a prototype filamentous nitrogen‐fixing cyanobacterium, in which nitrogen fixation and photosynthesis are spatially separated. Recent molecular and cellular studies have established the importance of molecular exchange between cells in the filament, but the routes involved are still under investigation. Two current models propose either a continuous periplasm or direct connections between adjacent cells whose integrity requires the protein SepJ. We used electron tomography to analyze the ultrastructure of the septum between vegetative cells in the Anabaena filament and were able to visualize intercellular connections that we term ‘SEPTOSOMES’. We observed that, whereas the existence of the septosome does not depend on the presence of SepJ, the spacing between the two plasma membranes of the septum was significantly decreased in a ΔsepJ mutant. In addition, we observed that the peptidoglycan layer of each cell enters the septum but the outer membrane does not. Thus, each cell in the filament is individually surrounded by a plasma membrane and a peptidoglycan layer, and physical cell–cell contacts are mediated by the septosome.

title: Phosphorylation and nitrogenase activity in isolated heterocysts from Anabaena variabilis (ATCC 29413)
abstract: Adenylate-pool composition, energy charge, and nitrogenase activity were examined in isolated heterocysts from Anabaena variabilis (ATCC 29413). ATP formation was detected as a light- or oxygen-induced increase in ATP concentration. No cofactors or substrates had to be added for photophosphorylation to occur, whereas oxidative phosphorylation was dependent on hydrogen and oxygen (Knallgas reaction). The increase in ATP concentration was reflected by a decrease in AMP concentration, accompanied by small changes in ADP levels. Thus, a regulation of the adenylate pool by a myokinase (adenylate kinase) has to be assumed. Upon dark-light transitions, the energy charge in heterocysts increased from values below 0.4 to values approaching 0.8. High energy-charge values, reached in the light only, allowed for high rates of acetylene reduction in the presence of hydrogen. The increase in the energy charge in the dark to approx. 0.64 by addition of oxygen (5% (vv) in the presence of hydrogen) resulted in low nitrogenase activities, generally not exceeding 1–3% of the light-induced rates. In the dark, oxygen concentrations above 10% were inhibitory to both ATP formation and acetylene reduction. Increasing light intensities led to a steep increase in energy charge followed by an increase in nitrogenase activity. Plotting enzyme activity versus energy charge, a nonlinear, asymptotic relationship was observed.

title: Cyanobacterial psbA families in Anabaena and Synechocystis encode trace, constitutive and UVB-induced D1 isoforms.
abstract: Cyanobacteria cope with UVB induced photoinhibition of Photosystem II by regulating multiple psbA genes to boost the expression of D1 protein (in Synechocystis sp. PCC6803), or to exchange the constitutive D1:1 protein to an alternate D1:2 isoform (in Synechococcus sp. PCC7942). To define more general patterns of cyanobacterial psbA expression, we applied moderately photoinhibitory UVB to Anabaena sp. PCC7120 and tracked the expression of its five psbA genes. psbAI, encoding a D1:1 protein isoform characterized by a Gln130, represented the majority of the psbA transcript pool under control conditions. psbAI transcripts decreased upon UVB treatment but the total psbA transcript pool increased 3.5 fold within 90 min as a result of sharply increased psbAII, psbAIV and psbAIII transcripts encoding an alternate D1:2 protein isoform characterized by Glu130, similar to that of Synechococcus. Upon UVB treatment the relaxation of flash induced chlorophyll fluorescence showed a characteristic acceleration of a decay phase likely associated with the exchange from the D1:1 protein isoform encoded by psbAI to the alternate D1:2 isoform encoded by psbAIV, psbAII and psbAIII. Throughout the UVB treatment the divergent psbA0 made only a trace contribution to the total psbA transcript pool. This suggests a similarity to the divergent psbAI gene from Synechocystis, whose natural expression we demonstrate for the first time at a trace level similar to psbA0 in Anabaena. These trace-expressed psbA genes in two different cyanobacteria raise questions concerning the functions of these divergent genes.

title: Strategies for psbA gene expression in cyanobacteria, green algae and higher plants: from transcription to PSII repair.
abstract: The Photosystem (PS) II of cyanobacteria, green algae and higher plants is prone to light-induced inactivation, the D1 protein being the primary target of such damage. As a consequence, the D1 protein, encoded by the psbA gene, is degraded and re-synthesized in a multistep process called PSII repair cycle. In cyanobacteria, a small gene family codes for the various, functionally distinct D1 isoforms. In these organisms, the regulation of the psbA gene expression occurs mainly at the level of transcription, but the expression is fine-tuned by regulation of translation elongation. In plants and green algae, the D1 protein is encoded by a single psbA gene located in the chloroplast genome. In chloroplasts of Chlamydomonas reinhardtii the psbA gene expression is strongly regulated by mRNA processing, and particularly at the level of translation initiation. In chloroplasts of higher plants, translation elongation is the prevalent mechanism for regulation of the psbA gene expression. The pre-existing pool of psbA transcripts forms translation initiation complexes in plant chloroplasts even in darkness, while the D1 synthesis can be completed only in the light. Replacement of damaged D1 protein requires also the assistance by a number of auxiliary proteins, which are encoded by the nuclear genome in green algae and higher plants. Nevertheless, many of these chaperones are conserved between prokaryotes and eukaryotes. Here, we describe the specific features and fundamental differences of the psbA gene expression and the regeneration of the PSII reaction center protein D1 in cyanobacteria, green algae and higher plants. This article is part of a Special Issue entitled Photosystem II.

