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The YggS/PLPBP protein (also called COG0325 or PLPHP) is a conserved pyridoxal 5ʹ-phosphate (PLP)-binding protein present in all 3 domains of life. Recent studies have demonstrated that disruption or mutation of this protein has multifaceted effects in various organisms, including vitamin B6-dependent epilepsy in humans. In Escherichia coli, disruption of this protein—encoded by yggS—perturbs Thr-Ile/Val metabolism, one-carbon metabolism, coenzyme A synthesis, and vitamin B6 homeostasis. This protein is critical for maintaining low levels of pyridoxine 5ʹ-phosphate (PNP) in various organisms. In the yggS-deficient E. coli strain, inhibition of PLP-dependent enzymes, such as the glycine cleavage system by PNP, is the root cause of metabolic perturbation. Our data suggest that the YggS/PLPBP protein may be involved in the balancing of B6 vitamers by mediating efficient turnover of protein-bound B6 vitamers. This paper reviews recent findings on the function of the YggS/PLPBP protein.

The pupae of lepidopterans contain high concentrations of endogenous d-serine. In the silkworm Bombyx mori, d-serine is negligible during the larval stage but increases markedly during the pupal stage, reaching 50% of the total free serine. However, the physiological function of d-serine and the enzyme responsible for its production is unknown. Herein, we identified a new type of pyridoxal 5′-phosphate (PLP)-dependent serine racemase (SR) that catalyses the racemization of l-serine to d-serine in B. mori. This silkworm SR (BmSR) has an N-terminal PLP-binding domain that is homologous to mammalian SR and a C-terminal putative ligand-binding regulatory-like domain (ACT-like domain) that is absent in mammalian SR. Similar to mammalian SRs, BmSR catalyses the racemization and dehydration of both serine isomers. However, BmSR is different from mammalian SRs as evidenced by its insensitivity to Mg2+/Ca2+ and Mg-ATP—which are required for activation of mammalian SRs—and high d-serine dehydration activity. At the pupal stage, the SR activity was predominantly detected in the fat body, which was consistent with the timing and localization of BmSR expression. The results are an important first step in elucidating the physiological significance of d-serine in lepidopterans.

cis-Prenyltransferases (cPTs) form linear polyprenyl pyrophosphates, the precursors of polyprenyl or dolichyl phosphates that are essential for cell function in all living organisms. Polyprenyl phosphate serves as a sugar carrier for peptidoglycan cell wall synthesis in bacteria, a role that dolichyl phosphate performs analogously for protein glycosylation in eukaryotes and archaea. Bacterial cPTs are characterized by their homodimeric structure, while cPTs from eukaryotes usually require two distantly homologous subunits for enzymatic activity. This study identifies the subunits of heteromeric cPT, Af1219 and Af0707, from a thermophilic sulphur-reducing archaeon, Archaeoglobus fulgidus. Both subunits are indispensable for cPT activity, and their protein–protein interactions were demonstrated by a pulldown assay. Gel filtration chromatography and chemical cross-linking experiments suggest that Af1219 and Af0707 likely form a heterotetramer complex. Although this expected subunit composition agrees with a reported heterotetrameric structure of human hCIT/NgBR cPT complex, the similarity of the quaternary structures is likely a result of convergent evolution.

The pyridoxal 5′-phosphate (PLP)-binding protein (PLPBP) plays an important role in vitamin B(6) homeostasis. Loss of this protein in organisms such as Escherichia coli and humans disrupts the vitamin B(6) pool and induces intracellular accumulation of pyridoxine 5′-phosphate (PNP), which is normally undetectable in wild-type cells. This accumulated PNP could affect diverse metabolic systems through the inhibition of some PLP-dependent enzymes. In this study, we investigated the as-yet-unclear mechanism of intracellular accumulation of PNP due to the loss of PLPBP protein encoded by yggS in E. coli. Genetic studies using several PLPBP-deficient strains of E. coli lacking a known enzyme(s) in the de novo or salvage pathways of vitamin B(6), including pyridoxine (amine) 5′-phosphate oxidase (PNPO), PNP synthase, pyridoxal kinase, and pyridoxal reductase, demonstrated that neither the flux from the de novo pathway nor the salvage pathway solely contributed to the PNP accumulation caused by the PLPBP mutation. Studies of the strains lacking both PLPBP and PNPO suggested that PNP shares the same pool with PMP, and showed that PNP levels are impacted by PMP levels and vice versa. Here, we show that disruption of PLPBP perturbs PMP homeostasis, which may result in PNP accumulation in the PLPBP-deficient strains. IMPORTANCE A PLP-binding protein (PLPBP) from the conserved COG0325 family has recently been recognized as a key player in vitamin B(6) homeostasis in various organisms. Loss of PLPBP disrupts vitamin B(6) homeostasis and perturbs diverse metabolisms, including amino acid and α-keto acid metabolism. Accumulation of PNP is a characteristic phenotype of PLPBP deficiency and is suggested to be a potential cause of the pleiotropic effects, but the mechanism of this accumulation has been poorly understood. In this study, we show that fluxes for PNP synthesis/metabolism are not responsible for the accumulation of PNP. Our results indicate that PLPBP is involved in the homeostasis of pyridoxamine 5′-phosphate, and that its disruption may lead to the accumulation of PNP in PLPBP deficiency.

The lateral costal artery and vein are under recognized yet potentially important vessels for physicians, especially cardiothoracic surgeons. This study sought to determine the prevalence and clinical, anatomical, and radiological features of lateral costal vessels. We retrospectively analyzed lateral costal vessels based on intraoperative images in patients who underwent thoracic surgery at our institute between January 2016 and March 2020. Clinical data and surgical videos were analyzed for patient characteristics, prevalence, length, laterality, and additional anatomical and radiological features. The overall prevalence of lateral costal vessels was 19% and was significantly higher in males than females (22% vs. 14%, p = 0.003). The lateral costal vessels extended beyond the 2nd intercostal space in 74% of the cases, with differing length between the right and left sides in bilateral cases. Lateral costal vessels could be identified intraoperatively using indocyanine green or preoperatively through three-dimensional computed tomography. The prevalence of lateral costal vessels is relatively high and should be acknowledged by physicians prior to procedures involving the vessels.

