Characterization of a phycoerythrin without alpha-subunits from a unicellular red alga

Confocal Microscopy in Ecophysiological Studies of Algae: A Door to Understanding Autofluorescence in Red Algae

Alga in the genus Chroothece have been reported mostly from aquatic or subaerial continental environments, where they grow in extreme conditions. The strain Chroothece mobilis MAESE 20.29 was exposed to different light intensities, red and green monochromatic light, ultraviolet (UV) radiation, high nitrogen concentrations, and high salinity to assess the effect of those environmental parameters on its growth. Confocal laser scanning microscopy (CLSM) was used as an “in vivo” noninvasive single-cell method for the study. The strain seemed to prefer fairly high light intensities and showed a significant increase in allophycocyanin (APC) and chlorophyll a [photosystem I (PSI) and photosystem II (PSII)] fluorescence with 330 and 789 μM/cm2/s intensities. Green monochromatic light promoted a significant increase in the fluorescence of APC and chlorophyll a (PSI and PSII). UV-A significantly decreased phycocyanin and increased APC, while UV-A + B showed a greater decreasing effect on c-Phycocyanin but did not significantly change concentrations of APC. The increase in nitrogen concentration in the culture medium significantly and negatively affected all pigments, and no effect was observed with an increase in salinity. Our data show that CLSM represents a very powerful tool for ecological research of microalgae in small volumes and may contribute to the knowledge of phycobiliproteins in vivo behavior and the parameters for the large-scale production of these pigments.

Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency

Diatoms, considered as one of the most diverse and largest groups of algae, can provide the means to reach a sustainable production of petrochemical substitutes and bioactive compounds. However, a prerequisite to achieving this goal is to increase the solar-to-biomass conversion efficiency of photosynthesis, which generally remains less than 5% for most photosynthetic organisms. We have developed and implemented a rapid and effective approach, herein referred to as intracellular spectral recompositioning (ISR) of light, which, through absorption of excess blue light and its intracellular emission in the green spectral band, can improve light utilization. We demonstrate that ISR can be used chemogenically, by using lipophilic fluorophores, or biogenically, through the expression of an enhanced green fluorescent protein (eGFP) in the model diatom Phaeodactylum tricornutum. Engineered P. tricornutum cells expressing eGFP achieved 28% higher efficiency in photosynthesis than the parental strain, along with an increased effective quantum yield and reduced nonphotochemical quenching (NPQ) induction levels under high-light conditions. Further, pond simulator experiments demonstrated that eGFP transformants could outperform their wild-type parental strain by 50% in biomass production rate under simulated outdoor sunlight conditions. Transcriptome analysis identified up-regulation of major photosynthesis genes in the engineered strain in comparison with the wild type, along with down-regulation of NPQ genes involved in light stress response. Our findings provide a proof of concept for a strategy of developing more efficient photosynthetic cell factories to produce algae-based biofuels and bioactive products.

Occurrence of a functionally stable photoharvesting single peptide allophycocyanin α-subunit (16.4 kDa) in the cyanobacterium Nostoc sp. R76DM

We report the occurrence of a functionally stable single peptide APC α-subunit in cyanobacterium Nostoc sp. R76DM.

A stable and functional single peptide phycoerythrin (15.45 kDa) from Lyngbya sp. A09DM

A functional and stable truncated-phycoerythrin (T-PE) was found as a result of spontaneous in vitro truncation. Truncation was noticed to occur during storage of purified native-phycoerythrin (N-PE) isolated from Lyngbya sp. A09DM. SDS and native-PAGE analysis revealed the truncation of N-PE, containing α (19.0 kDa)--and β (21.5 kDa)--subunits to the only single peptide of ∼15.45 kDa (T-PE). The peptide mass fingerprinting (PMF) and MS/MS analysis indicated that T-PE is the part of α-subunit of N-PE. UV-visible absorption peak of N-PE was found to split into two peaks (540 and 565 nm) after truncation, suggesting the alterations in its folded state. The emission spectra of both N-PE and T-PE show the emission band centered at 581 nm (upon excitation at 559 nm) suggested the maintenance of fluorescence even after significant truncation. Urea-induced denaturation and Gibbs-free energy (ΔGD°) calculations suggested that the folding and structural stability of T-PE was almost similar to that of N-PE. Presented bunch of evidences revealed the truncation in N-PE without perturbing its folding, structural stability and functionality (fluorescence), and thereby suggested its applicability in fluorescence based biomedical techniques where smaller fluorescence molecules are more preferable.

