Partial sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase and the phylogeny of Prochloron and Prochlorococcus (Prochlorales)

Novel integrative elements and genomic plasticity in ocean ecosystems

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.

Induction of Conjugation and Zygospore Cell Wall Characteristics in the Alpine Spirogyra mirabilis (Zygnematophyceae, Charophyta): Advantage under Climate Change Scenarios?

Extreme environments, such as alpine habitats at high elevation, are increasingly exposed to man-made climate change. Zygnematophyceae thriving in these regions possess a special means of sexual reproduction, termed conjugation, leading to the formation of resistant zygospores. A field sample of Spirogyra with numerous conjugating stages was isolated and characterized by molecular phylogeny. We successfully induced sexual reproduction under laboratory conditions by a transfer to artificial pond water and increasing the light intensity to 184 µmol photons m-2 s-1. This, however was only possible in early spring, suggesting that the isolated cultures had an internal rhythm. The reproductive morphology was characterized by light- and transmission electron microscopy, and the latter allowed the detection of distinctly oriented microfibrils in the exo- and endospore, and an electron-dense mesospore. Glycan microarray profiling showed that Spirogyra cell walls are rich in major pectic and hemicellulosic polysaccharides, and immuno-fluorescence allowed the detection of arabinogalactan proteins (AGPs) and xyloglucan in the zygospore cell walls. Confocal RAMAN spectroscopy detected complex aromatic compounds, similar in their spectral signature to that of Lycopodium spores. These data support the idea that sexual reproduction in Zygnematophyceae, the sister lineage to land plants, might have played an important role in the process of terrestrialization.

Identification of 13 Spirogyra species (Zygnemataceae) by traits of sexual reproduction induced under laboratory culture conditions

The genus Spirogyra is abundant in freshwater habitats worldwide, and comprises approximately 380 species. Species assignment is often difficult because identification is based on the characteristics of sexual reproduction in wild-collected samples and spores produced in the field or laboratory culture. We developed an identification procedure based on an improved methodology for inducing sexual conjugation in laboratory-cultivated filaments. We tested the modified procedure on 52 newly established and genetically different strains collected from diverse localities in Japan. We induced conjugation or aplanospore formation under controlled laboratory conditions in 15 of the 52 strains, which allowed us to identify 13 species. Two of the thirteen species were assignable to a related but taxonomically uncertain genus, Temnogyra, based on the unique characteristics of sexual reproduction. Our phylogenetic analysis demonstrated that the two Temnogyra species are included in a large clade comprising many species of Spirogyra. Thus, separation of Temnogyra from Spirogyra may be untenable, much as the separation of Sirogonium from Spirogyra is not supported by molecular analyses.

Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly

Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics (SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S-SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples.

Cyanobacteria of the genus prochlorothrix

Green cyanobacteria differ from the blue-green cyanobacteria by the possession of a chlorophyll-containing light-harvesting antenna. Three genera of the green cyanobacteria namely Acaryochloris, Prochlorococcus, and Prochloron are unicellular and inhabit marine environments. Prochlorococcus marinus attracts most attention due to its prominent role in marine primary productivity. The fourth genus Prochlorothrix is represented by the filamentous freshwater strains. Unlike the other green cyanobacteria, Prochlorothrix strains are remarkably rare: to date, living isolates have been limited to two European locations. Taking into account fluctuating blooms, morphological resemblance to Planktothrix and Pseudanabaena, and unsuccessful attempts to obtain enrichments of Prochlorothrix, the most successful strategy to search for this cyanobacterium involves PCR with environmental DNA and Prochlorothrix-specific primers. This approach has revealed a broader distribution of Prochlorothrix. Marker genes have been found in at least two additional locations. Despite of the growing evidence for naturally occurring Prochlorothrix, there are only a few cultured strains with one of them (PCC 9006) being claimed to be axenic. In multixenic cultures, Prochlorothrix is accompanied by heterotrophic bacteria indicating a consortium-type association. The genus Prochlorothrix includes two species: P. hollandica and P. scandica based on distinctions in genomic DNA, cell size, temperature optimum, and fatty acid composition of membrane lipids. In this short review the properties of cyanobacteria of the genus Prochlorothrix are described. In addition, the evolutionary scenario for green cyanobacteria is suggested taking into account their possible role in the origin of simple chloroplast.

