Characterization of five putative aspartate aminotransferase genes in the N2-fixing heterocystous cyanobacterium Anabaena sp. strain PCC 7120

DesC1 and DesC2, Δ9 Fatty Acid Desaturases of Filamentous Cyanobacteria: Essentiality and Complementarity

DesC1 and DesC2, which are fatty acid desaturases found in cyanobacteria, are responsible for introducing a double bond at the Δ9 position of fatty-acyl chains, which are subsequently esterified to the sn-1 and sn-2 positions of the glycerol moiety, respectively. However, since the discovery of these two desaturases in the Antarctic cyanobacterium Nostoc sp. SO-36, no further research has been reported. This study presents a comprehensive characterization of DesC1 and DesC2 through targeted mutagenesis and transformation using two cyanobacteria strains: Anabaena sp. PCC 7120, comprising both desaturases, and Synechocystis sp. PCC 6803, containing a single Δ9 desaturase (hereafter referred to as DesCs) sharing similarity with DesC1 in amino acid sequence. The results suggested that both DesC1 and DesC2 were essential in Anabaena sp. PCC 7120 and that DesC1, but not DesC2, complemented DesCs in Synechocystis sp. PCC 6803. In addition, DesC2 from Anabaena sp. PCC 7120 desaturated fatty acids esterified to the sn-2 position of the glycerol moiety in Synechocystis sp. PCC 6803.

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.

Identification of small RNAs involved in nitrogen fixation in Anabaena sp. PCC 7120 based on RNA-seq under steady state conditions

Purpose

Anabaena sp. PCC7120 is a genetically tractable model organism for nitrogen fixation and photosynthesis research. The importance of small regulatory RNAs (sRNAs) as mediators of a number of cellular processes in bacteria has begun to be recognized. Bacterial sRNA binds to target genes through base pairing, and play a regulatory role. Many studies have shown that bacterial sRNA can regulate cell stress response, carbon and nitrogen fixation, and so on. However, little is known about sRNAs in Anabaena sp. PCC 7120 regarded to nitrogen fixation under later steady state.

Methods

To provide a comprehensive study of sRNAs in this model organism, the sRNA (< 200 nt) extracted from Anabaena sp. PCC 7120 under nitrogen step-down treatment of 12 days, together with the sRNA from the control, was analyzed using deep RNA sequencing. Possible target genes regulated by all identified putative sRNAs were predicted by IntaRNA and further analyzed for functional categorizations for biological pathways.

Result

Totally, 14,132 transcripts were produced from the de novo assembly. Among them, transcripts that are located either in the intergenic region or antisense strand were kept, which resulted in 1219 sRNA candidates, for further analysis. RPKM-based differential expression analysis showed that 418 sRNAs were significantly differentially expressed between the samples from control (nitrogen addition, N+) and nitrogen depletion, (N−). Among them, 303 sRNAs were significantly upregulated, whereas 115 sRNAs were significantly downregulated. RT-PCR of 18 randomly chosen sRNAs showed a similar pattern as RNA-seq result, which confirmed the reliability of the RNA-seq data. In addition, the possible target genes regulated by unique sRNAs of Anabaena sp. PCC 7120 under nitrogen addition (N+) condition or that under nitrogen depletion (N−) condition were analyzed for functional categorization and biological pathways, which provided the evidences that sRNAs were indeed involved in many different metabolic pathways.

Conclusion

The information from the present study provides a valuable reference for understanding the sRNA-mediated regulation of the nitrogen fixation in Anabaena PCC 7120 under steady state conditions.