The YggS/Ybl036c/PLPBP family includes conserved pyridoxal 5′-phosphate (PLP)-binding proteins that plays a critical role in the homeostasis of vitamin B(6) and amino acids. Disruption of members of this family causes pleiotropic effects in many organisms by unknown mechanisms. In Escherichia coli, conditional lethality of the yggS and glyA (encoding serine hydroxymethyltransferase) has been described, but the mechanism of lethality was not determined. Strains lacking yggS and serA (3-phosphoglycerate dehydrogenase) were conditionally lethality in the M9-glucose medium supplemented with Gly. Analyses of vitamin B(6) pools found the high-levels of pyridoxine 5′-phosphate (PNP) in the two yggS mutants. Growth defects of the double mutants could be eliminated by overexpressing PNP/PMP oxidase (PdxH) to decrease the PNP levels. Further, a serA pdxH strain, which accumulates PNP in the presence of yggS, exhibited similar phenotype to serA yggS mutant. Together these data suggested the inhibition of the glycine cleavage (GCV) system caused the synthetic lethality. Biochemical assays confirmed that PNP disrupts the GCV system by competing with PLP in GcvP protein. Our data are consistent with a model in which PNP-dependent inhibition of the GCV system causes the conditional lethality observed in the glyA yggS or serA yggS mutants.

The analysis of the urine contents can be informative of physiological homoeostasis, and it has been speculated that the levels of urinary d-serine (d-ser) could inform about neurological and renal disorders. By analysing the levels of urinary d-ser using a d-ser dehydratase (DSD) enzyme, Ito et al. (Biosci. Rep.(2021) 41, BSR20210260) have described abundant levels of l-erythro-β-hydroxyasparagine (l-β-EHAsn), a non-proteogenic amino acid which is also a newly described substrate for DSD. The data presented support the endogenous production l-β-EHAsn, with its concentration significantly correlating with the concentration of creatinine in urine. Taken together, these results could raise speculations that l-β-EHAsn might have unexplored important biological roles. It has been demonstrated that l-β-EHAsn also inhibits serine racemase with Ki values (40 μM) similar to its concentration in urine (50 μM). Given that serine racemase is the enzyme involved in the synthesis of d-ser, and l-β-EHAsn is also a substrate for DSD, further investigations could verify if this amino acid would be involved in the metabolic regulation of pathways involving d-ser.

Mevalonate 3,5-bisphosphate decarboxylase is involved in the recently discovered Thermoplasma-type mevalonate pathway. The enzyme catalyzes the elimination of the 3-phosphate group from mevalonate 3,5-bisphosphate as well as concomitant decarboxylation of the substrate. This entire reaction of the enzyme resembles the latter half-reactions of its homologs, diphosphomevalonate decarboxylase and phosphomevalonate decarboxylase, which also catalyze ATP-dependent phosphorylation of the 3-hydroxyl group of their substrates. However, the crystal structure of mevalonate 3,5-bisphosphate decarboxylase and the structural reasons of the difference between reactions catalyzed by the enzyme and its homologs are unknown. In this study, we determined the X-ray crystal structure of mevalonate 3,5-bisphosphate decarboxylase from Picrophilus torridus, a thermoacidophilic archaeon of the order Thermoplasmatales. Structural and mutational analysis demonstrated the importance of a conserved aspartate residue for enzyme activity. In addition, although crystallization was performed in the absence of substrate or ligands, residual electron density having the shape of a fatty acid was observed at a position overlapping the ATP-binding site of the homologous enzyme, diphosphomevalonate decarboxylase. This finding is in agreement with the expected evolutionary route from phosphomevalonate decarboxylase (ATP-dependent) to mevalonate 3,5-bisphosphate decarboxylase (ATP-independent) through the loss of kinase activity. We found that the binding of geranylgeranyl diphosphate, an intermediate of the archeal isoprenoid biosynthesis pathway, evoked significant activation of mevalonate 3,5-bisphosphate decarboxylase, and several mutations at the putative geranylgeranyl diphosphate-binding site impaired this activation, suggesting the physiological importance of ligand binding as well as a possible novel regulatory system employed by the Thermoplasma-type mevalonate pathway.

YggS (COG0325) is a pyridoxal 5′-phosphate (PLP)-binding protein proposed to be involved in homeostasis of B6 vitamers. In Salmonella enterica, lack of yggS resulted in phenotypes that were distinct and others that were similar to those of a yggS mutant of Escherichia coli. Like other organisms, yggS mutants of S. enterica accumulate endogenous pyridoxine 5′-phosphate (PNP). Data herein show that strains lacking YggS accumulated ∼10-fold more PLP in growth medium than a parental strain. The deoxyxylulose 5-phosphate-dependent biosynthetic pathway for PLP and the PNP/pyridoxamine 5′-phosphate (PMP) oxidase credited with interconverting B6 vitamers were replaced with a single PLP synthase from Saccharomyces cerevisiae. The impact of a yggS deletion on the intracellular and extracellular levels of B6 vitamers in this restructured strain supported a role for PdxH in PLP homeostasis and led to a general model for YggS function in PLP-PMP cycling. Our findings uncovered broader consequences of a yggS mutation than previously reported and suggest that the accumulation of PNP is not a direct effect of lacking YggS but rather a downstream consequence. IMPORTANCE Pyridoxal 5′-phosphate (PLP) is an essential cofactor for enzymes in all domains of life. Perturbations in PLP or B6 vitamer content can be detrimental, notably causing B6-dependent epilepsy in humans. YggS homologs are broadly conserved and have been implicated in altered levels of B6 vitamers in multiple organisms. The biochemical activity of YggS, expected to be conserved across domains, is not yet known. Herein, a simplified heterologous pathway minimized metabolic variables and allowed the dissection of this system to generate new metabolic knowledge that will be relevant to understanding YggS.

