Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartic acid (cyanophycin): molecular cloning of the gene of Synechocystis sp. PCC 6803, expression in Escherichia coli, and biochemical characterization of the purified enzyme

Phosphoproteome modulation by nucleoside diphosphate kinase affects photosynthesis & stress tolerance of Nostoc PCC 7120

Nucleoside diphosphate kinase (Ndk/NDK/NDPK) is known to possess pleiotropic functions, one of which is that as a protein kinase, and has been shown to be involved in stress tolerance in plants. To assess its role in the cyanobacterium Nostoc PCC 7120, which is hitherto unreported, recombinant strain overexpressing Ndk, Anndk+ was generated. Phosphoproteomic analysis of Anndk+ and its comparison with that of the vector control, AnpAM, revealed differential phosphorylation at S/T/Y sites of proteins belonging to varied functional groups, with over 17 % phosphoproteins involved in photosynthesis. A total of 177 phosphopeptides and 117 phosphoproteins were identified, including newly identified phosphopeptides in any cyanobacteria. Compared to AnpAM, the Anndk+ cells exhibited (i) lower photosynthetic efficiency and electron transport rate at low PAR (photosynthetically active radiation), (ii) no change in photochemical quenching across PAR, (iii) but distinct non-photochemical quenching [zero Y(NPQ) and high Y(NO) in Anndk+ and high Y(NPQ) and low (NO) in AnpAM], and (iv) increased tolerance to γ-radiation, oxidative, salt and DCMU stresses. The observed modulation of phosphoproteome linked to physiological changes upon overexpression of Ndk in Nostoc could be a combination of direct protein kinase activity of Ndk and/or indirectly through other protein kinases and phosphatases whose phosphorylation status is mediated by Ndk. This is the first report on a direct correlation between Ndk levels, phosphorylation status of proteins and stress tolerance in any cyanobacteria.

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.

Characterization and functional evidence for Orf2 of Streptomyces sp. 139 as a novel dipeptidase E

Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.

Chlorophyll biosynthesis under the control of arginine metabolism

In natural environments, photosynthetic organisms adjust their metabolism to cope with the fluctuating availability of combined nitrogen sources, a growth-limiting factor. For acclimation, the dynamic degradation/synthesis of tetrapyrrolic pigments, as well as of the amino acid arginine, is pivotal; however, there has been no evidence that these processes could be functionally coupled. Using co-immunopurification and spectral shift assays, we found that in the cyanobacterium Synechocystis sp. PCC 6803, the arginine metabolism-related ArgD and CphB enzymes form protein complexes with Gun4, an essential protein for chlorophyll biosynthesis. Gun4 binds ArgD with high affinity, and the Gun4-ArgD complex accumulates in cells supplemented with ornithine, a key intermediate of the arginine pathway. Elevated ornithine levels restricted de novo synthesis of tetrapyrroles, which arrested the recovery from nitrogen deficiency. Our data reveal a direct crosstalk between tetrapyrrole biosynthesis and arginine metabolism that highlights the importance of balancing photosynthetic pigment synthesis with nitrogen homeostasis.

Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes

Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.

Recombinant Multi-l-Arginyl-Poly-l-Aspartate (Cyanophycin) as an Emerging Biomaterial

Multi-l-arginyl-poly-l-aspartate (MAPA) is a non-ribosomal polypeptide which synthesis is directed by cyanophycin synthetase, and its production can be achieved using recombinant microorganisms carrying the cphA gene. Along its poly-aspartate backbone, arginine or lysine links to each aspartate via an isopeptide bond. MAPA is a zwitterionic polyelectrolyte full of charged carboxylic, amine, and guanidino groups. In aqueous solution, MAPA exhibits dual thermal and pH responses similar to those stimuli-responsive polymers. Being biocompatible, the films containing MAPA can support cell proliferation and elicits minimal immune response in macrophages. Dipeptides from MAPA after enzymatic treatments can provide nutritional benefits. In light of the increasing interest in MAPA, this article focuses on the recent discovery of the function of cyanophycin synthetase and the potentials of MAPA as a biomaterial.

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.

Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation

Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.

Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments

Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.

Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota

The intestinal microbiota is a crucial environmental factor in the development of inflammatory bowel disease (IBD). The abundance of Faecalibacterium prausnitzii is significantly decreased in IBD patients, which is used as a biomarker for IBD diagnosis. However, this can be observed in both IBD and colorectal cancer, which would confound the diagnostic results. Thus, we first established a new model for predicting Crohn's disease (CD) with high precision according to gene characteristics based on single nucleotide variants (SNVs). Next, five gene markers belonging to two species, F. prausnitzii and Eubacterium rectale, that were enriched in the CD group were obtained to build a CD prediction model, and high accuracy in distinguishing the CD and control groups was observed in the discovery (area under curve [AUC] = 91.13%) and validation cohorts (AUC = 79.55%). The model still maintained high accuracy after expanding the healthy cohort (AUC = 89.75%). High disease specificity in distinguishing CD and CRC groups (AUC = 95.74%) was also proven. This study establishes a novel diagnostic method for predicting IBD that also provides unprecedented insight for the early, painless diagnosis of other non-communicable diseases.

Genomic comparison of Planktothrix agardhii isolates from a Lake Erie embayment

Planktothrix agardhii is a filamentous cyanobacterial species that dominates harmful algal blooms in Sandusky Bay, Lake Erie and other freshwater basins across the world. P. agardhii isolates were obtained from early (June) blooms via single filament isolation; eight have been characterized from 2016, and 12 additional isolates have been characterized from 2018 for a total of 20 new cultures. These novel isolates were processed for genomic sequencing, where reads were used to generate scaffolds and contigs which were annotated with DIAMOND BLAST hit, Pfam, and GO. Analyses include whole genome alignment to generate phylogenetic trees and comparison of genetic rearrangements between isolates. Nitrogen acquisition and metabolism was compared across isolates. Secondary metabolite production was genetically explored including microcystins, two types of aeruginosin clusters, anabaenopeptins, cyanopeptolins, microviridins, and prenylagaramides. Two common and 4 unique CRISPR-cas islands were analyzed for similar sequences across all isolates and against the known Planktothrix-specific cyanophage, PaV-LD. Overall, the uniqueness of each genome from Planktothrix blooms sampled from the same site and at similar times belies the unexplored diversity of this genus.

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.

S51 Family Peptidases Provide Resistance to Peptidyl-Nucleotide Antibiotic McC

Microcin C (McC)-like compounds are natural Trojan horse peptide-nucleotide antibiotics produced by diverse bacteria. The ribosomally synthesized peptide parts of these antibiotics are responsible for their facilitated transport into susceptible cells. Once inside the cell, the peptide part is degraded, releasing the toxic payload, an isoaspartyl-nucleotide that inhibits aspartyl-tRNA synthetase, an enzyme essential for protein synthesis. Bacteria that produce microcin C-like compounds have evolved multiple ways to avoid self-intoxication. Here, we describe a new strategy through the action of S51 family peptidases, which we name MccG. MccG cleaves the toxic isoaspartyl-nucleotide, rendering it inactive. While some MccG homologs are encoded by gene clusters responsible for biosynthesis of McC-like compounds, most are encoded by standalone genes whose products may provide a basal level of resistance to peptide-nucleotide antibiotics in phylogenetically distant bacteria.

Discovery of the non-cosmopolitan lineages in Candidatus Thermoprofundales

The recently proposed order Candidatus Thermoprofundales, currently containing only one family-level lineage Marine Benthic Group-D (MBG-D), is distributed in global subsurface ecosystems and ecologically important, but its diversity, evolution and metabolism remain largely unknown. Here we described two novel family-level specialized lineages in Ca. Thermoprofundales, JdFR-43 and HyVt, which are restricted to specific biotopes (primarily in marine hydrothermal vents and occasionally in oil reservoirs and hot springs) in contrast to the cosmopolitan lineage MBG-D. The comparative genomics revealed that the specialized lineages have streamlined genomes, higher GC contents, enriched genes associated with nucleotide biosynthesis, ribosome biogenesis and DNA repair and additional thermostable aminopeptidases, enabling them to adapt to high-temperature habitats such as marine hydrothermal vents, deep subsurface oil reservoirs and hot springs. On the contrary, the unique metabolic traits of the cosmopolitan MBG-D, motility, glycolysis, butanoate metabolism, secondary metabolites production and additional genes for specific peptides and carbohydrates degradation potentially enhance its response to environmental change. Substrate preference is found for most MAGs across all lineages with the ability to utilize both polysaccharides (chitin and starch) and proteinaceous substances, whereas JdFR-43 members from oil reservoirs can only utilize proteins. These results expand the diversity of Ca. Thermoprofundales significantly and further improve our understandings of the adaptations of Ca. Thermoprofundales to various environments. This article is protected by copyright. All rights reserved.

