Determination of the structure of the novel polypeptide containing aspartic acid and arginine which is found in Cyanobacteria

Synthetic biology toolkit of Ralstonia eutropha (Cupriavidus necator)

Synthetic biology encompasses many kinds of ideas and techniques with the common theme of creating something novel. The industrially relevant microorganism, Ralstonia eutropha (also known as Cupriavidus necator), has long been a subject of metabolic engineering efforts to either enhance a product it naturally makes (polyhydroxyalkanoate) or produce novel bioproducts (e.g., biofuels and other small molecule compounds). Given the metabolic versatility of R. eutropha and the existence of multiple molecular genetic tools and techniques for the organism, development of a synthetic biology toolkit is underway. This toolkit will allow for novel, user-friendly design that can impart new capabilities to R. eutropha strains to be used for novel application. This article reviews the different synthetic biology techniques currently available for modifying and enhancing bioproduction in R. eutropha. KEY POINTS: • R. eutropha (C. necator) is a versatile organism that has been examined for many applications. • Synthetic biology is being used to design more powerful strains for bioproduction. • A diverse synthetic biology toolkit is being developed to enhance R. eutropha's capabilities.

Bridging Nature and Engineering: Protein-Derived Materials for Bio-Inspired Applications

The sophisticated, elegant protein-polymers designed by nature can serve as inspiration to redesign and biomanufacture protein-based materials using synthetic biology. Historically, petro-based polymeric materials have dominated industrial activities, consequently transforming our way of living. While this benefits humans, the fabrication and disposal of these materials causes environmental sustainability challenges. Fortunately, protein-based biopolymers can compete with and potentially surpass the performance of petro-based polymers because they can be biologically produced and degraded in an environmentally friendly fashion. This paper reviews four groups of protein-based polymers, including fibrous proteins (collagen, silk fibroin, fibrillin, and keratin), elastomeric proteins (elastin, resilin, and wheat glutenin), adhesive/matrix proteins (spongin and conchiolin), and cyanophycin. We discuss the connection between protein sequence, structure, function, and biomimetic applications. Protein engineering techniques, such as directed evolution and rational design, can be used to improve the functionality of natural protein-based materials. For example, the inclusion of specific protein domains, particularly those observed in structural proteins, such as silk and collagen, enables the creation of novel biomimetic materials with exceptional mechanical properties and adaptability. This review also discusses recent advancements in the production and application of new protein-based materials through the approach of synthetic biology combined biomimetics, providing insight for future research and development of cutting-edge bio-inspired products. Protein-based polymers that utilize nature's designs as a base, then modified by advancements at the intersection of biology and engineering, may provide mankind with more sustainable products.

Cyanophycin and its biosynthesis: not hot but very cool

Covering: 1878 to early 2023Cyanophycin is a biopolymer consisting of a poly-aspartate backbone with arginines linked to each Asp sidechain through isopeptide bonds. Cyanophycin is made by cyanophycin synthetase 1 or 2 through ATP-dependent polymerization of Asp and Arg, or β-Asp-Arg, respectively. It is degraded into dipeptides by exo-cyanophycinases, and these dipeptides are hydrolyzed into free amino acids by general or dedicated isodipeptidase enzymes. When synthesized, chains of cyanophycin coalesce into large, inert, membrane-less granules. Although discovered in cyanobacteria, cyanophycin is made by species throughout the bacterial kingdom, and cyanophycin metabolism provides advantages for toxic bloom forming algae and some human pathogens. Some bacteria have developed dedicated schemes for cyanophycin accumulation and use, which include fine temporal and spatial regulation. Cyanophycin has also been heterologously produced in a variety of host organisms to a remarkable level, over 50% of the host's dry mass, and has potential for a variety of green industrial applications. In this review, we summarize the progression of cyanophycin research, with an emphasis on recent structural studies of enzymes in the cyanophycin biosynthetic pathway. These include several unexpected revelations that show cyanophycin synthetase to be a very cool, multi-functional macromolecular machine.

Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase

Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin synthetase (CphA1), and accumulates as a nitrogen reservoir during N₂ fixation by most cyanobacteria. A recent structural study showed that three constituent domains of CphA1 function as two distinct catalytic sites and an oligomerization interface in cyanophycin synthesis. However, it remains unclear how the ATP-dependent addition of aspartate to cyanophycin is initiated at the catalytic site of the glutathione synthetase-like domain. Here, we report the cryogenic electron microscopy structures of CphA1, including a complex with aspartate, cyanophycin primer peptide, and ATP analog. These structures reveal the aspartate binding mode and phosphate-binding loop movement to the active site required for the reaction. Furthermore, structural and mutational data show a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction.

