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PubMed2004

Consequences of a deletion in dspA on transcript accumulation in Synechocystis sp. strain PCC6803.

A sensor histidine kinase of Synechococcus sp. strain PCC7942, designated nblS, was previously identified and shown to be critical for the acclimation of cells to high-light and nutrient limitation conditions and to influence the expression of a number of light-responsive genes. The nblS orthologue in Synechocystis sp. strain PCC6803 is designated dspA (also called hik33). We have generated a dspA null mutant and analyzed global gene expression in both the mutant and wild-type strains under high- and low-light conditions. The mutant is aberrant for the expression of many genes encoding proteins critical for photosynthesis, phosphate and carbon acquisition, and the amelioration of stress conditions. Furthermore, transcripts from a number of genes normally detected only during exposure of wild-type cells to high-light conditions become partially constitutive in the low-light-grown dspA mutant. Other genes for which transcripts decline upon exposure of wild-type cells to high light are already lower in the mutant during growth in low light. These results suggest that DspA may influence gene expression in both a positive and a negative manner and that the dspA mutant behaves as if it were experiencing stress conditions (e.g., high-light exposure) even when maintained at near-optimal growth conditions for wild-type cells. This is discussed with respect to the importance of DspA for regulating the responses of the cell to environmental cues.

Bacterial Proteins↗
PubMed2004

A novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell.

A significant portion of the total carbon fixed in the biosphere is attributed to the autotrophic metabolism of prokaryotes. In cyanobacteria and many chemolithoautotrophic bacteria, CO(2) fixation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), most if not all of which is packaged in protein microcompartments called carboxysomes. These structures play an integral role in a cellular CO(2)-concentrating mechanism and are essential components for autotrophic growth. Here we report that the carboxysomal shell protein, CsoS3, from Halothiobacillus neapolitanus is a novel carbonic anhydrase (epsilon-class CA) that has an evolutionary lineage distinct from those previously recognized in animals, plants, and other prokaryotes. Functional CAs encoded by csoS3 homologues were also identified in the cyanobacteria Prochlorococcus sp. and Synechococcus sp., which dominate the oligotrophic oceans and are major contributors to primary productivity. The location of the carboxysomal CA in the shell suggests that it could supply the active sites of RuBisCO in the carboxysome with the high concentrations of CO(2) necessary for optimal RuBisCO activity and efficient carbon fixation in these prokaryotes, which are important contributors to the global carbon cycle.

Amino Acid Sequence↗
PubMed2004

The sufR gene (sll0088 in Synechocystis sp. strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria.

The suf operon is composed of four genes (sufB, sufC, sufD, and sufS) and is highly conserved in the genomes of cyanobacteria. Open reading frame sll0088 in Synechocystis sp. strain PCC 6803 is located near the 5' end of the suf operon but is transcribed in the direction opposite that of the suf operon. We previously reported the isolation of two independent suppressor strains of C14S(PsaC) that mapped to sll0088 and restored photoautotrophic growth. The protein encoded by sll0088 has two significant features: (i) a DNA-binding domain near the N terminus and (ii) four highly conserved cysteine residues near the C terminus. The protein has high sequence similarity to transcription regulatory proteins with a conserved DNA-binding domain and can be classified in the DeoR family of helix-loop-helix proteins. The protein falls into a further subclass that contains a C-X(12)-C-X(13)-C-X(14)-C motif near the C terminus, which may represent a metal-binding site. The expressed Sll0088 protein harbored an iron-sulfur cluster as shown by optical and electron paramagnetic resonance spectroscopy. Compared to the wild type, expression levels of the sufBCDS genes were elevated when cells were grown under conditions of oxidative and iron stress and were even higher in a null mutant of Synechococcus sp. strain PCC 7002 in which the sll0088 homolog was insertionally inactivated. In agreement with the proposed role of the sufBCDS genes in iron metabolism, the growth rate of the null mutant was significantly higher than that of the wild type under iron-limiting conditions. We propose that the protein encoded by sll0088 is a transcriptional repressor of the suf operon, and we name the gene sufR.

Amino Acid Sequence↗
PubMed2005

A novel mutation in kaiC affects resetting of the cyanobacterial circadian clock.