title: Photosynthetic components and activities of nitrogen-fixing isolated heterocysts of Anabaena cylindrica
abstract: Isolated heterocysts of the N2-fixing Anabaena cylindrica, prepared by a combination of lysozyme and Yeda press treatments, are metabolically active with over 90% of the measurable nitrogenase activity being located in the heterocyst preparations after disruption of the intact filaments. The photosynthetic activities of such isolated heterocysts are characterized by an inability to carry out the photolysis of water or to fix CO2. The lack of O2 evolution appears to be due in part to the depletion during heterocyst differentiation of Mn, a central component of the photosystem II reaction centre in O2-evolving algae. There is evidence that components of the photosynthetic electron transport chain on the reducing side of the photosystem II reaction centre are present and functional in heterocysts. These include cytochrome c554, plastocyanin, plastoquinone, cytochrome b559, P700, cytochrome b563, and iron-sulphur proteins which appear to correspond to centre A and centre B of higher plant chloroplasts. Soluble, or loosely bound ferredoxin is also present and involved in electron transport from ferredoxin to NADP. Isolated heterocysts photoreduce methylviologen when reduced 2,6-dichlorophenolindophenol and diphenylcarbazide serve as electron donors. They show P700 photo-oxidation and photoreduction, photosynthetic electron transport which is inhibited by 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone an antagonist of plastoquinone, photophosphorylation, oxidative phosphorylation and ferredoxin-NADP oxido-reductase mediated reactions. The photosynthetic modifications of the heterocyst are such that electron transport and the generation of ATP for nitrogenase can occur without concomitant O2 evolution and without nitrogenase having to compete with CO2 fixation for ATP and reductant.

title: Absence of photosystem 2 in heterocysts of the blue-green alga Anabaena.
abstract: Heterocysts of the filamentous blue-green alga Anabaena cylindrica have a high concentration of the System 1 reaction center P700 and are able to photooxidize a cytochrome. They have a low yield of chlorophyll a fluorescence, do not show light-induced changes in fluorescence yield, show a very low intensity of delayed light emission and do not show Hill-reaction activity. It is concluded that heterocysts contain Photosystem 1 only.

title: An assessment of photosynthetic downregulation in cyanobacteria from the Gunnera–Nostoc symbiosis
abstract: • The transition of Nostoc colonies from a free-living to a symbiotic condition, in the Nostoc–Gunnera association, involves a downregulation of photosynthesis, which is not associated with an altered heterocyst frequency or a loss of photosynthetic pigments. 
• Fluorescence assessments and measurements of Hill activity using the artificial electron acceptor 2,6-dichloro-p-benzoquinine (DCIP) indicate a major reduction in photosystem II (PSII) photochemistry in symbiotic vegetative cells. 
• The downregulation of PSII activity in symbiotic cells was associated with a smaller effective pool size of the primary electron acceptors (QA) and plastoquinone (PQ), and a reduction in the efficiency of light utilization by individual PSII units. The reduction in PSII electron transport was correlated with a partial degradation of the D1 protein and the presence of C-terminal degradation products. 
• While it has been proposed that PSII is absent in the symbiotic state, our results suggest that PSII units are present but their photochemical efficiency is much reduced. We suggest that modification to the D1 protein and a decrease in the effective pool size of the primary electron acceptors of PSII may signal a shift from an autotrophic to a heterotrophic mode of metabolism.

title: Structures and functions of the extrinsic proteins of photosystem II from different species
abstract: This minireview presents a summary of information available on the variety and binding properties of extrinsic proteins that form the oxygen-evolving complex of photosystem II (PSII) of cyanobacteria, red alga, diatom, green alga, euglena, and higher plants. In addition, the structure and function of extrinsic PsbO, PsbV, and PsbU proteins are summarized based on the crystal structure of thermophilic cyanobacterial PSII together with biochemical and genetic studies from various organisms.

title: Energy transfer from phycobiliproteins to photosystem I in vegetative cells and heterocysts of Anabaena variabilis.
abstract: The presence of phycobilins in heterocysts of Anabaena variabilis is established on the basis of absorption and fluorescence spectroscopy. At 77 K heterocysts exhibit fluorescence emission bands at 645 and 661 nm indicative of phycocyanin and allophycocyanin, respectively. Both allophycocyanin levels and fluorescence emission at 695 nm were low in heterocysts relative to whole filaments. In situ fluorescence microscopy confirmed the presence of phycobilins in individual heterocysts, but the pigment levels varied considerably among cells. Heterocysts exhibited Photosystem I activity, as evidenced by photooxidation of P-700, but no Photosystem II activity. The quantum efficiency of phycobilins in sensitizing P-700 photooxidation was 50-70% that of chlorophyll a. Phycoibins were also effective in promoting light-dependent reduction of acetylene to ethylene. The results are discussed in terms of the role of the heterocyst in nitrogen fixation and of the significance of energy transfer from phycobilins to Photosystem I in heterocysts.