CphA1 catalyzes the synthesis of cyanophycin polypeptide consisting of equimolar amounts of aspartate and arginine as a fixed nitrogen reservoir in cyanobacteria. Here, the authors solve the cryo-EM structures of CphA1, revealing the aspartate binding mode and protein dynamics required for cyanophycin elongation.

The structure of cyanophycinase in complex with a cyanophycin degradation intermediate

BACKGROUND

Cyanophycinases are serine protease family enzymes which are required for the metabolism of cyanophycin, the natural polymer multi-L-arginyl-poly(L-aspartic acid). Cyanophycinases degrade cyanophycin to β-Asp-Arg dipeptides, which enables use of this important store of fixed nitrogen.

METHODS

We used genetic code expansion to incorporate diaminopropionic acid into cyanophycinase in place of the active site serine, and determined a high-resolution structure of the covalent acyl-enzyme intermediate resulting from attack of cyanophycinase on a short cyanophycin segment.

RESULTS

The structure indicates that cyanophycin dipeptide residues P1 and P1' bind shallow pockets adjacent to the catalytic residues. We observe many cyanophycinase - P1 dipeptide interactions in the co-complex structure. Calorimetry measurements show that at least two cyanophycin dipeptides are needed for high affinity binding to cyanophycinase. We also characterized a putative cyanophycinase which we found to be structurally very similar but that shows no activity and could not be activated by mutation of its active site.

GENERAL SIGNIFICANCE

Despite its peptidic structure, cyanophycin is resistant to degradation by peptidases and other proteases. Our results help show how cyanophycinase can specifically bind and degrade this important polymer.

A cryptic third active site in cyanophycin synthetase creates primers for polymerization

Cyanophycin is a nitrogen reserve biopolymer in many bacteria that has promising industrial applications. Made by cyanophycin synthetase 1 (CphA1), it has a poly-L-Asp backbone with L-Arg residues attached to each aspartate sidechain. CphA1s are thought to typically require existing segments of cyanophycin to act as primers for cyanophycin polymerization. In this study, we show that most CphA1s will not require exogenous primers and discover the surprising cause of primer independence: CphA1 can make minute quantities of cyanophycin without primer, and an unexpected, cryptic metallopeptidase-like active site in the N-terminal domain of many CphA1s digests these into primers, solving the problem of primer availability. We present co-complex cryo-EM structures, make mutations that transition CphA1s between primer dependence and independence, and demonstrate that primer dependence can be a limiting factor for cyanophycin production in heterologous hosts. In CphA1, domains with opposite catalytic activities combine into a remarkable, self-sufficient, biosynthetic nanomachine.

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

Characterization of an efficient extracellular cyanophycinase and its encoding cphEStrept. gene from Streptomyces pratensis strain YSM

Until now, no enzymes were described that hydrolyze cyanophycin granular protein (CGP) from a species of the genus Streptomyces. An isolate able to hydrolyze CGP was identified as Streptomyces pratensis strain YSM. The CGPase from S. pratensis strain YSM had an optimum activity at 42 °C and pH 8.5, and was able to degrade CGP at a rate of 12 ± 0.3 μg/mL min. Additionally, this CGPase hydrolyzes water-soluble CGP significantly faster than water-insoluble CGP. The molecular mass of CGPase subunits from S. pratensis strain YSM as determined by SDS-PAGE was about 43 kDa, and the enzyme was entirely inhibited by serine-protease inhibitors. The CGPase coding gene (cphE_Strept.) was amplified from genomic DNA using primers designed form consensus sequence of putative CGPase sequences. The cphE_Strept. was 1427 bp encoding a CGPase of 420 amino acids that showed about 44% and 22% similarities to CGPase from Pseudomonas anguilliseptica BI and Synechocystis sp. PCC 6803, respectively. The catalytic triad and serine-protease residues (GXSXG) were identified in the CphE_Strept. sequence. Dipeptides and tetrapeptides were identified as hydrolysis products. Biotechnological exploitation of S. pratensis strain YSM for CGPase production might have an advantage due to the reduction of separation costs and its ability to degrade CGP in phosphate buffer saline using actively growing or resting cells.

Microbial production of cyanophycin: From enzymes to biopolymers

Cyanophycin is an attractive biopolymer with chemical and material properties that are suitable for industrial applications in the fields of food, medicine, cosmetics, nutrition, and agriculture. For efficient production of cyanophycin, considerable efforts have been exerted to characterize cyanophycin synthetases (CphAs) and optimize fermentations and downstream processes. In this paper, we review the characteristics of diverse CphAs from cyanobacteria and non-cyanobacteria. Furthermore, strategies for cyanophycin production in microbial strains, including Escherichia coli, Pseudomonas putida, Ralstonia eutropha, Rhizopus oryzae, and Saccharomyces cerevisiae, heterologously expressing different cphA genes are reviewed. Additionally, chemical and material properties of cyanophycin and its derivatives produced through biological or chemical modifications are reviewed in the context of their industrial applications. Finally, future perspectives on microbial production of cyanophycin are provided to improve its cost-effectiveness.

