Glutamate production from aerial nitrogen using the nitrogen-fixing bacterium Klebsiella oxytoca.

Glutamate is an essential biological compound produced for various therapeutic and nutritional applications. The current glutamate production process requires a large amount of ammonium, which is generated through the energy-consuming and CO2-emitting Haber-Bosch process; therefore, the development of bio-economical glutamate production processes is required. We herein developed a strategy for glutamate production from aerial nitrogen using the nitrogen-fixing bacterium Klebsiella oxytoca. We showed that a simultaneous supply of glucose and citrate as carbon sources enhanced the nitrogenase activity of K. oxytoca. In the presence of glucose and citrate, K. oxytoca strain that was genetically engineered to increase the supply of 2-oxoglutarate, a precursor of glutamate synthesis, produced glutamate extracellularly more than 1 g L-1 from aerial nitrogen. This strategy offers a sustainable and eco-friendly manufacturing process to produce various nitrogen-containing compounds using aerial nitrogen.

Discovery of type II polyketide synthase-like enzymes for the biosynthesis of cispentacin.

Type II polyketide synthases (PKSs) normally synthesize polycyclic aromatic compounds in nature, and the potential to elaborate further diverse skeletons was recently revealed by the discovery of a polyene subgroup. Here, we show a type II PKS machinery for the biosynthesis of a five-membered nonaromatic skeleton contained in the nonproteinogenic amino acid cispentacin and the plant toxin coronatine. We successfully produce cispentacin in a heterologous host and reconstruct its biosynthesis using seven recombinant proteins in vitro. Biochemical analyses of each protein reveal the unique enzymatic reactions, indicating that a heterodimer of type II PKS-like enzymes (AmcF-AmcG) catalyzes a single C2 elongation as well as a subsequent cyclization on the acyl carrier protein (AmcB) to form a key intermediate with a five-membered ring. The subsequent reactions, which are catalyzed by a collection of type II PKS-like enzymes, are also peculiar. This work further expands the definition of type II PKS and illuminates an unexplored genetic resource for natural products.

Non-coding RNAs and functional RNA elements in Thermus thermophilus.

To complete the ThermusQ database, small non-coding RNAs (ncRNAs) and functional RNA elements found in Thermus thermophilus were summarized with annotations. The well-known three ncRNAs, M1 RNA, tmRNA and SRP RNA, were annotated as ttj8_nc001 to ttj8_nc003, and 10 novel RNAs were annotated as ttj8_nc004 to ttj8_nc013. Antisense RNAs for some ORFs were annotated as ttj8_EST00001 to ttj8_EST00006. In addition, a set of conserved sequences found in T. thermophilus HB27 were also described.

Protein-protein interaction-mediated regulation of lysine biosynthesis of Thermus thermophilus through the function-unknown protein LysV.

Thermus thermophilus biosynthesizes lysine via α-aminoadipate as an intermediate using the amino-group carrier protein, LysW, to transfer the attached α-aminoadipate and its derivatives to biosynthetic enzymes. A gene named lysV, which encodes a hypothetical protein similar to LysW, is present in the lysine biosynthetic gene cluster. Although the knockout of lysV did not affect lysine auxotrophy, lysV homologs are conserved in the lysine biosynthetic gene clusters of microorganisms belonging to the phylum Deinococcus-Thermus, suggesting a functional role for LysV in lysine biosynthesis. Pulldown assays and crosslinking experiments detected interactions between LysV and all of the biosynthetic enzymes requiring LysW for reactions, and the activities of most of all these enzymes were affected by LysV. These results suggest that LysV modulates the lysine biosynthesis through protein-protein interactions.

Substrate Recognition Mechanism of a Trichostatin A-Forming Hydroxyamidotransferase.

The hydroxyamidotransferase TsnB9 catalyzes hydroxylamine transfer from l-glutamic acid γ-monohydroxamate to the carboxyl group of trichostatic acid to produce the terminal hydroxamic acid group of trichostatin A, which is a potent inhibitor of histone deacetylase (HDAC). The reaction catalyzed by TsnB9 is similar to that catalyzed by glutamine-dependent asparagine synthetase, but the trichostatic acid recognition mechanism remains unclear. Here, we determine the crystal structure of TsnB9 composed of the N-terminal glutaminase domain and the C-terminal synthetase domain. Two consecutive phenylalanine residues, which are not found in glutamine-dependent asparagine synthetase, in the N-terminal glutaminase domain structurally form the bottom of the hydrophobic pocket in the C-terminal synthetase domain. Mutational and computational analyses of TsnB9 suggest five aromatic residues, including the two consecutive phenylalanine residues, in the hydrophobic pocket are important for the recognition of the dimethylaniline moiety of trichostatic acid. These insights lead us to the discovery of hydroxyamidotransferase to produce terminal hydroxamic acid group-containing HDAC inhibitors different from trichostatin A.