title: Structure and regulation of genes encoding phycocyanin and allophycocyanin from Anabaena variabilis ATCC 29413
abstract: Gene clones encoding phycocyanin and allophycocyanin were isolated from an Anabaena variabilis ATCC 29413-Charon 30 library by using the phycocyanin (cpc) genes of Agmenellum quadruplicatum and the allophycocyanin (apc) genes of Cyanophora paradoxa as heterologous probes. The A. variabilis cpcA and cpcB genes occur together in the genome, as do the apcA and apcB genes; the two sets of genes are not closely linked, however. The cpc and apc genes appear to be present in only one copy per genome. DNA-RNA hybridization analysis showed that expression of the cpc and apc genes is greatly decreased during nitrogen starvation; within 1 h no cpc or apc mRNA could be detected. The source of nitrogen for growth did not influence expression of the genes; vegetative cells from nitrogen-fixing and ammonia-grown cultures had approximately the same levels of cpc and apc mRNAs. Heterocysts had less than 5% as much cpc mRNA as vegetative cells from nitrogen-fixing cultures. Northern hybridization (RNA blot) analysis showed that the cpc genes are transcribed to give an abundant 1.4-kilobase (kb) RNA as well as two less prominent 3.8- and 2.6-kb species. The apc genes gave rise to two transcripts, a 1.4-kb predominant RNA and a minor 1.75-kb form.

title: Protein-based organelles in bacteria: carboxysomes and related microcompartments
abstract: Many bacteria contain intracellular microcompartments with outer shells that are composed of thousands of protein subunits and interiors that are filled with functionally related enzymes. These microcompartments serve as organelles by sequestering specific metabolic pathways in bacterial cells. The carboxysome, a prototypical bacterial microcompartment that is found in cyanobacteria and some chemoautotrophs, encapsulates ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase, and thereby enhances carbon fixation by elevating the levels of CO2 in the vicinity of RuBisCO. Evolutionarily related, but functionally distinct, microcompartments are present in diverse bacteria. Although bacterial microcompartments were first observed more than 40 years ago, a detailed understanding of how they function is only now beginning to emerge.

title: Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation.
abstract: Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO(2) concentrations by employing a CO(2)-concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO(2)-fixing enzyme, RubisCO. The efficiency of CO(2) fixation by the sequestered RubisCO is enhanced by co-localization with a specialized carbonic anhydrase that catalyzes dehydration of the cytoplasmic bicarbonate and ensures saturation of RubisCO with its substrate, CO(2). There are two genetically distinct carboxysome types that differ in their protein composition and in the carbonic anhydrase(s) they employ. Here we review the existing information concerning the genomics, structure and enzymology of these uniquely adapted carbonic anhydrases, which are of fundamental importance in the global carbon cycle.

title: The Unique Cyanobacterial Protein OpcA Is an Allosteric Effector of Glucose-6-phosphate Dehydrogenase in Nostoc punctiformeATCC 29133*
abstract: Glucose-6-phosphate dehydrogenase (G6PD), encoded by zwf, is essential for nitrogen fixation and dark heterotrophic growth of the cyanobacterium Nostoc punctiforme ATCC 29133. In N. punctiforme,zwf is part of a four-gene operon transcribed in the orderfbp-tal-zwf-opcA. Genetic analyses indicated thatopcA is required for G6PD activity. To define the role ofopcA, the synthesis, aggregation state, and activity of G6PD in N. punctiforme strains expressing different amounts of G6PD and/or OpcA were examined. A single tetrameric form of G6PD was consistently observed for all strains, as well as for recombinantN. punctiforme His-G6PD purified from Escherichia coli, regardless of the quantity of OpcA present. However, His-G6PD and the G6PD of strain UCD 351, which lacks OpcA, had low affinities for glucose 6-phosphate (G6P) substrate (K m (app) = 65 and 85 mm, respectively) relative to wild-type N. punctiforme G6PD (K m (app) = 0.5 mm). Near wild-type affinities for G6P were observed for these enzymes when saturating amounts of His-OpcA- or OpcA-containing extract were added. Kinetic studies were consistent with OpcA acting as an allosteric activator of G6PD. A role in redox modulation of G6PD activity was also indicated, because thioredoxin-mediated inactivation and reactivation of His-G6PD occurred only when His-OpcA was present.

title: Transcriptional regulation of zwf, encoding glucose‐6‐phosphate dehydrogenase, from the cyanobacterium Nostoc punctiforme strain ATCC 29133
abstract: The gene encoding glucose‐6‐phosphate dehydrogenase (G6PD), zwf, in Nostocpunctiforme strain ATCC 29133 is part of a four‐gene operon that also encodes fructose bisphosphatase (fbp), transaldolase (tal ) and a gene product termed OpcA, which is cotranscribed with zwf and essential for G6PD activity. The effect of exogenous nitrogen and carbon sources on transcription of these genes was investigated. Growth in the presence of ammonium yielded low levels of transcripts encoding all genes of the operon, while growth under nitrogen‐fixing conditions resulted in a large increase of transcripts encoding for fbp and zwf–opcA. When cells are grown in the presence of fructose, levels of transcripts encoding tal and zwf–opcA were increased, relative to levels in ammonium‐grown cells. These results indicate that this facultatively heterotrophic cyanobacterium can respond to changes in its environment by altering transcription of genes involved in carbon catabolism. Primer extension identified five 5′ ends corresponding to the major regulated transcripts which we conclude arise from independent transcriptional start points.

title: Activities of enzymes of the oxidative and the reductive pentose phosphate pathways in heterocysts of a blue-green alga.
abstract: Preparations of heterocysts of Anabaena cylindrica Lemm. had 7- to 8-fold higher activities of glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, 2-fold more hexokinase activity, and 0.02 to 0.06 times as much ribulose diphosphate carboxylase and glyceraldehyde 3-phosphate dehydrogenase activities as did whole filaments per milligram soluble protein in cell-free extracts. Time courses of solubilization of glucose 6-phosphate dehydrogenase activity indicated that heterocysts contain 74 to 80% of the total activity of this enzyme in filaments.