Light is the most important factor controlling circadian systems in response to day-night cycles. In order to better understand the regulation of circadian rhythms by light in Synechococcus elongatus PCC 7942, we screened for mutants with defective phase shifting in response to dark pulses. Using a 5-h dark-pulse protocol, we identified a mutation in kaiC that we termed pr1, for phase response 1. In the pr1 mutant, a 5-h dark pulse failed to shift the phase of the circadian rhythm, while the same pulse caused a 10-h phase shift in wild-type cells. The rhythm in accumulation of KaiC was abolished in the pr1 mutant, and the rhythmicity of KaiC phosphorylation was reduced. Additionally, the pr1 mutant was defective in mediating the feedback inhibition of kaiBC. Finally, overexpression of mutant KaiC led to a reduced phase shift compared to that for wild-type KaiC. Thus, KaiC appears to play a role in resetting the cellular clock in addition to its documented role in the feedback regulation of circadian rhythms.

Bacterial Proteins↗
PubMed1968

Measurement of steady-state growth rates of a thermophilic alga directly in nature.

Steady-state growth rates of thermophilic algae can be determined directly in nature in the flowing waters of a hot spring channel by measuring the rate of loss of algal cells when the channel is darkened. The half time of the loss rate in the steady state is identical to the generation time. We studied the unicellular blue-green alga Synechococcus in Yellowstone National Park. Temperature and flow rate remained relatively constant throughout the experiment. Quantitative cores were taken and homogenized; the algal cells were then counted by use of a Petroff-Hausser counting chamber. After ascertaining that the algal population was in a steady state, the channel was darkened in such a way that neither flow rate nor temperature was altered. The population began to decrease within 1 day; the loss rate was exponential with time for 2 to 3 decades. Half times were then calculated from these loss rates. The growth rates found were considerably lower than those for the same organism in laboratory culture. The results suggest that in nature the organism may be an obligate phototroph. In two cases, after the algal populations decreased to an undetectable level, the dark covers were removed and the rate of recolonization was measured. The kinetics of recolonization were different from the kinetics of washout.

Cell Division↗
PubMed2004

Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments.

Prochlorococcus is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans. Here we present an overview of the pathways of nitrogen assimilation in Prochlorococcus, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems. The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase. However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged. Similarly, urease activities remain fairly constant under different conditions. The signal transduction protein P(II) is apparently not phosphorylated in Prochlorococcus, despite its conserved amino acid sequence. The genes amt1 and ntcA (coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in Prochlorococcus under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed. All of these unusual features could provide a physiological basis for the predominance of Prochlorococcus over Synechococcus in oligotrophic oceans.

Adaptation, Physiological↗
PubMed1977

Similar C-phycocyanins from two strains of thermotolerant cyanophyte Mastigocladus laminousus.

C-phycocyanin from two strains of the thermotolerant blue-green alga, Mastigocladus laminosus (NZ-DB2-m and I-30-m), that grow within different temperature ranges have been characterized with respect to aggregation, immunologic properties, subunit composition, and thermodenaturation. The critical thermal-denaturation temperature for phycocyanin from both strains of M. laminosus phycocyanin is 60 degrees C which is higher than that for mesophilic phyococyanin. Immunodiffusion studied have shown that these two strains of M. laminosus exhibit no antigenic differences and are closely related to the mesophilic Plectonema calothricoides and the thermophilic Synechococcus lividus (strains 3). Neither phenol nor alpha-naphthol has any effect on phycocyanin aggregation in these two strains of M. laminosus. There is also no enhancement of formation of large aggregates at their elevated temperature of cultivation. Furthermore, the phycocyanin of both strains of M. laminosus does not demonstrate any large amount of 19S or higher aggregates at any pH value. These observations suggest that the mode of adaptation of M. laminosus phycocyanin to high temperature is differnet from the previously encountered. It is also important to note that phycocyanin is essentially unchanged whether it is extracted from the same strain, M. laminosus (NZ-DBS-m), grown at either 50 degrees C or 37 degrees C.

Adaptation, Biological↗
PubMed1996

Genetics and molecular analysis of circadian rhythms.

