Analysis of natural populations of Prochlorococcus spp. in the northern Red Sea using phycoerythrin gene sequences

Marine cyanobacteria of the genus Prochlorococcus belong to one of two ecotypes that are specifically adapted to either low light (LL) or high light (HL) conditions. Previous analyses of the differences in pigmentation and gene complement revealed that LL-adapted ecotypes carry a gene cluster to produce a functional phycoerythrin, whereas in the fully sequenced genome of the HL-adapted strain MED4, only a single and free-standing cpeB gene occurs. This gene encodes a derived form of beta-phycoerythrin, the function of which has remained enigmatic so far. Here, an analysis of HL-adapted Prochlorococcus strains from different ocean provinces revealed the presence of a cpeB gene highly similar to that of MED4. To investigate whether the presence of particular phycoerythrin genes is a common characteristic of the LL- and HL-adapted ecotypes, primer sets targeting specific motifs in LL-cpeB and HL-cpeB were designed for polymerase chain reaction (PCR) analysis of Red Sea phytoplankton. A major PCR product for Prochlorococcus HL-cpeB was obtained from samples taken at 5-70 m depth and for LL-cpeB from 70-125 m. The high sensitivity of this approach allowed the detection of HL-cpeB down to 100 m and LL-cpeB as deep as 175 m. DNA sequence and phylogenetic analysis of 70 individual clones for HL-cpeB and of 68 clones for LL-cpeB revealed a monophyletic origin for the HL and LL sequences respectively. This study shows that cpeB sequences are suitable as very sensitive molecular markers for the study of natural populations of Prochlorococcus. The low sequence divergence of HL-cpeB among Prochlorococcus strains, which have been isolated from the Mediterranean Sea, the Arabian Sea and the Southern Pacific Ocean as well as in populations from the Red Sea, suggests the HL-cpeB gene to be conserved and its product to be functional in Prochlorococcus.     

Light-harvesting antenna function of phycoerythrin in prochlorococcus marinus

Prochlorococcus marinus strain CCMP 1375 is the sole prokaryote to possess phycoerythrin in addition to (divinyl-)chlorophyll a/b binding antenna complexes. Here we demonstrate, employing a spectrofluorimetric assay, that phycoerythrin serves a light-harvesting antenna function (transfers energy to chlorophylls).     

The divinyl-chlorophyll a/b-protein complexes of two strains of the oxyphototrophic marine prokaryote Prochlorococcus – characterization and response to changes in growth irradiance

Apoproteins of the antenna complexes of Prochlorococcus marinus clone SS120 (= CCMP 1375) and Prochlorococcus sp. clone MED4 (= CCMP 1378) cross-reacted with an antibody against the 30 kDa CP 5 complex of Prochlorothrix hollandica antenna. For the MED4 strain, which has a high divinyl-chlorophyll a to divinyl-chlorophyll b (DV-Chl a/b) ratio ranging from 11.4 to 15.0 (w/w), the major antenna proteins had an apparent molecular mass of 32.5 kDa. In contrast for the SS120 strain, which has a low DV-Chl a/b ratio ranging from 1.1 to 2.2, antenna apoproteins were observed in the range 34–38 kDa. For both strains, these apoproteins decreased at high growth irradiance but more markedly in the latter. Partially purified antenna fractions had a DV-Chl a/b ratio ca. 7-fold lower for SS120 than for MED4 at 30 mol photons m-2 s-1. For both strains, the 77 K fluorescence emission spectra of whole thylakoids displayed a major peak at 685 nm and a broad but very low shoulder above 700 nm. Energetic coupling of the antenna to both PS II and PSI reaction centers was demonstrated for SS120 by the strong contribution of DV-Chl b in both the 77 K excitation fluorescence spectra and the oxidized minus reduced absorption difference spectra of P700. The PS I to PS II ratio of Prochlorococcus SS120 was determined as being 0.7 ± 0.1 at low light.     