title: Simultaneous occurrence of two different glyceraldehyde-3-phosphate dehydrogenases in heterocystous N(2)-fixing cyanobacteria.
abstract: Enzyme activity determinations and Western and Northern blot analyses have shown the presence of two catalytically different glyceraldehyde-3-phosphate dehydrogenases (GAPDH) in both vegetative cells and heterocysts of several N(2)-fixing Anabaena strains: (a) the gap2-encoded NAD(P)-dependent GAPDH2 (EC 1.2.1.59), the enzyme involved in the photosynthetic carbon assimilation pathway, which is present at higher levels in vegetative cells, and (b) the gap3-encoded NAD-dependent GAPDH3 (EC 1.2.1.12), presumably involved in carbohydrate anabolism and catabolism, which is the predominant GAPDH in heterocysts. In contrast, the gap1-encoded GAPDH1, which is the other NAD-dependent cyanobacterial GAPDH, is virtually absent in both cell types. These findings are discussed in the context of carbon metabolism of heterocystous N(2)-fixing cyanobacteria.

title: Cellular Differentiation of Sucrose Metabolism in Anabaena variabilis
abstract: Upon treatment of whole filaments of Anabaena variabilis with a French pressure cell, the activity of sucrose synthase (UDP glucose; D-fructose 2-α-ᴅ-glucosyl transferase, EC 2.4.1.13) was found to be associated almost exclusively with the vegetative cells. The sucrose-cleaving enzyme, an alkaline invertase (β-ᴅ-fructofuranoside fructohydrolase, EC 3.2.1.26), appears to be localized solely within the heterocysts. The implications of these findings, in the light of relevant data from the literature, are summarized in a model representing the physiological differentiation and molecular exchange between vegetative cells and heterocysts.

title: Sucrose synthase and RuBisCo expression is similarly regulated by the nitrogen source in the nitrogen-fixing cyanobacterium Anabaena sp.
abstract: In higher plants and cyanobacteria, sucrose (Suc) metabolism is carried out by a similar set of enzymes. The function and regulation of Suc metabolism in cyanobacteria has begun to be elucidated. In strains of Anabaena sp., filamentous nitrogen-fixing cyanobacteria, Suc synthase (SuS, EC 2.4.1.13) controls Suc cell level through the cleavage of the disaccharide. The present work shows that there are two sus genes in Anabaena (Nostoc) sp. that are co-regulated regarding the nitrogen source; however, only susA accounts for the extractable SuS activity and for the control of the Suc level. Primer extension analysis has uncovered the sequence of the AnabaenasusA and susB ammonium-activated putative promoters, which share a high sequence similarity with that of rbcLS encoding ribulose bisphosphate carboxylase/oxygenase (EC 4.1.1.39) and other ammonium up-regulated genes. Moreover, susA and rbcLS expression is developmentally co-localized to the vegetative cells of the nitrogen-fixing cyanobacterial filaments. Our results strongly suggest the existence of a regulatory network that would coordinate the expression of key genes for Suc and nitrogen metabolism, carbon fixation, and development in Anabaena sp.

title: Role of NtcA, a cyanobacterial global nitrogen regulator, in the regulation of sucrose metabolism gene expression in Anabaena sp. PCC 7120
abstract: In the heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 (also known as Nostoc sp. PCC 7120), it has been shown that spsB and susA, the genes coding for proteins related to sucrose synthesis and cleavage, respectively, exhibit converse expression regarding the nitrogen source. In the nitrogen-fixing filament, spsB expression is mostly localized to the heterocysts and susA is only expressed in vegetative cells. The aim of this work was to investigate the participation of NtcA, a global nitrogen regulator that operates in cyanobacteria, in the regulation of sucrose metabolism genes in Anabaena sp. PCC 7120. The induction of spsB expression observed in the filaments upon combined-nitrogen depletion was abolished in an NtcA-deficient mutant. In vitro experiments showed that NtcA binds specifically but with different affinities to two sites in the spsB promoter region. When susA expression was analyzed after a combined-nitrogen starvation, the levels of mRNA, polypeptide and activity increased in the mutant in comparison with the wild-type strain. Also, NtcA interacted with one site in the promoter region of susA. We conclude that sucrose metabolism is coordinated at the transcriptional level with nitrogen metabolism, suggesting a global metabolism regulating role for NtcA.

title: Sucrose biosynthesis in a prokaryotic organism: Presence of two sucrose-phosphate synthases in Anabaena with remarkable differences compared with the plant enzymes.
abstract: Biosynthesis of sucrose-6-P catalyzed by sucrose-phosphate synthase (SPS), and the presence of sucrose-phosphate phosphatase (SPP) leading to the formation of sucrose, have both been ascertained in a prokaryotic organism: Anabaena 7119, a filamentous heterocystic cyanobacterium. Two SPS activities (SPS-I and SPS-II) were isolated by ion-exchange chromatography and partially purified. Four remarkable differences between SPSs from Anabaena and those from higher plants were shown: substrate specificity, effect of divalent cations, native molecular mass, and oligomeric composition. Both SPS-I and SPS-II accept Fru-6-P (K(m) for SPS-I = 0.8 +/- 0.1 mM; K(m) for SPS-II = 0.7 +/- 0.1 mM) and UDP-Glc as substrates (K(m) for SPS-I = 1.3 +/- 0.4 mM; K(m) for SPS-II = 4.6 +/- 0.4 mM), but unlike higher plant enzymes, they are not specific for UDP-Glc. GDP-Glc and TDP-Glc are also SPS-I substrates (K(m) for GDP-Glc = 1.2 +/- 0.2 mM and K(m) for TDP-Glc = 4.0 +/- 0.4 mM), and ADP-Glc is used by SPS-II (K(m) for ADP-Glc = 5.7 +/- 0.7 mM). SPS-I has an absolute dependence toward divalent metal ions (Mg2+ or Mn2+) for catalytic activity, not found in plants. A strikingly smaller native molecular mass (between 45 and 47 kDa) was determined by gel filtration for both SPSs, which, when submitted to SDS/PAGE, showed a monomeric composition. Cyanobacteria are, as far as the authors know, the most primitive organisms that are able to biosynthesize sucrose as higher plants do.