New types of ATP-grasp ligase are associated with the novel pathway for complicated mycosporine-like amino acid production in desiccation-tolerant cyanobacteria

Mycosporine-like amino acids (MAAs) were widespread in diverse organisms to attenuate UV radiation. We recently characterized the large, complicated MAA mycosporine-2-(4-deoxygadusolyl-ornithine) in desert cyanobacterium Nostoc flagelliforme. Synthesis of this MAA requires the five-gene cluster mysABDC2C3. Here, bioinformatic analysis indicated that mysC duplication within five-gene mys clusters is strictly limited to drought-tolerant cyanobacteria. Phylogenic analysis distinguished these duplicated MysCs into two clades that separated from canonical MysCs. Heterologous expression of N. flagelliforme mys genes in Escherichia coli showed that MysAB produces 4-deoxygadusol. The ATP-grasp ligase of MysC3 catalyses the linkage of the δ- or ε-amino group of ornithine/lysine to 4-deoxygadusol, yielding mycosporine-ornithine or mycosporine-lysine respectively. The ATP-grasp ligase of MysC2 strictly condenses the α-amino group of mycosporine-ornithine to another 4-deoxygadusol. MysD (D-Ala-D-Ala ligase) functions following MysC2 to catalyse the formation of mycosporine-2-(4-deoxygadusolyl-ornithine). High arginine content likely provides a greater pool of ornithine over other amino acids during rehydration of desiccated N. flagelliforme. Duplication of ATP-grasp ligases is specific for the use of substrates that have two amino groups (such as ornithine) for the production of complicated MAAs with multiple chromophores. This five-enzyme biosynthesis pathway for complicated MAAs is a novel adaptation of cyanobacteria for UV tolerance in drought environments.

Applications of bacteria and their derived biomaterials for repair and tissue regeneration

Microorganisms such as bacteria and their derived biopolymers can be used in biomaterials and tissue regeneration. Various methods have been applied to regenerate damaged tissues, but using probiotics and biomaterials derived from bacteria with improved economic-production efficiency and highly applicable properties can be a new solution in tissue regeneration. Bacteria can synthesize numerous types of biopolymers. These biopolymers possess many desirable properties such as biocompatibility and biodegradability, making them good candidates for tissue regeneration. Here, we reviewed different types of bacterial-derived biopolymers and highlight their applications for tissue regeneration.

Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective

Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.

Structural and functional diversity of asparaginases: Overview and recommendations for a revised nomenclature

Asparaginases (ASNases) are a large and structurally diverse group of enzymes ubiquitous amongst archaea, bacteria and eukaryotes, that catalyze hydrolysis of asparagine to aspartate and ammonia. Bacterial ASNases are important biopharmaceuticals for the treatment of acute lymphoblastic leukemia, although some patients experience adverse allergic side effects during treatment with these protein therapeutics. ASNases are currently divided into three families: plant-type ASNases, Rhizobium etli-type ASNases and bacterial-type ASNases. This system is outdated as both bacterial-type and plant-type families also include archaeal, bacterial and eukaryotic enzymes, each with their own distinct characteristics. Herein, phylogenetic studies allied to tertiary structural analyses are described with the aim of proposing a revised and more robust classification system that considers the biochemical diversity of ASNases. Accordingly, based on distinct peptide domains, phylogenetic data, structural analysis and functional characteristics, we recommend that ASNases now be divided into three new distinct classes containing subgroups according to structural and functional aspects. Using this new classification scheme, 25 ASNases were identified as candidates for future new lead discovery.

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.

Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena

In cyanobacteria, metabolic pathways that use the nitrogen-rich amino acid arginine play a pivotal role in nitrogen storage and mobilization. The N-terminal domains of two recently identified bacterial enzymes: ArgZ from Synechocystis and AgrE from Anabaena, have been found to contain an arginine dihydrolase. This enzyme provides catabolic activity that converts arginine to ornithine, resulting in concomitant release of CO2 and ammonia. In Synechocystis, the ArgZ-mediated ornithine-ammonia cycle plays a central role in nitrogen storage and remobilization. The C-terminal domain of AgrE contains an ornithine cyclodeaminase responsible for the formation of proline from ornithine and ammonia production, indicating that AgrE is a bifunctional enzyme catalyzing two sequential reactions in arginine catabolism. Here, the crystal structures of AgrE in three different ligation states revealed that it has a tetrameric conformation, possesses a binding site for the arginine dihydrolase substrate l-arginine and product l-ornithine, and contains a binding site for the coenzyme NAD(H) required for ornithine cyclodeaminase activity. Structure-function analyses indicated that the structure and catalytic mechanism of arginine dihydrolase in AgrE are highly homologous with those of a known bacterial arginine hydrolase. We found that in addition to other active-site residues, Asn-71 is essential for AgrE's dihydrolase activity. Further analysis suggested the presence of a passage for substrate channeling between the two distinct AgrE active sites, which are situated ∼45 Å apart. These results provide structural and functional insights into the bifunctional arginine dihydrolase-ornithine cyclodeaminase enzyme AgrE required for arginine catabolism in Anabaena.