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.

Mucinolytic bacteria modulate host-microbiota symbiosis and dysbiosis through their ability to degrade mucin O-glycans. However, how and to what extent bacterial enzymes are involved in the breakdown process remains poorly understood. Here we focus on a glycoside hydrolase family 20 sulfoglycosidase (BbhII) from Bifidobacterium bifidum, which releases N-acetylglucosamine-6-sulfate from sulfated mucins. Glycomic analysis showed that, in addition to sulfatases, sulfoglycosidases are involved in mucin O-glycan breakdown in vivo and that the released N-acetylglucosamine-6-sulfate potentially affects gut microbial metabolism, both of which were also supported by a metagenomic data mining analysis. Enzymatic and structural analysis of BbhII reveals the architecture underlying its specificity and the presence of a GlcNAc-6S-specific carbohydrate-binding module (CBM) 32 with a distinct sugar recognition mode that B. bifidum takes advantage of to degrade mucin O-glycans. Comparative analysis of the genomes of prominent mucinolytic bacteria also highlights a CBM-dependent O-glycan breakdown strategy used by B. bifidum.

Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.

(2,6)-Diamino-(5,7)-dihydroxyheptanoic acid (DADH), a non-proteinogenic amino acid, is converted to 1-azabicyclo[3.1.0]hexane ring-containing amino acids that are subsequently incorporated into ficellomycin and vazabitide A. The present study revealed that the sugar aminotransferase-like enzymes Fic25 and Vzb9, with a high amino acid sequence identity (56%) to each other, synthesized stereoisomers of DADH with (6S) and (6R) configurations, respectively. The crystal structure of the Fic25 complex with a PLP-(6S)-N2-acetyl-DADH adduct indicated that Asn45 and Gln197 (Asn205 and Ala53 in Vzb9) were located at positions that affected the stereochemistry of DADH being synthesized. A modeling study suggested that amino acid substitutions between Fic25 and Vzb9 allowed the enzymes to bind to the substrate with almost 180° rotation in the C5-C7 portions of the DADH molecules, accompanied by a concomitant shift in their C1-C4 portions. In support of this result, the replacement of two corresponding residues in Fic25 and Vzb9 increased (6R) and (6S) stereoselectivities, respectively. The different stereochemistry at C6 of DADH resulted in a different stereochemistry/orientation of the aziridine portion of the 1-azabicyclo[3.1.0]hexane ring, which plays a crucial role in biological activity, between ficellomycin and vazabitide A. A phylogenic analysis suggested that Fic25 and Vzb9 evolved from sugar aminotransferases to produce unusual building blocks for expanding the structural diversity of secondary metabolites.

Complete Biosynthetic Pathway of the Phosphonate Phosphonothrixin: Two Distinct Thiamine Diphosphate-Dependent Enzymes Divide the Work to Form a C-C Bond.

Phosphonates often exhibit biological activities by mimicking the phosphates and carboxylates of biological molecules. The phosphonate phosphonothrixin (PTX), produced by the soil-dwelling bacterium Saccharothrix sp. ST-888, exhibits herbicidal activity. In this study, we propose a complete biosynthetic pathway for PTX by reconstituting its biosynthesis in vitro. Our intensive analysis demonstrated that two dehydrogenases together reduce phosphonopyruvate (PnPy) to 2-hydroxy-3-phosphonopropanoic acid (HPPA) to accelerate the thermodynamically unfavorable rearrangement of phosphoenolpyruvate (PEP) to PnPy. The next four enzymes convert HPPA to (3-hydroxy-2-oxopropyl)phosphonic acid (HOPA). In the final stage of PTX biosynthesis, the "split-gene" transketolase homologue, PtxB5/6, catalyzes the transfer of a two-carbon unit attached to the thiamine diphosphate (TPP) cofactor (provided by the acetohydroxyacid synthase homologue, PtxB7) to HOPA to produce PTX. This study reveals a unique C-C bond formation in which two distinct TPP-dependent enzymes, PtxB5/6 and PtxB7, divide the work to transfer an acetyl group, highlighting an unprecedented biosynthetic strategy for natural products.

Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination.

Natural products containing an aziridine ring, such as mitomycin C and azinomycin B, exhibit antitumor activities by alkylating DNA via their aziridine rings; however, the biosynthetic mechanisms underlying the formation of these rings have not yet been elucidated. We herein investigated the biosynthesis of vazabitide A, the structure of which is similar to that of azinomycin B, and demonstrated that Vzb10/11, with no similarities to known enzymes, catalyzed the formation of the aziridine ring via sulfate elimination. To elucidate the detailed reaction mechanism, crystallization of Vzb10/11 and the homologous enzyme, AziU3/U2, in the biosynthesis of azinomycin B was attempted, and the structure of AziU3/U2, which had a new protein fold overall, was successfully determined. The structural analysis revealed that these enzymes adjusted the dihedral angle between the amino group and the adjacent sulfate group of the substrate to almost 180° and enhanced the nucleophilicity of the C6-amino group temporarily, facilitating the SN2-like reaction to form the aziridine ring. The present study reports for the first time the molecular basis for aziridine ring formation.

A Natural Dihydropyridazinone Scaffold Generated from a Unique Substrate for a Hydrazine-Forming Enzyme.

Nitrogen-nitrogen bond-containing functional groups are rare, but they are found in a considerably wide class of natural products. Recent clarifications of the biosynthetic routes for such functional groups shed light onto overlooked biosynthetic genes distributed across the bacterial kingdom, highlighting the presence of yet-to-be identified natural products with peculiar functional groups. Here, the genome-mining approach targeting a unique hydrazine-forming gene led to the discovery of actinopyridazinones A (1) and B (2), the first natural products with dihydropyridazinone rings. The structure of actinopyridazinone A was unambiguously established by total synthesis. Biosynthetic studies unveiled the structural diversity of natural hydrazines derived from this family of N-N bond-forming enzymes.

Cryptic Oxidative Transamination of Hydroxynaphthoquinone in Natural Product Biosynthesis.

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a group of versatile enzymes that catalyze various reactions, but only a small number of them react with O2. Here, we report an unprecedented PLP-dependent enzyme, NphE, that catalyzes both transamination and two-electron oxidation using O2 as an oxidant. Our intensive analysis reveals that NphE transfers the l-glutamate-derived amine to 1,3,6,8-tetrahydroxynaphthalene-derived mompain to form 8-amino-flaviolin (8-AF) via a highly conjugated quinonoid intermediate that is reactive with O2. During the NphE reaction, O2 is reduced to yield H2O2. An integrated technique involving NphE structure prediction by AlphaFold v2.0 and molecular dynamics simulation suggested the O2-accessible cavity. Our in vivo results demonstrated that 8-AF is a genuine biosynthetic intermediate for the 1,3,6,8-tetrahydroxynaphthalene-derived meroterpenoid naphterpin without an amino group, which was supported by site-directed mutagenesis. This study clearly establishes the NphE reaction product 8-AF as a common intermediate with a cryptic amino group for the biosynthesis of terpenoid-polyketide hybrid natural products.

Structural Basis for the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed by Squalene Synthase-Like Enzymes.

Some enzymes annotated as squalene synthase catalyze the prenylation of carbazole-3,4-quinone-containing substrates in bacterial secondary metabolism. Their reaction mechanisms remain unclear because of their low sequence similarity to well-characterized aromatic substrate prenyltransferases (PTs). We determined the crystal structures of the carbazole PTs, and these revealed that the overall structure is well superposed on those of squalene synthases. In contrast, the stacking interaction between the prenyl donor and acceptor substrates resembles those observed in aromatic substrate PTs. Structural and mutational analyses suggest that the Ile and Asp residues are essential for the hydrophobic and hydrophilic interactions with the carbazole-3,4-quinone moiety of the prenyl acceptor, respectively, and a deprotonation mechanism of an intermediary σ-complex involving a catalytic triad is proposed. Our results provide a structural basis for a new subclass of aromatic substrate PTs.

Immune gene activation by NPR and TGA transcriptional regulators in the model monocot Brachypodium distachyon.