Reversible Self-Assembly Nanovesicle of UCST Response Prepared with Multi-l-arginyl-poly-l-aspartate Conjugated with Polyethylene Glycol

Multi-L-arginyl-poly-L-aspartate (MAPA), also known as cyanophycin, containing a backbone of polyaspartate with arginine and lysine as side chains, was prepared with recombinant Escherichia coli. The insoluble part (iMAPA) was conjugated with polyethylene glycol (PEG) at two different levels, high (iMAPA(PEG)h) and low (iMAPA(PEG)l). Both levels of conjugation exhibited UCST (upper critical solution temperature)-type responses in the pH range of 3-10 at a concentration of 2 mg/mL. The cloud-point temperature of each conjugate also showed a positive correlation with concentration in PBS, falling between 20 to 58 °C at a concentration from 0.1 to 3 mg/mL. Hysteresis was observed to follow approximate paths under the same condition during repeated heating and cooling. Notably, the reversible formation of core-shell vesicles appeared at room temperature in PBS with a size of around 25 to 60 nm, as measured by DLS and observed under TEM. The reversibility was further employed to encapsulate doxorubicin (Dox) at different weight ratios of Dox to iMAPA(PEG)h. An encapsulation efficiency could reach as high as 70% with an equivalent loading capacity of 1.5 mg Dox/mg iMAPA(PEG)h. The Dox-loaded vesicles stayed stable at 4 °C for up to 4 weeks, with a minimal leakage below 2% and a slightly dilated morphology. Temperature-triggered release of Dox from the vesicles could be achieved by a step change of 5 °C successively from 37 to 62 °C in an effort to induce an initial 10% release at 37 °C gradually to complete release at 62 °C.

Cyanophycin Synthesis Optimizes Nitrogen Utilization in the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6803

Cyanophycin is a carbon/nitrogen storage polymer widely distributed in most cyanobacterial strains and in a few heterotrophic bacteria. It is a nonribosomal polypeptide consisting of equimolar amounts of aspartate and arginine. Here, we focused on the physiological function and cell biology of cyanophycin in the unicellular nondiazotrophic cyanobacterium Synechocystis sp. strain PCC 6803. To study the cellular localization of the cyanophycin-synthesizing enzyme CphA during cyanophycin synthesis and degradation, we fused it to green fluorescent protein. When CphA was inactive, it localized diffusely in the cytoplasm. When cyanophycin synthesis was triggered, CphA first aggregated into foci and later localized on the surface of cyanophycin granules. In the corresponding cell extracts, localization of CphA on the cyanophycin granule surface required Mg²⁺ During cyanophycin degradation, CphA dissociated from the granule surface and returned to its inactive form in the cytoplasm. To investigate the physiological role of cyanophycin, we compared wild-type cells with a CphA-deficient mutant. Under standard laboratory conditions, the ability to synthesize cyanophycin did not confer a growth advantage. To mimic the situation in natural habitats, cells were cultured with a fluctuating and limiting nitrogen supplementation and/or day/night cycles. Under all of these conditions, cyanophycin provided a fitness advantage to the wild type over the mutant lacking cyanophycin. During resuscitation from nitrogen starvation, wild-type cells accumulated cyanophycin during the night and used it as an internal nitrogen source during the day. This demonstrates that cyanophycin can be used as a temporary nitrogen storage to uncouple nitrogen assimilation from photosynthesis.IMPORTANCE We clarified the elusive biological function of cyanophycin in the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803. Cyanophycin is a dynamic carbon/nitrogen storage polymer (multi-arginyl-l-polyaspartate) that is conditionally present in most cyanobacteria and a few heterotrophic bacteria as cellular inclusion granules. Here, we show that the cyanophycin-synthesizing enzyme CphA in the nonactive state localizes diffusely in the cytoplasm. When cyanophycin synthesis is triggered, active CphA first aggregates into foci and then covers the surface of mature cyanophycin granules, which in vitro requires Mg²⁺ as a cofactor. Cyanophycin accumulation enables Synechocystis sp. to optimize nitrogen assimilation under nitrogen-poor conditions, in particular when the nitrogen supply fluctuates and during day/night cycles, by allowing continuous nitrogen assimilation and storage. Therefore, cyanophycin provides the wild-type cyanobacterium with a clear fitness advantage over non-cyanophycin-producing cells in natural environments with fluctuating nitrogen supply.