The CO2-concentrating mechanism of Synechococcus WH5701 is composed of native and horizontally-acquired components

The cyanobacterial CO(2)-concentrating mechanism (CCM) is an effective adaptation that increases the carbon dioxide (CO(2)) concentration around the primary photosynthetic enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RuBisCO). α-Cyanobacteria (those containing Form1-A RuBisCO within cso-type α-carboxysomes) have a limited CCM composed of a small number of Ci-transporters whereas β-cyanobacteria (those species containing Form-1B RuBisCO within ccm-type β-carboxysomes) exhibit a more diverse CCM with a greater variety in Ci-transporter complement and regulation. In the coastal species Synechococcus sp. WH5701 (α-cyanobacteria), the minimal α-cyanobacterial CCM has been supplemented with β-cyanobacterial Ci transporters through the process of horizontal gene transfer (HGT). These transporters are transcriptionally regulated in response to external Ci-depletion however this change in transcript abundance is not correlated with a physiological induction. WH5701 exhibits identical physiological responses grown at 4% CO(2) (K (1/2) ≈ 31 μM Ci) and after induction with 0.04% CO(2) (K (1/2) ≈ 29 μM Ci). Insensitivity to external Ci concentration is an unusual characteristic of the WH5701 CCM which is a result of evolution by HGT. Our bioinformatic and physiological data support the hypothesis that WH5701 represents a clade of α-cyanobacterial species in transition from the marine/oligotrophic environment to a coastal/freshwater environment.

Ribulose-1,5-bisphosphate carboxylase/oxygenase from thermophilic cyanobacterium Thermosynechococcus elongatus

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) can be divided into two branches: the "red-like type" of marine algae and the "green-like type" of cyanobacteria, green algae, and higher plants. We found that the "green-like type" rubisco from the thermophilic cyanobacterium Thermosynechococcus elongatus has an almost 2-fold higher specificity factor compared with rubiscos of mesophilic cyanobacteria, reaching the values of higher plants, and simultaneously revealing an improvement in enzyme thermostability. The difference in the activation energies at the transition stages between the oxygenase and carboxylase reactions for Thermosynechococcus elongatus rubisco is very close to that of Galdieria partita and significantly higher than that of spinach. This is the first characterization of a "green-like type" rubisco from thermophilic organism.

The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like gamma-proteobacterium

BACKGROUND

Paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living Prochlorococcus and Synechococcus species (PS-clade). Members of the PS-clade of cyanobacteria contain a proteobacterial form 1A RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (HGT) of a carboxysomal operon. In rDNA-phylogenies, the Paulinella chromatophore diverged basal to the PS-clade, raising the question whether the HGT occurred before or after the split of the chromatophore ancestor.

RESULTS

Phylogenetic analyses of the almost complete rDNA operon with an improved taxon sampling containing most known cyanobacterial lineages recovered the Paulinella chromatophore as sister to the complete PS-clade. The sequence of the complete carboxysomal operon of Paulinella was determined. Analysis of RubisCO large subunit (rbcL) sequences revealed that Paulinella shares the proteobacterial form 1A RubisCO with the PS-clade. The gamma-proteobacterium Nitrococcus mobilis was identified as sister of the Paulinella chromatophore and the PS-clade in the RubisCO phylogeny. Gene content and order in the carboxysomal operon correlates well with the RubisCO phylogeny demonstrating that the complete carboxysomal operon was acquired by the common ancestor of the Paulinella chromatophore and the PS-clade through HGT. The carboxysomal operon shows a significantly elevated AT content in Paulinella, which in the rbcL gene is confined to third codon positions. Combined phylogenies using rbcL and the rDNA-operon resulted in a nearly fully resolved tree of the PS-clade.

