A TPR-family membrane protein gene is required for light-activated heterotrophic growth of the cyanobacterium Synechocystis sp. PCC 6803

Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics

Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.

Selective loss of photosystem I and formation of tubular thylakoids in heterotrophically grown red alga Cyanidioschyzon merolae

We previously found that glycerol is required for heterotrophic growth in the unicellular red alga Cyanidioschyzon merolae. Here, we analyzed heterotrophically grown cells in more detail. Sugars or other organic substances did not support the growth in the dark. The growth rate was 0.4 divisions day^-1 in the presence of 400 mM glycerol, in contrast with 0.5 divisions day^-1 in the phototrophic growth. The growth continued until the sixth division. Unlimited heterotrophic growth was possible in the medium containing DCMU and glycerol in the light. Light-activated heterotrophic culture in which cells were irradiated by intermittent light also continued without an apparent limit. In the heterotrophic culture in the dark, chlorophyll content drastically decreased, as a result of inability of dark chlorophyll synthesis. Photosynthetic activity gradually decreased over 10 days, and finally lost after 19 days. Low-temperature fluorescence measurement and immunoblot analysis showed that this decline in photosynthetic activity was mainly due to the loss of Photosystem I, while the levels of Photosystem II and phycobilisomes were maintained. Accumulated triacylglycerol was lost during the heterotrophic growth, while keeping the overall lipid composition. Observation by transmission electron microscopy revealed that a part of thylakoid membranes turned into pentagonal tubular structures, on which five rows of phycobilisomes were aligned. This might be a structure that compactly conserve phycobilisomes and Photosystem II in an inactive state, probably as a stock of carbon and nitrogen. These results suggest that C. merolae has a unique strategy of heterotrophic growth, distinct from those found in other red algae.

Axenic Biofilm Formation and Aggregation by Synechocystis sp. Strain PCC 6803 Are Induced by Changes in Nutrient Concentration and Require Cell Surface Structures

Phototrophic biofilms are key to nutrient cycling in natural environments and bioremediation technologies, but few studies describe biofilm formation by pure (axenic) cultures of a phototrophic microbe. The cyanobacterium Synechocystis sp. strain PCC 6803 (here Synechocystis) is a model microorganism for the study of oxygenic photosynthesis and biofuel production. We report here that wild-type (WT) Synechocystis caused extensive biofilm formation in a 2,000-liter outdoor nonaxenic photobioreactor under conditions attributed to nutrient limitation. We developed a biofilm assay and found that axenic Synechocystis forms biofilms of cells and extracellular material but only when cells are induced by an environmental signal, such as a reduction in the concentration of growth medium BG11. Mutants lacking cell surface structures, namely type IV pili and the S-layer, do not form biofilms. To further characterize the molecular mechanisms of cell-cell binding by Synechocystis, we also developed a rapid (8-h) axenic aggregation assay. Mutants lacking type IV pili were unable to aggregate, but mutants lacking a homolog to Wza, a protein required for type 1 exopolysaccharide export in Escherichia coli, had a superbinding phenotype. In WT cultures, 1.2× BG11 medium induced aggregation to the same degree as 0.8× BG11 medium. Overall, our data support that Wza-dependent exopolysaccharide is essential to maintain stable, uniform suspensions of WT Synechocystis cells in unmodified growth medium and that this mechanism is counteracted in a pilus-dependent manner under altered BG11 concentrations.IMPORTANCE Microbes can exist as suspensions of individual cells in liquids and also commonly form multicellular communities attached to surfaces. Surface-attached communities, called biofilms, can confer antibiotic resistance to pathogenic bacteria during infections and establish food webs for global nutrient cycling in the environment. Phototrophic biofilm formation is one of the earliest phenotypes visible in the fossil record, dating back over 3 billion years. Despite the importance and ubiquity of phototrophic biofilms, most of what we know about the molecular mechanisms, genetic regulation, and environmental signals of biofilm formation comes from studies of heterotrophic bacteria. We aim to help bridge this knowledge gap by developing new assays for Synechocystis, a phototrophic cyanobacterium used to study oxygenic photosynthesis and biofuel production. With the aid of these new assays, we contribute to the development of Synechocystis as a model organism for the study of axenic phototrophic biofilm formation.