Developing a Genetically Encoded, Cross-Species Biosensor for Detecting Ammonium and Regulating Biosynthesis of Cyanophycin

Responding to nitrogen status is essential for all living organisms. Bacteria have evolved various complex and exquisite regulatory systems to control nitrogen metabolism. However, natural nitrogen regulatory systems, owing to their complexity, often function only in their original hosts and do not respond properly when transferred to another species. By harnessing the Lactococcus GlnRA system, we developed a genetically encoded, cross-species ammonium biosensor that displays a dynamic range up to 9-fold upon detection of ammonium ion. We demonstrated applications of this ammonium biosensor in three different species (Escherichia coli, Pseudomonas putida, and Synechocystis sp.) to detect different nitrogen sources. This ammonium sensor was further used to regulate the biosynthesis of a nitrogen-rich polymer, cyanophycin, based on ammonium concentration. Given the importance of nitrogen responses, the developed biosensor should be broadly applicable to synthetic biology and bioengineering.

Expression of CphB- and CphE-type cyanophycinases in cyanophycin-producing tobacco and comparison of their ability to degrade cyanophycin in plant and plant extracts

Increasing the arginine (Arg) content in plants used as feed or food is of interest, since the supplementation of food with conditionally essential Arg has been shown to have nutritional benefits. An increase was achieved by the expression of the Arg-rich bacterial storage component, cyanophycin (CGP), in the chloroplast of transgenic plants. CGP is stable in plants and its degradation into β-aspartic acid (Asp)-Arg dipeptides, is solely catalyzed by bacterial cyanophycinases (CGPase). Dipeptides can be absorbed by animals even more efficiently than free amino acids (Matthews and Adibi 1976; Wenzel et al. 2001). The simultaneous production of CGP and CGPase in plants could be a source of β-Asp-Arg dipeptides if CGP degradation can be prevented in planta or if dipeptides are stable in the plants. We have shown for the first time that it is possible to co-express CGP and CGPase in the same plant without substrate degradation in planta by transient expression of the cyanobacterial CGPase CPHB (either in the plastid or cytosol), and the non-cyanobacterial CGPase CPHE (cytosol) in CGP-producing Nicotiana tabacum plants. We compared their ability to degrade CGP in planta and in crude plant extracts. No CGP degradation appeared prior to cell homogenization independent of the CGPase produced. In crude plant extracts, only cytosolic CPHE led to a fast degradation of CGP. CPHE also showed higher stability and in vitro activity compared to both CPHB variants. This work is the next step to increase Arg in forage plants using a stable, Arg-rich storage protein.

Complete Genome Sequence of Bacillus horikoshii Strain 20a from Cuatro Cienegas, Coahuila, Mexico

We sequenced the Bacillus horikoshii 20a genome, isolated from sediment collected in Cuatro Cienegas, Mexico. We identified genes involved in establishing antagonistic interactions in microbial communities (antibiotic resistance and bacteriocins) and genes related to the metabolism of cyanophycin, a reserve compound and spore matrix material potentially relevant for survival in an oligotrophic environment.

Stable production of cyanophycinase in Nicotiana benthamiana and its functionality to hydrolyse cyanophycin in the murine intestine

Food supplementation with the conditionally essential amino acid arginine (Arg) has been shown to have nutritional benefits. Degradation of cyanophycin (CGP), a peptide polymer used for nitrogen storage by cyanobacteria, requires cyanophycinase (CGPase) and results in the release of β-aspartic acid (Asp)-Arg dipeptides. The simultaneous production of CGP and CGPase in plants could be a convenient source of Arg dipeptides. Different variants of the cphB coding region from Thermosynechococcus elongatus BP-1 were transiently expressed in Nicotiana benthamiana plants. Translation and enzyme stability were optimized to produce high amounts of active CGPase. Protein stability was increased by the translational fusion of CGPase to the green fluorescent protein (GFP) or to the transit peptide of the small subunit of RuBisCO for peptide production in the chloroplasts. Studies in mice showed that plant-expressed CGP fed in combination with plant-made CGPase was hydrolysed in the intestine, and high levels of ß-Asp-Arg dipeptides were found in plasma, demonstrating dipeptide absorption. However, the lack of an increase in Asp and Arg or its metabolite ornithine in plasma suggests that Arg from CGP was not bioavailable in this mouse group. Intestinal degradation of CGP by CGPase led to low intestinal CGP content 4 h after consumption, but after ingestion of CGP alone, high CGP concentrations remained in the large intestine; this indicated that intact CGP was transported from the small to the large intestine and that CGP was resistant to colonic microbes.

Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

Bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (AMD) from the lignite-mining district in Lusatia (East Germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus "Ferrovum" and a group comprising Gallionella-like strains. Since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of "Ferrovum" and a strain of the heterotrophic acidophile Acidiphilium in order to obtain insight into the life style of these novel bacteria. Here we report on attempts to undertake a similar study on Gallionella-like acidophiles from AMD. Isolates belonging to the family Gallionellaceae are still restricted to the microaerophilic and neutrophilic iron oxidizers Sideroxydans and Gallionella. Availability of genomic or metagenomic sequence data of acidophilic strains of these genera should, therefore, be relevant for defining adaptive strategies in pH homeostasis. This is particularly the case since complete genome sequences of the neutrophilic strains G. capsiferriformans ES-2 and S. lithotrophicus ES-1 permit the direct comparison of the metabolic capacity of neutrophilic and acidophilic members of the same genus and, thus, the detection of biochemical features that are specific to acidophilic strains to support life under acidic conditions. Isolation attempts undertaken in this study resulted in the microaerophilic enrichment culture ADE-12-1 which, based on 16S rRNA gene sequence analysis, consisted of at least three to four distinct Gallionellaceae strains that appear to be closely related to the neutrophilic iron oxidizer S. lithotrophicus ES-1. Key hypotheses inferred from the metabolic reconstruction of the metagenomic sequence data of these acidophilic Sideroxydans strains include the putative role of urea hydrolysis, formate oxidation and cyanophycin decarboxylation in pH homeostasis.

Peculiarities and impacts of expression of bacterial cyanophycin synthetases in plants

Cyanophycin (CP) can be successfully produced in plants by the ectopic expression of the CphA synthetase from Thermosynechococcus elongatus BP-1 (Berg et al. 2000), yielding up to 6.8 % of dry weight (DW) in tobacco leaf tissue and 7.5 % in potato tubers (Huehns et al. 2008, 2009). Though, high amounts of the polymer lead to phenotypical abnormalities in both crops. The extension of abnormalities and the maximum amount of CP tolerated depend on the compartment that CP production is localized at the tissue/crop in which CP was produced (Huehns et al. 2008, 2009; Neumann et al. 2005). It cannot be ascribed to a depletion of arginine, lysine, or aspartate, the substrates for CP synthesis.

Cyanophycin mediates the accumulation and storage of fixed carbon in non-heterocystous filamentous cyanobacteria from coniform mats

Thin, filamentous, non-heterocystous, benthic cyanobacteria (Subsection III) from some marine, lacustrine and thermal environments aggregate into macroscopic cones and conical stromatolites. We investigate the uptake and storage of inorganic carbon by cone-forming cyanobacteria from Yellowstone National Park using high-resolution stable isotope mapping of labeled carbon (H(13)CO3 (-)) and immunoassays. Observations and incubation experiments in actively photosynthesizing enrichment cultures and field samples reveal the presence of abundant cyanophycin granules in the active growth layer of cones. These ultrastructurally heterogeneous granules rapidly accumulate newly fixed carbon and store 18% of the total particulate labeled carbon after 120 mins of incubation. The intracellular distribution of labeled carbon during the incubation experiment demonstrates an unexpectedly large contribution of PEP carboxylase to carbon fixation, and a large flow of carbon and nitrogen toward cyanophycin in thin filamentous, non-heterocystous cyanobacteria. This pattern does not occur in obvious response to a changing N or C status. Instead, it may suggest an unusual interplay between the regulation of carbon concentration mechanisms and accumulation of photorespiratory products that facilitates uptake of inorganic C and reduces photorespiration in the dense, surface-attached communities of cyanobacteria from Subsection III.

Increased lysine content is the main characteristic of the soluble form of the polyamide cyanophycin synthesized by recombinant Escherichia coli

Cyanophycin, a polyamide of cyanobacterial or noncyanobacterial origin consisting of aspartate, arginine, and lysine, was synthesized in different recombinant strains of Escherichia coli expressing cphA from Synechocystis sp. strain PCC 6308 or PCC 6803, Anabaena sp. strain PCC 7120, or Acinetobacter calcoaceticus ADP1. The molar aspartate/arginine/lysine ratio of the water-soluble form isolated from a recombinant strain expressing CphA6308 was 1:0.5:0.5, with a lysine content higher than any ever described before. The water-insoluble form consisted instead of mainly aspartate and arginine residues and had a lower proportion of lysine, amounting to a maximum of only 5 mol%. It could be confirmed that the synthesis of soluble cyanobacterial granule polypeptide (CGP) is independent of the origin of cphA. Soluble CGP isolated from all recombinant strains contained a least 17 mol% lysine. The total CGP portion of cell dry matter synthesized by CphA6308 from recombinant E. coli was about 30% (wt/wt), including 23% (wt/wt) soluble CGP, by using terrific broth complex medium for cultivation at 30°C for 72 h. Enhanced production of soluble CGP instead of its insoluble form is interesting for further application and makes recombinant E. coli more attractive as a suitable source for the production of polyaspartic acid or dipeptides. In addition, a new low-cost, time-saving, effective, and common isolation procedure for mainly soluble CGP, suitable for large-scale application, was established in this study.