CONCLUSION

The HGT of the carboxysomal operon predated the divergence of the chromatophore ancestor from the PS-clade. Following HGT and divergence of the chromatophore ancestor, diversification of the PS-clade into at least three subclades occurred. The gamma-proteobacterium Nitrococcus mobilis represents the closest known relative to the donor of the carboxysomal operon. The isolated position of the Paulinella chromatophore in molecular phylogenies as well as its elevated AT content suggests that the Paulinella chromatophore has already undergone typical steps in the reductive evolution of an endosymbiont.

Fine structure and phylogeny of green algal photobionts in the microfilamentous genus Psoroglaena (Verrucariaceae, lichen-forming ascomycetes)

According to the literature the microfilamentous thalli of lichen-forming ascomycetes of the genus Psoroglaena are assumed to harbour vivid green "prochlorophyte" cyanobacterial photobionts. As this would be the first report of terrestrial "prochlorophytes" we investigated the fine structure and two molecular markers (SSU rDNA and rbcL) of the photobionts of P. stigonemoides (Orange) Henssen and P. epiphylla Lücking. Both Psoroglaena spp. had unicellular green algal photobionts, representatives of the Trebouxiophyceae. The photobiont of P. stigonemoides is closely related to the non-symbiotic auxenochlorella protothecoides and to a Chlorella endosymbiont of the freshwater polyp Hydra viridis. The putative photobiont of P. epiphylla may be related to Chlorella luteoviridis, C. saccharophila, and a Pseudochlorella isolate. In contrast to other microfilamentous lichens, which derive their shape from filamentous green algae or cyanobacterial colonies overgrown and ensheathed by the fungal partner, Psoroglaena mycobionts position their unicellular photobiont in uni- or multiseriate rows which strongly resemble the situation in filamentous cyanobacterial colonies.

Host specificity and phylogeography of the prochlorophyte Prochloron sp., an obligate symbiont in didemnid ascidians

Prochloron is an oxygenic photosynthetic bacterium that lives in obligate symbiosis with didemnid ascidians, such as Diplosoma spp., Lissoclinum spp. and Trididemnum spp. This study investigated the genetic diversity of the genus Prochloron by constructing a phylogenetic tree based on the 16S rRNA gene sequences of 27 isolates from 11 species of didemnid ascidians collected from Japan, Australia and the USA. The 27 isolates formed three phylogenetic groups: 22 of the samples were identified to be closely related members of Prochloron. Two samples, isolated from Trididemnum nubilum and Trididemnum clinides, were found to belong to the species Synechocystis trididemni, the closest relative of Prochloron. Three isolates formed a separate group from both Prochloron sp. and S. trididemni, potentially indicating a new symbiotic phylotype. Genomic polymorphism analysis, employing cyanobacterium-specific highly iterative palindrome 1 repeats, could not delineate the isolates further. For the Prochloron sp. isolates, the phylogenetic outcome was independent of host species and geographic origin of the sample indicating a low level of host specificity, low genetic variation within the taxon and possibly a lack of a host-symbiont relationship during reproductive dispersal. This study contributes significantly to the understanding of Prochloron diversity and phylogeny, and implications for the evolutionary relationship of prochlorophytes, cyanobacteria and chloroplasts are also discussed.

Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium

In an age of comparative microbial genomics, knowledge of the near-native architecture of microorganisms is essential for achieving an integrative understanding of physiology and function. We characterized and compared the three-dimensional architecture of the ecologically important cyanobacterium Prochlorococcus in a near-native state using cryo-electron tomography and found that closely related strains have diverged substantially in cellular organization and structure. By visualizing native, hydrated structures within cells, we discovered that the MED4 strain, which possesses one of the smallest genomes (1.66 Mbp) of any known photosynthetic organism, has evolved a comparatively streamlined cellular architecture. This strain possesses a smaller cell volume, an attenuated cell wall, and less extensive intracytoplasmic (photosynthetic) membrane system compared to the more deeply branched MIT9313 strain. Comparative genomic analyses indicate that differences have evolved in key structural genes, including those encoding enzymes involved in cell wall peptidoglycan biosynthesis. Although both strains possess carboxysomes that are polygonal and cluster in the central cytoplasm, the carboxysomes of MED4 are smaller. A streamlined cellular structure could be advantageous to microorganisms thriving in the low-nutrient conditions characteristic of large regions of the open ocean and thus have consequences for ecological niche differentiation. Through cryo-electron tomography we visualized, for the first time, the three-dimensional structure of the extensive network of photosynthetic lamellae within Prochlorococcus and the potential pathways for intracellular and intermembrane movement of molecules. Comparative information on the near-native structure of microorganisms is an important and necessary component of exploring microbial diversity and understanding its consequences for function and ecology.