Fingerprinting cities: differentiating subway microbiome functionality

BACKGROUND

Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project participants collected samples from subway surfaces in different cities and performed metagenomic sequencing. Previous studies focused on taxonomic composition of these microbiomes and no explicit functional analysis had been done till now.

RESULTS

As a part of the 2018 CAMDA challenge, we functionally profiled the available ~ 400 subway metagenomes and built predictor for city origin. In cross-validation, our model reached 81% accuracy when only the top-ranked city assignment was considered and 95% accuracy if the second city was taken into account as well. Notably, this performance was only achievable if the similarity of distribution of cities in the training and testing sets was similar. To assure that our methods are applicable without such biased assumptions we balanced our training data to account for all represented cities equally well. After balancing, the performance of our method was slightly lower (76/94%, respectively, for one or two top ranked cities), but still consistently high. Here we attained an added benefit of independence of training set city representation. In testing, our unbalanced model thus reached (an over-estimated) performance of 90/97%, while our balanced model was at a more reliable 63/90% accuracy. While, by definition of our model, we were not able to predict the microbiome origins previously unseen, our balanced model correctly judged them to be NOT-from-training-cities over 80% of the time. Our function-based outlook on microbiomes also allowed us to note similarities between both regionally close and far-away cities. Curiously, we identified the depletion in mycobacterial functions as a signature of cities in New Zealand, while photosynthesis related functions fingerprinted New York, Porto and Tokyo.

CONCLUSIONS

We demonstrated the power of our high-speed function annotation method, mi-faser, by analysing ~ 400 shotgun metagenomes in 2 days, with the results recapitulating functional signals of different city subway microbiomes. We also showed the importance of balanced data in avoiding over-estimated performance. Our results revealed similarities between both geographically close (Ofa and Ilorin) and distant (Boston and Porto, Lisbon and New York) city subway microbiomes. The photosynthesis related functional signatures of NYC were previously unseen in taxonomy studies, highlighting the strength of functional analysis.

Seasonal Gene Expression and the Ecophysiological Implications of Toxic Microcystis aeruginosa Blooms in Lake Taihu

Harmful cyanobacterial blooms represent an increasing threat to freshwater resources globally. Despite increased research, the physiological basis of how the dominant bloom-forming cyanobacteria, Microcystis spp., proliferate and then maintain high population densities through changing environmental conditions is poorly understood. In this study, we examined the transcriptional profiles of the microbial community in Lake Taihu, China at 9 stations sampled monthly from June to October in 2014. To target Microcystis populations, we collected metatranscriptomic data and mapped reads to the M. aeruginosa NIES 843 genome. Our results revealed significant temporal gene expression patterns, with many genes separating into either early or late bloom clusters. About one-third of genes observed from M. aeruginosa were differentially expressed between these two clusters. Conductivity and nutrient availability appeared to be the environmental factors most strongly associated with these temporal gene expression shifts. Compared with the early bloom season (June and July), genes involved in N and P transport, energy metabolism, translation, and amino acid biosynthesis were down-regulated during the later season (August to October). In parallel, genes involved in regulatory functions as well as transposases and the production of microcystin and extracellular polysaccharides were up-regulated in the later season. Our observation indicates an eco-physiological shift occurs within the Microcystis spp. transcriptome as cells move from the rapid growth of early summer to bloom maintenance in late summer and autumn.

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.

Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans

Arsenic, a representative toxic metalloid, is responsible for serious global health problems. Most organisms possess arsenic resistance strategies to mitigate this toxicity. Here, we reported a microorganism, strain AS8, from heavy metal/metalloid-contaminated soil that is able to oxidize arsenite, and investigated its physiological and genomic traits. Its cells were rod-shaped and Gram-negative, and formed small beige-pigmented colonies. 16S rRNA-based phylogenetic analysis indicated that the strain belongs to the genus Herminiimonas and is closely related to Herminiimonas glaciei UMB49^T (98.7% of 16S rRNA gene sequence similarity), Herminiimonas arsenicoxydans ULPAs1^T (98.4%), and Herminiimonas saxobsidens NS11^T (98.4%). Under chemolithoheterotrophic conditions, the strain utilized some organic acids and amino acids as carbon and/or nitrogen sources but not electron sources. Further, the strain grew as a sulfur oxidizer in a complex medium (trypticase soy agar). Unexpectedly, most carbohydrates failed to support its growth as sole carbon sources. Genome sequencing supported these observations, and very few ABC transporters capable of oligo/monosaccharide uptake were identified in the AS8 genome. The genome harbored genes required for the colonization, flagella biosynthesis, urea degradation, and heavy metal and antibiotic resistance. Based on these polyphasic and genomic analyses, we propose that the strain AS8 be named Herminiimonas arsenitoxidans.

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.

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.

Analysis of the Spore Membrane Proteome in Clostridium perfringens Implicates Cyanophycin in Spore Assembly

Heat-resistant endospore formation plays an important role in Clostridium perfringens-associated foodborne illnesses. The spores allow the bacterium to survive heating during normal cooking processes, followed by germination and outgrowth of the bacterium in contaminated foods. To identify proteins associated with germination and other spore functions, a comparative spore membrane proteome analysis of dormant and germinated spores of C. perfringens strain SM101 was performed by using gel-based protein separation and liquid chromatography coupled with matrix-assisted laser desorption ionization-tandem time of flight (MALDI-TOF/TOF) mass spectrometry. A total of 494 proteins were identified, and 117 of them were predicted to be integral membrane or membrane-associated proteins. Among these membrane proteins, 16 and 26 were detected only in dormant and germinated spores, respectively. One protein that was detected only in germinated spore membranes was the enzyme cyanophycinase, a protease that cleaves the polymer cyanophycin, which is composed of l-arginine-poly(l-aspartic acid), to β-Asp-Arg. Genes encoding cyanophycinase and cyanophycin synthetase have been observed in many species of Clostridium, but their role has not been defined. To determine the function of cyanophycin in C. perfringens, a mutation was introduced into the cphA gene, encoding cyanophycin synthetase. In comparison to parent strain SM101, the spores of the mutant strain retained wild-type levels of heat resistance, but fewer spores were made, and they were smaller, suggesting that cyanophycin synthesis plays a role in spore assembly. Although cyanophycin could not be extracted from sporulating C. perfringens cells, an Escherichia coli strain expressing the cphA gene made copious amounts of cyanophycin, confirming that cphA encodes a cyanophycin synthetase.

IMPORTANCE

Clostridium perfringens is a common cause of food poisoning, and germination of spores after cooking is thought to play a significant role in the disease. How C. perfringens controls the germination process is still not completely understood. We characterized the proteome of the membranes from dormant and germinated spores and discovered that large-scale changes occur after germination is initiated. One of the proteins that was detected after germination was the enzyme cyanophycinase, which degrades the storage compound cyanophycin, which is found in cyanobacteria and other prokaryotes. A cyanophycin synthetase mutant was constructed and found to make spores with altered morphology but normal heat resistance, suggesting that cyanophycin plays a different role in C. perfringens than it does in cyanobacteria.

Carbon assimilation and accumulation of cyanophycin during the development of dormant cells (akinetes) in the cyanobacterium Aphanizomenon ovalisporum

Akinetes are spore-like non-motile cells that differentiate from vegetative cells of filamentous cyanobacteria from the order Nostocales. They play a key role in the survival and distribution of these species and contribute to their perennial blooms. Here, we demonstrate variations in cellular ultrastructure during akinete formation concomitant with accumulation of cyanophycin; a copolymer of aspartate and arginine that forms storage granules. Cyanophycin accumulation is initiated in vegetative cells few days post-exposure to akinete inducing conditions. This early accumulated cyanophycin pool in vegetative cells disappears as a nearby cell differentiates to an akinete and stores large pool of cyanophycin. During the akinete maturation, the cyanophycin pool is further increased and comprise up to 2% of the akinete volume. The cellular pattern of photosynthetic activity during akinete formation was studied by a nano-metric scale secondary ion mass spectrometry (NanoSIMS) analysis in (13)C-enriched cultures. Quantitative estimation of carbon assimilation in vegetative cells and akinetes (filament-attached and -free) indicates that vegetative cells maintain their basal activity while differentiating akinetes gradually reduce their activity. Mature-free akinetes practically lost their photosynthetic activity although small fraction of free akinetes were still photosynthetically active. Additional (13)C pulse-chase experiments indicated rapid carbon turnover during akinete formation and de novo synthesis of cyanophycin in vegetative cells 4 days post-induction of akinete differentiation.