Characterization of the Photosystem I subunits PsaI and PsaL from two strains of the marine oxyphototrophic prokaryote Prochlorococcus

A 25 kDa protein associated with Photosystem I (PS I) of the divinyl-chlorophyll a/b-containing oxychlorobacterium Prochlorococcus marinus SS120 (CCMP 1375) was isolated, and the amino acid sequences of the N-terminus and one internal peptide were determined. Polymerase chain reaction (PCR) with degenerate primers yielded a 92 bp fragment, which was used to isolate the complete gene from a genomic library. The corresponding gene was isolated from a library of Prochlorococcus sp. MED4 (CCMP 1378). In both Prochlorococcus strains, the gene encodes a protein of 199 amino acids. The gene products show a strong sequence similarity to the PS I subunit PsaL. The N-terminus contains a hydrophilic domain that has not been found in PsaL proteins from other organisms. In both strains, sequences encoding a protein similar to PsaI were found upstream of the psaL gene. Both genes are transcribed in the same direction.     

Photophysical properties of Prochlorococcus marinus SS120 divinyl chlorophylls and phycoerythrin in vitro and in vivo

Prochlorococcus marinus SS120 is an ecologically important and biochemically intriguing marine cyanobacterium. In addition to divinyl chlorophylls (DV-Chls) a and b it possesses a particular form of phycoerythrin (PE), but no other phycobilins and therefore no complete phycobilisomes. Here, a spectroscopic characterisation of these DV-Chls and PE is provided. Comparison of fluorescence quantum yields, excited state lifetimes and absorption characteristics indicate similar light-harvesting properties of the DV-Chls as their monovinyl counterparts. PE, which is present only in tiny amounts, was purified and considerably enriched. A phycourobilin to phycoerythrobilin ratio of 3:1 chromophores per (alphabeta) PE monomer is suggested. The in vitro fluorescence lifetime of PE is 1.74 ns. In vivo time-resolved fluorescence measurements with synchrotron radiation were used to investigate the possible role of PE in light-harvesting. The fluorescence decay time for PE is about 550 ps, indicating an unusually slow excitation energy transfer. The decay time slowed to 1 ns after addition of glycerol to cell cultures. The contribution of PE to total light-harvesting capacity was estimated to be about one (alphabeta) PE monomer per 330 DV-Chl b molecules. Thus, the capacity of PE to function primarily as a photosynthetic light-harvesting pigment in P. marinus SS120 is low.     

Glucosylglycerate: a secondary compatible solute common to marine cyanobacteria from nitrogen-poor environments

The synthesis and accumulation of compatible solutes represent an essential part of the salt acclimation strategy of microorganisms. Glucosylglycerol is considered to be the typical compatible solute among marine cyanobacteria. However, genes that encode enzymes for the synthesis of glucosylglycerol were not detected in the genome sequences of marine picoplanktonic Prochlorococcus strains. Instead, we noticed the presence of genes that putatively encode for glucosylglycerate (GGA) synthesis among Prochlorococcus and most other closely related marine picocyanobacteria. Recombinant proteins from Prochlorococcus marinus SS120 and Synechococcus sp. PCC 7002 exhibited glucosyl-phosphoglycerate synthase (GpgS) activity, and GpgS is a key enzyme of GGA synthesis. GGA accumulation was found to be salt- as well as nitrogen-regulated in the coastal strain Synechococcus sp. PCC 7002. Moreover, GGA was also detected in all picoplanktonic Prochlorococcus and Synechococcus strains harbouring gpgS genes, especially under N-limiting conditions. These results suggest that marine picocyanobacteria acquired the capacity to synthesize the negatively charged compound GGA during their evolution. Our results establish GGA as the fifth most widespread compatible solute among cyanobacteria. Additionally, GGA appears to replace glutamate as an anion to counter monovalent cations in marine picocyanobacteria from N-poor environments.     

Nitrogen deprivation strongly affects photosystem II but not phycoerythrin level in the divinyl-chlorophyll b-containing cyanobacterium Prochlorococcus marinus

Effects of nitrogen limitation on Photosystem II (PSII) activities and on phycoerythrin were studied in batch cultures of the marine oxyphotobacterium Prochlorococcus marinus. Dramatic decreases in photochemical quantum yields (F(V)/F(M)), the amplitude of thermoluminescence (TL) B-band, and the rate of Q(A) reoxidation were observed within 12 h of growth in nitrogen-limited conditions. The decline in F(V)/F(M) paralleled changes in the TL B-band amplitude, indicative of losses in PSII activities and formation of non-functional PSII centers. These changes were accompanied by a continuous reduction in D1 protein content. In contrast, nitrogen deprivation did not cause any significant reduction in phycoerythrin content. Our results refute phycoerythrin as a nitrogen storage complex in Prochlorococcus. Regulation of phycoerythrin gene expression in Prochlorococcus is different from that in typical phycobilisome-containing cyanobacteria and eukaryotic algae investigated so far.     