Influence of form IA RubisCO and environmental dissolved inorganic carbon on the delta13C of the clam-chemoautotroph symbiosis Solemya velum

Many nutritive symbioses between chemoautotrophic bacteria and invertebrates, such as Solemya velum, have delta(13)C values of approximately -30 to -35%, considerably more depleted than phytoplankton. Most of the chemoautotrophic symbionts fix carbon with a form IA ribulose 1,5-bisphosphate carboxylase (RubisCO). We hypothesized that this form of RubisCO discriminates against (13)CO(2) to a greater extent than other forms. Solemya velum symbiont RubisCO was cloned and expressed in Escherichia coli, purified and characterized. Enzyme from this recombinant system fixed carbon most rapidly at pH 7.5 and 20-25 degrees C. Surprisingly, this RubisCO had an epsilon-value (proportional to the degree to which the enzyme discriminates against (13)CO(2)) of 24.4 per thousand, similar to form IB RubisCOs, and higher than form II RubisCOs. Samples of interstitial water from S. velum's habitat were collected to determine whether the dissolved inorganic carbon (DIC) could contribute to the negative delta(13)C values. Solemya velum habitat DIC was present at high concentrations (up to approximately 5 mM) and isotopically depleted, with delta(13)C values as low as approximately -6%. Thus environmental DIC, coupled with a high degree of isotopic fractionation by symbiont RubisCO likely contribute to the isotopically depleted delta(13)C values of S. velum biomass, highlighting the necessity of considering factors at all levels (from environmental to enzymatic) in interpreting stable isotope ratios.

Physiological diversity and niche adaptation in marine Synechococcus

During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.

Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences

Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.

Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms

The phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated from seven samples, including samples from the Mid-Atlantic Ridge and various deep-sea habitats around Japan. The kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent mussel, Bathymodiolus sp., and the seep vestimentiferan tubeworm, Lamellibrachia sp. The RuBisCO genes that encode both form I and form II large subunits (cbbL and cbbM) were amplified by PCR from the seven deep-sea sample DNA populations, cloned, and sequenced. From each sample, 50 cbbL clones and 50 cbbM clones, if amplified, were recovered and sequenced to group them into operational taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total cbbL clones, and a total of 24 OTUs were recorded from the 250 total cbbM clones. All the current OTUs have the characteristic RuBisCO amino acid motif sequences that exist in other RuBisCOs. The recorded OTUs were related to different RuBisCO groups of proteobacteria, cyanobacteria, and eukarya. The diversity of the RuBisCO genes may be correlated with certain characteristics of the microbial habitats. The RuBisCO sequences from the symbiont-bearing tissues showed a phylogenetic relationship with those from the ambient bacteria. Also, the RuBisCO sequences of known species of thiobacilli and those from widely distributed marine habitats were closely related to each other. This suggests that the Thiobacillus-related RuBisCO may be distributed globally and contribute to the primary production in the deep sea.

Molecular and physiological responses of two classes of marine chromophytic phytoplankton (Diatoms and prymnesiophytes) during the development of nutrient-stimulated blooms

Generic taxon-specific DNA probes that target an internal region of the gene (rbcL) encoding the large subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RubisCO) were developed for two groups of marine phytoplankton (diatoms and prymnesiophytes). The specificity and utility of the probes were evaluated in the laboratory and also during a 1-month mesocosm experiment in which we investigated the temporal variability in RubisCO gene expression and primary production in response to inorganic nutrient enrichment. We found that the onset of successive bloom events dominated by each of the two classes of chromophyte algae was associated with marked taxon-specific increases in rbcL transcription rates. These observations suggest that measurements of RubisCO gene expression can provide an early indicator of the development of phytoplankton blooms and may also be useful in predicting which taxa are likely to dominate a bloom.

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.