Features of the biotechnologically relevant polyamide family "cyanophycins" and their biosynthesis in prokaryotes and eukaryotes

Cyanophycin, inclusions in cyanobacteria discovered by the Italian scientist Borzi in 1887, were characterized as a polyamide consisting of aspartic acid and arginine. Its synthesis in cyanobacteria was analyzed regarding growth conditions, responsible gene product, requirements, polymer structure and properties. Heterologous expression of diverse cyanophycin synthetases (CphA) in Escherichia coli enabled further enzyme characterization. Cyanophycin is a polyamide with variable composition and physiochemical properties dependent on host and cultivation conditions in contrast to the extracellular polyamides poly-γ-glutamic acid and poly-ε-l-lysine. Furthermore, recombinant prokaryotes and transgenic eukaryotes, including plants expressing different cphA genes, were characterized as suitable for production of insoluble cyanophycin regarding higher yields and modified composition for other requirements and applications. In addition, cyanophycin was characterized as a source for the synthesis of polyaspartic acid or N-containing bulk chemicals and dipeptides upon chemical treatment or degradation by cyanophycinases, respectively. Moreover, water-soluble cyanophycin derivatives with altered amino acid composition were isolated from transgenic plants, yeasts and recombinant bacteria. Thereby, the range of dipeptides could be extended by biological processes and by chemical modification, thus increasing the range of applications for cyanophycin and its dipeptides, including agriculture, food supplementations, medical and cosmetic purposes, synthesis of the polyacrylate substitute poly(aspartic acid) and other applications.

Intercellular diffusion of a fluorescent sucrose analog via the septal junctions in a filamentous cyanobacterium

Many filamentous cyanobacteria produce specialized nitrogen-fixing cells called heterocysts, which are located at semiregular intervals along the filament with about 10 to 20 photosynthetic vegetative cells in between. Nitrogen fixation in these complex multicellular bacteria depends on metabolite exchange between the two cell types, with the heterocysts supplying combined-nitrogen compounds but dependent on the vegetative cells for photosynthetically produced carbon compounds. Here, we used a fluorescent tracer to probe intercellular metabolite exchange in the filamentous heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. We show that esculin, a fluorescent sucrose analog, is incorporated by a sucrose import system into the cytoplasm of Anabaena cells. The cytoplasmic esculin is rapidly and reversibly exchanged across vegetative-vegetative and vegetative-heterocyst cell junctions. Our measurements reveal the kinetics of esculin exchange and also show that intercellular metabolic communication is lost in a significant fraction of older heterocysts. SepJ, FraC, and FraD are proteins located at the intercellular septa and are suggested to form structures analogous to gap junctions. We show that a ΔsepJ ΔfraC ΔfraD triple mutant shows an altered septum structure with thinner septa but a denser peptidoglycan layer. Intercellular diffusion of esculin and fluorescein derivatives is impaired in this mutant, which also shows a greatly reduced frequency of nanopores in the intercellular septal cross walls. These findings suggest that FraC, FraD, and SepJ are important for the formation of junctional structures that constitute the major pathway for feeding heterocysts with sucrose.

IMPORTANCE

Anabaena and its relatives are filamentous cyanobacteria that exhibit a sophisticated form of prokaryotic multicellularity, with the formation of differentiated cell types, including normal photosynthetic cells and specialized nitrogen-fixing cells called heterocysts. The question of how heterocysts communicate and exchange metabolites with other cells in the filament is key to understanding this form of bacterial multicellularity. Here we provide the first information on the intercellular exchange of a physiologically important molecule, sucrose. We show that a fluorescent sucrose analog can be imported into the Anabaena cytoplasm by a sucrose import system. Once in the cytoplasm, it is rapidly and reversibly exchanged among all of the cells in the filament by diffusion across the septal junctions. Photosynthetically produced sucrose likely follows the same route from cytoplasm to cytoplasm. We identify some of the septal proteins involved in sucrose exchange, and our results indicate that these proteins form structures functionally analogous to metazoan gap junctions.