The nonexpressor of pathogenesis-related (NPR) gene family is well known to play a crucial role in transactivation of TGA transcription factors for salicylic acid (SA)-responsive genes, including pathogenesis-related protein 1 (PR1), during plants' immune response after pathogen attack in the model dicot Arabidopsis thaliana. However, little is known about NPR gene functions in monocots. We therefore explored the functions of NPRs in SA signaling in the model monocot Brachypodium distachyon. BdNPR1 and BdNPR2/3 share structural similarities with A. thaliana AtNPR1/2 and AtNPR3/4 subfamilies, respectively. The transcript level of BdNPR2 but not BdNPR1/3 appeared to be positively regulated in leaves in response to methyl salicylate. Reporter assays in protoplasts showed that BdNPR2 positively regulated BdTGA1-mediated activation of PR1. This transactivation occurred in an SA-dependent manner through SA binding at Arg468 of BdNPR2. In contrast, BdNPR1 functioned as a suppressor of BdNPR2/BdTGA1-mediated transcription of PR1. Collectively, our findings reveal that the TGA-promoted transcription of SA-inducible PR1 is orchestrated by the activator BdNPR2 and the repressor BdNPR1, which function competitively in B. distachyon.

Preliminary Clinical Outcome of One-level Mobi-C Total Disc Replacement in Japanese Population.

INTRODUCTION: In 2018, the first Mobi-CⓇ total disk replacement (TDR) case was performed in Japan. In this study, we examined the preliminary clinical outcome of Mobi-CⓇ for degenerative cervical spine disease. METHODS: We examined 24 consecutive patients who underwent 1-level TDR after 2018 and followed up for more than 6 months after surgery. The evaluation criteria included age, gender, diagnosis, follow-up period, surgical level, implant size, surgery time, intraoperative bleeding volume, complications, revision surgery, imaging findings, JOA score, and various questionnaires. RESULTS: The mean age was 52.7 years, 13 males and 11 females. There were 15 cases of cervical disk herniation and 9 cases of cervical spondylosis. The mean follow-up period was 17.4 months. Surgical levels were C3/4 in 4 cases, C4/5 in 2 cases, C5/6 in 16 cases, and C6/7 in 2 cases. The mean operation time was 138.5 minutes, the amount of intraoperative bleeding was 32.1 ml, and there were no serious intraoperative complications. The range of motion of the affected level increased significantly, from 6.6 degrees preoperatively to 12.2 degrees at final follow-up. No patients required revision surgery at final follow-up, and there were no cases of heterotopic ossification or adjacent segment disease. One patient exhibited radiculopathy due to mild subsidence 1 year after surgery, and 1 had asymptomatic contact of device plates. Preoperative and final JOA scores improved from 11.7 to 15.8 points, and NRS improved from 4.3 to 1.3 points for neck pain and 4.3 to 1.7 points for arm pain. Preoperative and final NDI improved from 39.7% to 14.0%, and EQ-5D improved from 0.602 to 0.801. CONCLUSIONS: The short-term treatment outcomes of Mobi-CⓇ TDR were generally favorable. Spine surgeons should comply with guidelines when introducing this procedure and strive to adopt this new technology in Japan.

Dynamic alignment changes during level walking in patients with dropped head syndrome: analyses using a three-dimensional motion analysis system.

In patients with dropped head syndrome (DHS), cervical malalignment is one of the risk factors for impaired horizontal gaze and restrictions to ambulation. The characteristics of gait in patients with DHS have not been clarified biomechanically from the viewpoint of dynamic alignment and lower limb kinematics. This study aimed to clarify kinematic and kinetic differences during level walking in patients with DHS compared to the healthy elderly. Twelve patients with DHS and healthy elderly individuals performed level walking at a self-selected speed. Spatiotemporal, kinematic, and kinetic data were recorded using a three-dimensional motion analysis system. Statistical analysis was performed to compare these data between the two groups, respectively. Compared with the healthy elderly, stride length and peak hip-joint extension angle in patients with DHS were significantly shorter and smaller. The thorax was also significantly tilted backwards. Peak ankle-joint plantar-flexion moment was significantly smaller despite larger dorsiflexion angle compared with the healthy elderly. The walking of DHS patients demonstrated kinematic and kinetic characteristics of the lower limb joints and alignment of the thorax and pelvis corresponding to their short stride and walking speed.

Pollen shells and soluble factors play non-redundant roles in the development of allergic conjunctivitis in mice.