YggS (COG0325) is a pyridoxal 5′-phosphate (PLP)-binding protein proposed to be involved in homeostasis of B(6) vitamers. In Salmonella enterica, lack of yggS resulted in phenotypes that were distinct and others that were similar to those of a yggS mutant of Escherichia coli. Like other organisms, yggS mutants of S. enterica accumulate endogenous pyridoxine 5′-phosphate (PNP). Data herein show that strains lacking YggS accumulated ∼10-fold more PLP in growth medium than a parental strain. The deoxyxylulose 5-phosphate-dependent biosynthetic pathway for PLP and the PNP/pyridoxamine 5′-phosphate (PMP) oxidase credited with interconverting B(6) vitamers were replaced with a single PLP synthase from Saccharomyces cerevisiae. The impact of a yggS deletion on the intracellular and extracellular levels of B(6) vitamers in this restructured strain supported a role for PdxH in PLP homeostasis and led to a general model for YggS function in PLP-PMP cycling. Our findings uncovered broader consequences of a yggS mutation than previously reported and suggest that the accumulation of PNP is not a direct effect of lacking YggS but rather a downstream consequence. IMPORTANCE Pyridoxal 5′-phosphate (PLP) is an essential cofactor for enzymes in all domains of life. Perturbations in PLP or B(6) vitamer content can be detrimental, notably causing B(6)-dependent epilepsy in humans. YggS homologs are broadly conserved and have been implicated in altered levels of B(6) vitamers in multiple organisms. The biochemical activity of YggS, expected to be conserved across domains, is not yet known. Herein, a simplified heterologous pathway minimized metabolic variables and allowed the dissection of this system to generate new metabolic knowledge that will be relevant to understanding YggS.

Pyridoxal 5′-phosphate (PLP) is the biologically active form of vitamin B6 and an essential cofactor in all organisms. In Escherichia coli, PLP is synthesized via the deoxyxylulose 5-phosphate (DXP)-dependent pathway that includes seven enzymatic steps and generates pyridoxine 5′-phosphate as an intermediate. Additionally, E. coli is able to salvage pyridoxal, pyridoxine, and pyridoxamine B6 vitamers to produce PLP using kinases PdxK/PdxY and pyridox(am)ine phosphate oxidase (PdxH). We found that E. coli strains blocked in PLP synthesis prior to the formation of pyridoxine 5′-phosphate (PNP) required significantly less exogenous pyridoxal (PL) than strains lacking pdxH and identified the conversion of PL to pyridoxine (PN) during cultivation to be the cause. Our data showed that PdxI, shown to have PL reductase activity in vitro, was required for the efficient salvage of PL in E. coli. The pdxI+ E. coli strains converted exogenous PL to PN during growth, while pdxI mutants did not. In total, the data herein demonstrated that PdxI is a critical enzyme in the salvage of PL by E. coli. IMPORTANCE The biosynthetic pathway of pyridoxal 5′-phosphate (PLP) has extensively been studied in Escherichia coli, yet limited information is available about the vitamin B6 salvage pathway. We show that the protein PdxI (YdbC) is the primary pyridoxal (PL) reductase in E. coli and is involved in the salvage of PL. The orthologs of PdxI occur in a wide range of bacteria and plants, suggesting that PL reductase in the B6 salvage pathway is more widely distributed than previously expected.

Background: D-serine, the enantiomer of L-serine, was identified in mammals 20 years ago. Although a close relationship between D-serine and renal dysfunction has been shown, the clinical implications of urinary D- and L-serine in humans are poorly understood. The aim of this study was to evaluate the relationship between urinary D- and L-serine with well-known renal biomarkers, and clarify the prognostic value of D- and L-serine for renal events. Methods: This cross-sectional, prospective study included 65 patients with atherosclerotic risk factors, who were followed up for a median of 16 months. The primary endpoint was a composite of end-stage renal disease and a decline in estimated glomerular filtration rate (eGFR) ≥ 25% from baseline. Results: Urinary D-serine concentrations showed a better correlation with eGFR than did urinary L-serine, whereas neither urinary D- nor L-serine correlated with tubular markers such as urinary liver-type fatty acid-binding protein and N-acetyl-beta-D-glucosaminidase. A Cox regression analysis revealed that low urinary D-serine levels were significantly associated with the primary endpoint after adjusting for confounding factors (hazard ratio 12.60; 95% confidence interval, 3.49–45.51). Conclusions: Urinary D-serine is associated with glomerular filtration and can be a prognostic biomarker of renal dysfunction in patients with atherosclerotic risk factors.

The modified mevalonate pathway is believed to be the upstream biosynthetic route for isoprenoids in general archaea. The partially identified pathway has been proposed to explain a mystery surrounding the lack of phosphomevalonate kinase and diphosphomevalonate decarboxylase by the discovery of a conserved enzyme, isopentenyl phosphate kinase. Phosphomevalonate decarboxylase was considered to be the missing link that would fill the vacancy in the pathway between mevalonate 5-phosphate and isopentenyl phosphate. This enzyme was recently discovered from haloarchaea and certain Chroloflexi bacteria, but their enzymes are close homologs of diphosphomevalonate decarboxylase, which are absent in most archaea. In this study, we used comparative genomic analysis to find two enzymes from a hyperthermophilic archaeon, Aeropyrum pernix , that can replace phosphomevalonate decarboxylase. One enzyme, which has been annotated as putative aconitase, catalyzes the dehydration of mevalonate 5-phosphate to form a previously unknown intermediate, trans -anhydromevalonate 5-phosphate. Then, another enzyme belonging to the UbiD-decarboxylase family, which likely requires a UbiX-like partner, converts the intermediate into isopentenyl phosphate. Their activities were confirmed by in vitro assay with recombinant enzymes and were also detected in cell-free extract from A. pernix . These data distinguish the modified mevalonate pathway of A. pernix and likely, of the majority of archaea from all known mevalonate pathways, such as the eukaryote-type classical pathway, the haloarchaea-type modified pathway, and another modified pathway recently discovered from Thermoplasma acidophilum .