Functional characterization of aminotransferase involved in serine and aspartate metabolism in a halotolerant cyanobacterium, Aphanothece halophytica

Aminotransferases catalyze the reversible pyridoxal phosphate-dependent transfer of amino groups from amino acids to oxo acids and play important roles for the balance between carbon and nitrogen metabolism. In this report, four aminotransferases (Ap1-Ap4) from a halotolerant cyanobacterium Aphanothece halophytica were examined. The results revealed that Ap1 and Ap2 exhibited the aspartate:2-oxoglutarate aminotransferase (AspAT) activity whereas Ap2 catalyzed further aminotransferase activities with alanine (AlaAT) and LL-diaminopimelate (an intermediate for the synthesis of Lys/peptidoglycan) as amino donors. Ap4 exhibited bifunctional aminotransferase with phosphoserine (PSAT) and glycine (GGAT) as amino donors. No activity was observed for Ap3. We identified third gene encoding phosphoserine phosphatase (PSP) in phosphorylate serine biosynthetic pathway. The levels of mRNA for Ap2 and ApMurE encoding UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase were increased after salt stress. These results suggest the link among photorespiratory metabolite (serine, glycine, glyoxylate), phosphorylate serine biosynthetic pathway and aspartate metabolism via aminotransferases for the synthesis of peptidoglycan and betaine under salt stress conditions.

Metalloproteins in the Biology of Heterocysts

Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.

Catabolic pathway of arginine in Anabaena involves a novel bifunctional enzyme that produces proline from arginine

Arginine participates widely in metabolic processes. The heterocyst-forming cyanobacterium Anabaena catabolizes arginine to produce proline and glutamate, with concomitant release of ammonium, as major products. Analysis of mutant Anabaena strains showed that this catabolic pathway is the product of two genes, agrE (alr4995) and putA (alr0540). The predicted PutA protein is a conventional, bifunctional proline oxidase that produces glutamate from proline. In contrast, AgrE is a hitherto unrecognized enzyme that contains both an N-terminal α/β propeller domain and a unique C-terminal domain of previously unidentified function. In vitro analysis of the proteins expressed in Escherichia coli or Anabaena showed arginine dihydrolase activity of the N-terminal domain and ornithine cyclodeaminase activity of the C-terminal domain, overall producing proline from arginine. In the diazotrophic filaments of Anabaena, β-aspartyl-arginine dipeptide is transferred from the heterocysts to the vegetative cells, where it is cleaved producing aspartate and arginine. Both agrE and putA were found to be expressed at higher levels in vegetative cells than in heterocysts, implying that arginine is catabolized by the AgrE-PutA pathway mainly in the vegetative cells. Expression in Anabaena of a homolog of the C-terminal domain of AgrE obtained from Methanococcus maripaludis enabled us to identify an archaeal ornithine cyclodeaminase.

Identification of two genes required for heptadecane production in a N2-fixing cyanobacterium Anabaena sp. strain PCC 7120

Cyanobacteria photosynthetically produce long-chain hydrocarbons, which are considered as infrastructure-compatible biofuels. However, native cyanobacteria do not produce these hydrocarbons at sufficient rates or yields to warrant commercial deployment. This research sought to identify specific genes required for photosynthetic production of alkanes to enable future metabolic engineering for commercially viable production of alkanes. The two putative genes (alr5283 and alr5284) required for long-chain hydrocarbon production in Anabaena sp. PCC 7120 were knocked out through a double crossover approach. The knockout mutant abolished the production of heptadecane (C₁₇H₃₆). The mutant is able to be complemented by a plasmid bearing the two genes along with their native promoters only. The complemented mutant restored photosynthetic production of heptadecane. This combined genetic and metabolite (alkanes) profiling approach may be broadly applicable to characterization of knockout mutants, using N₂-fixing cyanobacteria as a cellular factory driven by solar energy to produce a wide range of commodity chemicals and drop-in-fuels from atmospheric gases (CO₂ and N₂ gas) and mineralized water.

Co-overexpression of response regulator genes slr1037 and sll0039 improves tolerance of Synechocystis sp. PCC 6803 to 1-butanol

In this study, two response regulator (RR) encoding genes slr1037 as well as sll0039 were co-overexpressed in Synechocystis sp. PCC 6803 by metabolic engineering and the 1-butanol tolerance was successfully improved by 133%. Aiming to explore the possible mechanisms for the enhancing 1-butanol tolerance, a quantitative iTRAQ-LC-MS/MS proteomics approach was then employed, identifying 216 up-regulated and 99 down-regulated proteins compared to wild type after 1-butanol treatment. This study mapped the potential target genes regulated by Slr1037 and Sll0039 and demonstrated the feasibility of engineering response regulators for modifying the biofuel tolerance in cyanobacteria.