title: Sucrose-phosphate phosphatase from Anabaena sp. strain PCC 7120: isolation of the protein and gene revealed significant structural differences from the higher-plant enzyme
abstract: The present study describes the first isolation and characterization of a prokaryotic protein and gene for sucrose-phosphate phosphatase (SPP), the enzyme that catalyzes the terminal step in sucrose synthesis. For gene isolation, a 2,015-bp DNA fragment containing an open reading frame with about 31% amino acid identity to Synechocystis SPS was amplified from Anabaena sp. PCC 7120 DNA. Surprisingly, expression of the putative gene in Escherichia coli demonstrated that it encoded an SPP protein. The expressed protein cross-reacted with antibodies against the native form of Anabaena SPP and its biochemical properties were identical to those of the enzyme purified from the cyanobacterial cells. Comparisons of the Anabaena SPP with the higher-plant enzyme revealed important differences in the C-terminal region, molecular mass, subunit composition and immunoreactivity. Nevertheless, two conserved motifs, including four invariant aspartate residues similar to those found in members of the phosphohydrolase superfamily, were identified in the Anabaena SPP deduced amino acid sequence.

title: Carbon Cycling in Anabaena sp. PCC 7120. Sucrose Synthesis in the Heterocysts and Possible Role in Nitrogen Fixation1[OA]
abstract: Nitrogen (N) available to plants mostly originates from N2 fixation carried out by prokaryotes. Certain cyanobacterial species contribute to this energetically expensive process related to carbon (C) metabolism. Several filamentous strains differentiate heterocysts, specialized N2-fixing cells. To understand how C and N metabolism are regulated in photodiazotrophically grown organisms, we investigated the role of sucrose (Suc) biosynthesis in N2 fixation in Anabaena sp. PCC 7120 (also known as Nostoc sp. PCC 7120). The presence of two Suc-phosphate synthases (SPS), SPS-A and SPS-B, directly involved in Suc synthesis with different glucosyl donor specificity, seems to be important in the N2-fixing filament. Measurement of enzyme activity and polypeptide levels plus reverse transcription-polymerase chain reaction experiments showed that total SPS expression is greater in cells grown in N2 versus combined N conditions. Only SPS-B, however, was seen to be active in the heterocyst, as confirmed by analysis of green fluorescent protein reporters. SPS-B gene expression is likely controlled at the transcriptional initiation level, probably in relation to a global N regulator. Metabolic control analysis indicated that the metabolism of glycogen and Suc is likely interconnected in N2-fixing filaments. These findings suggest that N2 fixation may be spatially compatible with Suc synthesis and support the role of the disaccharide as an intermediate in the reduced C flux in heterocyst-forming cyanobacteria.

title: Cyanobacterial alkaline/neutral invertases. Origin of sucrose hydrolysis in the plant cytosol?
abstract: The aim of this work was to investigate the occurrence of invertase (Inv) in cyanobacteria. We describe the first isolation and characterization of prokaryotic alkaline/neutral Inv (A/N-Inv) genes. Two genes (invA and invB) were identified in Anabaena sp. PCC 7120, which share about 50–56% identity with plant A/N-Inv and encode proteins of about 53–55 kDa. The identification of these proteins was confirmed by biochemical and immunological studies with recombinant proteins and with the enzymes isolated from Anabaena cells. Expression analysis supported the important role of A/N-Inv in nitrogen-fixing growth conditions. Nevertheless, A/N-Inv activities were shown in all filamentous and unicellular cyanobacteria investigated, regardless of their capacity to fix dinitrogen. Searches in complete sequenced genomes showed that A/N-Inv homologues are restricted to cyanobacterial species and plants. In particular, filamentous nitrogen-fixing strains display two A/N-Inv genes and unicellular strains have only one. Phylogenetic analysis leads us to suggest that modern plant A/N-Inv might have originated from an orthologous ancestral gene after the endosymbiotic origin of chloroplasts.

title: Sucrose is involved in the diazotrophic metabolism of the heterocyst‐forming cyanobacterium Anabaena sp
abstract: Sucrose synthase (SuS) expression was studied in the filamentous, nitrogen‐fixing cyanobacterium Anabaena sp. PCC 7119. SuS activity, SusA polypeptide, and susA mRNA levels were lower in cells cultured diazotrophically than in the presence of combined nitrogen. An insertional susA mutant presented a dramatic increase in sucrose levels, whereas the disaccharide was not detectable in a susA overexpressing strain, indicating that SusA is involved in the cleavage of sucrose in vivo. Diazotrophic growth was impaired in the susA overexpressing strain, suggesting a role for sucrose in diazotrophic metabolism and the involvement of SusA in the control of carbon flux in the N2‐fixing filament.