Combination of environmental stress and localization of L-asparaginase in Arthrospira platensis for production improvement

The diverse applications of l-asparaginase have led us to explore new sources of this enzyme. Arthrospira platensis has been scarcely reported as a new candidate for l-asparaginase production. In the present study, we localized l-asparaginase in A. platensis and enhanced its production. Enzyme localization was conducted by culturing cells in SOT medium and extracting the enzymes from different parts of the cell. The Taguchi method (factors studied: nitrogen, iron, sodium chloride, and temperature shock) using an L9 orthogonal array was designed for improving l-asparaginase production. The highest specific activity of l-asparaginase was found in subcellular, cytoplasmic extracts (0.166 ± 0.029 U/mg). Optimization data revealed that the highest production of l-asparaginase (0.275 ± 0.005 U) was attained by NaNO₃, NaCl, and FeSO₄·7H₂O at concentrations, 1.875 g/l, 0.25 M, and 0.0075 g/l, respectively, with 1-h temperature shock at 22 °C in the dark. Results revealed more than twofold higher production of l-asparaginase than that under the normal condition. In summary, l-asparaginase appeared dominantly in the cytoplasmic region and its production could be induced by employing combined stress conditions with a Taguchi experimental design. To our best knowledge, this is the first report on l-asparaginase production in cyanobacteria of the subclass Oscillatoriophycideae.

Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst-forming cyanobacterium Anabaena

Arginine decarboxylase produces agmatine, and arginase and agmatinase are ureohydrolases that catalyze the production of ornithine and putrescine from arginine and agmatine, respectively, releasing urea. In the genome of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, ORF alr2310 putatively encodes an ureohydrolase. Cells of Anabaena supplemented with [¹⁴C]arginine took up and catabolized this amino acid generating a set of labeled amino acids that included ornithine, proline, and glutamate. In an alr2310 deletion mutant, an agmatine spot appeared and labeled glutamate increased with respect to the wild type, suggesting that Alr2310 is an agmatinase rather than an arginase. As determined in cell-free extracts, agmatinase activity could be detected in the wild type but not in the mutant. Thus, alr2310 is the Anabaena speB gene encoding agmatinase. The Δalr2310 mutant accumulated large amounts of cyanophycin granule polypeptide, lacked nitrogenase activity, and did not grow diazotrophically. Growth tests in solid media showed that agmatine is inhibitory for Anabaena, especially under diazotrophic conditions, suggesting that growth of the mutant is inhibited by non-metabolized agmatine. Measurements of incorporation of radioactivity from [¹⁴C]leucine into macromolecules showed, however, a limited inhibition of protein synthesis in the Δalr2310 mutant. Analysis of an Anabaena strain producing an Alr2310-GFP (green fluorescent protein) fusion showed expression in vegetative cells but much less in heterocysts, implying compartmentalization of the arginine decarboxylation pathway in the diazotrophic filaments of this heterocyst-forming cyanobacterium.

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.

Compartmentalized cyanophycin metabolism in the diazotrophic filaments of a heterocyst-forming cyanobacterium

Heterocyst-forming cyanobacteria are multicellular organisms in which growth requires the activity of two metabolically interdependent cell types, the vegetative cells that perform oxygenic photosynthesis and the dinitrogen-fixing heterocysts. Vegetative cells provide the heterocysts with reduced carbon, and heterocysts provide the vegetative cells with fixed nitrogen. Heterocysts conspicuously accumulate polar granules made of cyanophycin [multi-L-arginyl-poly (L-aspartic acid)], which is synthesized by cyanophycin synthetase and degraded by the concerted action of cyanophycinase (that releases β-aspartyl-arginine) and isoaspartyl dipeptidase (that produces aspartate and arginine). Cyanophycin synthetase and cyanophycinase are present at high levels in the heterocysts. Here we created a deletion mutant of gene all3922 encoding isoaspartyl dipeptidase in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. The mutant accumulated cyanophycin and β-aspartyl-arginine, and was impaired specifically in diazotrophic growth. Analysis of an Anabaena strain bearing an All3922-GFP (green fluorescent protein) fusion and determination of the enzyme activity in specific cell types showed that isoaspartyl dipeptidase is present at significantly lower levels in heterocysts than in vegetative cells. Consistently, isolated heterocysts released substantial amounts of β-aspartyl-arginine. These observations imply that β-aspartyl-arginine produced from cyanophycin in the heterocysts is transferred intercellularly to be hydrolyzed, producing aspartate and arginine in the vegetative cells. Our results showing compartmentalized metabolism of cyanophycin identify the nitrogen-rich molecule β-aspartyl-arginine as a nitrogen vehicle in the unique multicellular system represented by the heterocyst-forming cyanobacteria.