Investigations on three genes in Ralstonia eutropha H16 encoding putative cyanophycin metabolizing enzymes

The genome sequence of the facultative chemolithoautotrophic bacterium Ralstonia eutropha H16 exhibited two coding sequences with high homologies to cyanophycin synthetases (CphA) as well as one gene coding for a putative cyanophycinase (CphB). To investigate whether or not the genes cphA H16 (H16_A0774), cphA'H16 (H16_A0775) and cphB H16 (H16_B1013) encode active cyanophycin (CGP) metabolism proteins, several functional analyses were performed. Extensive in silico analysis revealed that all characteristic motifs are conserved within CphAH16, whereas CphA'H16 misses a large part of the so-called J-loop present in other active cyanophycin synthetases. Although transcription of both genes was demonstrated by RT-PCR, and heterologously expressed cphA genes led to light-scattering inclusions in recombinant cells of Escherichia coli, no CGP could be isolated from the cells or detected by HPLC analysis. For all enzyme assay experiments carried out, significant enzyme activities were determined for CphA and CphA' in recombinant E. coli cells if crude cell extracts were applied. Homologous expression of cphA genes in cells of R. eutropha H16∆phaC1 did not result in the formation of light-scattering inclusions, and no CGP could be isolated from the cells or detected by HPLC analysis. No transcription of cphB encoding a putative cyanophycinase could be detected by RT-PCR analysis and no overexpression was achieved in several strains of E. coli. Furthermore, no enzyme activity was detected by using CGP overlay agar plates.

Isolation of cyanophycin from tobacco and potato plants with constitutive plastidic cphATe gene expression

A chimeric cyanophycin synthetase gene composed of the cphATe coding region from the cyanobacterium Thermosynechococcus elongatus BP-1, the constitutive 35S promoter and the plastid targeting sequence of the integral photosystem II protein PsbY was transferred to the tobacco variety Petit Havanna SRI and the commercial potato starch production variety Albatros. The resulting constitutive expression of cyanophycin synthetase leads to polymer contents in potato leaf chloroplasts of up to 35 mg/g dry weight and in tuber amyloplasts of up to 9 mg/g dry weight. Both transgenic tobacco and potato were used for the development of isolation methods applicable for large-scale extraction of the polymer. Two different procedures were developed which yielded polymer samples of 80 and 90% purity, respectively.

Production optimization of cyanophycinase ChpEal from Pseudomonas alcaligenes DIP1

Pseudomonas alcaligenes DIP1 produces an extracellular cyanophycinase (CphE_al). The corresponding gene (cphE_al) was identified from subclones of a genomic DNA gene library by heterologously expressing the functionally active enzyme in Escherichia coli. The nucleotide sequence of the gene (1260 base pairs) was determined indicating a theoretical mass of 43.6 kDa (mature CphE_al) plus a leader peptide of 2,6 kDa which corresponds well to the apparent molecular mass of 45 kDa as revealed by SDS-PAGE. The enzyme exhibited a high sequence identity of 91% with the extracellular cyanophycinase from P. anguilliseptica strain BI and carried an N-terminal Sec secretion signal peptide. Analysis of the amino acid sequence of cphE revealed a putative catalytic triad consisting of the serine motif GXSXG plus a histidine and a glutamate residue, suggesting a catalytic mechanism similar to serine-type proteases. The cyanophycinase (CphE_al) was heterologously produced in two different E. coli strains (Top10 and BL21(DE3)) from two plasmid vectors (pBBR1MCS-4 and pET-23a(+)). The signal peptide of CphE_al was cleaved in E. coli, suggesting active export of the protein at least to the periplasm. Substantial enzyme activity was also present in the culture supernatants. The extracellular cyanophycinase activities in E. coli were higher than activities in the wild type P. alcaligenes DIP1 in complex LB medium. Highest extracellular enzyme production was achieved with E. coli BL21(DE3) expressing CphE_al from pBBR1MCS-4. Using M9 minimal medium was less effective, but the relatively low cost of mineral salt media makes these results important for the industrial-scale production of dipeptides from cyanophycin.