The first part of this review summarizes the two best understood aspects of the two best understood circadian systems, the feedback oscillators of Neurospora and Drosophila, concentrating on what we know about the frequency (frq), period (per) and timeless (tim) genes. In the second part, the general circadian genetic and molecular literature is surveyed, with an eye to describing what is known from a variety of systems about input to the oscillator (entrainment), and how the oscillator might work and be temperature compensated, in emerging systems including Synechococcus, Gonyaulax, Arabidopsis, hamsters, and mice. Finally, the conversation of the molecular components of clocks is analyzed: both frq and per are widely conserved in their respective phylogenetic classes. Pharmacological data suggests that most other organisms use a day-phased oscillator of the type seen in Neurospora rather than a night-phased oscillator such as in Drosophila.

Animals↗
PubMed2003

A cyanobacterial circadian timing mechanism.

Cyanobacteria such as Synechococcus elongatus PCC 7942 exhibit 24-h rhythms of gene expression that are controlled by an endogenous circadian clock that is mechanistically distinct from those described for diverse eukaryotes. Genetic and biochemical experiments over the past decade have identified key components of the circadian oscillator, input pathways that synchronize the clock with the daily environment, and output pathways that relay temporal information to downstream genes. The mechanism of the cyanobacterial circadian clock that is emerging is based principally on the assembly and disassembly of a large complex at whose heart are the proteins KaiA, KaiB, and KaiC. Signal transduction pathways that feed into and out of the clock employ protein domains that are similar to those in two-component regulatory systems of bacteria.

Circadian Rhythm↗
PubMed2005

Identification of cyanobacterial non-coding RNAs by comparative genome analysis.

BACKGROUND: Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria. RESULTS: Based on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin. CONCLUSION: This is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.

Base Sequence↗
PubMed1993

A cyanobacterial gene encoding a protein with extensive homology to mammalian phosphoribosylpyrophosphate synthetase.

Phosphoribosylpyrophosphate (PRibPP) is the primary precursor in the biosynthesis of purine and pyrimidine nucleotides. The synthesis of PRibPP is catalysed by a ubiquitous PRibPP synthetase in many organisms. We provide evidence that a cyanobacterium, Synechococcus sp., has a gene encoding a protein with striking homology to mammalian PRibPP synthetases.

Amino Acid Sequence↗
PubMed2006

Characterization of the nitrate-nitrite transporter of the major facilitator superfamily (the nrtP gene product) from the cyanobacterium Nostoc punctiforme strain ATCC 29133.

The products of the NpR1527 and NpR1526 genes of the filamentous, diazotrophic, fresh-water cyanobacterium Nostoc punctiforme strain ATCC 29133 were identified as a nitrate transporter (NRT) and nitrate reductase (NR) respectively, by complementation of nitrate assimilation mutants of the cyanobacterium Synechococcus elongatus strain PCC 7942. While other fresh-water cyanobacteria, including S. elongatus, have an ATP-binding cassette (ABC)-type NRT, the NRT of N. punctiforme belongs to the major facilitator superfamily, being orthologous to the one found in marine cyanobacteria (NrtP). Unlike the ABC-type NRT, which transports both nitrate and nitrite with high affinity, Nostoc NrtP transported nitrate preferentially over nitrite. NrtP was distinct from ABC-type NRT also in its insensitivity to ammonium-promoted regulation at the post-translational level. The nitrate reductase of N. punctiforme was, on the other hand, inhibited upon addition of ammonium to medium, lending ammonium sensitivity to nitrate assimilation.

Anion Transport Proteins↗
PubMed2003

Flow cytometric determination of size and complex refractive index for marine particles: comparison with independent and bulk estimates.

We advance a method to determine the diameter D and the complex refractive index (n + n'i) of marine particles from flow cytometric measurements of forward scattering, side scattering, and chlorophyll fluorescence combined with Mie theory. To understand better the application of Mie theory with its assumptions to flow cytometry (FCM) measurements of phytoplankton cells, we evaluate our flow cytometric-Mie (FCM-Mie) method by comparing results from a variety of phytoplankton cultures with independent estimates of cell D and with estimates of n and n' from the inversion of bulk measurements. Cell D initially estimated from the FCM-Mie method is lower than independent estimates, and n and n' are generally higher than bulk estimates. These differences reflect lower forward scattering and higher side scattering for single-cell measurements than predicted by Mie theory. The application of empirical scattering corrections improves FCM-Mie estimates of cell size, n, and n'; notably size is determined accurately for cells grown in both high- and low-light conditions, and n' is correlated with intracellular chlorophyll concentration. A comparison of results for phytoplankton and mineral particles suggests that differences in n between these particle types can be determined from FCM measurements. In application to natural mixtures of particles, eukaryotic pico/nanophytoplankton and Synechococcus have minimum mean values of n' in surface waters, and nonphytoplankton particles have higher values of n than phytoplankton at all depths.