Analysis of the hli gene family in marine and freshwater cyanobacteria

Certain cyanobacteria thrive in natural habitats in which light intensities can reach 2000 micromol photon m(-2) s(-1) and nutrient levels are extremely low. Recently, a family of genes designated hli was demonstrated to be important for survival of cyanobacteria during exposure to high light. In this study we have identified members of the hli gene family in seven cyanobacterial genomes, including those of a marine cyanobacterium adapted to high-light growth in surface waters of the open ocean (Prochlorococcus sp. strain Med4), three marine cyanobacteria adapted to growth in moderate- or low-light (Prochlorococcus sp. strain MIT9313, Prochlorococcus marinus SS120, and Synechococcus WH8102), and three freshwater strains (the unicellular Synechocystis sp. strain PCC6803 and the filamentous species Nostoc punctiforme strain ATCC29133 and Anabaena sp. [Nostoc] strain PCC7120). The high-light-adapted Prochlorococcus Med4 has the smallest genome (1.7 Mb), yet it has more than twice as many hli genes as any of the other six cyanobacterial species, some of which appear to have arisen from recent duplication events. Based on cluster analysis, some groups of hli genes appear to be specific to either marine or freshwater cyanobacteria. This information is discussed with respect to the role of hli genes in the acclimation of cyanobacteria to high light, and the possible relationships among members of this diverse gene family.     

Phycoerythrins of the oxyphotobacterium Prochlorococcus marinus are associated to the thylakoid membrane and are encoded by a single large gene cluster

An intrinsic divinyl-chlorophyll a/b antenna and a particular form of phycobiliprotein, phycoerythrin (PE) III, coexist in the marine oxyphotobacterium Prochlorococcus marinus CCMP 1375. The genomic region including the cpeB/A operon of P. marinus was analysed. It encompasses 10153 nucleotides that encode three structural phycobiliproteins and at least three (possibly five) different polypeptides analogous to cyanobacterial or red algal proteins involved either in the linkage of subunits or the synthesis and attachment of chromophoric groups. This gene cluster is part of the chromosome and is located within a distance of less than 110 kb from a previously characterized region containing the genes aspA-psbA-aroC. Whereas the Prochlorococcus phycobiliproteins are characterized by distinct deletions and amino acid replacements with regard to analogous proteins from other organisms, the gene arrangement resembles the organization of phycobiliprotein genes in some other cyanobacteria, in particular marine Synechococcus strains. The expression of two of the Prochlorococcus polypeptides as recombinant proteins in Escherichia coli allowed the production of individual homologous antisera to the Prochlorococcus and PE subunits. Experiments using these sera show that the Prochlorococcus PEs are specifically associated to the thylakoid membrane and that the protein level does not significantly vary as a function of light irradiance or growth phase.     

Identification of chlorophyllide a oxygenase in the Prochlorococcus genome by a comparative genomic approach

Chl b is a major photosynthetic pigment of peripheral antenna complexes in chlorophytes and prochlorophytes. Chl b is synthesized by chlorophyllide a oxygenase (CAO), an enzyme that has been identified from higher plants, moss, green algae and two groups of prochlorophytes, Prochlorothrix and Prochloron. Based on these results, we previously proposed the hypothesis that all of the Chl b synthesis genes have a common origin. However, the CAO gene is not found in whole genome sequences of Prochlorococcus although a gene which is distantly related to CAO was reported. If Prochlorococcus employs a different enzyme, a Chl synthesis gene should have evolved several times on the different phylogenetic lineages of Prochlorococcus and other Chl b-containing organisms. To examine these hypotheses, we identified a Prochlorococcus Chl b synthesis gene by using a combination of bioinformatics and molecular genetics techniques. We first identified Prochlorococcus-specific genes by comparing the whole genome sequences of Prochlorococcus marinus MED4, MIT9313 and SS120 with Synechococcus sp. WH8102. Synechococcus is closely related to Prochlorococcus phylogenetically, but it does not contain a Chl b synthesis gene. By examining the sequences of Prochlorococcus-specific genes, we found a candidate for the Chl b synthesis gene and introduced it into Synechocystis sp. PCC6803. The transformant cells accumulated Chl b, indicating that the gene product catalyzes Chl b synthesis. In this study, we discuss the evolution of CAO based upon the molecular phylogenetic studies we performed.     