Escherichia coli YggS (COG0325) is a member of the highly conserved pyridoxal 5′-phosphate (PLP)-binding protein (PLPBP) family. Recent studies suggested a role for this protein family in the homeostasis of vitamin B6 and amino acids. The deletion or mutation of a member of this protein family causes pleiotropic effects in many organisms and is causative of vitamin B6-dependent epilepsy in humans. To date, little has been known about the mechanism by which lack of YggS results in these diverse phenotypes. In this study, we determined that the pyridoxine (PN) sensitivity observed in yggS-deficient E. coli was caused by the pyridoxine 5′-phosphate (PNP)-dependent overproduction of Val, which is toxic to E. coli. The data suggest that the yggS mutation impacts Val accumulation by perturbing the biosynthetic of Thr from homoserine (Hse). Exogenous Hse inhibited the growth of the yggS mutant, caused further accumulation of PNP, and increased the levels of some intermediates in the Thr-Ile-Val metabolic pathways. Blocking the Thr biosynthetic pathway or decreasing the intracellular PNP levels abolished the perturbations of amino acid metabolism caused by the exogenous PN and Hse. Our data showed that a high concentration of intracellular PNP is the root cause of at least some of the pleiotropic phenotypes described for a yggS mutant of E. coli. IMPORTANCE Recent studies showed that deletion or mutation of members of the YggS protein family causes pleiotropic effects in many organisms. Little is known about the causes, mechanisms, and consequences of these diverse phenotypes. It was previously shown that yggS mutations in E. coli result in the accumulation of PNP and some metabolites in the Ile/Val biosynthetic pathway. This work revealed that some exogenous stresses increase the aberrant accumulation of PNP in the yggS mutant. In addition, the current report provides evidence indicating that some, but not all, of the phenotypes of the yggS mutant in E. coli are due to the elevated PNP level. These results will contribute to continuing efforts to determine the molecular functions of the members of the YggS protein family.

d-Aspartate is found in the nervous and reproductive system and participates in various physiological roles. While several lines of evidence suggest that this amino acid has an endogenous origin, the enzyme responsible for mammalian d-Asp biosynthesis has not yet been identified. We show that mammalian serine racemase (SRR), the primary enzyme responsible for brain d-Ser production, catalyses Asp racemization via a two-base mechanism. We observed that overexpression of SRR in rat pheochromocytoma PC12 cells resulted in an increase in intracellular d-Asp compared with control cells, demonstrating that SRR functions as an Asp racemase in the cells. To investigate the impact of endogenous SRR on endogenous d-Asp levels in the cells, we generated SRR-knockout (SRR-KO) PC12 cells. The SRR-KO cells exhibited decreased intracellular d-Ser levels, but production levels of d-Asp were unaffected. In contrast, SRR-KO mice showed significantly decreased d-Asp levels in their frontal cortices and hippocampi, where SRR is normally highly expressed, while d-Asp levels in the cerebellum and testes remained unchanged. Our results indicate that SRR indeed acts as a d-Asp biosynthetic enzyme in some organs and/or tissues, and also provide evidences that there should be some additional enzyme for d-Asp synthesis in mammals.

The modified mevalonate pathway is believed to be the upstream biosynthetic route for isoprenoids in general archaea. The partially identified pathway has been proposed to explain a mystery surrounding the lack of phosphomevalonate kinase and diphosphomevalonate decarboxylase by the discovery of a conserved enzyme, isopentenyl phosphate kinase. Phosphomevalonate decarboxylase was considered to be the missing link that would fill the vacancy in the pathway between mevalonate 5-phosphate and isopentenyl phosphate. This enzyme was recently discovered from haloarchaea and certain Chroloflexi bacteria, but their enzymes are close homologs of diphosphomevalonate decarboxylase, which are absent in most archaea. In this study, we used comparative genomic analysis to find two enzymes from a hyperthermophilic archaeon, Aeropyrum pernix, that can replace phosphomevalonate decarboxylase. One enzyme, which has been annotated as putative aconitase, catalyzes the dehydration of mevalonate 5-phosphate to form a previously unknown intermediate, trans-anhydromevalonate 5-phosphate. Then, another enzyme belonging to the UbiD-decarboxylase family, which likely requires a UbiX-like partner, converts the intermediate into isopentenyl phosphate. Their activities were confirmed by in vitro assay with recombinant enzymes and were also detected in cell-free extract from A. pernix. These data distinguish the modified mevalonate pathway of A. pernix and likely, of the majority of archaea from all known mevalonate pathways, such as the eukaryote-type classical pathway, the haloarchaea-type modified pathway, and another modified pathway recently discovered from Thermoplasma acidophilum.

In mammals, D-Ser is synthesized by serine racemase (SR) and degraded by D-amino acid oxidase (DAO). D-Ser acts as an endogenous ligand for N-methyl-D-aspartate (NMDA)- and δ2 glutamate receptors, and is involved in brain functions such as learning and memory. Although SR homologs are highly conserved in eukaryotes, little is known about the significance of D-Ser in non-mammals. In contrast to mammals, the slime mold Dictyostelium discoideum genome encodes SR, DAO, and additionally D-Ser specific degradation enzyme D-Ser dehydratase (DSD), but not NMDA- and δ2 glutamate receptors. Here, we studied the significances of D-Ser and DSD in D. discoideum. Enzymatic assays demonstrated that DSD is 460- and 1,700-fold more active than DAO and SR, respectively, in degrading D-Ser. Moreover, in dsd-null cells D-Ser degradation activity is completely abolished. In fact, while in wild-type D. discoideum intracellular D-Ser levels were considerably low, dsd-null cells accumulated D-Ser. These results indicated that DSD but not DAO is the primary enzyme responsible for D-Ser decomposition in D. discoideum. We found that dsd-null cells exhibit delay in development and arrest at the early culmination stage. The efficiency of spore formation was considerably reduced in the mutant cells. These phenotypes were further pronounced by exogenous D-Ser but rescued by plasmid-borne expression of dsd. qRT-PCR analysis demonstrated that mRNA expression of key genes in the cAMP signaling relay is perturbed in the dsd knockout. Our data indicate novel roles for D-Ser and/or DSD in the regulation of cAMP signaling in the development processes of D. discoideum.