Production of cyanophycin in Rhizopus oryzae through the expression of a cyanophycin synthetase encoding gene

Cyanophycin or cyanophycin granule peptide is a protein that results from non-ribosomal protein synthesis in microorganisms such as cyanobacteria. The amino acids in cyanophycin can be used as a feedstock in the production of a wide range of chemicals such as acrylonitrile, polyacrylic acid, 1,4-butanediamine, and urea. In this study, an auxotrophic mutant (Rhizopus oryzae M16) of the filamentous fungus R. oryzae 99-880 was selected to express cyanophycin synthetase encoding genes. These genes originated from Synechocystis sp. strain PCC6803, Anabaena sp. strain PCC7120, and a codon optimized version of latter gene. The genes were under control of the pyruvate decarboxylase promoter and terminator elements of R. oryzae. Transformants were generated by the biolistic transformation method. In only two transformants both expressing the cyanophycin synthetase encoding gene from Synechocystis sp. strain PCC6803 was a specific enzyme activity detected of 1.5 mU/mg protein. In one of these transformants was both water-soluble and insoluble cyanophycin detected. The water-soluble fraction formed the major fraction and accounted for 0.5% of the dry weight. The water-insoluble CGP was produced in trace amounts. The amino acid composition of the water-soluble form was determined and constitutes of equimolar amounts of arginine and aspartic acid.

Establishment of cyanophycin biosynthesis in Pichia pastoris and optimization by use of engineered cyanophycin synthetases

Two strains of the methylotrophic yeast Pichia pastoris were used to establish cyanophycin (multi-L-arginyl-poly-L-aspartic acid [CGP]) synthesis and to explore the applicability of this industrially widely used microorganism for the production of this polyamide. Therefore, the CGP synthetase gene from the cyanobacterium Synechocystis sp. strain PCC 6308 (cphA(6308)) was expressed under the control of the alcohol oxidase 1 promoter, yielding CGP contents of up to 10.4% (wt/wt), with the main fraction consisting of the soluble form of the polymer. To increase the polymer contents and to obtain further insights into the structural or catalytic properties of the enzyme, site-directed mutagenesis was applied to cphA(6308) and the mutated gene products were analyzed after expression in P. pastoris and Escherichia coli, respectively. CphA(6308)Delta1, which was truncated by one amino acid at the C terminus; point mutated CphA(6308)C595S; and the combined double-mutant CphA(6308)Delta1C595S protein were purified. They exhibited up to 2.5-fold higher enzyme activities of 4.95 U/mg, 3.20 U/mg, and 4.17 U/mg, respectively, than wild-type CphA(6308) (2.01 U/mg). On the other hand, CphA proteins truncated by two (CphA(6308)Delta2) or three (CphA(6308)Delta3) amino acids at the C terminus showed similar or reduced CphA enzyme activity in comparison to CphA(6308). In flask experiments, a maximum of 14.3% (wt/wt) CGP was detected after the expression of CphA(6308)Delta1 in P. pastoris. For stabilization of the expression plasmid, the his4 gene from Saccharomyces cerevisiae was cloned into the expression vector used and the constructs were transferred to histidine auxotrophic P. pastoris strain GS115. Parallel fermentations at a one-to-one scale revealed 26 degrees C and 6.0 as the optimal temperature and pH, respectively, for CGP synthesis. After optimization of fermentation parameters, medium composition, and the length of the cultivation period, CGP contents could be increased from 3.2 to 13.0% (wt/wt) in cells of P. pastoris GS115 expressing CphA(6308) and up to even 23.3% (wt/wt) in cells of P. pastoris GS115 expressing CphA(6308)Delta1.

Tuber-specific cphA expression to enhance cyanophycin production in potatoes

The production of biodegradable polymers that can be used to substitute petrochemical compounds in commercial products in transgenic plants is an important challenge for plant biotechnology. Nevertheless, it is often accompanied by reduced plant fitness. To decrease the phenotypic abnormalities of the sprout and to increase polymer production, we restricted cyanophycin accumulation to the potato tubers by using the cyanophycin synthetase gene (cphA(Te)) from Thermosynechococcus elongatus BP-1, which is under the control of the tuber-specific class 1 promoter (B33). Tuber-specific cytosolic (pB33-cphA(Te)) as well as tuber-specific plastidic (pB33-PsbY-cphA(Te)) expression resulted in significant polymer accumulation solely in the tubers. In plants transformed with pB33-cphA(Te), both cyanophycin synthetase and cyanophycin were detected in the cytoplasm leading to an increase up to 2.3% cyanophycin of dry weight and resulting in small and deformed tubers. In B33-PsbY-cphA(Te) tubers, cyanophycin synthetase and cyanophycin were exclusively found in amyloplasts leading to a cyanophycin accumulation up to 7.5% of dry weight. These tubers were normal in size, some clones showed reduced tuber yield and sometimes exhibited brown sunken staining starting at tubers navel. During a storage period over of 32 weeks of one selected clone, the cyanophycin content was stable in B33-PsbY-cphA(Te) tubers but the stress symptoms increased. However, all tubers were able to germinate. Nitrogen fertilization in the greenhouse led not to an increased cyanophycin yield, slightly reduced protein content, decreased starch content, and changes in the amounts of bound and free arginine and aspartate, as compared with control tubers were observed.