title: Sucrose synthase is involved in the conversion of sucrose to polysaccharides in filamentous nitrogen-fixing cyanobacteria
abstract: Higher plants and cyanobacteria metabolize sucrose (Suc) by a similar set of enzymes. Suc synthase (SuS, UDP-glucose: d-fructose 2-α-d-glucosyl transferase, EC 2.4.1.13) catalyses the synthesis and cleavage of Suc, and in higher plants, it plays an important role in polysaccharides biosynthesis and carbon allocation. In this work, we have studied the functional relationship between SuS and the metabolism of polysaccharides in filamentous nitrogen-fixing cyanobacteria. We show that the nitrogen and carbon sources and light regulate the expression of the SuS encoding gene (susA), in a similar way that they regulate the accumulation of polysaccharides. Furthermore, glycogen content in an Anabaena sp. mutant strain with an insertion inactivation of susA was lower than in the wild type strain under diazotrophic conditions, while both glycogen and polysaccharides levels were higher in a mutant strain constitutively overexpressing susA. We also show that there are soluble and membrane-bound forms of SuS in Anabaena. Taken together, these results strongly suggest that SuS is involved in the Suc to polysaccharides conversion according to nutritional and environmental signals in filamentous nitrogen-fixing cyanobacteria.

title: A membrane-associated form of sucrose synthase and its potential role in synthesis of cellulose and callose in plants.
abstract: Sucrose synthase (SuSy; EC 2.4.1.13; sucrose + UDP reversible UDPglucose + fructose) has always been studied as a cytoplasmic enzyme in plant cells where it serves to degrade sucrose and provide carbon for respiration and synthesis of cell wall polysaccharides and starch. We report here that at least half of the total SuSy of developing cotton fibers (Gossypium hirsutum) is tightly associated with the plasma membrane. Therefore, this form of SuSy might serve to channel carbon directly from sucrose to cellulose and/or callose synthases in the plasma membrane. By using detached and permeabilized cotton fibers, we show that carbon from sucrose can be converted at high rates to both cellulose and callose. Synthesis of cellulose or callose is favored by addition of EGTA or calcium and cellobiose, respectively. These findings contrast with the traditional observation that when UDPglucose is used as substrate in vitro, callose is the major product synthesized. Immunolocalization studies show that SuSy can be localized at the fiber surface in patterns consistent with the deposition of cellulose or callose. Thus, these results support a model in which SuSy exists in a complex with the beta-glucan synthases and serves to channel carbon from sucrose to glucan.

title: Morphological and ultrastructural changes in vegetative cells and heterocysts of Anabaena variabilis grown with fructose
abstract: The morphology and ultrastructure of Anabaena variabilis grown in medium with and without 40 mM fructose were compared. Vegetative cells and young heterocysts in fructose-supplemented medium were significantly larger, were filled with glycogen granules, and had fewer thylakoids. Developing heterocysts contained large numbers of glycogen granules well into mature stages, and envelope formation was precocious. As heterocysts enlarged in fructose medium, their shape became more broadly oblong compared with the more rectangular heterocysts in fructose-free medium.

title: Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in Anabaena sp. Strain PCC 7120
abstract: As demonstrated with alr2835 (hepA) and alr2834 (hepC) mutants, heterocysts of Anabaena sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep+ phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox+ phenotype). Transpositions presumptively responsible for a Fox− phenotype were localized in open reading frames (ORFs) near hepA and hepC. A mutation in each of nine of these ORFs was complemented by a clone bearing only that single, intact ORF. Heterocysts of the nine mutants were found to lack an envelope polysaccharide layer. Complementation of mutations in alr2832 and alr2840 may have resulted from recombination. However, alr2825, alr2827, alr2831, alr2833, alr2837, alr2839, and alr2841, like hepA and hepC, are required for a Hep+ Fox+ phenotype.

title: Genetic evidence of a major role for glucose-6-phosphate dehydrogenase in nitrogen fixation and dark growth of the cyanobacterium Nostoc sp. strain ATCC 29133
abstract: Heterocysts, sites of nitrogen fixation in certain filamentous cyanobacteria, are limited to a heterotrophic metabolism, rather than the photoautotrophic metabolism characteristic of cyanobacterial vegetative cells. The metabolic route of carbon catabolism in the supply of reductant to nitrogenase and for respiratory electron transport in heterocysts is unresolved. The gene (zwf) encoding glucose-6-phosphate dehydrogenase (G6PD), the initial enzyme of the oxidative pentose phosphate pathway, was inactivated in the heterocyst-forming, facultatively heterotrophic cyanobacterium, Nostoc sp. strain ATCC 29133. The zwf mutant strain had less than 5% of the wild-type apparent G6PD activity, while retaining wild-type rates of photoautotrophic growth with NH4+ and of dark O2 uptake, but it failed to grow either under N2-fixing conditions or in the dark with organic carbon sources. A wild-type copy of zwf in trans in the zwf mutant strain restored only 25% of the G6PD specific activity, but the defective N2 fixation and dark growth phenotypes were nearly completely complemented. Transcript analysis established that zwf is in an operon also containing genes encoding two other enzymes of the oxidative pentose phosphate cycle, fructose-1,6-bisphosphatase and transaldolase, as well as a previously undescribed gene (designated opcA) that is cotranscribed with zwf. Inactivation of opcA yielded a growth phenotype identical to that of the zwf mutant, including a 98% decrease, relative to the wild type, in apparent G6PD specific activity. The growth phenotype and lesion of G6PD activity in the opcA mutant were complemented in trans with a wild-type copy of opcA. In addition, placement in trans of a multicopy plasmid containing the wild-type copies of both zwf and opcA in the zwf mutant resulted in an approximately 20-fold stimulation of G6PD activity, relative to the wild type, complete restoration of nitrogenase activity, and a slight stimulation of N2-dependent photoautotrophic growth and fructose-supported dark growth. These results unequivocally establish that G6PD, and most likely the oxidative pentose phosphate pathway, represents the essential catabolic route for providing reductant for nitrogen fixation and respiration in differentiated heterocysts and for dark growth of vegetative cells. Moreover, the opcA gene product is involved by an as yet unknown mechanism in G6PD synthesis or catalytic activity.