NICHE ADAPTATION OF PROCHLOROCOCCUS ECOTYPES: INSIGHTS THROUGH COMPARATIVE GENOMICS

Hess, W. R.¹*, Rocap, G.², Steglich, C.¹, Post, A.², Ting, C. S.³ & Chisholm, S. W.^{2,3 1}Humboldt-University Berlin, Germany; Institute of Biology, Chausseestr. 117, D-10115 Berlin, Germany; ²Massachusetts Institute of Technology, Department of Civil and Environmental Engineering and ³Department of Biology, Massachusetts Institute of Technology, 15 Vassar Street, 48-425 MIT, Cambridge MA 02139, USA Prochlorococcus is an extremely small, chlorophyll b-containing oceanic cyanobacterium. Specific ecotypes of Prochlorococcus have adapted to different ecological conditions with regard to factors as light or the available nutrients. Such differentially adapted ecotypes are less than 3% divergent in their 16S rRNA sequences, which invites speculation as to how their specific gene content has diverged to reflect the particular niche of each strain. Complete genome sequences have been determined of two Prochlorococcus strains, MED4 and MIT9313. These two strains are representatives of high and low light-adapted ecotypes. Intriguing similarities between both genomes include their small size and compact organization (MED4: 1.7 Mbp and MIT9313: 2.3 Mbp), a gene cluster for RubisCo and carboxysomal proteins that is of obviously non-cyanobacterial origin, or genes for two different lycopene cyclases explaining how Prochlorococcus synthesizes alpha-carotene, a carotenoid that is not common to cyanobacteria. Several genes and operons which in cyanobacteria are involved in light harvesting, nitrate utilization or in the generation of circadian rhythms have been reduced to a different degree in the two compared genomes. MED4 has many more genes encoding high light inducible proteins and photolyases. In contrast, MIT9313 possesses more genes to build up more complex light harvesting structures, including a gene cluster to produce chromophorylated phycoerythrin. The latter represents an intermediate between the phycobiliproteins of non-chlorophyll b containing cyanobacteria and a degenerated phycoerythrin present in MED4. Screening of natural samples from the Red Sea suggests that a highly similar phycoerythrin form is wide-spread among high light-adapted ecotypes.     

Glucose uptake and its effect on gene expression in prochlorococcus

The marine cyanobacteria Prochlorococcus have been considered photoautotrophic microorganisms, although the utilization of exogenous sugars has never been specifically addressed in them. We studied glucose uptake in different high irradiance- and low irradiance-adapted Prochlorococcus strains, as well as the effect of glucose addition on the expression of several glucose-related genes. Glucose uptake was measured by adding radiolabelled glucose to Prochlorococcus cultures, followed by flow cytometry coupled with cell sorting in order to separate Prochlorococcus cells from bacterial contaminants. Sorted cells were recovered by filtration and their radioactivity measured. The expression, after glucose addition, of several genes (involved in glucose metabolism, and in nitrogen assimilation and its regulation) was determined in the low irradiance-adapted Prochlorococcus SS120 strain by semi-quantitative real time RT-PCR, using the rnpB gene as internal control. Our results demonstrate for the first time that the Prochlorococcus strains studied in this work take up glucose at significant rates even at concentrations close to those found in the oceans, and also exclude the possibility of this uptake being carried out by eventual bacterial contaminants, since only Prochlorococcus cells were used for radioactivity measurements. Besides, we show that the expression of a number of genes involved in glucose utilization (namely zwf, gnd and dld, encoding glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase and lactate dehydrogenase, respectively) is strongly increased upon glucose addition to cultures of the SS120 strain. This fact, taken together with the magnitude of the glucose uptake, clearly indicates the physiological importance of the phenomenon. Given the significant contribution of Prochlorococcus to the global primary production, these findings have strong implications for the understanding of the phytoplankton role in the carbon cycle in nature. Besides, the ability of assimilating carbon molecules could provide additional hints to comprehend the ecological success of Prochlorococcus.     