GC constituents and relative codon expressed amino acid composition in cyanobacterial phycobiliproteins

The genomic as well as structural relationship of phycobiliproteins (PBPs) in different cyanobacterial species are determined by nucleotides as well as amino acid composition. The genomic GC constituents influence the amino acid variability and codon usage of particular subunit of PBPs. We have analyzed 11 cyanobacterial species to explore the variation of amino acids and causal relationship between GC constituents and codon usage. The study at the first, second and third levels of GC content showed relatively more amino acid variability on the levels of G3+C3 position in comparison to the first and second positions. The amino acid encoded GC rich level including G rich and C rich or both correlate the codon variability and amino acid availability. The fluctuation in amino acids such as Arg, Ala, His, Asp, Gly, Leu and Glu in α and β subunits was observed at G1C1 position; however, fluctuation in other amino acids such as Ser, Thr, Cys and Trp was observed at G2C2 position. The coding selection pressure of amino acids such as Ala, Thr, Tyr, Asp, Gly, Ile, Leu, Asn, and Ser in α and β subunits of PBPs was more elaborated at G3C3 position. In this study, we observed that each subunit of PBPs is codon specific for particular amino acid. These results suggest that genomic constraint linked with GC constituents selects the codon for particular amino acids and furthermore, the codon level study may be a novel approach to explore many problems associated with genomics and proteomics of cyanobacteria.

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers

Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.

Purification, characterization and comparison of phycoerythrins from three different marine cyanobacterial cultures

The present study is focused on purification, characterization and comparison of phycoerythrins from three different marine cyanobacterial cultures--hormidium sp. A27 DM, Lyngbya sp. A09 DM and Halomicronema sp. A32 DM. 'Phycoerythrin' was successfully purified and characterized. On SDS-PAGE, the PE purified from all three young cultures showed four bands--corresponding to α and β subunits of each of PE-I and PE-II. However, phycoerythrin purified after prolonged growth of Phormidium sp. A27 DM and Halomicronema sp. A32DM showed only one band corresponding to 14 kDa whereas Lyngbya sp. A09 DM continued to produce uncleaved phycoerythrin. The absorption spectra of purified PEs from all the three young and old cultures showed variations however the fluorescence studies of the purified PEs in all cases gave the emission spectra at around 580 nm. The described work is of great importance to understand the role of phycoerythrin in adapting cyanobacteria to stress conditions.

Cloning, expression and characterization of phycoerythrin gene fromCeramium boydenn

Phycobiliproteins function as a major light harvesting protein-pigment complex in the cyanobacteria and the eukaryotic algae. Phycoerythrin (PE) is a kind of phycobiliproteins, widely located in all rhodophytes, some species of cyanobacteria and cryptophytes, and different ecotypes of Prochlorococcus populations. PeBA encoding beta and alpha subunits of PE from Ceramium boydenn was cloned and sequenced in this research. A peBA specific PCR primer was synthesized, based on the peBA gene conserved sequences. The beta subunit encoding gene (peB) contained an open reading frame of 534 bp, while the alpha subunit (peA) was 495 bp. Recombinant expression plasmid pET-peAB was constructed and expressed in Escherichia coli BL21. The molecular weight of expressive product of peB and peA was about 23.3 and 18.2 KD, respectively. Results of codon usage analysis show that G + C content is heterogeneous among different groups of PE and spacers have dramatically lower G + C contents than coding regions. Also there is a high variance in G + C content among sequences at the third position sites. It is also found in this paper that several sequence regions, which might reflect functional or structural requirements of the PE organization, and several residues known for their functional importance are conserved in almost all the sequences.

Exploiting genomic patterns to discover new supramolecular protein assemblies

Bacterial microcompartments are supramolecular protein assemblies that function as bacterial organelles by compartmentalizing particular enzymes and metabolic intermediates. The outer shells of these microcompartments are assembled from multiple paralogous structural proteins. Because the paralogs are required to assemble together, their genes are often transcribed together from the same operon, giving rise to a distinctive genomic pattern: multiple, typically small, paralogous proteins encoded in close proximity on the bacterial chromosome. To investigate the generality of this pattern in supramolecular assemblies, we employed a comparative genomics approach to search for protein families that show the same kind of genomic pattern as that exhibited by bacterial microcompartments. The results indicate that a variety of large supramolecular assemblies fit the pattern, including bacterial gas vesicles, bacterial pili, and small heat-shock protein complexes. The search also retrieved several widely distributed protein families of presently unknown function. The proteins from one of these families were characterized experimentally and found to show a behavior indicative of supramolecular assembly. We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data.