The branched-chain α-ketoacid dehydrogenase (BCKDH) complex regulates branched-chain amino acid (BCAA) catabolism by controlling the second step of this catabolic pathway. In the present study, we examined the in vivo effects of treatment with an mTORC1 inhibitor, rapamycin, on cardiac BCKDH complex activity in mice. Oral administration of leucine in control mice significantly activated the cardiac BCKDH complex with an increase in cardiac concentrations of leucine and α-ketoisocaproate. However, rapamycin treatment significantly suppressed the leucine-induced activation of the complex despite similar increases in cardiac leucine and α-ketoisocaproate levels. Rapamycin treatment fully inhibited mTORC1 activity, measured by the phosphorylation state of ribosomal protein S6 kinase 1. These results suggest that mTORC1 is involved in the regulation of cardiac BCAA catabolism.

Single-port laparoscopic appendectomy (SILS-A) is now being performed in a great number of patients. However, SILS-A requires extended operation time and does not markedly decrease postoperative pain or improve cosmesis. To solve these problems, we developed a new technique for laparoscopic appendectomy that relies on 2 ports in a single incision plus 1 puncture (POP-SILS), and we can prove that this useful technique allows SILS-A to be easier and more cosmetic. The cases of 112 patients treated by laparoscopic appendectomy (LA) at our hospital between 2010 and 2013 were studied retrospectively. Forty-one were cases of locally complicated appendicitis, and 71 were cases of simple appendicitis. In laparoscopic appendectomy with POP-SILS, we maintain instrument triangulation using two 5-mm ports in the umbilicus and needle instruments that are introduced by puncture above the pubic bone. We studied the safety and usefulness of this method from the standpoint of operation time, postoperative stay, and complications. From 2010 to 2013, we performed 77 POP-SILS-LAs. Thirty-five patients required 1 or more additional ports or underwent conventional LA. The time required for POP-SILS-LA was 54 minutes (range, 23–209) in cases of simple appendicitis. Even in 17 cases of locally complicated appendicitis, POP-SILS-LA was successful. There was no statistical difference in surgical complications between POP-SILS-LA and multiport LA. Both the umbilical scar and the puncture scar eventually became invisible. The outcomes in our patient series showed POP-SILS-LA to be a safe and beneficial, minimally invasive approach to laparoscopic appendectomy.

The Brevibacillus brevis BBR47_28440 gene (referred to as ddlR) encodes an MocR/GabR family transcriptional regulator consisting of an N-terminal helix-turn-helix DNA binding domain and a C-terminal aminotransferase-like domain. The ddlR gene is located just upstream of the d-alanyl-d-alanine ligase gene (ddl) in the B. brevis genome, and these two genes form an operon. Gel-shift assays indicated that purified DdlR binds specifically to the DNA region that includes putative -35 and -10 regions of the ddlR promoter. A 6-bp inverted repeat that overlaps the -10 region of the ddlR promoter was found to be important for the binding. In vivo reporter assays confirmed that DdlR is an activator of the ddlR-ddl operon. Spectroscopic analyses indicated that purified DdlR is a pyridoxal 5'-phosphate binding transcriptional regulator that has dipeptide binding ability for d-alanyl-d-alanine, the enzymatic product of Ddl, and glycylglycine. DdlR is capable of forming a dipeptide-pyridoxal 5'-phosphate external aldimine, but it lacks aminotransferase activity. Bioinformatic analyses suggest that DdlR-mediated transcriptional regulation of ddlR and ddl may occur in multiple bacterial systems such as Actinobacteria and Bacillus species.

Bacillus subtilis GabR is a transcriptional regulator consisting of a helix-turn-helix N-terminal DNA-binding domain, a pyridoxal 5'-phosphate (PLP)-binding C-terminal domain that has a structure homologous to aminotransferases, and a linker of 29 amino acid residues. In the presence of γ-aminobutyrate (GABA), GabR activates the transcription of gabT and gabD, which encode GABA aminotransferase and succinate semialdehyde dehydrogenase, respectively. We expressed N-terminal and C-terminal domain fragments (named N'-GabR and C'-GabR) in Escherichia coli cells, and obtained N'-GabR as a soluble monomer and C'-GabR as a soluble dimer. Spectroscopic studies suggested that C'-GabR contains PLP and binds to d-Ala, β-Ala, d-Asn and d-Gln, as well as GABA, although the intact GabR binds only to GABA. N'-GabR does not bind to the DNA fragment containing the GabR-binding sequence regardless of the presence or absence of C'-GabR. A fusion protein consisting of N'-GabR and 2-aminoadipate aminotransferase of Thermus thermophilus bound to the DNA fragment. These results suggested that each domain of GabR could be an independent folding unit. The C-terminal domain provides the N-terminal domain with DNA-binding ability via dimerization. The N-terminal domain controls the ligand specificity of the C-terminal domain. Connection by the linker is indispensable for the mutual interaction of the domains.