Metabolic engineering of Saccharomyces cerevisiae for production of novel cyanophycins with an extended range of constituent amino acids

Cyanophycin (multi-l-arginyl-poly-l-aspartic acid; also known as cyanophycin grana peptide [CGP]) is a putative precursor for numerous biodegradable technically used chemicals. Therefore, the biosynthesis and production of the polymer in recombinant organisms is of special interest. The synthesis of cyanophycin derivatives consisting of a wider range of constituents would broaden the applications of this polymer. We applied recombinant Saccharomyces cerevisiae strains defective in arginine metabolism and expressing the cyanophycin synthetase of Synechocystis sp. strain PCC 6308 in order to synthesize CGP with citrulline and ornithine as constituents. Strains defective in arginine degradation (Car1 and Car2) accumulated up to 4% (wt/wt) CGP, whereas strains defective in arginine synthesis (Arg1, Arg3, and Arg4) accumulated up to 15.3% (wt/wt) of CGP, which is more than twofold higher than the previously content reported in yeast and the highest content ever reported in eukaryotes. Characterization of the isolated polymers by different analytical methods indicated that CGP synthesized by strain Arg1 (with argininosuccinate synthetase deleted) consisted of up to 20 mol% of citrulline, whereas CGP from strain Arg3 (with ornithine carbamoyltransferase deleted) consisted of up to 8 mol% of ornithine, and CGP isolated from strain Arg4 (with argininosuccinate lyase deleted) consisted of up to 16 mol% lysine. Cultivation experiments indicated that the incorporation of citrulline or ornithine is enhanced by the addition of low amounts of arginine (2 mM) and also by the addition of ornithine or citrulline (10 to 40 mM), respectively, to the medium.

Establishment of a novel anabolism-based addiction system with an artificially introduced mevalonate pathway: complete stabilization of plasmids as universal application in white biotechnology

Plasmid stability in recombinant microorganisms is a very important requirement for highly efficient plasmid-based production processes in biotechnology. To stably maintain plasmids, we developed in this study an efficient and stringent novel anabolism-based addiction system, which can be widely used. This novel addiction system is based on two components: (i) an Escherichia coli HMS174(DE3) knockout mutant of the ispH gene coding for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) of the deoxyxylulose 5-phosphate (DXP) pathway, impairing the synthesis of isopentenyl pyrophosphate (IPP) and (ii) a completely synthetic and episomal mevalonate (MVA) pathway as an alternative supplier of essential IPP. The latter is encoded by a plasmid that contains the genes for HMG-CoA reductases from Lactococcus lactis and Staphylococcus aureus plus HMG-CoA-synthase, MVA kinase, MVP kinase and MVPP decarboxylase from S. aureus. This plasmid should then also harbor the genes for the protein or for the pathway that will be produced or that will be utilized for production of a chemical. To demonstrate the functionality of this addiction system, a mutated cyanophycin synthetase gene (cphA(6308)C595S) was used. To determine plasmid stabilities, flasks experiments in media supplied or not supplied with antibiotics were carried out with the knockout mutant and two control strains, one harboring plasmid pCOLADuet-1::MVA1-5::cphA(6308) and the other harboring a conventional expression plasmid pET-23a::cphA(6308). As revealed by measuring the colony-forming units of aliquots spread on solid media with or without antibiotics, the knockout mutant revealed a plasmid stability of 100% whereas the control strains exhibited plasmid stabilities of only 64% and 2%, respectively. Radiometric enzyme activity measurements for CphA revealed only 95% and 12.5% of the activity in the control strains harboring pCOLADuet-1::MVA1-5::cphA(6308) and pET-23a::cphA(6308), respectively, in comparison to the activity measured in the knockout mutant. The knockout mutant synthesized 9.5% (w/w of cell dry weight (CDW)) of cyanophycin, and the control strain harboring pCOLADuet-1::MVA1-5::cphA(6308) synthesized 13.6% (w/w of CDW) after growth without antibiotics.

Transformation of cyanobacteria

Cyanobacteria are a diverse and successful group of bacteria defined by their ability to carry out oxygenic photosynthesis. They occupy diverse ecological niches and are important primary producers in the oceans. Cyanobacteria are amenable to genetic manipulation. Some strains are naturally transformable. Many others have been transformed in the lab by conjugation or electroporation. The ability to transform cyanobacteria has been determinant in the development of the molecular biology of these organisms and has been the basis of many of their biotechnological applications. Cyanobacteria are the source of natural products and toxins of potential use and can be engineered to synthesize substances of biotechnological interest. Their high protein and vitamin content makes them useful as a dietary supplement. Because of their ability to occupy diverse ecological niches, they can be used to deliver to the medium substances of interest or as biosensors.