title: Pathway of nitrogen metabolism after fixation of 13N-labeled nitrogen gas by the cyanobacterium, Anabaena cylindrica.
abstract: Methods have been developed for identifying the pathway of assimilation of N2-derived nitrogen. The products of fixation of 13N-labeled nitrogen gas ([13N]N2), and the distribution of 13N within glutamine, were determined after short periods of labeling (approximately 1 to 120 s) and also in pulse-chase experiments. Ammonia, the amide nitrogen of glutamine, and the alpha-amino nitrogen of glutamate, in that order, were the first observed products of fixation of N2 by the cyanobacterium (blue-green alga), Anabaena cylindrica. This sequence of the formation of nitrogenous products was confirmed by the use of inhibitors. The presence of 1 mM methionine sulfoximine permitted continued formation of 13NH3, while virtually preventing 13N-labeling of amino acids. In the presence of 1 mM azaserine, glutamine was labeled, but not other amino acids. Our observations demonstrate unequivocally that N2-derived nitrogen fixed by this organism is metabolized initially by the glutamine synthetase/glutamate synthase pathway.

title: The isocitrate dehydrogenase from cyanobacteria
abstract: The present communication describes the properties of isocitrate dehydrogenase in crude extracts from the unicellular Anacystis nidulans and from heterocysts and vegetative cells of Nostoc muscorum and Anabaena cylindrica. The activity levels of this enzyme are much higher in heterocysts than in vegetative cells of N. muscorum and A. cylindrica. Isocitrate dehydrogenase is virtually inactive in vegetative cells of A. cylindrica. The enzyme is negatively regulated by the reduction charge and scarcely affected by oxoglutarate in the three cyanobacteria. The inhibition by ATP and ADP is competitive with respect to isocitrate and NADP+ in A. cylindrica and N. muscorum and noncompetitive in A. nidulans. Isocitrate dehydrogenase from the three cyanobacteria seems to be a hysteretic enzyme. All the experimental data suggest that the major physiological role of isocitrate and the isocitrate dehydrogenase in heterocysts is not to generate reducing equivalents for N2-fixation. Oxoglutarate formed by the enzyme reaction is likely required for the biosynthesis of glutamate inside the heterocysts. Thioredoxin preparations from spinach chloroplasts or from A. cylindrica activate isocitrate dehydrogenase from either heterocysts or vegetative cells of A. cylindrica. Activation is completed within seconds and requires dithiothreitol besides thioredoxin. The thioredoxin preparation which activates isocitrate dehydrogenase also activates NADP+-dependent malate dehydrogenase from spinach chloroplasts or heterocysts of A. cylindrica. Isocitrate dehydrogenase from A. cylindrica is deactivated by oxidized glutathione. It is speculated that isocitrate dehydrogenase and thioredoxin play a role in the differentiation of vegetative cells to heterocysts.

title: Posttranscriptional Regulation of Glutamine Synthetase in the Filamentous Cyanobacterium Anabaena sp. PCC 7120: Differential Expression between Vegetative Cells and Heterocysts
abstract: Genes homologous to those implicated in glutamine synthetase (GS) regulation by protein-protein interaction in the cyanobacterium Synechocystis sp. strain PCC 6803 are conserved in several cyanobacterial sequenced genomes. We investigated this GS regulatory mechanism in Anabaena sp. strain PCC 7120. In this strain the system operates with only one GS inactivation factor (inactivation factor 7A [IF7A]), encoded by open reading frame (ORF) asl2329 (gifA). Following addition of ammonium, expression of gifA is derepressed, leading to the synthesis of IF7A, and consequently, GS is inactivated. Upon ammonium removal, the GS activity returns to the initial level and IF7A becomes undetectable. The global nitrogen control protein NtcA binds to the gifA promoter. Constitutive high expression levels of gifA were found in an Anabaena ntcA mutant (CSE2), indicating a repressor role for NtcA. In vitro studies demonstrate that Anabaena GS is not inactivated by Synechocystis IFs (IF7 and IF17), indicating the specificity of the system. We constructed an Anabaena strain expressing a second inactivating factor, containing the amino-terminal part of IF17 from Synechocystis fused to IF7A. GS inactivation in this strain is more effective than that in the wild type (WT) and resembles that observed in Synechocystis. Finally we found differential expression of the IF system between heterocysts and vegetative cells of Anabaena.