Development of Synechocystis sp. PCC 6803 as a phototrophic cell factory

Cyanobacteria (blue-green algae) play profound roles in ecology and biogeochemistry. One model cyanobacterial species is the unicellular cyanobacterium Synechocystis sp. PCC 6803. This species is highly amenable to genetic modification. Its genome has been sequenced and many systems biology and molecular biology tools are available to study this bacterium. Recently, researchers have put significant efforts into understanding and engineering this bacterium to produce chemicals and biofuels from sunlight and CO₂. To demonstrate our perspective on the application of this cyanobacterium as a photosynthesis-based chassis, we summarize the recent research on Synechocystis 6803 by focusing on five topics: rate-limiting factors for cell cultivation; molecular tools for genetic modifications; high-throughput system biology for genome wide analysis; metabolic modeling for physiological prediction and rational metabolic engineering; and applications in producing diverse chemicals. We also discuss the particular challenges for systems analysis and engineering applications of this microorganism, including precise characterization of versatile cell metabolism, improvement of product rates and titers, bioprocess scale-up, and product recovery. Although much progress has been achieved in the development of Synechocystis 6803 as a phototrophic cell factory, the biotechnology for “Compounds from Synechocystis” is still significantly lagging behind those for heterotrophic microbes (e.g., Escherichia coli).

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.

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.

The Sakaguchi reaction product quenches phycobilisome fluorescence, allowing determination of the arginine concentration in cells of Anabaena strain PCC 7120

The filamentous cyanobacterium Anabaena fixes nitrogen in specialized cells called heterocysts. The immediate product of fixation, ammonia, is known to be assimilated by addition to glutamate to make glutamine. How fixed nitrogen is transported along the filament to the 10 to 20 vegetative cells that separate heterocysts is unknown. N-fixing heterocysts accumulate an insoluble polymer containing aspartate and arginine at the cell poles. Lockau's group has proposed that the polymer is degraded at the poles to provide a mobile carrier, arginine, to the vegetative cells (R. Richter, M. Hejazi, R. Kraft, K. Ziegler, and W. Lockau, Eur. J. Biochem. 263:163-169, 1999). We wished to use the Sakaguchi reaction for arginine to determine the relative cellular concentration of arginine along the filament. At present, the methods for measuring absorption of the Sakaguchi reaction product at 520 nm are insufficiently sensitive for that purpose. However, that product quenches the fluorescence of phycobiliproteins, which we have adapted to a determination of arginine. Our results are consistent with the proposal that arginine is a principal nitrogen carrier from heterocysts to vegetative cells in Anabaena.

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.

Poly(aspartate) hydrolases: biochemical properties and applications

Thermally synthesized poly(aspartate) (tPAA) shows potential for use in a wide variety of products and applications as a biodegradable replacement for non-biodegradable polycarboxylates, such as poly(acrylate). The tPAA molecule has unnatural structures, and the relationship between its biodegradability and structures has been investigated. Two tPAA-degrading bacteria, Sphingomonas sp. KT-1 and Pedobacter sp. KP-2, were isolated from river water; from them, two PAA-hydrolyzing enzymes, PAA hydrolases-1 and -2, were purified and biologically and genetically characterized. Interestingly, not only are PAA hydrolases-1 from those two strains novel in terms of structural genes and substrate specificities (they specifically cleave the amide bond between β-aspartate units in tPAA), they also probably play a central role in tPAA biodegradation by both strains. In green polymer chemistry, one active area of research is the use of purified enzymes for the enzyme-catalyzed synthesis of polypeptides by taking advantage of their substrate specificities. Recently, β-peptides have attracted academic and industrial interest as functional materials as they possess both functions of α-peptides and excellent metabolic stability. As one of the attractive applications of PAA hydrolases, we report here the enzyme-catalyzed synthesis of poly(α-ethyl β-aspartate), which is composed of only β-linkages and belongs to β-peptides, using the unique substrate specificity of the enzyme from Pedobacter sp. KP-2.