Ophthalmic acid (OA; l -γ-glutamyl- l -2-aminobutyryl-glycine) is an analog of glutathione (GSH; l -γ-glutamyl- l -cysteinyl-glycine) in which the cysteine moiety is replaced by l -2-aminobutyrate. OA is a useful peptide for the pharmaceutical and/or food industries. Herein, we report a method for the production of OA using engineered Escherichia coli cells. yggS -deficient E. coli , which lacks the highly conserved pyridoxal 5′-phosphate-binding protein YggS and naturally accumulates OA, was selected as the starting strain. To increase the production of OA, we overexpressed the OA biosynthetic enzymes glutamate-cysteine ligase (GshA) and glutathione synthase (GshB), desensitized the product inhibition of GshA, and eliminated the OA catabolic enzyme γ-glutamyltranspeptidase. The production of OA was further enhanced by the deletion of miaA and ridA with the aim of increasing the availability of ATP and attenuating the unwanted degradation of amino acids, respectively. The final strain developed in this study successfully produced 277 μmol/liter of OA in 24 h without the formation of by-products in a minimal synthetic medium containing 1 mM each glutamate, 2-aminobutyrate, and glycine. IMPORTANCE Ophthalmic acid (OA) is a peptide that has the potential for use in the pharmaceutical and/or food industries. An efficient method for the production of OA would allow us to expand our knowledge about its physiological functions and enable the industrial/pharmaceutical application of this compound. We demonstrated the production of OA using Escherichia coli cells in which OA biosynthetic enzymes and degradation enymes were engineered. We also showed that unique approaches, including the use of a Δ yggS mutant as a starting strain, the establishment of an S495F mutation in GshA, and the deletion of ridA or miaA , facilitated the efficient production of OA in E. coli .

(E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) is an intermediate of the methylerythritol phosphate pathway. Utilization of HMBPP by lycopene elongase from Corynebacterium glutamicum, which is a UbiA-family prenyltransferase responsible for C50 carotenoid biosynthesis, was investigated using an Escherichia coli strain that contained the exogenous mevalonate pathway as well as the carotenoid biosynthetic pathway. Inhibition of the endogenous methylerythritol phosphate pathway resulted in loss of the production of C50 carotenoid flavuxanthin, while C40 lycopene formation was retained. Overexpression of E. coli ispH gene, which encodes HMBPP reductase, also decreased the production of flavuxanthin in E. coli cells. These results indicate the preference of lycopene elongase for HMBPP instead of the previously proposed substrate, dimethylallyl diphosphate. Furthermore, several (all-E)-prenyl diphosphate synthases, which are classified in a distinct family of prenyltransferase, were demonstrated to accept HMBPP, which implies that the compound is more widely used as a prenyl donor substrate than was previously expected., Published online: 01 Dec 2017. ファイル公開：2018/12/01

In mammals, D-Ser is synthesized by serine racemase (SR) and degraded by D-amino acid oxidase (DAO). D-Ser acts as an endogenous ligand for N-methyl-D-aspartate (NMDA)- and δ2 glutamate receptors, and is involved in brain functions such as learning and memory. Although SR homologs are highly conserved in eukaryotes, little is known about the significance of D-Ser in non-mammals. In contrast to mammals, the slime mold Dictyostelium discoideum genome encodes SR, DAO, and additionally D-Ser specific degradation enzyme D-Ser dehydratase (DSD), but not NMDA- and δ2 glutamate receptors. Here, we studied the significances of D-Ser and DSD in D. discoideum. Enzymatic assays demonstrated that DSD is 460- and 1,700-fold more active than DAO and SR, respectively, in degrading D-Ser. Moreover, in dsd-null cells D-Ser degradation activity is completely abolished. In fact, while in wild-type D. discoideum intracellular D-Ser levels were considerably low, dsd-null cells accumulated D-Ser. These results indicated that DSD but not DAO is the primary enzyme responsible for D-Ser decomposition in D. discoideum. We found that dsd-null cells exhibit delay in development and arrest at the early culmination stage. The efficiency of spore formation was considerably reduced in the mutant cells. These phenotypes were further pronounced by exogenous D-Ser but rescued by plasmid-borne expression of dsd. qRT-PCR analysis demonstrated that mRNA expression of key genes in the cAMP signaling relay is perturbed in the dsd knockout. Our data indicate novel roles for D-Ser and/or DSD in the regulation of cAMP signaling in the development processes of D. discoideum.

Summary MocR/GabR family proteins are widely distributed prokaryotic transcriptional regulators containing pyridoxal 5′-phosphate (PLP), a coenzyme form of vitamin B6. The Bacillus subtilis GabR, probably the most extensively studied MocR/GabR family protein, consists of an N-terminal DNA-binding domain and a PLP-binding C-terminal domain that has a structure homologous to aminotransferases. GabR suppresses transcription of gabR and activates transcription of gabT and gabD, which encode γ-aminobutyrate (GΑΒΑ) aminotransferase and succinate semialdehyde dehydrogenase, respectively, in the presence of PLP and GABA. In this study, we examined the mechanism underlying GabR-mediated gabTD transcription with spectroscopic, crystallographic and thermodynamic studies, focusing on the function of the aminotransferase domain. Spectroscopic studies revealed that GABA forms an external aldimine with the PLP in the aminotransferase domain. Isothermal calorimetry demonstrated that two GabR molecules bind to the 51-bp DNA fragment that contains the GabR-binding region. GABA minimally affected ΔGbinding upon binding of GabR to the DNA fragment but greatly affected the contributions of ΔH and ΔS to ΔGbinding. GABA forms an external aldimine with PLP and causes a conformational change in the aminotransferase domain, and this change likely rearranges GabR binding to the promoter and thus activates gabTD transcription.