Journal Article↗
PubMed2003

Estimation of scattering error in spectrophotometric measurements of light absorption by aquatic particles from three-dimensional radiative transfer simulations.

We present an approach based on three-dimensional Monte Carlo radiative transfer simulations for estimating scattering error in measurements of light absorption by aquatic particles with a typical laboratory double-beam spectrophotometer. The scattering error is calculated by combining the weighting function describing the angular distribution of photon losses that are due to scattering on suspended particles with the volume scattering function of particles. We applied this method to absorption measurements made on marine phytoplankton, a diatom Thalassiosira pseudonana and a cyanobacterium Synechococcus. Assuming that the scattering phase function is described by the Henyey-Greenstein formula, we determined the backscatter probability of phytoplankton, which yields the best correction for scattering error at a light wavelength of 750 nm, where true absorption is null. The backscattering ratio estimated for both phytoplankton species is significantly higher than previously reported data based on Mie-scattering calculations for homogeneous spheres. Depending on the type of particles, the corrected absorption spectra obtained with our method may be similar or significantly different from spectra obtained with the null-point correction based on wavelength-independent scattering error.

Journal Article↗
PubMed1987

Isolation and localization of N4-methylasparagine in phycobiliproteins from the cyanobacterium Mastigocladus laminosus.

The occurrence of post-translationally methylated asparagine residues in beta AP from Anabaena variabilis, Synechococcus PCC 6301 and Porphyridium cruentum has recently been reported (Klotz, A.V., Leary, J.A. & Glazer, A.N. (1986) J. Biol. Chem. 261, 15891-15894). We reinvestigated the amino-acid compositions of all phycobiliproteins from Mastigocladus laminosus. During total hydrolysis of beta AP, beta 16.2 and beta PC one mol methylamine per mol protein was released. These proteins were chemically and enzymatically fragmented and the sequences of the fragments containing the modified asparagine residue were determined by automated Edman degradation. Residues beta AP72, beta 16.2 72 and beta PC 72 were identified as N4-methylasparagine. This derivative of asparagine was also found at a homologous position in beta PE of Calothrix. In the x-ray structure model of C-phycocyanin (PC) the residue beta PC 72 points towards the chromophore beta 84, presumably having an effect on the spectroscopic characteristics of this light harvesting pigment protein complex.

Amino Acid Sequence↗
PubMedDate not supplied

Multiple functions of thioredoxins.

Reduced thioredoxins from microbial and plant cells, both of cytoplasmic or chloroplast origin, are interchangeable in stimulating such diverse enzyme activities as ribonucleoside diphosphate reductase (E. coli), PAPS sulfotransferase (Synechococcus), and fructose-1,6-bis-phosphatase (from spinach) in vitro. It is suggested that reduced thioredoxins are unspecific, multifunctional cellular proteins while in contrast the oxidized froms require specific enzymes for their reduction.

Bacterial Proteins↗
PubMed1979

Distribution of thioredoxins in Cyanobacteria.

The presence of thioredoxin was demonstrated in 20 strains of cyanobacteria as well as in one phototrophic bacterium Rhodopseudomonas sulfidophila and in Thiobacillus denitrificans. Thioredoxin activity was not found in Cyanophora paradoxa and in Porphyridium cruentum using the thioredoxin-dependent PAPS-sulfotransferase activity from Synechococcus 6301 as assay system.

Bacterial Proteins↗
PubMedDate not supplied

PAPS-reductase from Escherichia coli: characterization of the enzyme as probe for thioredoxins.

PAPS-reductase from Escherichia coli was employed to detect thioredoxins from pro- and eukaryotic organisms. A simple method for the isolation of this enzyme and properties of the enzymatic assay were described. A comparison between thioredoxins detected by the PAPS-reductase and the Fructose-bisphosphatase or NADP malate dehydrogenase was used to assess the validity of the test. The high cross-reactivity of the bacterial enzyme was useful in the purification of heterologous thioredoxins from spinach, Synechococcus, and Saccharomyces cerevisiae.

Bacterial Proteins↗