IMMUNOLOGICAL AND ULTRASTRUCTURAL CHARACTERIZATION OF THE PHOTOSYNTHETIC COMPLEXES OF THE PROCHLOROPHYTE PROCHLOROCOCCUS (OXYCHLOROBACTERIA)

Ultrastructural features and immunological properties of some thylakoid proteins were examined in two strains of the prochlorophyte Prochlorococcus and compared to those of other photosynthetic prokaryotes and eukaryotes. Both strains exhibited two or three rows of tightly appressed thylakoidal membranes, located at the cell periphery. However, thylakoids were concentrically arranged in the strain from the Sargasso Sea (SARG) and horseshoe-shaped in the Mediterranean isolate (CCMP 1378). Although lacking phycobilisomes, both cell types shared with cyanobacteria the presence of carboxysome-like structures and glycogen granules as storage compounds. The main thylakoid polypeptides separated by sodium dodecyl sulfate—polyacrylamide gel electrophoresis were characterized by Western blotting using several antibodies. The 30-kDa polypeptide of the light-harvesting complex (LHC) of Prochlorococcus showed a weak positive immunological cross-reaction with an antibody raised against the 32-kDa apoprotein of the LHC of the prochlorophyte Prochlorothrix hollandica. In contrast, it showed no immunological relationships with the chlorophyll a/b (Chl a/b) LHCs of green algae and higher plants. Protein membranes from Prochlorococcus strongly cross-reacted with antibodies raised against reaction center polypeptides of photosystems II and I (PSs II and I) of other photosynthetic organisms, confirming the high degree of conservation of these basic compounds of the photosynthetic machinery during evolution. Immunolocalization of thylakoid proteins showed that the LHC proteins, the major PS II reaction center proteins (CP 43 and D2), and the PS I reaction center proteins were equally distributed within the thylakoid membranes in contrast to the segregation observed in higher plants and green alga thylakoids. We also identified ribulose-1, 5-bisphosphate carboxylase/oxygenase in the carboxysomes. These results suggest that Prochlorococcus is more closely related to cyanobacteria than to green plastids even though it contains Chl b.     

Glutamine synthetase from the marine cyanobacteria Prochlorococcus spp: characterization,phylogeny and response to nutrient limitation

The regulation of glutamine synthetase (EC 6.3.1.2) from Prochlorococcus was previously shown to exhibit unusual features: it is not upregulated by nitrogen starvation and it is not inactivated by darkness (El Alaoui et al. (2001) Appl Environ Microbiol 67: 2202-2207). These are probably caused by adaptations to oligotrophic environments, as confirmed in this work by the marked decrease in the enzymatic activity when cultures were subjected to iron or phosphorus starvation. In order to further understand the adaptive features of ammonium assimilation in this cyanobacterium, glutamine synthetase was purified from two Prochlorococcus strains: PCC 9511 (high-light adapted) and SS120 (low-light adapted). We obtained approximately 100-fold purified samples of glutamine synthetase electrophoretically homogeneous, with a yield of approximately 30%. The estimated molecular mass of the subunits was roughly the same for both strains: 48.3 kDa. The apparent Km constants for the biosynthetic activity were 0.30 mM for ammonium, 1.29 mM for glutamate and 1.35 mM for ATP; the optimum pH was 8.0. Optimal temperature was surprisingly high (55 degrees C). Phylogenetic analysis of glnA from three Prochlorococcus strains (MED4, MIT9313 and SS120) showed they group closely with marine Synechococcus isolates, in good agreement with other studies based on 16 S RNA sequences. All of our results suggest that the structure and kinetics of glutamine synthetase in Prochlorococcus have not been significantly modified during the evolution within the cyanobacterial radiation, in sharp contrast with its regulatory properties.     

Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1

Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.     

Prochlorococcus, a marine photosynthetic prokaryote of global significance.

The minute photosynthetic prokaryote Prochlorococcus, which was discovered about 10 years ago, has proven exceptional from several standpoints. Its tiny size (0.5 to 0.7 microm in diameter) makes it the smallest known photosynthetic organism. Its ubiquity within the 40 degrees S to 40 degrees N latitudinal band of oceans and its occurrence at high density from the surface down to depths of 200 m make it presumably the most abundant photosynthetic organism on Earth. Prochlorococcus typically divides once a day in the subsurface layer of oligotrophic areas, where it dominates the photosynthetic biomass. It also possesses a remarkable pigment complement which includes divinyl derivatives of chlorophyll a (Chl a) and Chl b, the so-called Chl a2 and Chl b2, and, in some strains, small amounts of a new type of phycoerythrin. Phylogenetically, Prochlorococcus has also proven fascinating. Recent studies suggest that it evolved from an ancestral cyanobacterium by reducing its cell and genome sizes and by recruiting a protein originally synthesized under conditions of iron depletion to build a reduced antenna system as a replacement for large phycobilisomes. Environmental constraints clearly played a predominant role in Prochlorococcus evolution. Its tiny size is an advantage for its adaptation to nutrient-deprived environments. Furthermore, genetically distinct ecotypes, with different antenna systems and ecophysiological characteristics, are present at depth and in surface waters. This vertical species variation has allowed Prochlorococcus to adapt to the natural light gradient occurring in the upper layer of oceans. The present review critically assesses the basic knowledge acquired about Prochlorococcus both in the ocean and in the laboratory.     

In silico comparison of bacterial strains using mutual information

Fast-sequencing throughput methods have increased the number of completely sequenced bacterial genomes to about 400 by December 2006, with the number increasing rapidly. These include several strains. In silico methods of comparative genomics are of use in categorizing and phylogenetically sorting these bacteria. Various word-based tools have been used for quantifying the similarities and differences between entire genomes. The simple di-nucleotide frequency comparison, codon specificity and k-mer repeat detection are among some of the well-known methods. In this paper, we show that the Mutual Information function, which is a measure of correlations and a concept from Information Theory, is very effective in determining the similarities and differences among genome sequences of various strains of bacteria such as the plant pathogen Xylella fastidiosa, marine Cyanobacteria Prochlorococcus marinus or animal and human pathogens such as species of Ehrlichia and Legionella. The short-range three-base periodicity, small sequence repeats and long-range correlations taken together constitute a genome signature that can be used as a technique for identifying new bacterial strains with the help of strains already catalogued in the database. There have been several applications of using the Mutual Information function as a measure of correlations in genomics but this is the first whole genome analysis done to detect strain similarities and differences.     

Isolation and characterization of Photosystem I from two strains of the marine oxychlorobacterium Prochlorococcus

Photosystem I (PS I) complexes from two strains of the marine photosynthetic prokaryote Prochlorococcus, MED4 (= clone CCMP1378) and SS120 (= clone CCMP1375), were isolated by centrifugation on sucrose gradients after detergent treatment. The PS I-enriched fractions of both strains contained about 100 chlorophyll molecules per P700. Electron microscopy showed that the PS I complexes were in a trimeric form. The characteristic long wavelength fluorescence emission of PS I at 77 K, currently observed in chloroplasts and most cyanobacteria was absent both in intact cells and in PS I preparations of both strains. The major proteins of the PS I-enriched fractions were identified immunologically as PsaA and PsaB. Two proteins with apparent molecular masses of about 21 and 25 kDa were present in PS I preparations of Prochlorococcus, whereas the small PS I subunits in cyanobacteria all have molecular masses below 18 kDa. The 25 kDa protein showed a strong cross-reaction with a heterologous antibody against PsaL. Relatedness of the 21 kDa protein to PsaF was demonstrated by internal protein sequencing. Although only trace amounts of the major divinyl-Chl a/b-binding antenna complexes were present in the PS I preparations, significant amounts of divinyl-Chl b were observed in this fraction. The putative organization of this Chl b in PS I is discussed.