d-Aspartate is an endogenous free amino acid in the brain, endocrine tissues, and exocrine tissues in mammals, and it plays several physiological roles. In the testis, d-aspartate is detected in elongate spermatids, Leydig cells, and Sertoli cells, and implicated in the synthesis and release of testosterone. In the hippocampus, d-aspartate strongly enhances N-methyl-d-aspartate receptor-dependent long-term potentiation and is involved in learning and memory. The existence of aspartate racemase, a candidate enzyme for d-aspartate production, has been suggested. Recently, mouse glutamic-oxaloacetic transaminase 1-like 1 (Got1l1) has been reported to synthesize substantially d-aspartate from l-aspartate and to be involved in adult neurogenesis. In this study, we investigated the function of Got1l1 in vivo by generating and analyzing Got1l1 knockout (KO) mice. We also examined the enzymatic activity of recombinant Got1l1 in vitro. We found that Got1l1 mRNA is highly expressed in the testis, but it is not detected in the brain and submandibular gland, where d-aspartate is abundant. The d-aspartate contents of wild-type and Got1l1 KO mice were not significantly different in the testis and hippocampus. The recombinant Got1l1 expressed in mammalian cells showed l-aspartate aminotransferase activity, but lacked aspartate racemase activity. These findings suggest that Got1l1 is not the major aspartate racemase and there might be an as yet unknown d-aspartate-synthesizing enzyme.

The details of the mediastinal fascia have been scarcely described and the bronchopericardial membrane is the only known structure that is present between the bronchi and the pericardium. However, the anatomical description of this structure is unclear. This study aimed to investigate the fascial structures between the bronchi and the pericardium based on surgical findings. The connective tissues in the mid-mediastinum were observed surgically when lung lobectomy, including mediastinal lymph node dissection for lung cancer, was performed at our institute from April 2011 to March 2016. In total, 96 lobectomies were performed in 94 patients. A firm fibrous structure connecting the tracheobronchus and the fibrous pericardium was observed. It fixes the central bronchi to the pericardium and is composed of three parts. The largest part exists in front of the carina, its appearance is membranous, and runs behind the pulmonary artery. The other parts run over the right pulmonary artery and diverge at its superior trunk. The location at which all these structures fuse to the pericardium is the venous part of the hilum cordis (VHC). The results showed that connections of the dense fibrous tissues existed between the tracheobronchus and VHC. The structure not only works as a ligament that fixes the bronchi to the mid-mediastinum, but also divides the mid-mediastinum into two compartments: the Barety and subcarinal spaces. The anatomy of the structure observed in this study differs from the previous description of the bronchopericardial membrane.

This is a prospective clinical study aimed at introducing a method to visualise the location of an air leak and to identify the bulla responsible on three-dimensional (3-D) cine CT. In 10 patients with spontaneous pneumothorax, dynamic 320-detector row CT was performed with injection of 0.9% saline into the affected pleural cavity via a preplaced chest tube. In eight cases, 3-D cine CT thoracography revealed the location of the air leak and the bulla responsible (7 cases: air stream sign; 1 case: repeated collapse and expansion of a bulla with the patient's breathing).

Escherichia coli YggS is a highly conserved pyridoxal 5′-phosphate (PLP)-binding protein whose biochemical function is currently unknown. A previous study with a yggS-deficient E. coli strain (ΔyggS) demonstrated that YggS controls l-Ile- and l-Val-metabolism by modulating 2-ketobutyrate (2-KB), l-2-aminobutyrate (l-2-AB), and/or coenzyme A (CoA) availability in a PLP-dependent fashion. In this study, we found that ΔyggS accumulates an unknown metabolite as judged by amino acid analyses. LC/MS and MS/MS analyses of the compound with propyl chloroformate derivatization, and co-chromatography analysis identified this compound as γ-l-glutamyl-l-2-aminobutyryl-glycine (ophthalmic acid), a glutathione (GSH) analogue in which the l-Cys moiety is replaced by l-2-AB. We also determine the metabolic consequence of the yggS mutation. Absence of YggS initially increases l-2-AB availability, and then causes ophthalmic acid accumulation and CoA limitation in the cell. The expression of a γ-glutamylcysteine synthetase and a glutathione synthetase in a ΔyggS background causes high-level accumulation of ophthalmic acid in the cells (∼1.2 nmol/mg cells) in a minimal synthetic medium. This opens the possibility of a first fermentative production of ophthalmic acid.

Shewanella livingstonensis Ac10, a psychrotrophic bacterium isolated from Antarctic seawater, grows well at low temperatures close to 0°C. The bacterium is useful as a host in a low-temperature protein expression system. It is also useful as a model microorganism to investigate the mechanisms of microbial cold-adaptation. Versatile genetic manipulation techniques would be useful to investigate the biology of this bacterium and to develop its applications. In this study, we developed a method for targeted gene deletion and insertion by using the gene coding for orotidine-5'-phosphate decarboxylase (pyrF), which is involved in pyrimidine synthesis. We found that S. livingstonensis Ac10 is sensitive to 5-fluoroorotic acid (5-FOA), which is converted to a highly toxic compound by the product of pyrF. A uracil-auxotrophic strain resistant to 5-FOA was constructed by deleting pyrF, thus allowing the use of a plasmid-borne copy of pyrF for selection of recombinants. We constructed the pyrF complementation suicide plasmid pKKP, which contains pyrF, the R6K replication origin, the mob site of RP4, an antibiotic marker gene, and a multiple cloning site. To demonstrate pyrF-based gene replacement, we deleted the internal region of orf5, the gene coding for an eicosapentaenoic acid (EPA) synthesis enzyme. We also successfully inserted a His6-tag-coding sequence into orf8, the gene coding for another EPA synthesis enzyme. This system allows the markerless deletion and insertion of desired sequences at specific sites in the genome, which remarkably facilitates genetic manipulation of this bacterium.

