Metabolic analysis reveals the contribution of mechanosensitive channel MscM to extracellular release of glutamate in glycogen-deficient Synechococcus elongatus.

In bacteria, mechanosensitive channels mediate extracellular release of osmolytes, including glutamate, functioning as safety valves upon osmotic downshift. In cyanobacteria, the role of mechanosensitive channels has not been completely elucidated. Recently, the glycogen-deficient ΔglgC mutant of Synechococcus elongatus PCC 7942 was found to release glutamate extracellularly, giving rise to a hypothesis that the role of mechanosensitive channels in cyanobacteria is conserved.

Glycogen deficiency enhances carbon partitioning into glutamate for an alternative extracellular metabolic sink in cyanobacteria.

Glycogen serves as a metabolic sink in cyanobacteria. Glycogen deficiency causes the extracellular release of distinctive metabolites such as pyruvate and 2-oxoglutarate upon nitrogen depletion; however, the mechanism has not been fully elucidated. This study aimed to elucidate the mechanism of carbon partitioning in glycogen-deficient cyanobacteria.

Effect of chronic administration with human thioredoxin-1 transplastomic lettuce on diabetic mice.

Scope: Human thioredoxin-1 (hTrx-1) is a defensive protein induced by various stresses and exerts antioxidative and anti-inflammatory effects. Previously, we described a transplastomic lettuce overexpressing hTrx-1 that exerts a protective effect against oxidative damage in a pancreatic β-cell line. In this study, we treated diabetic mice (Akita mice) with exogenous hTrx-1 and evaluated the effects.

Reaction of ribulose biphosphate carboxylase/oxygenase assembled on a DNA scaffold.

Ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO), an enzyme in the Calvin-Benson-Bassham cycle of photosynthesis, catalyzes the first step of CO fixation in plants, algae, and photosynthetic bacteria. Despite of the important function in the global carbon cycle, RuBisCO suffers from a slow reaction rate and a competing reaction with O which draw attentions to improve the enzyme efficiency. In this study, a RuBisCO dimer from Rhodospirillum rubrum was assembled on a DNA scaffold using a dimeric DNA binding protein as an adaptor.

Learning RuBisCO's birth and subsequent environmental adaptation.

It is believed that organisms that first appeared after the formation of the earth lived in a very limited environment, making full use of the limited number of genes. From these early organisms' genes, more were created by replication, mutation, recombination, translocation, and transmission of other organisms' DNA; thus, it became possible for ancient organisms to grow in various environments. The photosynthetic CO-fixing enzyme RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) began to function in primitive methanogenic archaea and has been evolved as a central CO-fixing enzyme in response to the large changes in CO and O concentrations that occurred in the subsequent 4 billion years.

Revisiting the methionine salvage pathway and its paralogues.

Methionine is essential for life. Its chemistry makes it fragile in the presence of oxygen. Aerobic living organisms have selected a salvage pathway (the MSP) that uses dioxygen to regenerate methionine, associated to a ratchet-like step that prevents methionine back degradation.

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea.

Two enzymes are considered to be unique to the photosynthetic Calvin-Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term 'reductive hexulose-phosphate' (RHP) pathway.

Potato yield enhancement through intensification of sink and source performances.

The combined total annual yield of six major crops (maize, rice, wheat, cassava, soybean, and potato; Solanum tuberosum L.) amounts to 3.1 billion tons.

Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme.

APIP, Apaf-1 interacting protein, has been known to inhibit two main types of programmed cell death, apoptosis and pyroptosis, and was recently found to be associated with cancers and inflammatory diseases. Distinct from its inhibitory role in cell death, APIP was also shown to act as a 5-methylthioribulose-1-phosphate dehydratase, or MtnB, in the methionine salvage pathway. Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.

MtnBD is a multifunctional fusion enzyme in the methionine salvage pathway of Tetrahymena thermophila.

To recycle reduced sulfur to methionine in the methionine salvage pathway (MSP), 5-methylthioribulose-1-phosphate is converted to 2-keto-4-methylthiobutyrate, the methionine precursor, by four steps; dehydratase, enolase, phosphatase, and dioxygenase reactions (catalyzed by MtnB, MtnW, MtnX and MtnD, respectively, in Bacillus subtilis). It has been proposed that the MtnBD fusion enzyme in Tetrahymena thermophila catalyzes four sequential reactions from the dehydratase to dioxygenase steps, based on the results of molecular biological analyses of mutant yeast strains with knocked-out MSP genes, suggesting that new catalytic function can be acquired by fusion of enzymes. This result raises the question of how the MtnBD fusion enzyme can catalyze four very different reactions, especially since there are no homologous domains for enolase and phosphatase (MtnW and MtnX, respectively, in B.

Plausible novel ribose metabolism catalyzed by enzymes of the methionine salvage pathway in Bacillus subtilis.

The methionine salvage pathway (MSP) recycles reduced sulfur from 5-methylthioribose. Here we propose a novel ribose metabolic pathway performed by MSP enzymes of Bacilli. MtnK, an initial catalyst of MSP, had significant ribose kinase activity, with Vmax and Km values of 2.