RNase P RNA from Prochlorococcus marinus: contribution of substrate domains to recognition by a cyanobacterial ribozyme

The molecular organisation of the Prochlorococcus marinus rnpB gene and the catalytic activity of the encoded RNA were characterised. Kinetic parameters for several pre-tRNA substrates were comparable to those from other eubacterial RNase P RNAs, although unusually high cation concentrations were required. The CCA-end of pre-tRNAs is essential for efficient turnover despite the lack of the canonical binding motif in P. marinus RNase P RNA. A trnR gene is located only 38 nt upstream the rnpB 5' end on the complementary strand. This arrangement resembles those in the plastids of Cyanophora and Porphyra but not in any other bacterium.

Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities

The phytoplankton of the world's oceans play an integral part in global carbon cycling and food webs by conversion of carbon dioxide into organic carbon. They accomplish this task through the action of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Here we have investigated the phylogenetic diversity in the form I rbcL locus in natural phytoplankton communities of the open ocean and representative clones of marine autotrophic picoplankton by mRNA or DNA amplification and sequencing of a 480 to 483 bp internal fragment of this gene. Five gene sequences were recovered from nucleic acids of natural phytoplankton communities of the Gulf of Mexico. The rbcL genes of two Prochlorococcus isolates and one Synechococcus strain (WH8007) were also sequenced. Sequences were aligned with the database of rbcL genes and subjected to both neighbor-joining and parsimony analyses. The five sequences from the natural phytoplankton community spanned nearly the entire diversity of characterized form I rbcL genes, with some sequences closely related to isolates such as Synechococcus and Prochlorococcus (forms IA and I) and prymnesiophyte algae (form ID), while other sequences were deeply rooted. Unexpectedly, the deep euphotic zone contained an organism that possesses a transcriptionally active rbcL gene closely related to that of a recently characterized manganese-oxidizing bacterium, suggesting that such chemoautotrophs may contribute to the diversity of carbon-fixing organisms in the marine euphotic zone.

Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the key reaction of the Calvin reductive pentose phosphate cycle and as such is responsible for life as we know it. This enzyme has been intensively studied for decades. Evidence that RubisCO phylogenies are incongruent with those derived from other macromolecules has been accumulating and recent discoveries have driven home this point. Here we review findings regarding RubisCO phylogeny and discuss these in the context of the important biochemical and structural features of the enzyme. The implications for the engineering of improved RubisCO enzymes are considered.

Regulation, unique gene organization, and unusual primary structure of carbon fixation genes from a marine phycoerythrin-containing cyanobacterium

Marine phycoerythrin-containing cyanobacteria are major contributors to the overall productivity of the oceans. The present study indicates that the structural genes of the carbon assimilatory system are unusually arranged and possess a unique primary structure compared to previously studied cyanobacteria. Southern blot analyses of Synechococcus sp. strain WH7803 chromosomal DNA digests, using the ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit gene from Synechococcus sp. strain PCC6301 as a heterologous probe, revealed the presence of a 6.4 kb HindIII fragment that was detectable at only low stringency. Three complete open reading frames (ORFs) were detected within this fragment. Two of these ORFs potentially encode the Synechococcus sp. strain WH7803 rbcL and rbcS genes. The third ORF, situated immediately upstream from rbcL, potentially encodes a homologue of the ccmK gene from Synechococcus sp. strain PCC7942. The deduced amino acid sequences of each of these ORFs are more similar to homologues among the beta/gamma purple bacteria than to existing cyanobacterial homologues and phylogenetic analysis of the Rubisco large and small subunit sequences confirmed an unexpected relationship to sequences from among the beta/gamma purple bacteria. This is the first instance in which the possibility has been considered that an operon encoding three genes involved in carbon fixation may have been laterally transferred from a purple bacterium. Analysis of mRNA extracted from cells grown under diel conditions indicated that rbcL, rbcS and ccmK were regulated at the transcriptional level; specifically Rubisco transcripts were highest during the midday period, decreased at later times during the light period and eventually reached a level where they were all but undetectable during the dark period. Primer extension analysis indicated that the ccmK, rbcL and rbcS genes were co-transcribed.