We often perceive odors of smoking at seats for non-smokers of cafes and restaurants. A new ventilation system was developed by using the knowledge that neither flow separation nor backward flow could occur in case of increasing velocity distribution near walls. Air was supplied with uniform velocity distribution from the whole surface of one side wall and exhausted from the slits set at upper and lower positions of the opposite side wall. The effects were examined experimentally and by means of CFD, and it was confirmed that neither separation nor backward flow occurred even when furniture was set. Furthermore, it was examined experimentally and was confirmed that supplying unsteady flow was effective to prevent the growth of wakes behind obstacles and to decrease the amount of remaining smoke there, when Strouhal number based on the frequency of unsteady flow and the characteristic length of obstacle was about 0.2. These findings seemed useful to ventilate passenger cabins of airplanes or trains, where many seats were arranged densely.

症例1は79歳，男性．主訴は腹痛，食欲不振．イレウスの診断でイレウス管留置し消化管減圧後にイレウス管造影を施行し内ヘルニアと診断．第3病日に腹腔鏡下手術施行．S状結腸間膜左葉に約4cmの欠損孔を認め，同部に回腸が嵌頓しており，S状結腸間膜内ヘルニアと診断．腹腔鏡下に嵌頓した回腸を整復しヘルニア門を縫合し手術を終了．術後第11病日に退院となった．症例2は，80歳，男性で主訴は左下腹部痛．症例1と同様にイレウス管による減圧後に造影施行し内ヘルニアと診断．第9病日，腹腔鏡下手術施行．S状結腸間膜左葉に約3cmのヘルニア門を認め，8cm長の回腸が嵌頓していた．腹腔鏡下に嵌頓を整復，ヘルニア門を縫合閉鎖した．術後第6病日に退院となった．S状結腸間膜内ヘルニアはまれな疾患であり，イレウス管による消化管減圧後に腹腔鏡下に根治しえた症例を2例経験したので，文献的考察を含め報告する．

d -Serine acts as a co-agonist of the N -methyl- d -aspartate (NMDA) receptor, an excitatory glutamate receptor in the mammalian brain that is thought to be involved in higher brain functions such as memory and study. A relationship between the concentration of d -serine in cerebrospinal fluid and neurological disorders such as schizophrenia and amyotrophic lateral sclerosis has been hypothesized. A simple and accurate d -serine assay system would be useful in the study and diagnosis of these diseases. Previously, we developed an enzymatic assay of d -serine using d -serine dehydratase from Saccharomyces cerevisiae , lactate dehydrogenase and NADH. Although this method can detect 10 μM d -serine, a 10-fold increase in sensitivity is required for the assay to be useful for the study and diagnosis of neurological disorders. In this study, we increased the sensitivity of this assay to detect submicromolar concentrations of d -serine. In the new assay, d -serine dehydratase converts d -serine to pyruvate, which is in turn oxidized by pyruvate oxidase. Then, in the presence of horseradish peroxidase, hydrogen peroxide formed during the oxidation converts 10-acetyl-3,7-dihydroxy-phenoxazine (Amplex ® Red) to resorufin, which exhibits a strong fluorescence. We show that this improved assay can be used to determine the concentration of d -serine in calf serum.

Single crystals of MgAl2–xBxO4 (x = 0.0, 0.11 and 0.13) spinel were synthesized under high pressure (5 and 11 GPa) and high temperature (1873 and 1273 K) using a 1000 ton “6–8” type uniaxial split-sphere apparatus. Single-crystal X-ray diffraction measurements were carried out using a laboratory diffractometer with a Weissenberg-type imaging plate detector and using a four-circle diffractometer with synchrotron radiation at Photon Factory, Japan. The maximum content of boron was about x = 0.13 at 1273K and 11GPa. The smallest boron ion occupies the octahedral site in top priority in the spinel solid solution of the Mg/Al/B systems. The B3+ ions can replace considerably bigger Al3+ ion under pressure. We estimated the cation distribution of each site from the reproduction of the observed average distance using the observed local bond lengths for Mg–O and Al–O and the normal B–O distance. The chemical formula of boron-bearing spinels are estimated as (Mg0.47,Al0.53)[Al1.36,Mg0.53,B0.11]O4 (x = 0.11) and (Mg0.50,Al0.50)[Al1.37,Mg0.50,B0.13]O4 (x = 0.13), respectively. These spinel solid solutions are largely disordered crystals and the inversion parameter grow up to 0.5 in the tetrahedral site. The temperature factor Beq for oxygen site in boron-bearing spinels were significantly larger than that in pure MgAl2O4 spinel. Only the positional shifts of oxygen ions have, therefore, been relaxing the disorder in structure.

これまでアンケート調査および腰痛検診にて介護士における腰痛の実態調査を行い，日常生活動作（ADL)に支障をきたすほどの器質的疾患を有する腰痛はなかったこと，一部の介護作業姿勢が腰椎に影響を及ぼしていることを報告した．今回，同じ施設でRoland-Morris Disability Questionnaire（以下RDQ)日本語版を用いて腰痛の調査を行った．対象は，男性319人，女性575人，年齢は19歳から60歳であった．回答が得られたのは，892人（99.8％)であった．RDQ 0点が598人（全体の67.0％)，1～2点が149人（16.7％)，3～4点が70人（7.8％)，5点以上が75人（7.3％)であった．質問の項目別にみると，腰痛を和らげるために，何回も姿勢を変えるが162人，腰痛のため家の仕事をするときは力仕事をしないようにしているが103人，ほとんどいつも腰が痛いが94人，腰痛のため，いつもより横になって休むことが多いが74人，腰痛のためいつもよりゆっくり階段を上るが74人，腰痛のため寝返りが打ちにくいが73人，腰痛のため靴下やストッキングをはくとき苦労するが68人と多かった．これに対し，腰痛のため，服を着るのを誰かに手伝ってもらうが2人，腰痛のためあまり食欲がないが4人，腰痛のため1日大半を座って過ごすが5人，腰痛のため，大半の間，ベッド（布団)の中にいるが6人，腰痛のため，いつもより人に対していらいらしたり腹が立ったりするが7人と少なかった．2次検診を希望したのが42人（4.7％)であった．調査の結果，QOLにかなりの支障をきたすほどの腰痛を有する者は少ないことがわかった．