title: The Presence of Glutamate Dehydrogenase Is a Selective Advantage for the Cyanobacterium Synechocystis sp. Strain PCC 6803 under Nonexponential Growth Conditions
abstract: The unicellular cyanobacterium Synechocystis sp. strain PCC 6803 has two putative pathways for ammonium assimilation: the glutamine synthetase-glutamate synthase cycle, which is the main one and is finely regulated by the nitrogen source; and a high NADP-dependent glutamate dehydrogenase activity (NADP-GDH) whose contribution to glutamate synthesis is uncertain. To investigate the role of the latter, we used two engineered mutants, one lacking and another overproducing NADP-GDH. No major disturbances in the regulation of nitrogen-assimilating enzymes or in amino acids pools were detected in the null mutant, but phycobiline content, a sensitive indicator of the nutritional state of cyanobacterial cells, was significantly reduced, indicating that NADP-GDH plays an auxiliary role in ammonium assimilation. This effect was already prominent in the initial phase of growth, although differences in growth rate between the wild type and the mutants were observed at this stage only at low light intensities. However, the null mutant was unable to sustain growth at the late stage of the culture at the point when the wild type showed the maximum NADP-GDH activity, and died faster in ammonium-containing medium. Overexpression of NADP-GDH improved culture proliferation under moderate ammonium concentrations. Competition experiments between the wild type and the null mutant confirmed that the presence of NADP-GDH confers a selective advantage toSynechocystis sp. strain PCC 6803 in late stages of growth.

title: The Sakaguchi Reaction Product Quenches Phycobilisome Fluorescence, Allowing Determination of the Arginine Concentration in Cells of Anabaena Strain PCC 7120
abstract: The filamentous cyanobacterium Anabaena fixes nitrogen in specialized cells called heterocysts. The immediate product of fixation, ammonia, is known to be assimilated by addition to glutamate to make glutamine. How fixed nitrogen is transported along the filament to the 10 to 20 vegetative cells that separate heterocysts is unknown. N-fixing heterocysts accumulate an insoluble polymer containing aspartate and arginine at the cell poles. Lockau's group has proposed that the polymer is degraded at the poles to provide a mobile carrier, arginine, to the vegetative cells (R. Richter, M. Hejazi, R. Kraft, K. Ziegler, and W. Lockau,  1999). We wished to use the Sakaguchi reaction for arginine to determine the relative cellular concentration of arginine along the filament. At present, the methods for measuring absorption of the Sakaguchi reaction product at 520 nm are insufficiently sensitive for that purpose. However, that product quenches the fluorescence of phycobiliproteins, which we have adapted to a determination of arginine. Our results are consistent with the proposal that arginine is a principal nitrogen carrier from heterocysts to vegetative cells in Anabaena.

title: Cyclic electron flow around Photosystem II in vivo
abstract: The oxygen flash yield (YO2) and photochemical yield of PS II (ΦPS II) were simultaneously detected in intact Chlorella cells on a bare platinum oxygen rate electrode. The two yields were measured as a function of background irradiance in the steady-state and following a transition from light to darkness. During steady-state illumination at moderate irradiance levels, YO2 and ΦPS II followed each other, suggesting a close coupling between the oxidation of water and QA reduction (Falkowski et al. (1988) ). Following a light-to-dark transition, however, the relationship between QA reduction and the fraction of PS II reaction centers capable of evolving O2 became temporarily uncoupled. ΦPS II recovered to the preillumination levels within 5–10 s, while the YO2 required up to 60 s to recover under aerobic conditions. The recovery of YO2 was independent of the redox state of QA, but was accompanied by a 30% increase in the functional absorption cross-section of PS II (σPS II). The hysteresis between YO2 and the reduction of QA during the light-to-dark transition was dependent upon the reduction level of the plastoquinone pool and does not appear to be due to a direct radiative charge back-reaction, but rather is a consequence of a transient cyclic electron flow around PS II. The cycle is engaged in vivo only when the plastoquinone pool is reduced. Hence, the plastoquinone pool can act as a clutch that disconnects the oxygen evolution from photochemical charge separation in PS II.

title: Over-expression of the β-carboxysomal CcmM protein in Synechococcus PCC7942 reveals a tight co-regulation of carboxysomal carbonic anhydrase (CcaA) and M58 content
abstract: Carboxysomes, containing the cell’s complement of RuBisCO surrounded by a specialized protein shell, are a central component of the cyanobacterial CO2-concentrating mechanism. The ratio of two forms of the β-carboxysomal protein CcmM (M58 and M35) may affect the carboxysomal carbonic anhydrase (CcaA) content. We have over-expressed both M35 and M58 in the β-cyanobacterium Synechococcus PCC7942. Over-expression of M58 resulted in a marked increase in the amount of this protein in carboxysomes at the expense of M35, with a concomitant increase in the observed CcaA content of carboxysomes. Conversely, M35 over-expression diminished M58 content of carboxysomes and led to a decrease in CcaA content. Carboxysomes of air-grown wild-type cells contained slightly elevated CcaA and M58 content and slightly lower M35 content compared to their 2% CO2-grown counterparts. Over a range of CcmM expression levels, there was a strong correlation between M58 and CcaA content, indicating a constant carboxysomal M58:CcaA stoichiometry. These results also confirm a role for M58 in the recruitment of CcaA into the carboxysome and suggest a tight regulation of M35 and M58 translation is required to produce carboxysomes with an appropriate CA content. Analysis of carboxysomal protein ratios, resulting from the afore-mentioned over-expression studies, revealed that β-carboxysomal protein stoichiometries are relatively flexible. Determination of absolute protein quantities supports the hypothesis that M35 is distributed throughout the β-carboxysome. A modified β-carboxysome packing model is presented.