NblA gene expression in Synechocystis PCC 6803 strains lacking DspA (Hik33) and a NblR-like protein

Cyanobacteria respond to nutrient-limiting conditions by degrading their phycobilisomes (PBS), the light-harvesting complexes for photosynthesis. In Synechococcus sp. PCC 7942, the expression of nblA, an essential gene in this process, is controlled by the response regulator NblR and the sensor NblS. Here we study the effect of inactivation of dspA (an nblS homologue) and an nblR-like gene on phycobilisome degradation in Synechocystis sp. PCC 6803, under nitrogen starvation. In each mutant, the expression of nblA was found to be unaffected and sequential PBS degradation occurred after nitrogen deprivation (although it was slightly delayed). Our results demonstrate that dspA and nblR-like do not exert a major control of PBS degradation in Synechocystis sp. PCC 6803.

Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium Synechococcus sp. strain WH8102

The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II). Although the allophycocyanin appears to be similar to that found commonly in freshwater cyanobacteria, the phycocyanin is simpler since it possesses only one complete set of alpha and beta subunits and two rod-core linkers (CpcG1 and CpcG2). It is therefore probably made of a single hexameric disk per rod. In contrast, we have found two novel putative phycoerythrin-associated linker polypeptides that appear to be specific for marine Synechococcus spp. The first one (SYNW2000) is unusually long (548 residues) and apparently results from the fusion of a paralog of MpeC, a phycoerythrin II linker, and of CpeD, a phycoerythrin-I linker. The second one (SYNW1989) has a more classical size (300 residues) and is also an MpeC paralog. A biochemical analysis revealed that, like MpeC, these two novel linkers were both chromophorylated with phycourobilin. Our data suggest that they are both associated (partly or totally) with phycoerythrin II, and we propose to name SYNW2000 and SYNW1989 MpeD and MpeE, respectively. We further show that acclimation of phycobilisomes to high light leads to a dramatic reduction of MpeC, whereas the two novel linkers are not significantly affected. Models for the organization of the rods are proposed.

The NblAI protein from the filamentous cyanobacterium Tolypothrix PCC 7601: regulation of its expression and interactions with phycobilisome components

Cyanobacteria respond to changes in light or nutrient availability by modifications in their photosynthetic light harvesting antenna. In unicellular cyanobacteria a small polypeptide (NblA) is required for phycobilisome degradation following environmental stresses. In the filamentous strain Tolypothrix sp. PCC 7601 the nblAI gene, encoding a NblA homologue, is located upstream of the operon coding for phycoerythrin (cpeBA). The nblAI transcripts all originate from a single transcription start point; their intracellular levels vary according to nitrogen regimes but not with light spectral quality. Using recombinant His-tagged NblAI protein, we found that in vitro NblAI has affinity for both phycocyanin and phycoerythrin subunits from Tolypothrix sp. PCC 7601, but not for allophycocyanin from this cyanobacterium or for phycobiliproteins from other cyanobacterial species. We also observed that although nblAI is mainly expressed under nitrogen starvation, NblAI polypeptides are always present in the cell; a significant portion of them co-purify with phycobilisome preparations but only if cells were grown under red light. Our data indicate that NblAI attaches to the phycobilisomes even under non-inducing conditions and suggest a preferential affinity of NblAI for phycocyanin.

Nitrogen or sulfur starvation differentially affects phycobilisome degradation and expression of the nblA gene in Synechocystis strain PCC 6803

Nitrogen (N) limitation in cyanobacteria is well documented: a reduced growth rate is observed, accompanied by a cessation of phycobiliprotein synthesis and an ordered degradation of phycobilisomes (PBS). This leads to a dramatic bleaching phenomenon known as chlorosis. In Synechococcus strain PCC 7942, bleaching due to PBS degradation is also observed under sulfur (S) or phosphorus (P) limitation, and all three are under the control of the nblA gene product, a 59-amino-acid polypeptide which is overexpressed under N, S, and P starvation (J. L. Collier, and A. R. Grossman, EMBO J. 13:1039-1047, 1994). Cyanobase sequence data for Synechocystis strain PCC 6803 indicate the presence of two tandem open reading frames (sll0452 and sll0453) homologous to nblA. We cloned the two genes, identified a unique 5' mRNA end suggestive of a single transcription start site, and studied nblA expression under conditions of N or S starvation by Northern hybridization: transcripts were detected only under N starvation (no signal is detected in replete medium or with S starvation), whether nblA1 or nblA2 was used as a probe. Mutations in nblA1 and nblA2 were constructed by insertion of a kanamycin cassette; both mutations were nonbleaching under N starvation. Synechocystis strain PCC 6803 does not bleach under S starvation, consistent with the absence of nblA induction in these conditions. These results were confirmed by analysis of the PBS components: sequential degradation of phycocyanin and associated linkers was observed only under conditions of N starvation. This indicates differences between Synechocystis strain PCC 6803 and Synechococcus strain PCC 7942 in their regulatory and signaling pathways leading to N- and S-starved phenotypes.