Two regulatory networks mediated by light and glucose involved in glycolytic gene expression in cyanobacteria

Fructose 1,6-bisphosphate aldolase (FBA) is an enzyme involved in both glycolytic and photosynthetic reactions in photosynthetic organisms. In prokaryotes, the bidirectional reaction proceeds in the same cellular compartment, i.e. the cytoplasm. Expression of the FBA gene, fbaA, is induced through two independent pathways, stimulated by continuous light and by glucose plus pulsed light (GPL), in a cyanobactrium, Synechocystis sp. PCC 6803. Under GPL conditions, glucose can be replaced by glucose analogs that are not even metabolized in a cell. Analyses of transcripts in deletion mutants suggested that both a histidine kinase, Hik8, and a response regulator, Sll1330, played important roles as signal components in fbaA expression under GPL conditions, but not under photosynthetic conditions. Analysis of a transformant in which sll1330 expression was enhanced demonstrated that fbaA expression was induced at least partially even without glucose, but for its further induction a pulsed light stimulus was required. These results substantiated that there are two light-dependent regulatory pathways for aldolase gene expression in this cyanobacterium.

The N-acetylmuramic acid 6-phosphate etherase gene promotes growth and cell differentiation of cyanobacteria under light-limiting conditions

Inactivation of sll0861 in Synechocystis sp. strain PCC 6803 or the homologous gene alr2432 in Anabaena sp. strain PCC 7120 had no effect on the growth of these organisms at a light intensity of 30 micromol photons m(-2) s(-1) but reduced their growth at a light intensity of 5 or 10 micromol photons m(-2) s(-1). In Anabaena, inactivation of the gene also significantly reduced the rate of heterocyst differentiation under low-light conditions. The predicted products of sll0861 and alr2432 and homologs of these genes showed similarity to N-acetylmuramic acid 6-phosphate etherase (MurQ), an enzyme involved in peptidoglycan recycling, in Escherichia coli. E. coli murQ and the cyanobacterial homologs could functionally substitute for each other. We hypothesize that murQ in cyanobacteria promotes low-light adaptation through reutilization of peptidoglycan degradation products.

The functional divergence of two glgP homologues in Synechocystis sp. PCC 6803

Glycogen phosphorylase (GlgP, EC 2.4.1.1) catalyzes the cleavage of glycogen into glucose-1-phosphate (Glc-1-P), the first step in glycogen catabolism. Two glgP homologues are found in the genome of Synechocystis sp. PCC 6803, a unicellular cyanobacterium: sll1356 and slr1367. We report on the different functions of these glgP homologues. sll1356, rather than slr1367, is essential for growth at high temperatures. On the other hand, when CO2-fixation and the supply of glucose are both limited, slr1367 is the key factor in glycogen metabolism. In cells growing autotrophically, sll1356 plays a more important role in glycogen digestion than slr1367. This functional divergence is also supported by a phylogenetic analysis of glgP homologues in cyanobacteria.

PratA, a periplasmic tetratricopeptide repeat protein involved in biogenesis of photosystem II in Synechocystis sp. PCC 6803

The light reactions of oxygenic photosynthesis are mediated by multisubunit pigment-protein complexes situated within the specialized thylakoid membrane system. The biogenesis of these complexes is regulated by transacting factors that affect the expression of the respective subunit genes and/or the assembly of their products. Here we report on the analysis of the PratA gene from the cyanobacterium Synechocystis sp. PCC 6803 that encodes a periplasmic tetratricopeptide repeat protein of formerly unknown function. Targeted inactivation of PratA resulted in drastically reduced photosystem II (PSII) content. Protein pulse labeling experiments of PSII subunits indicated that the C-terminal processing of the precursor of the reaction center protein D1 is compromised in the pratA mutant. Moreover, a direct interaction of PratA and precursor D1 was demonstrated by applying yeast two-hybrid analyses. This suggests that PratA represents a factor facilitating D1 maturation via the endoprotease CtpA. The periplasmic localization of PratA supports a model that predicts the initial steps of PSII biogenesis to occur at the plasma membrane of cyanobacterial cells.