His267 is involved in carbamylation and catalysis of RuBisCO-like protein from Bacillus subtilis.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and RuBisCO-like protein (RLP) from Bacillus subtilis catalyze mechanistically similar enolase reactions. Both enzymes require carbamylation of the ε-amino group of the active site lysine during activation to generate the binding site of the essential Mg(2+) ion. His267 forms a possible hydrogen bond with the carbamate of the active site Lys176 in B.

Shape-based alignment of genomic landscapes in multi-scale resolution.

Due to dramatic advances in DNA technology, quantitative measures of annotation data can now be obtained in continuous coordinates across the entire genome, allowing various heterogeneous 'genomic landscapes' to emerge. Although much effort has been devoted to comparing DNA sequences, not much attention has been given to comparing these large quantities of data comprehensively. In this article, we introduce a method for rapidly detecting local regions that show high correlations between genomic landscapes.

Generation of transplastomic lettuce with enhanced growth and high yield.

We generated transplastomic lettuce plants expressing cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) in chloroplasts. Their photosynthetic capacity and productivity were increased 1.3-fold and 1.

Production of biologically active human thioredoxin 1 protein in lettuce chloroplasts.

The production of human therapeutic proteins in plants provides opportunities for low-cost production, and minimizes the risk of contamination from potential human pathogens. Chloroplast genetic engineering is a particularly promising strategy, because plant chloroplasts can produce large amounts of foreign target proteins. Oxidative stress is a key factor in various human diseases.

A DEAD box protein is required for formation of a hidden break in Arabidopsis chloroplast 23S rRNA.

In plant chloroplasts, the ribosomal RNA (rRNA) of the large subunit of the ribosome undergoes post-maturation fragmentation processing. This processing consists of site-specific cleavage that generates gapped, discontinuous rRNA molecules. However, the molecular mechanism underlying introduction of the gap structure (the 'hidden break') is poorly understood.

Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences.

We developed an accurate method to predict nucleosome positioning from genome sequences by refining the previously developed method of Peckham et al. (2007). Here, we used the relative fragment frequency index we developed and a support vector machine to screen for nucleosomal and linker DNA sequences.

An evolutionally conserved Lys122 is essential for function in Rhodospirillum rubrum bona fide RuBisCO and Bacillus subtilis RuBisCO-like protein.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and RuBisCO-like protein (RLP) catalyze similar enolase-type reactions. Both enzymes have a conserved non-catalytic Lys122 or Arg122 on the beta-strand E lying in the interface between the N- and C-terminal domains. We used site-directed mutagenesis to analyze the function of Lys122 in the form II Rhodospirillum rubrum RuBisCO (RrRuBisCO) and Bacillus subtilis RLP (BsRLP).

Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.

2,3-Diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1P enolase), a RuBisCO-like protein (RLP), catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate. The crystal structure of the apo decarbamylated form (E form) of Bacillus subtilis DK-MTP-1P enolase (Bs-DK-MTP-1P enolase) has been determined at 2.3 A resolution.

A phosphofructokinase B-type carbohydrate kinase family protein, NARA5, for massive expressions of plastid-encoded photosynthetic genes in Arabidopsis.

To date, there have been no reports on screening for mutants defective in the massive accumulation of Rubisco in higher plants. Here, we describe a screening method based on the toxic accumulation of ammonia in the presence of methionine sulfoximine, a specific inhibitor of glutamine synthetase, during photorespiration initiated by the oxygenase reaction of Rubisco in Arabidopsis (Arabidopsis thaliana). Five recessive mutants with decreased amounts of Rubisco were identified and designated as nara mutants, as they contained a mutation in genes necessary for the achievement of Rubisco accumulation.

Structural and functional similarities between a ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Bacillus subtilis and photosynthetic RuBisCO.

The sequences classified as genes for various ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO)-like proteins (RLPs) are widely distributed among bacteria, archaea, and eukaryota. In the phylogenic tree constructed with these sequences, RuBisCOs and RLPs are grouped into four separate clades, forms I-IV. In RuBisCO enzymes encoded by form I, II, and III sequences, 19 conserved amino acid residues are essential for CO(2) fixation; however, 1-11 of these 19 residues are substituted with other amino acids in form IV RLPs.

Crystallization and preliminary X-ray analysis of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.

2,3-Diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1P enolase) from Bacillus subtilis was crystallized using the hanging-drop vapour-diffusion method. Crystals grew using PEG 3350 as the precipitant at 293 K. The crystals diffracted to 2.

RuBisCO-like proteins as the enolase enzyme in the methionine salvage pathway: functional and evolutionary relationships between RuBisCO-like proteins and photosynthetic RuBisCO.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme in the fixation of CO(2) in the Calvin cycle of plants. Many genome projects have revealed that bacteria, including Bacillus subtilis, possess genes for proteins that are similar to the large subunit of RuBisCO. These RuBisCO homologues are called RuBisCO-like proteins (RLPs) because they are not able to catalyse the carboxylase or the oxygenase reactions that are catalysed by photosynthetic RuBisCO.