PURPOSE: We aimed to clarify the role of particulate allergen exposure to the conjunctiva in the development of allergic conjunctivitis. METHODS: We administered ragweed pollen suspension, pollen extract, pollen shell, particulate air pollutants, and their combinations to the mouse conjunctiva five days a week without prior sensitization. Clinical signs were scored. Histological changes, cellular infiltrations, mRNA expressions, lymph node cell recall responses, and serum immunoglobulin levels were assessed. Immune cell-depleting antibodies and ST2 knockout mice were used to investigate the cellular and molecular requirements. RESULTS: Pollen suspension, but not the extract or shell alone, induced robust eosinophilic conjunctivitis, accompanied by a proliferative response of epithelial cells. A combination of pollen extract and shell completely restored eosinophil accumulation. In addition, eosinophilic conjunctivitis was induced by a mixture of particulate air pollutants and pollen extract. Mechanistically, eosinophil accumulation was ameliorated by deficiency of the IL-33 receptor ST2 and abolished by depleting CD4+ T cells. Pollen shells, but not the extract, induced IL-33 release from conjunctival epithelial cells in vivo. CONCLUSIONS: Our results indicate the non-redundant roles for the allergens' particulate properties and soluble factors in the development of allergic conjunctivitis.

Sequential MRI Changes After Lateral Lumbar Interbody Fusion in Spondylolisthesis with Mild and Severe Lumbar Spinal Stenosis.

OBJECTIVE: We assessed the sequential magnetic resonance imaging changes of indirect neural decompression after minimally invasive lumbar lateral interbody fusion (LIF) combined with posterior percutaneous pedicle screw (PPS) fixation for degenerative spondylolisthesis (DS) according to the severity of preoperative lumbar spinal stenosis. METHODS: A total of 43 patients (mean age, 68.7 years; 16 men and 27 women) with DS who had undergone LIF and closed reduction with PPS fixation were enrolled. The intervertebral levels were divided into the moderate stenosis (MS) group (preoperative cross-sectional area [CSA] of the thecal sac >50 mm2) and severe stenosis (SS) group (CSA ≤50 mm2). The CSA, ligamentum flavum thickness, and diameter of the thecal sac at the affected level were measured on cross-sectional magnetic resonance images at baseline, immediately postoperatively, and 2 years postoperatively. RESULTS: For the 31 and 29 intervertebral levels in the MS and SS groups, the mean CSA at baseline, immediately postoperatively, and 2 years postoperatively was 76.9 mm2 and 35.8 mm2, 104.3 mm2 and 81.4 mm2, and 130.9 mm2 and 105.7 mm2, respectively. The mean ligamentum flavum thicknesses at 2 years postoperatively became thinner than that immediately after surgery in both groups (P < 0.01). The mean diameter of the thecal sac at 2 years was longer than that immediately after surgery in both groups (MS group, P < 0.05; SS group, P < 0.01) The expansion ratio of the CSA at 2 years postoperatively was significantly greater in the SS group than that in the MS group (P < 0.01). CONCLUSIONS: Sequential enlargement of the spinal canal was obtained by the thinning of the ligamentum flavum after LIF and PPS fixation in patients with DS with both mild and severe stenosis. The effect of indirect neural decompression was equivalent even in those with severe lumbar spinal stenosis.

Idiopathic dorsal spinal cord herniation perforating the lamina: a case report and review of the literature.

Spinal cord herniation (SCH) is a rare condition associated with tethering of the spinal cord at the ventral dural defect. Idiopathic dorsal spinal cord herniation (IDSCH) is an extremely rare clinical entity. Here, we report the first case of IDSCH perforating the lamina in a patient with a history of ossification of the ligamentum flavum and diffuse idiopathic skeletal hyperostosis. Untethering of the spinal cord was performed by removing the surrounded ossified dura. Although urological symptoms and impaired proprioception remained, progressive neurological deterioration was prevented. Because this disease condition is extremely rare, it should be differentiated from ventral SCH.

A Rare Case of Nontraumatic Atlantoaxial Rotatory Fixation in an Adult Patient Treated by a Closed Reduction: A Case Report.

CASE: A 42-year-old woman presented with a severe neck pain and torticollis due to uncertain etiology. Because her radiographs and computed tomography revealed atlantoaxial rotatory fixation (AARF) that is an extremely rare condition in the adult population, a nonsurgical treatment was initially applied. Because 3 weeks of indirect traction failed, closed reduction was performed under general anesthesia at 2 months after onset, and her symptoms markedly improved without any complications and recurrence. CONCLUSION: Closed reduction under general anesthesia for nontraumatic AARF in adult patients might be an effective treatment option, even for chronic cases or intractable cases by traction treatment.